Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 129 of 135
Found at i:41877472 original size:11 final size:11
Alignment explanation
Indices: 41877458--41877482 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41877448 ATTGTTTAAT
41877458 ATATTATTCAA
1 ATATTATTCAA
41877469 ATATTATTCAA
1 ATATTATTCAA
41877480 ATA
1 ATA
41877483 CAGTAACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATTATTCAA
Found at i:41880299 original size:15 final size:15
Alignment explanation
Indices: 41880279--41880310 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41880269 AGTTGAGAGG
41880279 AATTTTTTTAATTTT
1 AATTTTTTTAATTTT
*
41880294 AATTTTTTTATTTTT
1 AATTTTTTTAATTTT
41880309 AA
1 AA
41880311 ACTTGCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
AATTTTTTTAATTTT
Found at i:41889357 original size:25 final size:24
Alignment explanation
Indices: 41889300--41889358 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
41889290 AAAAATAGGT
* *
41889300 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
41889323 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
41889347 TATTTTAATAAT
1 TATATT-ATAAT
41889359 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:41889369 original size:15 final size:14
Alignment explanation
Indices: 41889350--41889439 Score: 60
Period size: 15 Copynumber: 6.2 Consensus size: 14
41889340 TAATTCATAT
41889350 TTTAATAATAATTA
1 TTTAATAATAATTA
*
41889364 TATTAAAAAT-ATTA
1 T-TTAATAATAATTA
* *
41889378 TTAAATTATATATTA
1 TTTAATAATA-ATTA
* *
41889393 TTTTATTAA-ATTATA
1 -TTTAATAATAAT-TA
41889408 TTTAATAATAATTA
1 TTTAATAATAATTA
41889422 TGTTAA-AATATATTA
1 T-TTAATAATA-ATTA
41889437 TTT
1 TTT
41889440 TTGTTAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
13 5 0.09
14 23 0.40
15 25 0.43
16 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (14 bp):
TTTAATAATAATTA
Found at i:41889419 original size:58 final size:62
Alignment explanation
Indices: 41889319--41889438 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 62
41889309 TTTTTCTAAT
41889319 ATTATATATTATAATTTTTACTAATTCATATTTTAATAATAATTATATTAAAA-ATATTATTAA
1 ATTATATATTAT-ATTTTTAC-AATTCATATTTTAATAATAATTATATTAAAATATATTATTAA
*
41889382 ATTATATATTAT-TTTATTA-AATT-ATA-TTTAATAATAATTATGTTAAAATATATTATT
1 ATTATATATTATATTT-TTACAATTCATATTTTAATAATAATTATATTAAAATATATTATT
41889439 TTTGTTAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
58 21 0.39
59 11 0.20
60 4 0.07
61 3 0.06
62 3 0.06
63 12 0.22
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (62 bp):
ATTATATATTATATTTTTACAATTCATATTTTAATAATAATTATATTAAAATATATTATTAA
Found at i:41890300 original size:15 final size:15
Alignment explanation
Indices: 41890258--41890311 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 15
41890248 ATATTTTAAA
**
41890258 TAAAAAATAAAATTT
1 TAAAAAATAATTTTT
41890273 TAAAAATTATAATTTTT
1 TAAAAA--ATAATTTTT
*
41890290 TAAAAAATAATCTCTT
1 TAAAAAATAAT-TTTT
41890306 TAAAAA
1 TAAAAA
41890312 TCAAAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 11 0.33
16 9 0.27
17 13 0.39
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAAAATAATTTTT
Found at i:41890333 original size:35 final size:32
Alignment explanation
Indices: 41890258--41890333 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
41890248 ATATTTTAAA
* *
41890258 TAAAAAATAAAATTTTAAAAATTATAATTTTT
1 TAAAAAATAAAATTTTAAAAATCAAAATTTTT
**
41890290 TAAAAAATAATCTCTTTAAAAATCAAAATATTATT
1 TAAAAAATAAAAT-TTTAAAAATCAAAAT-TT-TT
41890325 TAAAAAATA
1 TAAAAAATA
41890334 TAAAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 11 0.30
33 13 0.35
34 2 0.05
35 11 0.30
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAAAATTTTAAAAATCAAAATTTTT
Found at i:41890911 original size:28 final size:29
Alignment explanation
Indices: 41890854--41890909 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
41890844 ATCGAAATCT
* *
41890854 TATTTATTTTTATATTAATTTTTTATAAA
1 TATTTATTTTTACATTAATTTTATATAAA
*
41890883 TATTTTTTTTTACA-TAATTTTA-ATAAA
1 TATTTATTTTTACATTAATTTTATATAAA
41890910 ATTGAATGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 7 0.29
29 12 0.50
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TATTTATTTTTACATTAATTTTATATAAA
Found at i:41897969 original size:2 final size:2
Alignment explanation
Indices: 41897962--41897995 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41897952 TATGTACTAA
41897962 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
41897996 TTCATTCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41899011 original size:31 final size:31
Alignment explanation
Indices: 41898973--41899047 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
41898963 ACAGCCAAAA
* * **
41898973 TCACTAAACTATTAGCAA-TTTTACATTTTGG
1 TCACTAAACTATTAGAAAGCTTT-CATTTAAG
*
41899004 TCACTAAACTATTTGAAAGCTTTCATTTAAG
1 TCACTAAACTATTAGAAAGCTTTCATTTAAG
41899035 TCACTAAACTATT
1 TCACTAAACTATT
41899048 CAAAATTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 35 0.92
32 3 0.08
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (31 bp):
TCACTAAACTATTAGAAAGCTTTCATTTAAG
Found at i:41907319 original size:24 final size:24
Alignment explanation
Indices: 41907292--41907359 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
41907282 TTAAAATCTG
*
41907292 TCTAGGCTTGTAAGAGCTAATCAT
1 TCTAGGCTCGTAAGAGCTAATCAT
*
41907316 TCTAAGCTCGTAAGAGCTAATCAT
1 TCTAGGCTCGTAAGAGCTAATCAT
* *
41907340 TTTGGGCTCGTAAGAGCTAA
1 TCTAGGCTCGTAAGAGCTAA
41907360 ATGTCATCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (24 bp):
TCTAGGCTCGTAAGAGCTAATCAT
Found at i:41909347 original size:14 final size:14
Alignment explanation
Indices: 41909328--41909359 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
41909318 AATAAGAAGA
41909328 TTTCTTCCAAAACT
1 TTTCTTCCAAAACT
41909342 TTTCTTCCAAAACT
1 TTTCTTCCAAAACT
41909356 TTTC
1 TTTC
41909360 CTTTACCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTCTTCCAAAACT
Found at i:41911742 original size:24 final size:24
Alignment explanation
Indices: 41911705--41911763 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
41911695 TTAAACTTTG
*
41911705 TCTGGGCTCATAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
* *
41911729 TCTGGGTTCGTAAGAGCTAATTAT
1 TCTGGGCTCGTAAGAGCTAATCAT
41911753 TCTGGGCTCGT
1 TCTGGGCTCGT
41911764 GTTGGCTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAATCAT
Found at i:41913656 original size:21 final size:20
Alignment explanation
Indices: 41913632--41913682 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
41913622 AAATTGTCTA
41913632 ATAACTTTCATAATATTTTTT-
1 ATAACTTT-ATAAT-TTTTTTC
* *
41913653 ATAAATAATATAATTTTTTTC
1 ATAACT-TTATAATTTTTTTC
41913674 ATAACTTTA
1 ATAACTTTA
41913683 GAAATTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAACTTTATAATTTTTTTC
Found at i:41913752 original size:21 final size:20
Alignment explanation
Indices: 41913723--41913761 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
41913713 TAAAATAAAT
41913723 TATAATATTTTTATGAATAAG
1 TATAATATTTTTAT-AATAAG
*
41913744 TATATTATTTTTATAATA
1 TATAATATTTTTATAATA
41913762 TATAGCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TATAATATTTTTATAATAAG
Found at i:41915277 original size:17 final size:17
Alignment explanation
Indices: 41915257--41915289 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41915247 TTATAGAACC
41915257 AAAAAA-ATCATTATATT
1 AAAAAATAT-ATTATATT
41915274 AAAAAATATATTATAT
1 AAAAAATATATTATAT
41915290 ATATAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAAATATATTATATT
Found at i:41924342 original size:39 final size:39
Alignment explanation
Indices: 41924288--41924366 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
41924278 CTATGAAAAG
41924288 TTACAAAATCGTCACCCAATTATTCAATTTTGTCTTTTC
1 TTACAAAATCGTCACCCAATTATTCAATTTTGTCTTTTC
41924327 TTACAAAATCGTCACCCAATTATTCAATTTTGTCTTTTC
1 TTACAAAATCGTCACCCAATTATTCAATTTTGTCTTTTC
41924366 T
1 T
41924367 GATCACCAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (39 bp):
TTACAAAATCGTCACCCAATTATTCAATTTTGTCTTTTC
Found at i:41930781 original size:90 final size:89
Alignment explanation
Indices: 41930616--41930782 Score: 192
Period size: 90 Copynumber: 1.9 Consensus size: 89
41930606 ATTAATGGTT
* * * * *
41930616 ATTAAAGCATACAAACTAAAATTTATCAATTCAAAAATTATAGGAATACTACATTCACAACTTAG
1 ATTAAAGCATACAAACTAAAATTTATCAATTCAAAAATTACAAGAATACGACATTCACAAATTAC
*
41930681 GCCGAGTACACTTATTTAACAACA
66 GCCGAATACACTTATTTAACAACA
* * * * *
41930705 ATTAAAGTATACAAATTAATATTTGATCAATTTGAAAAA-TACAAGAATACGATATTCACAAATT
1 ATTAAAGCATACAAACTAAAATTT-ATCAA-TTCAAAAATTACAAGAATACGACATTCACAAATT
**
41930769 ACGTTGAATACACT
64 ACGCCGAATACACT
41930783 AAAATTGATC
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
89 21 0.33
90 35 0.56
91 7 0.11
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (89 bp):
ATTAAAGCATACAAACTAAAATTTATCAATTCAAAAATTACAAGAATACGACATTCACAAATTAC
GCCGAATACACTTATTTAACAACA
Found at i:41930948 original size:89 final size:89
Alignment explanation
Indices: 41930782--41930948 Score: 194
Period size: 89 Copynumber: 1.9 Consensus size: 89
41930772 TTGAATACAC
* * * * * *
41930782 TAAAATTGATCAATTCGAAAATTATCAAAATATTGAATTCACAATTTATACAAAGTACACTGATT
1 TAAAATTGATCAATCCGAAAATTATCAAAATACTAAATTCACAACTTACACAAAGTACACTGACT
* *
41930847 TAACATCTACTAAAATATATAGAT
66 CAACAACTACTAAAATATATAGAT
* * * *
41930871 TAAAATTGATCAATCCGGAAATTA-CAAGAATACTAAATTCATAACTTACCCAATA-TACATTGA
1 TAAAATTGATCAATCCGAAAATTATCAA-AATACTAAATTCACAACTTACACAA-AGTACACTGA
41930934 CTCAACAACTACTAA
64 CTCAACAACTACTAA
41930949 GGTATAAAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
88 3 0.05
89 60 0.94
90 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.31
Consensus pattern (89 bp):
TAAAATTGATCAATCCGAAAATTATCAAAATACTAAATTCACAACTTACACAAAGTACACTGACT
CAACAACTACTAAAATATATAGAT
Found at i:41938526 original size:22 final size:23
Alignment explanation
Indices: 41938501--41938547 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 23
41938491 GTATGTTAAA
41938501 TTAAAGAGTAAA-TTAATT-ATTT
1 TTAAAGA-TAAATTTAATTCATTT
*
41938523 TT-AATATAAATTTAATTCATTT
1 TTAAAGATAAATTTAATTCATTT
41938545 TTA
1 TTA
41938548 TGTTAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 4 0.19
21 9 0.43
22 8 0.38
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
TTAAAGATAAATTTAATTCATTT
Found at i:41938637 original size:20 final size:20
Alignment explanation
Indices: 41938612--41938652 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41938602 ATATATATCT
41938612 CATCAAGACCAAGTTTTAAC
1 CATCAAGACCAAGTTTTAAC
41938632 CATCAAGACCAAGTTTTAAC
1 CATCAAGACCAAGTTTTAAC
41938652 C
1 C
41938653 TTAGAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (20 bp):
CATCAAGACCAAGTTTTAAC
Found at i:41945114 original size:9 final size:9
Alignment explanation
Indices: 41945097--41945140 Score: 79
Period size: 9 Copynumber: 4.9 Consensus size: 9
41945087 ACCTCAATTG
*
41945097 TATATAAAA
1 TATAAAAAA
41945106 TATAAAAAA
1 TATAAAAAA
41945115 TATAAAAAA
1 TATAAAAAA
41945124 TATAAAAAA
1 TATAAAAAA
41945133 TATAAAAA
1 TATAAAAA
41945141 TTAAAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
TATAAAAAA
Found at i:41948511 original size:23 final size:23
Alignment explanation
Indices: 41948441--41948609 Score: 157
Period size: 23 Copynumber: 7.3 Consensus size: 23
41948431 ACGGAACAAG
* *
41948441 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
41948462 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
41948487 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
41948510 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
41948533 CGGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
41948556 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
41948579 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
41948602 CAGAGAGC
1 CAGAGAGC
41948610 GCGCTAGTGT
Statistics
Matches: 124, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
21 15 0.12
23 89 0.72
24 1 0.01
25 13 0.10
26 6 0.05
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:41948543 original size:46 final size:46
Alignment explanation
Indices: 41948487--41948609 Score: 176
Period size: 46 Copynumber: 2.7 Consensus size: 46
41948477 TGCTGGGCAA
*
41948487 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * * *
41948533 CGGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
*
41948579 CAGAGAGCACGAGAC-GTGCTAAACAGAGAGC
1 CAGAGAGCAC-ACACAGTGCTAAACAGAGAGC
41948610 GCGCTAGTGT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
46 65 0.97
47 2 0.03
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (46 bp):
CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:41948560 original size:69 final size:66
Alignment explanation
Indices: 41948441--41948585 Score: 184
Period size: 69 Copynumber: 2.1 Consensus size: 66
41948431 ACGGAACAAG
* *
41948441 CAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGTGC
1 CAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAAAGTGC
41948506 TAAA
63 TAAA
*
41948510 CAGAGAGTACACAAAGTACTAATCGGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAAGTG
*
41948574 CTAAT
62 CTAAA
41948579 CAGAGAG
1 CAGAGAG
41948586 CACGAGACGT
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
68 2 0.03
69 38 0.56
70 11 0.16
71 10 0.15
72 7 0.10
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (66 bp):
CAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGTGCTAA
A
Found at i:41955324 original size:52 final size:52
Alignment explanation
Indices: 41955229--41955520 Score: 404
Period size: 52 Copynumber: 5.6 Consensus size: 52
41955219 GTAAATGCAA
* * *
41955229 AAGGTCTGATAACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
41955281 AAGGCCCGATGATTATGTGTCATCATGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * *
41955333 ATGGTCCAATGACTATGTGTCATCGTGAGTGTACGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
41955385 ATGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACAGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * *
41955437 GAGGTCCGATAACTATGTGTCATCGTGAGCATATGAATCCTTTTCGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
41955489 GAGGTTCGATAACTATGTGTCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
41955521 CAAATGAGAA
Statistics
Matches: 213, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 213 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.36
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:41959591 original size:24 final size:24
Alignment explanation
Indices: 41959534--41959592 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
41959524 TTTAGCCAAC
*
41959534 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCTAGAATGATTAGCTCTT
* *
41959558 ACGAGTCTAGAGTGATTAGCTCTT
1 ACGAGCCTAGAATGATTAGCTCTT
41959582 ACGAGCCTAGA
1 ACGAGCCTAGA
41959593 TAGAGTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (24 bp):
ACGAGCCTAGAATGATTAGCTCTT
Found at i:41963516 original size:19 final size:19
Alignment explanation
Indices: 41963486--41963536 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
41963476 TTCATATATT
41963486 TTTTAGAATTTTAAAAATTA
1 TTTTA-AATTTTAAAAATTA
*
41963506 TTTTAAATTTTTGAAAATTA
1 TTTTAAA-TTTTAAAAATTA
*
41963526 TTTTGAATTTT
1 TTTTAAATTTT
41963537 TTTAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
TTTTAAATTTTAAAAATTA
Found at i:41963544 original size:20 final size:20
Alignment explanation
Indices: 41963494--41963537 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
41963484 TTTTTTAGAA
*
41963494 TTTTAAAAATTATTTTAAAT
1 TTTTGAAAATTATTTTAAAT
*
41963514 TTTTGAAAATTATTTTGAAT
1 TTTTGAAAATTATTTTAAAT
41963534 TTTT
1 TTTT
41963538 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTGAAAATTATTTTAAAT
Found at i:41963545 original size:10 final size:10
Alignment explanation
Indices: 41963500--41963547 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
41963490 AGAATTTTAA
*
41963500 AAATTATTTT
1 AAATTTTTTT
**
41963510 AAATTTTTGA
1 AAATTTTTTT
*
41963520 AAATTATTTT
1 AAATTTTTTT
*
41963530 GAATTTTTTT
1 AAATTTTTTT
41963540 AAATTTTT
1 AAATTTTT
41963548 GTTGAGAGAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (10 bp):
AAATTTTTTT
Found at i:41973971 original size:1 final size:1
Alignment explanation
Indices: 41973967--41973991 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
41973957 TTTTTTTTTT
41973967 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
41973992 TAAATTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:41975617 original size:22 final size:23
Alignment explanation
Indices: 41975579--41975621 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
41975569 CAAATTCAAG
41975579 TACCAAATCGAAAAAAAATTATA
1 TACCAAATCGAAAAAAAATTATA
*
41975602 TACCAAAT-TAAAAAAAATTA
1 TACCAAATCGAAAAAAAATTA
41975622 AATTCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.23
Consensus pattern (23 bp):
TACCAAATCGAAAAAAAATTATA
Found at i:41975684 original size:3 final size:3
Alignment explanation
Indices: 41975678--41975706 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41975668 AAAAAATGTC
41975678 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41975707 AGGCATGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41978018 original size:13 final size:14
Alignment explanation
Indices: 41978000--41978031 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41977990 TGAAATTATT
41978000 TTTTTA-AAAATAA
1 TTTTTAGAAAATAA
41978013 TTTTTAGAAAATAA
1 TTTTTAGAAAATAA
41978027 TTTTT
1 TTTTT
41978032 TTAATAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TTTTTAGAAAATAA
Found at i:41978078 original size:33 final size:32
Alignment explanation
Indices: 41978041--41978113 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
41978031 TTTAATAGTT
*
41978041 AATATTTTCTGATGTTTGAATGAATTTATAT-AA
1 AATATTTTCTGATGTTTG-ATAAATTTAT-TGAA
* *
41978074 AATATTTTTTTGTTGTTTGATAAATTTATTGAA
1 AATA-TTTTCTGATGTTTGATAAATTTATTGAA
41978107 AATATTT
1 AATATTT
41978114 CATAAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 4 0.11
33 19 0.54
34 12 0.34
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.53
Consensus pattern (32 bp):
AATATTTTCTGATGTTTGATAAATTTATTGAA
Found at i:41978476 original size:15 final size:15
Alignment explanation
Indices: 41978456--41978509 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
41978446 TACTACAAAA
41978456 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
41978471 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
41978488 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
41978505 ATATT
1 ATATT
41978510 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:41978614 original size:16 final size:19
Alignment explanation
Indices: 41978589--41978644 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
41978579 TAAAATTGAA
41978589 ATATTAAATAATTTATTAA-
1 ATATT-AATAATTTATTAAT
41978608 A-A-TAATAAATTATATTAATT
1 ATATTAAT-AATT-TATTAA-T
41978628 ATATTAATAATTTATTA
1 ATATTAATAATTTATTA
41978645 TATGACTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 5 0.16
18 7 0.23
19 1 0.03
20 6 0.19
21 5 0.16
22 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTAATAATTTATTAAT
Found at i:41990867 original size:92 final size:90
Alignment explanation
Indices: 41990747--41990916 Score: 241
Period size: 90 Copynumber: 1.9 Consensus size: 90
41990737 CACACTACCA
* * *
41990747 TTATATCACGTAACAATGCCATACATATATATACACAGAAGTAATTGCCATTCATCTTTGCTTAA
1 TTATAACACGTAACAATGCC--ACATATATAGACACAGAAGTAATTGCAATTCATCTTTGCTTAA
* *
41990812 GCTACCGTGCAACCTTGACATCTTCTG
64 CCAACCGTGCAACCTTGACATCTTCTG
* * * *
41990839 TTATAACACTTAACAATGCCATATATATAGACACATAAGTATTTGCAATTCATCTTTGCTTAACC
1 TTATAACACGTAACAATGCCACATATATAGACACAGAAGTAATTGCAATTCATCTTTGCTTAACC
41990904 AACCGTGCAACCT
66 AACCGTGCAACCT
41990917 CCGTTATAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
90 51 0.74
92 18 0.26
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (90 bp):
TTATAACACGTAACAATGCCACATATATAGACACAGAAGTAATTGCAATTCATCTTTGCTTAACC
AACCGTGCAACCTTGACATCTTCTG
Found at i:41990994 original size:81 final size:81
Alignment explanation
Indices: 41990838--41990994 Score: 244
Period size: 81 Copynumber: 1.9 Consensus size: 81
41990828 GACATCTTCT
* * *
41990838 GTTATAACACTTAACAATGCCATATATATAGACACATAAGTATTTGCAATTCATCTTTGCTTAAC
1 GTTATAACACATAACAATGCCATATATATACACACATAAGTATTTGCAATTCATCTTTGCTTAAA
*
41990903 CAACCGTGCAACCTCC
66 CAACCATGCAACCTCC
*
41990919 GTTATAACACATAACAATTG-CATATATATACACACATAAGTATTTGCAATTCATTTTTGCTTAA
1 GTTATAACACATAACAA-TGCCATATATATACACACATAAGTATTTGCAATTCATCTTTGCTTAA
*
41990983 ACTACCATGCAA
65 ACAACCATGCAA
41990995 TCTTAACATC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
81 67 0.97
82 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (81 bp):
GTTATAACACATAACAATGCCATATATATACACACATAAGTATTTGCAATTCATCTTTGCTTAAA
CAACCATGCAACCTCC
Found at i:41993873 original size:71 final size:71
Alignment explanation
Indices: 41993784--41993952 Score: 284
Period size: 71 Copynumber: 2.4 Consensus size: 71
41993774 CATACCTTAA
* *
41993784 CTTCAATGTTGATTGGTCTCGAGACAATATGTATTTTGTCTTGAGATAAGGTTCCTTTAAAGCAT
1 CTTCGATGTTGGTTGGTCTCGAGACAATATGTATTTTGTCTTGAGATAAGGTTCCTTTAAAGCAT
41993849 TTTTAG
66 TTTTAG
*
41993855 CTTCGATGTTGGTTGGTCTCGAGACGATATGTATTTTGTCTTGAGATAAGGTTCCTTTAAAGCAT
1 CTTCGATGTTGGTTGGTCTCGAGACAATATGTATTTTGTCTTGAGATAAGGTTCCTTTAAAGCAT
41993920 TTTTAG
66 TTTTAG
* * *
41993926 TTTTGATGTTGGTTTGTCTCGAGACAA
1 CTTCGATGTTGGTTGGTCTCGAGACAA
41993953 CCATGCTTGT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (71 bp):
CTTCGATGTTGGTTGGTCTCGAGACAATATGTATTTTGTCTTGAGATAAGGTTCCTTTAAAGCAT
TTTTAG
Found at i:41997227 original size:21 final size:21
Alignment explanation
Indices: 41997179--41997240 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
41997169 TTTTTTACTA
* *
41997179 ATACAAGTGTCAATTCTACCG
1 ATACAAGTTTCACTTCTACCG
41997200 A-AGCAAGTTTCACTTCTACCG
1 ATA-CAAGTTTCACTTCTACCG
**
41997221 ATACAAGTTTTTCTTCTACC
1 ATACAAGTTTCACTTCTACC
41997241 AACACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (21 bp):
ATACAAGTTTCACTTCTACCG
Found at i:41998051 original size:40 final size:42
Alignment explanation
Indices: 41997987--41998079 Score: 154
Period size: 40 Copynumber: 2.3 Consensus size: 42
41997977 GTTACCAGTA
*
41997987 TACGATGCTACACACAATCATCGATACGGTATAACTATTCCC
1 TACGATGCTACACACAATCATCGATACAGTATAACTATTCCC
*
41998029 TACGATGCTAC-C-CAATCATCGATACAGTATAACTGTTCCC
1 TACGATGCTACACACAATCATCGATACAGTATAACTATTCCC
41998069 TACGATGCTAC
1 TACGATGCTAC
41998080 TTACACCAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 37 0.76
41 1 0.02
42 11 0.22
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (42 bp):
TACGATGCTACACACAATCATCGATACAGTATAACTATTCCC
Found at i:42031192 original size:28 final size:28
Alignment explanation
Indices: 42031137--42031192 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
42031127 GACCAATTCA
* *
42031137 AAAAGTATAAGATTAAAATTGATCAAAT
1 AAAAGTACAAGATTAAAATTGATAAAAT
*
42031165 AAAAGTACAATGATT-AAATTTATAAAAT
1 AAAAGTACAA-GATTAAAATTGATAAAAT
42031193 TTACAATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (28 bp):
AAAAGTACAAGATTAAAATTGATAAAAT
Found at i:42032898 original size:537 final size:541
Alignment explanation
Indices: 42031878--42032965 Score: 1760
Period size: 537 Copynumber: 2.0 Consensus size: 541
42031868 AATAATACTG
* *
42031878 TAATGTGAAAATGTACTAAATTTGAAACCAAAATAGTCGATGTTTTGGACTGGAAAAAATAATTA
1 TAATATGAAAATGTACTAAATTTGAAACCAAAATAGTCGATGTTTTGGACTGGAAAAAAAAATTA
** *
42031943 ATTTAAATAGTAATGTAATGAATAAATTTAATATGAATATATTAACTTATTAAACTTGTTTTTTT
66 ATTTAAATAGTAATGTAACAAATAAATTTAATATGAATATATTAACTTATTAAACTTGTTTTTTA
*
42032008 TTTCTGTAAAATTCAATTTTTTTAAAGATAAATTTGGTACTAAATCATGGACGAAGTCATAAATT
131 TTTCTGTAAAATTCAATTTTTTTAAAGATAAATTTGGTACTAAACCATGGACGAAGTCATAAATT
*
42032073 TTTTAGGGAAGGAAGTTAAGATATATATTTTTATATCATATATTAATTTAAAATTTTATAAATTT
196 TTTTAGGGAAGCAAGTTAAGATATATATTTTTATATCATATATTAATTTAAAATTTTATAAATTT
* ** * *
42032138 AAGAAGATTGAAGCAACAATTTTTCTATTTTGGAGAGGATTAGGGGTTTGTCTGCCCTCACTTTT
261 AAGAAGATTGAAGCAACAATTTTTCTATTTTGGAGAGGATTAAGGGCCTGTCTGCCCCCACTCTT
* * *
42032203 TGCCCCTATAATAAACCGACAAGAAAGTTAAAACCAATTAAGACAAACACCAAACACTTGGTGAC
326 TGCCCCTATAATAAACCGAAAAGAAAGTTAAAACCAATTAAAACAAACACCAAACACTTGATGAC
* * * * *
42032268 TATTGTTGAATGTCACGGTTTAATATTAGAGGCATTTATTATAATAAAAAATACAAAAGATGTCT
391 CATTGTTGAATGCCACGGTTTAATATTAGAGGCATTCATTACAACAAAAAATACAAAAGATGTCT
*
42032333 CATCATGCGACTCTCTTTAATATTTCAAACTTTCTG-TAA-ATTTTTTTTTTCAATTTTTTTTGT
456 CATCATGCGACTCTCTTTAATATTTCAAACTTTCTGTTAATATTTTTTTTTTCAATTTTTATTGT
*
42032396 ATTTGTCCACTTAGAAAAAAC
521 ATTTGTCCACCTAGAAAAAAC
*
42032417 TAATATGAAAATGTACTAAATTTGAAACCAAAGTAGTCGATGTTTTGGACT-GAAAAAAAAATTT
1 TAATATGAAAATGTACTAAATTTGAAACCAAAATAGTCGATGTTTTGGACTGGAAAAAAAAA-TT
42032481 AATTTAAATAGTAATGTAACAAATAAATTTAATATGAATATATTAACTTATTAAACTTGTTTTTT
65 AATTTAAATAGTAATGTAACAAATAAATTTAATATGAATATATTAACTTATTAAACTTGTTTTTT
* *
42032546 ATTTCTGTAAAATTCAA-TTTTTTAAAGATAAATTTGGTACTAAACCATGGGCGAAGTCATAATT
130 ATTTCTGTAAAATTCAATTTTTTTAAAGATAAATTTGGTACTAAACCATGGACGAAGTCATAAAT
*
42032610 TTTTTAGGG-ATCAAGGTTAAGATATATATTTTTATATCATATATTAATTTAAAATTTTATAAAT
195 TTTTTAGGGAAGCAA-GTTAAGATATATATTTTTATATCATATATTAATTTAAAATTTTATAAAT
* * *
42032674 TTAGGAAGATTGAAGCAATAATTTTTC-ATTTTGGAGAGGGTTAAGGGCCTGTCTGCCCCCA-TC
259 TTAAGAAGATTGAAGCAACAATTTTTCTATTTTGGAGAGGATTAAGGGCCTGTCTGCCCCCACT-
* * *
42032737 CTTTGCCCTTGTAATAAACCGATAAAG-AAGTTGAAACCAATTAAAACAAACACCAAACACTTGA
323 CTTTGCCCCTATAATAAACCGA-AAAGAAAGTTAAAACCAATTAAAACAAACACCAAACACTTGA
* * *
42032801 TGACCATTGTTGAATGCCACGGTTTAATATTAGAGGCATTCGTTACAACAAAAAGTATAAAAGAT
387 TGACCATTGTTGAATGCCACGGTTTAATATTAGAGGCATTCATTACAACAAAAAATACAAAAGAT
*
42032866 GTCTCATCATGCGACTCTCTTTAATATTTCAAACTTTCTGTTAATATTTTTTTTTTCGATTTTTA
452 GTCTCATCATGCGACTCTCTTTAATATTTCAAACTTTCTGTTAATATTTTTTTTTTCAATTTTTA
42032931 TTGTATTTGTCCACCTAGAAAAAAC
517 TTGTATTTGTCCACCTAGAAAAAAC
42032956 TAATATGAAA
1 TAATATGAAA
42032966 GGATAAAGCC
Statistics
Matches: 507, Mismatches: 36, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
536 1 0.00
537 182 0.36
538 142 0.28
539 182 0.36
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (541 bp):
TAATATGAAAATGTACTAAATTTGAAACCAAAATAGTCGATGTTTTGGACTGGAAAAAAAAATTA
ATTTAAATAGTAATGTAACAAATAAATTTAATATGAATATATTAACTTATTAAACTTGTTTTTTA
TTTCTGTAAAATTCAATTTTTTTAAAGATAAATTTGGTACTAAACCATGGACGAAGTCATAAATT
TTTTAGGGAAGCAAGTTAAGATATATATTTTTATATCATATATTAATTTAAAATTTTATAAATTT
AAGAAGATTGAAGCAACAATTTTTCTATTTTGGAGAGGATTAAGGGCCTGTCTGCCCCCACTCTT
TGCCCCTATAATAAACCGAAAAGAAAGTTAAAACCAATTAAAACAAACACCAAACACTTGATGAC
CATTGTTGAATGCCACGGTTTAATATTAGAGGCATTCATTACAACAAAAAATACAAAAGATGTCT
CATCATGCGACTCTCTTTAATATTTCAAACTTTCTGTTAATATTTTTTTTTTCAATTTTTATTGT
ATTTGTCCACCTAGAAAAAAC
Found at i:42034792 original size:70 final size:71
Alignment explanation
Indices: 42034569--42034843 Score: 349
Period size: 71 Copynumber: 3.9 Consensus size: 71
42034559 TAAAATTAAT
* * *
42034569 TGAAACATACACCAAACACTTGGTGACCATCTTTGAATGTCATGGTTTAAAATCAGAGACATCTG
1 TGAAACAGACACCAAACACTTGGTGACCATCTTTAAATGTCATGGTTTAATATCAGAGACATCTG
*
42034634 TCTAAC
66 TCTCAC
* * * * * ** * *
42034640 TGAAACAAACACCAAACACTTGATGGCCATATTTGAATGTCATAATTTAATATCAGAAATATCTG
1 TGAAACAGACACCAAACACTTGGTGACCATCTTTAAATGTCATGGTTTAATATCAGAGACATCTG
42034705 TCTCAC
66 TCTCAC
42034711 TGAAATC-GACACCAAACACTTGGTGACCATCTTTAAATGTCAT-GTTTAATATCAGAGACATCT
1 TGAAA-CAGACACCAAACACTTGGTGACCATCTTTAAATGTCATGGTTTAATATCAGAGACATCT
*
42034774 ATCTCAC
65 GTCTCAC
* * * *
42034781 TGAAACAGACACCAAACACTTGATTG-TCATCTTTAAATTTCATGGTTTAATATCAAAGACATC
1 TGAAACAGACACCAAACACTTG-GTGACCATCTTTAAATGTCATGGTTTAATATCAGAGACATC
42034844 AGTTACAATA
Statistics
Matches: 177, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
69 1 0.01
70 58 0.33
71 117 0.66
72 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (71 bp):
TGAAACAGACACCAAACACTTGGTGACCATCTTTAAATGTCATGGTTTAATATCAGAGACATCTG
TCTCAC
Found at i:42034830 original size:141 final size:142
Alignment explanation
Indices: 42034577--42034835 Score: 403
Period size: 141 Copynumber: 1.8 Consensus size: 142
42034567 ATTGAAACAT
* *
42034577 ACACCAAACACTTGGTGACCATCTTTGAATGTCATGGTTTAAAATCAGAGACATCTGTCTAACTG
1 ACACCAAACACTTGGTGACCATCTTTAAATGTCATGGTTTAAAATCAGAGACATCTATCTAACTG
*
42034642 AAACAAACACCAAACACTTGATGGCCATATTTGAATGTCATAATTTAATATCAGAAATATCTGTC
66 AAACAAACACCAAACACTTGATGGCCATATTTAAATGTCATAATTTAATATCAGAAATATCTGTC
42034707 TCACTGAAATCG
131 TCACTGAAATCG
* *
42034719 ACACCAAACACTTGGTGACCATCTTTAAATGTCAT-GTTTAATATCAGAGACATCTATCTCACTG
1 ACACCAAACACTTGGTGACCATCTTTAAATGTCATGGTTTAAAATCAGAGACATCTATCTAACTG
* * * * * **
42034783 AAACAGACACCAAACACTTGATTGTCATCTTTAAATTTCATGGTTTAATATCA
66 AAACAAACACCAAACACTTGATGGCCATATTTAAATGTCATAATTTAATATCA
42034836 AAGACATCAG
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
141 71 0.68
142 34 0.32
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (142 bp):
ACACCAAACACTTGGTGACCATCTTTAAATGTCATGGTTTAAAATCAGAGACATCTATCTAACTG
AAACAAACACCAAACACTTGATGGCCATATTTAAATGTCATAATTTAATATCAGAAATATCTGTC
TCACTGAAATCG
Found at i:42036182 original size:71 final size:71
Alignment explanation
Indices: 42036092--42036375 Score: 309
Period size: 71 Copynumber: 4.0 Consensus size: 71
42036082 GAATTTAAAC
* * * *
42036092 CTAATTGAAACATAA-ACCAAACATTTGGTAGCCATCTTTAAATGTTATGATTTAATATCAGAGA
1 CTAACTGAAACA-AACACCAAACACTTGGTAGCCATCTTTGAATGTCATGATTTAATATCAGAGA
*
42036156 TATCTGT
65 CATCTGT
* * * * * * * * *
42036163 TTAACTAAAACAAACACCAAACACTTAGTGGTCATATTTGAATGTCATTATTTAATATCAAATAC
1 CTAACTGAAACAAACACCAAACACTTGGTAGCCATCTTTGAATGTCATGATTTAATATCAGAGAC
42036228 ATCTGT
66 ATCTGT
* * *
42036234 CTAACTGAAACAGACACTAAACACTTGGTAGCCATCTTTGAATGTCATGGTTTAATATCAGAGAC
1 CTAACTGAAACAAACACCAAACACTTGGTAGCCATCTTTGAATGTCATGATTTAATATCAGAGAC
*
42036299 ATCCGT
66 ATCTGT
* * * * * * * * *
42036305 CTAACTGGAATAGACACCAAACGCTTGATGGCCATCTTTGAATGTCATGGTTTAATTTCAGAGGC
1 CTAACTGAAACAAACACCAAACACTTGGTAGCCATCTTTGAATGTCATGATTTAATATCAGAGAC
42036370 ATCTGT
66 ATCTGT
42036376 TACAATAAAA
Statistics
Matches: 176, Mismatches: 36, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
70 2 0.01
71 174 0.99
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (71 bp):
CTAACTGAAACAAACACCAAACACTTGGTAGCCATCTTTGAATGTCATGATTTAATATCAGAGAC
ATCTGT
Found at i:42036288 original size:142 final size:142
Alignment explanation
Indices: 42036092--42036352 Score: 344
Period size: 142 Copynumber: 1.8 Consensus size: 142
42036082 GAATTTAAAC
* * * * *
42036092 CTAATTGAAACATAAACCAAACATTTGGTAGCCATCTTTAAATGTTATGATTTAATATCAGAGAT
1 CTAACTGAAACAGAAACCAAACACTTGGTAGCCATCTTTAAATGTCATGATTTAATATCAGAGAC
* * *
42036157 ATCTGTTTAACTAAAACAAACACCAAACACTT-AGTGGTCATATTTGAATGTCATTATTTAATAT
66 ATCCGTCTAACTAAAACAAACACCAAACACTTGA-TGGCCATATTTGAATGTCATTATTTAATAT
42036221 CAAATACATCTGT
130 CAAATACATCTGT
* * * *
42036234 CTAACTGAAACAGACACTAAACACTTGGTAGCCATCTTTGAATGTCATGGTTTAATATCAGAGAC
1 CTAACTGAAACAGAAACCAAACACTTGGTAGCCATCTTTAAATGTCATGATTTAATATCAGAGAC
** * * * *
42036299 ATCCGTCTAACTGGAATAGACACCAAACGCTTGATGGCCATCTTTGAATGTCAT
66 ATCCGTCTAACTAAAACAAACACCAAACACTTGATGGCCATATTTGAATGTCAT
42036353 GGTTTAATTT
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
142 99 0.99
143 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (142 bp):
CTAACTGAAACAGAAACCAAACACTTGGTAGCCATCTTTAAATGTCATGATTTAATATCAGAGAC
ATCCGTCTAACTAAAACAAACACCAAACACTTGATGGCCATATTTGAATGTCATTATTTAATATC
AAATACATCTGT
Found at i:42038172 original size:223 final size:222
Alignment explanation
Indices: 42037784--42038389 Score: 892
Period size: 223 Copynumber: 2.7 Consensus size: 222
42037774 GCAAGTAATA
* * ** *
42037784 TCTTGTATTAAACCAATAAGAAATTTAAAACTAATTGAAACAGACAAAAAACACTTTGTGG-CTA
1 TCTTGTACTAAACCAATAAG-AATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTC-A
* * * * * * * *
42037848 TTTTTGAATGCCACAGTTTAATGTTAGAGGCATCTTTGTTACAATAAAAAACACAAAAGATGGCT
64 GTTTTGAATGCTACGGTTTAATGTCAGAAGCATCTCTGTTACAGTAAAAAGCACAAAAGATGGCT
* * * * *
42037913 TGTCACATGACTATATTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTCAATTTTTGTTGTG
129 TGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCAATTAATTTTTTTTTCAATTTTTGTTGTG
* *
42037978 TTTATCCACCTACTTGTCCCCTCTTTCCC
194 TTTATCCACCTACTTGCCCCCTCATTCCC
42038007 TCTTGTACTAAACCAATAATGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTCAG
1 TCTTGTACTAAACCAATAA-GAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTCAG
*
42038072 TTTTGAATGCTACGGTTTAATGTCAGAAGCATCTCTGTTACGGTAAAAAGCACAAAAGATGGCTT
65 TTTTGAATGCTACGGTTTAATGTCAGAAGCATCTCTGTTACAGTAAAAAGCACAAAAGATGGCTT
*
42038137 GTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCAATTAATTTTTTTTTCGATTTTTGTTGTGT
130 GTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCAATTAATTTTTTTTTCAATTTTTGTTGTGT
*
42038202 TTATCCACCTATTTGCCCCCTCATTCCC
195 TTATCCACCTACTTGCCCCCTCATTCCC
*
42038230 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGTCAG
1 TCTTGTACTAAACCAATAA-GAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTCAG
* * *
42038295 TTTTGAATGCTATGGTTTAATGTCA-AAGGCATCTCTCTTACAGTAAAAAGCACAAAAGATGACT
65 TTTTGAATGCTACGGTTTAATGTCAGAA-GCATCTCTGTTACAGTAAAAAGCACAAAAGATGGCT
* *
42038359 TGTCACGTGGTTGCCTTTAATACTTCTCAAA
129 TGTCACGTGGCTGTCTTTAATACTTCTCAAA
42038390 AAGTGGCCAT
Statistics
Matches: 349, Mismatches: 31, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
222 2 0.01
223 345 0.99
224 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (222 bp):
TCTTGTACTAAACCAATAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTCAGT
TTTGAATGCTACGGTTTAATGTCAGAAGCATCTCTGTTACAGTAAAAAGCACAAAAGATGGCTTG
TCACGTGGCTGTCTTTAATACTTCTCAAACTTTCAATTAATTTTTTTTTCAATTTTTGTTGTGTT
TATCCACCTACTTGCCCCCTCATTCCC
Found at i:42038564 original size:197 final size:198
Alignment explanation
Indices: 42038201--42039006 Score: 670
Period size: 197 Copynumber: 4.0 Consensus size: 198
42038191 TTTTGTTGTG
** * * ** * *
42038201 TTTATCCACCTATTTGCCCCCTCATTCCCTCTTGTACTAAACCAATAAGGAATCTAAAACTAATT
1 TTTATCCACCTGCTTGTCCCCTCCTTTTCTCTTGTACTAAATCAATAAGGAATCTAAAATTAATT
* * * * * *
42038266 GAAACAAACACCAAACACTTGGTG-GTCAGTTTTGAATGCTATGGTTTAATGTCAAAGGCATCTC
66 GAAACAGACACCAAACACTTGGTGACT-ATTTTTGAATGCCACGATTTAATGTCAAAGGCATCTC
* * *
42038330 TCTTACAGTAAAAAGCACAAAAGATGACTTGTCACGTGGTTGCCTTTAATACTTCTCAAAAAGTG
130 TCTTACAATAAAAAGCACAAAAGATGACCTGTCACGTGATTGCCTTTAATACTTCTCAAAAAGTG
42038395 GCCA
195 GCCA
*
42038399 TTTATCCACCTGCTTG-CCCCTCCTTTTCTCTTGTACTAAATCAATAAGGAATTTAAAATTAATT
1 TTTATCCACCTGCTTGTCCCCTCCTTTTCTCTTGTACTAAATCAATAAGGAATCTAAAATTAATT
* * *
42038463 GAAACAGACACCAAATACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAGAGGTATCTCT
66 GAAACAGACACCAAACACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAAAGGCATCTCT
* * * *** **
42038528 GTTACAATAAAAAGCACAAAAGATGGCCTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTCA
131 CTTACAATAAAAAGCACAAAAGATGACCTGTCACGTGATTGCCTTTAATACTTCTCAAAAAGTGG
*
42038593 CTTAA
196 C--CA
* * ** * ** * * * * * *** * * **
42038598 TGTTTTTTTCGATTTTTGTTGTGTTTATCCACCTATTTGCCCCCT-CATTCCCTC-TTGTACTAA
1 ----TTTATCCA--CCTGCT-TG--TCCCCTCCT-TTT--CTCTTGTACTAAATCAAT-AAGGAA
* * ** * * * * *
42038661 ACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTG-GTCAGTTTTGAATGC
53 TCTAA-AATTAAT-TGAAAC--A--GACACCAA-A-----CACTTGGTGACT-ATTTTTGAATGC
* * * * * *
42038725 TATGGTTTAATGTCAAAGGCATCTCTCTTACAGTAAAAAGCACAAAAGATGACTTGTCACGTGGT
105 CACGATTTAATGTCAAAGGCATCTCTCTTACAATAAAAAGCACAAAAGATGACCTGTCACGTGAT
42038790 TGCCTTTAATACTTCTCAAAAAGTGGCCA
170 TGCCTTTAATACTTCTCAAAAAGTGGCCA
*
42038819 TTTATCCACCTGCTTG-CCCCTCCTTTTCTCTTGTACTAAATCAATAAGGAATTTAAAATTAATT
1 TTTATCCACCTGCTTGTCCCCTCCTTTTCTCTTGTACTAAATCAATAAGGAATCTAAAATTAATT
* * *
42038883 GAAACAGACACCAAATACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAGAGGTATCTCT
66 GAAACAGACACCAAACACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAAAGGCATCTCT
* * *
42038948 GTTACAATAAAAAGCACAAAAGATGGCCTGTCACGTGATTGTCTTTAATACTTCTCAAA
131 CTTACAATAAAAAGCACAAAAGATGACCTGTCACGTGATTGCCTTTAATACTTCTCAAA
42039007 CTTTCACTTA
Statistics
Matches: 458, Mismatches: 117, Indels: 67
0.71 0.18 0.10
Matches are distributed among these distances:
197 244 0.53
198 16 0.03
199 1 0.00
202 1 0.00
203 12 0.03
205 4 0.01
206 2 0.00
207 5 0.01
208 8 0.02
209 14 0.03
210 8 0.02
211 14 0.03
212 8 0.02
213 5 0.01
214 2 0.00
215 4 0.01
217 12 0.03
218 1 0.00
221 1 0.00
222 1 0.00
223 95 0.21
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (198 bp):
TTTATCCACCTGCTTGTCCCCTCCTTTTCTCTTGTACTAAATCAATAAGGAATCTAAAATTAATT
GAAACAGACACCAAACACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAAAGGCATCTCT
CTTACAATAAAAAGCACAAAAGATGACCTGTCACGTGATTGCCTTTAATACTTCTCAAAAAGTGG
CCA
Found at i:42038785 original size:420 final size:421
Alignment explanation
Indices: 42037978--42039479 Score: 2280
Period size: 420 Copynumber: 3.6 Consensus size: 421
42037968 TTTTGTTGTG
* * * *
42037978 TTTATCCACCTACTTGTCCCCT-CTTTCCCTCTTGTACTAAACCAATAATGAATCTAAAACTAAT
1 TTTATCCACCTGCTTGCCCCCTCCTTT-CCTCTTGTACTAAACCAATAAGGAATTTAAAACTAAT
* * * * * *
42038042 TGAAACAGACACCAAACACTTGGTG-GTCAGTTTTGAATGCTACGGTTTAATGTCAGAAGCATCT
65 TGAAACAGACACCAAATACTTGGTGACT-ATTTTTGAATGCCACGATTTAATGTCAGAGGCATCT
** * **
42038106 CTGTTACGGTAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTT
129 CTGTTACAATAAAAAGCACAAAAGATGGCCTGTCACGTGATTGTCTTTAATACTTCTCAAACTTT
* * *
42038171 CAATTAATTTTTTTTTCGATTTTTGTTGTGTTTATCCACCTATTTGCCCCCTCATTCCCTCTTGT
194 CACTTAATGTTTTTTTCGATTTTTGTTGTATTTATCCACCTATTTGCCCCCTCATTCCCTCTTGT
42038236 ACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGTCAGTTTTGA
259 ACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGTCAGTTTTGA
42038301 ATGCTATGGTTTAATGTCAAAGGCATCTCTCTTACAGTAAAAAGCACAAAAGATGACTTGTCACG
324 ATGCTATGGTTTAATGTCAAAGGCATCTCTCTTACAGTAAAAAGCACAAAAGATGACTTGTCACG
42038366 TGGTTGCCTTTAATACTTCTCAAAAAGTGGCCA
389 TGGTTGCCTTTAATACTTCTCAAAAAGTGGCCA
* * *
42038399 TTTATCCACCTGCTTG-CCCCTCCTTTTCTCTTGTACTAAATCAATAAGGAATTTAAAATTAATT
1 TTTATCCACCTGCTTGCCCCCTCCTTTCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATT
*
42038463 GAAACAGACACCAAATACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAGAGGTATCTCT
66 GAAACAGACACCAAATACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAGAGGCATCTCT
42038528 GTTACAATAAAAAGCACAAAAGATGGCCTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTCA
131 GTTACAATAAAAAGCACAAAAGATGGCCTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTCA
*
42038593 CTTAATGTTTTTTTCGATTTTTGTTGTGTTTATCCACCTATTTGCCCCCTCATTCCCTCTTGTAC
196 CTTAATGTTTTTTTCGATTTTTGTTGTATTTATCCACCTATTTGCCCCCTCATTCCCTCTTGTAC
42038658 TAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGTCAGTTTTGAAT
261 TAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGTCAGTTTTGAAT
42038723 GCTATGGTTTAATGTCAAAGGCATCTCTCTTACAGTAAAAAGCACAAAAGATGACTTGTCACGTG
326 GCTATGGTTTAATGTCAAAGGCATCTCTCTTACAGTAAAAAGCACAAAAGATGACTTGTCACGTG
42038788 GTTGCCTTTAATACTTCTCAAAAAGTGGCCA
391 GTTGCCTTTAATACTTCTCAAAAAGTGGCCA
* * *
42038819 TTTATCCACCTGCTTG-CCCCTCCTTTTCTCTTGTACTAAATCAATAAGGAATTTAAAATTAATT
1 TTTATCCACCTGCTTGCCCCCTCCTTTCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATT
*
42038883 GAAACAGACACCAAATACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAGAGGTATCTCT
66 GAAACAGACACCAAATACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAGAGGCATCTCT
42038948 GTTACAATAAAAAGCACAAAAGATGGCCTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTCA
131 GTTACAATAAAAAGCACAAAAGATGGCCTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTCA
* ** ***
42039013 CTTAATGTTTTTTTTTTTCTGATTTTTGTTGTATCTATCCACCTGCTTGCCTTTTC-TTCCCTCT
196 CTTAATG----TTTTTTTC-GATTTTTGTTGTATTTATCCACCTATTTGCCCCCTCATTCCCTCT
* * * * * *
42039077 TGTACTAAATCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACTCTTGGCGATCAATTT
256 TGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGTCAGTTT
* *** * *
42039142 TGAATGTTACAATTTAATGTCAGAGGCATCTCTGC-TACAATAAAAAAGCACAAAAGATGACTTG
321 TGAATGCTATGGTTTAATGTCAAAGGCATCTCT-CTTACAGT-AAAAAGCACAAAAGATGACTTG
** *
42039206 TCACGTGGTTATCTTTAATACTTCTCAAAAGGTGGCCA
384 TCACGTGGTTGCCTTTAATACTTCTCAAAAAGTGGCCA
** * * *
42039244 TTTATCCATGTGCTTGCCCCCTCATTCCCTCTTGTACTAAACCAATAAGAAATTTAAAACTAATT
1 TTTATCCACCTGCTTGCCCCCTCCTTTCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATT
* * *
42039309 GAAACAGACACCAAACT-CTTGGTGGCTATTTTTGAATGCCACGGTTTAACGTCAGAGGCATCTC
66 GAAACAGACACCAAA-TACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAGAGGCATCTC
** * * *
42039373 TGTTACAATAAAAAATACAAAAGATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTC
130 TGTTACAATAAAAAGCACAAAAGATGGCCTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTC
* * *
42039438 ACTTAATATTTTTTTTCGATTTTTATTTTATTTATCCACCTA
195 ACTTAAT-GTTTTTTTCGATTTTTGTTGTATTTATCCACCTA
42039480 CTGAAAGAAA
Statistics
Matches: 1005, Mismatches: 64, Indels: 23
0.92 0.06 0.02
Matches are distributed among these distances:
420 579 0.58
421 20 0.02
422 21 0.02
423 8 0.01
424 108 0.11
425 101 0.10
426 167 0.17
427 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (421 bp):
TTTATCCACCTGCTTGCCCCCTCCTTTCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATT
GAAACAGACACCAAATACTTGGTGACTATTTTTGAATGCCACGATTTAATGTCAGAGGCATCTCT
GTTACAATAAAAAGCACAAAAGATGGCCTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTCA
CTTAATGTTTTTTTCGATTTTTGTTGTATTTATCCACCTATTTGCCCCCTCATTCCCTCTTGTAC
TAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGTCAGTTTTGAAT
GCTATGGTTTAATGTCAAAGGCATCTCTCTTACAGTAAAAAGCACAAAAGATGACTTGTCACGTG
GTTGCCTTTAATACTTCTCAAAAAGTGGCCA
Found at i:42039313 original size:199 final size:198
Alignment explanation
Indices: 42039069--42039432 Score: 577
Period size: 199 Copynumber: 1.8 Consensus size: 198
42039059 TTGCCTTTTC
* *
42039069 TTCCCTCTTGTACTAAATCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACTCTTGGC-
1 TTCCCTCTTGTACTAAACCAATAAGAAATCTAAAACTAATTGAAACAGACACCAAACTCTTGGCG
* ** *
42039133 GATCAATTTTGAATGTTACAATTTAATGTCAGAGGCATCTCTGCTACAATAAAAAAGCACAAAAG
66 GCT-AATTTTGAATGCCACAATTTAACGTCAGAGGCATCTCTGCTACAATAAAAAA-CACAAAAG
42039198 ATGACTTGTCACGTGGTTATCTTTAATACTTCTCAAAAGGTGGCCATTTATCCATGTGCTTGCCC
129 ATGACTTGTCACGTGGTTATCTTTAATACTTCTCAAAAGGTGGCCATTTATCCATGTGCTTGCCC
42039263 CCTCA
194 CCTCA
* *
42039268 TTCCCTCTTGTACTAAACCAATAAGAAATTTAAAACTAATTGAAACAGACACCAAACTCTTGGTG
1 TTCCCTCTTGTACTAAACCAATAAGAAATCTAAAACTAATTGAAACAGACACCAAACTCTTGGCG
* ** * *
42039333 GCTATTTTTGAATGCCACGGTTTAACGTCAGAGGCATCTCTGTTACAATAAAAAATACAAAAGAT
66 GCTAATTTTGAATGCCACAATTTAACGTCAGAGGCATCTCTGCTACAATAAAAAACACAAAAGAT
*
42039398 GACTTGTCACGTGGTTGTCTTTAATACTTCTCAAA
131 GACTTGTCACGTGGTTATCTTTAATACTTCTCAAA
42039433 CTTTCACTTA
Statistics
Matches: 150, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
198 43 0.29
199 105 0.70
200 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (198 bp):
TTCCCTCTTGTACTAAACCAATAAGAAATCTAAAACTAATTGAAACAGACACCAAACTCTTGGCG
GCTAATTTTGAATGCCACAATTTAACGTCAGAGGCATCTCTGCTACAATAAAAAACACAAAAGAT
GACTTGTCACGTGGTTATCTTTAATACTTCTCAAAAGGTGGCCATTTATCCATGTGCTTGCCCCC
TCA
Found at i:42041235 original size:55 final size:53
Alignment explanation
Indices: 42041150--42041270 Score: 188
Period size: 55 Copynumber: 2.2 Consensus size: 53
42041140 ATTGTACGAT
42041150 GAAAATACTAATTTTGAAGCAAAAATAGTCAACATTTTGGACTTAATATATTGATG
1 GAAAATA-T-ATTTTGAAGCAAAAATAGTCAACATTTTGGAC-TAATATATTGATG
* *
42041206 GAAAAATATATTTTGAAGCAAAAATAGTCAATATTTTGGACTATTATATTGATG
1 G-AAAATATATTTTGAAGCAAAAATAGTCAACATTTTGGACTAATATATTGATG
42041260 GAAAATATATT
1 GAAAATATATT
42041271 AATTAAAATC
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
53 10 0.16
54 13 0.21
55 31 0.50
56 2 0.03
57 6 0.10
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (53 bp):
GAAAATATATTTTGAAGCAAAAATAGTCAACATTTTGGACTAATATATTGATG
Found at i:42042562 original size:211 final size:209
Alignment explanation
Indices: 42041667--42044615 Score: 3172
Period size: 211 Copynumber: 14.0 Consensus size: 209
42041657 CCTCCTTCCC
* * * ** *
42041667 TCTTCTACTAAATCAATAAGGAATCTAAAATTAATTGAAACAGACATAAAACACTT-GTGACTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
42041731 TTTTGAATGACAC-GATTTAATGTCAGAGGCATCTCTATTACAATAAAAAGCACAAAA-ATGGCT
66 TTTTGAATGCCACAG-TTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCT
* * * * ** *
42041794 TGTCATGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTTCCGATTTTTGTTC
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTT-TTATTTTTGTTG
*
42041859 TATTTATCCACCTGCTTCCACTCCTTCT
194 TA-TT-T--A------TCCACT--TGCT
*
42041887 CTCTTGTACTAAACTAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTA
1 -TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTA
* * *
42041952 TTTTTGAATGCCAC-GATTTAATGTCAAAGGCATCTCTCTTACAAAAAAAAGCACAAAAGATGGC
65 TTTTTGAATGCCACAG-TTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGC
* *
42042016 TTGTCACGTGGCTGTCTTTAATACTTCTCAAATTTTCACTTAATGTTTTTATTTTTTATTTTTGT
129 TTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATG-TTTT-TTTTTTATTTTTGT
42042081 TGTATTTATCCACTTGCT
192 TGTATTTATCCACTTGCT
* * * * *
42042099 TCTTGTTCTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACGCTAAACACTTTGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
**
42042164 TTTTGAATGCCACAGTTTAATGTCAGAGATATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * *
42042229 G-CACGTGGTTGCCTTTAATACTTCTCAAATTTTAACTT-A----TTTTTTTTATTTTTGTTGTA
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTATTTTTGTTGTA
* *
42042288 -TTATCCACTCGTT
196 TTTATCCACTTGCT
* * *
42042301 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAATA-ATCACCAAACACTTGGTGACTA
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGA-CACCAAACACTTGGTGGCTA
* * * * *
42042365 TTTTTGAATGCCACAGTTTAATGTTAGAGGCATCTCTATTACAATAAAAAGCACAAATGACGGTT
65 TTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCT
* * *
42042430 TGTCACGTCGTTGCCTTTAATACTTCTCAAACTTTCACTTAATGTATTTTATTTTTATTTTTTTT
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGT-TTTT-TTTTTATTTTTGTT
*
42042495 GTATCTATCCACTTGCT
193 GTATTTATCCACTTGCT
* *
42042512 TCTTGTTCTAAACCAATAAGGAATCTAAAACTACTTGAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
42042577 TTTT-AATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAACGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* *
42042641 GTCACGTGGTTGTCTTTAATAGTTCTCAAACTTTCACTTAAT-TTTTTTTTTAATTTTTGTTGTA
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTATTTTTGTTGTA
**
42042705 TTTATCCACTCACT
196 TTTATCCACTTGCT
* * *
42042719 TATTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTAGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * *
42042784 TTTTGAATGCCACAGTTTAATGTCAGATGCATCTTTGTTACAATAGAAAGCACAAAAGGTGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
** * *
42042849 CCCATGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATG------TTTT-TTTTTGTTGCA
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTATTTTTGTTGTA
*
42042907 TTTATCCACTTGTT
196 TTTATCCACTTGCT
* *
42042921 TCTTGTACTAAACCAATAAGGAATCTAAAGCTAATTGAAAGAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * * * * * * * *
42042986 TTCTGAATTCCACGGGTTAATTTTAGACGCATCCCTATTACAATAAAAAACACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
**
42043051 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAAT-TTTTTTTTAAATTTTTGTTGT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTT-AATGTTTTTTTTTTATTTTTGTTGT
*
42043115 ATTTATCCACTCGCT
195 ATTTATCCACTTGCT
* * *
42043130 TCTTGTTCTAAACCAATAAGGAATCT-AAACTAATTGAAACAAACACCAAACACTTAGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
42043194 TTTTGAATGCCACAGTTTAATATCAGAGGCATCTCTGTTATAATAAAAAGTACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* *
42043259 GTCACGTGATTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTATTTTATTTTTGTTG
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-GTTTTTT-TTTTATTTTTGTTG
*
42043324 TATTTATCCACTTGTT
194 TATTTATCCACTTGCT
* * *
42043340 TCTTGTACTAAACCAATAAGGAACCTAAAACTAATTGAAACAGACACCAAAAACTTGGTGACTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * *
42043405 TTTTGAATGCCACAGTTTAATGTCAGAGGTATCTCTATTATAGTAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * *
42043470 GTTACGTGGTTGTCTTTAATAATTCTCAAACTTTCA-TCTAATG---TTTTTTTATTTTTGTTAT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACT-TAATGTTTTTTTTTTATTTTTGTTGT
42043531 ATTTATCCA------
195 ATTTATCCACTTGCT
* * *
42043540 -CTTGTACTAAACCAATAAGGAATCTAAAATTAATTGAAACAAACACCAAACACTTGGTGGCTGT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
42043604 TTTTGAATGCCACAGTTTAATGACAGAGGCATCTCTTTTACAA-AAAAACGCACAAAAGATGGCT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAA-GCACAAAAGATGGCT
** * *
42043668 TGTCACGTGACTATCTTTAATACTTCTCAAACTTTCACTTAATGGTTTTTTTCTTCGATTTTTGT
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-GTTTTTTT-TT-TATTTTTGT
*
42043733 TGTGTTTATCCACCTGCTTGTCCCCTTCTT
192 TGTATTTATCCA----CTTG-------C-T
* * *
42043763 CCCTCTTGTACTAAACCAATAATGAATCTAAAACTAATTGAAACAAACACCAAACACTTGATGG-
1 ---TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGC
* * * * * *
42043827 TCAGTTTTGAATGCTACGGTTTAATGTCAGAGGTATTTCTGTTACAGTAAAAAGCACAAAAGATG
63 T-ATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATG
* ** *
42043892 GCTTATCACGTGACTGTCTTTAATACTTCTCAAACTTTCAATTAATGTTTTTTTTTTCGATTTTT
127 GCTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTT--ATTTTT
*
42043957 GTTGTGTTTATCCACCTGCTTGCCCCCTCATT
190 GTTGTATTTATCCA----CTTG------C--T
* * * *
42043989 ACCTCTTGGACTAAACCAATAAGGAATCTAAAACTAATTGCAACAAACATCAAACACTTGGTGGC
1 ---TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGC
* *
42044054 TATTTTTGAATGTCACAGTTTAATGTCAGAGGCATCTCTGTT--AATATAAAAGTACAAAAGATG
63 TATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATA-AAAAGCACAAAAGATG
* * * ** * *** * ** ** *
42044117 GCTTATCACGTGGCTGTCTTTAATATTTCTCAAA-----AGGT--GGCCATTTATCCACCTGT-T
127 GCTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTATTTTTGT
**** * * *
42044174 TGCCCCT-T-C-CGTCCC
192 TGTATTTATCCACTTGCT
* * *
42044189 TCTTGTACTAAACCAATAAGAAATTTAAAACTAATTAAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
42044254 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTATAATAAAAAAGCACAAAAGATGACT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAAT-AAAAAGCACAAAAGATGGCT
* **
42044319 TGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTCCGGTTTTTGTT
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTT--TATTTTTGTT
* *
42044384 GTGTTTATCCTCCTGCTTGCCTCCTCCTT
193 GTATTTA---TCC-ACTTG-------C-T
* * * * * *
42044413 CCCTCTTGTACTGACCCAATAAGGAATTTAAAACTAATTGCAATAGACACCAAACACTTTGTGGC
1 ---TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGC
* * * *
42044478 TATTTTTGAATGCCACGGGTTAATGTCAGAAGCATCTCTGTTATAATAAAAAGCACAAAAGATGG
63 TATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGG
* * ** * * * ***
42044543 CTTTTTACGTGACTGTCTTTAATACTCCTCAAATTTTTACTTAAT-TTTTTTTGCGATTTTTGTT
128 CTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTATTTTTGTT
42044607 GTATTTATC
193 GTATTTATC
42044616 TGCTTACTGA
Statistics
Matches: 2351, Mismatches: 278, Indels: 199
0.83 0.10 0.07
Matches are distributed among these distances:
197 95 0.04
198 5 0.00
199 196 0.08
200 3 0.00
201 1 0.00
202 297 0.13
203 62 0.03
204 7 0.00
205 18 0.01
206 28 0.01
207 98 0.04
208 227 0.10
209 62 0.03
210 194 0.08
211 323 0.14
212 5 0.00
213 2 0.00
214 8 0.00
215 4 0.00
216 5 0.00
218 5 0.00
220 5 0.00
221 50 0.02
222 61 0.03
223 64 0.03
224 18 0.01
225 66 0.03
226 188 0.08
227 249 0.11
228 5 0.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (209 bp):
TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTATTTTTGTTGTA
TTTATCCACTTGCT
Found at i:42042924 original size:620 final size:617
Alignment explanation
Indices: 42041666--42044615 Score: 3193
Period size: 620 Copynumber: 4.7 Consensus size: 617
42041656 CCCTCCTTCC
* * * ** *
42041666 CTCTTCTACTAAATCAATAAGGAATCTAAAATTAATTGAAACAGACATAAAACACTT-GTGACTA
1 CTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTA
*
42041730 TTTTTGAATGACAC-GATTTAATGTCAGAGGCATCTCTATTACAATAAAAAGCACAAAA-ATGGC
66 TTTTTGAATGCCACAG-TTTAATGTCAGAGGCATCTCTATTACAATAAAAAGCACAAAAGATGGC
* * *
42041793 TTGTCATGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAA--TATTTTTTTTCCGATTTTTG
130 TTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTATTTTTTTT--TA-TTTT-
* * * *
42041856 TTCTATTTATCCACCTGCTTCCACTCCTTCTCTCTTGTACTAAACTAATAAGGAATCTAAAACTA
191 TT-T-TGTAT----CT--ATCCACT--TGCT-TCTTGTACTAAACCAATAAGGAATCTAAAACTA
*
42041921 ATTGAAACAGACACCAAACACTTGGTGGCTATTTTTGAATGCCAC-GATTTAATGTCAAAGGCAT
245 ATTGAAACAGACACCAAACACTTGGTGGCTATTTTTGAATGCCACAG-TTTAATGTCAGAGGCAT
* * * *
42041985 CTCTCTTACAAAAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAATT
309 CTCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGACTGTCTTTAATACTTCTCAAACT
* * * *
42042050 TTCACTTAATGTTTTTATTTTTTATTTTTGTTGTATTTATCCACTTGCTTCTTGTTCTAAACCAA
374 TTCACTTAA--TTTTT-TTTTTGATTTTTGTTGTATTTATCCACTCGCTTATTGTACTAAACCAA
* * * *
42042115 TAAAGAATCTAAAACTAATTGAAACAGACGCTAAACACTTTGTGGCTATTTTTGAATGCCACAGT
436 TAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGT
** * *
42042180 TTAATGTCAGAGATATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTGCACGTGGTTGCCTTT
501 TTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTTCACGTGGTTGTCTTT
* * * * * *
42042245 AATACTTCTCAAATTTTAACTTATTTTTTTTATTTTTGTTGTATTATCCACTCGT
566 AATACTTCTCAAACTTTCACTTA-ATGTTTT-TTTTTGTTGCATTAT-CACTTGT
* * * *
42042300 TTCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAATA-ATCACCAAACACTTGGTGACT
1 CTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGA-CACCAAACACTTGGTGGCT
* * * *
42042364 ATTTTTGAATGCCACAGTTTAATGTTAGAGGCATCTCTATTACAATAAAAAGCACAAATGACGGT
65 ATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTATTACAATAAAAAGCACAAAAGATGGC
* * *
42042429 TTGTCACGTCGTTGCCTTTAATACTTCTCAAACTTTCACTTAATGTATTTTATTTTTATTTTTTT
130 TTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTATTTT-TTTTTATTTTTTT
* *
42042494 TGTATCTATCCACTTGCTTCTTGTTCTAAACCAATAAGGAATCTAAAACTACTTGAAACAGACAC
194 TGTATCTATCCACTTGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACAC
*
42042559 CAAACACTTGGTGGCTATTTTT-AATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAA
259 CAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAA
* ** *
42042623 AAGCACAAACGATGGCTTGTCACGTGGTTGTCTTTAATAGTTCTCAAACTTTCACTTAATTTTTT
324 AAGCACAAAAGATGGCTTGTCACGTGACTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTT
* * *
42042688 TTTTAATTTTTGTTGTATTTATCCACTCACTTATTGTTCTAAACCAATAAGGAATCTAAAACTAA
389 TTTTGATTTTTGTTGTATTTATCCACTCGCTTATTGTACTAAACCAATAAGGAATCTAAAACTAA
* *
42042753 TTGAAACAGACACCAAACACTTGGTAGCTATTTTTGAATGCCACAGTTTAATGTCAGATGCATCT
454 TTGAAACAGACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCT
* * * * *
42042818 TTGTTACAATAGAAAGCACAAAAGGTGGCTTCCCATGTGGTTGTCTTTAATACTTCTCAAACTTT
519 CTGTTACAATAAAAAGCACAAAAGATGGCTT-TCACGTGGTTGTCTTTAATACTTCTCAAACTTT
42042883 CACTTAATGTTTTTTTTTGTTGCATTTATCCACTTGT
583 CACTTAATGTTTTTTTTTGTTGCA-TTAT-CACTTGT
* * *
42042920 TTCTTGTACTAAACCAATAAGGAATCTAAAGCTAATTGAAAGAGACACCAAACACTTGGTGGCTA
1 CTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTA
* * * * * * * * *
42042985 TTTCTGAATTCCACGGGTTAATTTTAGACGCATCCCTATTACAATAAAAAACACAAAAGATGGCT
66 TTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTATTACAATAAAAAGCACAAAAGATGGCT
* *
42043050 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA---ATTTTTTTTTAAATTTTTGT
131 TGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTATTTTTTTTT--ATTTTTTT
* * * *
42043112 TGTATTTATCCACTCGCTTCTTGTTCTAAACCAATAAGGAATCT-AAACTAATTGAAACAAACAC
194 TGTATCTATCCACTTGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACAC
* * *
42043176 CAAACACTTAGTGGCTATTTTTGAATGCCACAGTTTAATATCAGAGGCATCTCTGTTATAATAAA
259 CAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAA
* *
42043241 AAGTACAAAAGATGGCTTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTT
324 AAGCACAAAAGATGGCTTGTCACGTGACTGTCTTTAATACTTCTCAAACTTTCACTT-A-ATTTT
* * * * *
42043306 TTTATTTTATTTTTGTTGTATTTATCCACTTGTTTCTTGTACTAAACCAATAAGGAACCTAAAAC
387 TTT-TTTGATTTTTGTTGTATTTATCCACTCGCTTATTGTACTAAACCAATAAGGAATCTAAAAC
* * *
42043371 TAATTGAAACAGACACCAAAAACTTGGTGACTATTTTTGAATGCCACAGTTTAATGTCAGAGGTA
451 TAATTGAAACAGACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCA
* * * * *
42043436 TCTCTATTATAGTAAAAAGCACAAAAGATGGCTTGTTACGTGGTTGTCTTTAATAATTCTCAAAC
516 TCTCTGTTACAATAAAAAGCACAAAAGATGGCTT-TCACGTGGTTGTCTTTAATACTTCTCAAAC
* * *
42043501 TTTCA-TCTAATGTTTTTTTATTTTTG--TTAT-ATTTAT
580 TTTCACT-TAATGTTTTTTT-TTGTTGCATTATCACTTGT
* * *
42043537 CCACTTGTACTAAACCAATAAGGAATCTAAAATTAATTGAAACAAACACCAAACACTTGGTGGCT
1 -CTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCT
* * *
42043602 GTTTTTGAATGCCACAGTTTAATGACAGAGGCATCTCTTTTACAA-AAAAACGCACAAAAGATGG
65 ATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTATTACAATAAAAA-GCACAAAAGATGG
* * *
42043666 CTTGTCACGTGACTATCTTTAATACTTCTCAAACTTTCACTTAATGGT-TTTTTTCTTCGATTTT
129 CTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAAT-GTATTTTTT-TT-TATTTT
* * * *
42043730 TGTTGTGTTTATCCACCTGCTTGTCCCCTTCTTCCCTCTTGTACTAAACCAATAATGAATCTAAA
191 TTTTGTATCTATCCA----CTTG-------C-T---TCTTGTACTAAACCAATAAGGAATCTAAA
* * * * *
42043795 ACTAATTGAAACAAACACCAAACACTTGATGG-TCAGTTTTGAATGCTACGGTTTAATGTCAGAG
241 ACTAATTGAAACAGACACCAAACACTTGGTGGCT-ATTTTTGAATGCCACAGTTTAATGTCAGAG
* * * *
42043859 GTATTTCTGTTACAGTAAAAAGCACAAAAGATGGCTTATCACGTGACTGTCTTTAATACTTCTCA
305 GCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGACTGTCTTTAATACTTCTCA
* *
42043924 AACTTTCAATTAATGTTTTTTTTTTCGATTTTTGTTGTGTTTATCCACCTGCTTGCCCCCTCATT
370 AACTTTCACTTAA--TTTTTTTTTT-GATTTTTGTTGTATTTATCCA-CT-C--G------C-TT
* * * *
42043989 ACCTCTTGGACTAAACCAATAAGGAATCTAAAACTAATTGCAACAAACATCAAACACTTGGTGGC
421 A----TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGC
* *
42044054 TATTTTTGAATGTCACAGTTTAATGTCAGAGGCATCTCTGTT--AATATAAAAGTACAAAAGATG
482 TATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATA-AAAAGCACAAAAGATG
* * * ** * ***** * * *
42044117 GCTTATCACGTGGCTGTCTTTAATATTTCTCAAAAGGTGGC-CATTTATCCACCTGTTTG--CCC
546 GCTT-TCACGTGGTTGTCTTTAATACTTCTC-AAA-CTTTCAC-TTAATGTTTTTTTTTGTTGCA
* * **
42044179 CT-TC-CGTCC
607 TTATCACTTGT
* * *
42044188 CTCTTGTACTAAACCAATAAGAAATTTAAAACTAATTAAAACAGACACCAAACACTTGGTGGCTA
1 CTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTA
* * * *
42044253 TTTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTATAATAAAAAAGCACAAAAGATGAC
66 TTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTATTACAAT-AAAAAGCACAAAAGATGGC
**
42044318 TTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGT-TTTTTTTTCCGGTTTTTG
130 TTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTATTTTTTTT--TATTTTT-
* * * * *
42044382 TTGTGTTTATCCTCCTGCTTGC-CTCCTCCTTCCCTCTTGTACTGACCCAATAAGGAATTTAAAA
192 TT-TG--TAT-CT-AT-C---CACT--TGC-T---TCTTGTACTAAACCAATAAGGAATCTAAAA
* * * * * *
42044446 CTAATTGCAATAGACACCAAACACTTTGTGGCTATTTTTGAATGCCACGGGTTAATGTCAGAAGC
242 CTAATTGAAACAGACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGC
* * * *
42044511 ATCTCTGTTATAATAAAAAGCACAAAAGATGGCTTTTTACGTGACTGTCTTTAATACTCCTCAAA
307 ATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGACTGTCTTTAATACTTCTCAAA
* * **
42044576 TTTTTACTTAATTTTTTTTGCGATTTTTGTTGTATTTATC
372 CTTTCACTTAATTTTTTTTTTGATTTTTGTTGTATTTATC
42044616 TGCTTACTGA
Statistics
Matches: 1993, Mismatches: 237, Indels: 159
0.83 0.10 0.07
Matches are distributed among these distances:
616 5 0.00
617 53 0.03
618 286 0.14
619 15 0.01
620 325 0.16
621 250 0.13
622 7 0.00
623 91 0.05
624 67 0.03
625 6 0.00
627 6 0.00
629 2 0.00
632 1 0.00
633 6 0.00
634 48 0.02
635 63 0.03
636 75 0.04
637 153 0.08
638 8 0.00
639 4 0.00
641 1 0.00
647 18 0.01
648 10 0.01
649 2 0.00
650 268 0.13
651 101 0.05
652 105 0.05
653 7 0.00
654 3 0.00
655 3 0.00
656 1 0.00
657 2 0.00
660 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (617 bp):
CTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTA
TTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTATTACAATAAAAAGCACAAAAGATGGCT
TGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTATTTTTTTTTATTTTTTTTG
TATCTATCCACTTGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCA
AACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAA
GCACAAAAGATGGCTTGTCACGTGACTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTT
TTGATTTTTGTTGTATTTATCCACTCGCTTATTGTACTAAACCAATAAGGAATCTAAAACTAATT
GAAACAGACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCT
GTTACAATAAAAAGCACAAAAGATGGCTTTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCAC
TTAATGTTTTTTTTTGTTGCATTATCACTTGT
Found at i:42043178 original size:410 final size:412
Alignment explanation
Indices: 42041667--42044615 Score: 3072
Period size: 410 Copynumber: 7.0 Consensus size: 412
42041657 CCTCCTTCCC
* * * ** *
42041667 TCTTCTACTAAATCAATAAGGAATCTAAAATTAATTGAAACAGACATAAAACACTT-GTGACTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
42041731 TTTTGAATGACACGATTTAATGTCAGAGGCATCTCTATTACAATAAAAAGCACAAAA-ATGGCTT
66 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * * * *
42041795 GTCATGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTTCCGATTTTTGTTCT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA-ATTTTTTTTTCGATTTTTGTTGT
* *
42041860 ATTTATCCACCTGCTTCCACTCCTTCTCTCTTGTACTAAACTAATAAGGAATCTAAAACTAATTG
195 A-TT-T--A------TCCACT-C-GCT-TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTG
* *
42041925 AAACAGACACCAAACACTTGGTGGCTATTTTTGAATGCCAC-GATTTAATGTCAAAGGCATCTCT
247 AAACAAACACCAAACACTTGGTGGCTATTTTTGAATGCCACAG-TTTAATGTCAGAGGCATCTCT
* * *
42041989 CTTACAAAAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAATTTTCA
311 GTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCA
42042054 CTTAATGTTTTTATTTTTTATTTTTGTTGTATTTATCCACTTGCT
376 CTTAATG--------TTTTATTTTTGTTGTATTTATCCACTTGCT
* * * * *
42042099 TCTTGTTCTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACGCTAAACACTTTGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* **
42042164 TTTTGAATGCCACAGTTTAATGTCAGAGATATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * *
42042229 G-CACGTGGTTGCCTTTAATACTTCTCAAATTTTAACTT--A-TTTTTTTT--ATTTTTGTTGTA
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAATTTTTTTTTCGATTTTTGTTGTA
* * * *
42042288 -TTATCCACTCGTTTCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAATAATCACCAAA
196 TTTATCCACTCGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAA
* * *
42042352 CACTTGGTGACTATTTTTGAATGCCACAGTTTAATGTTAGAGGCATCTCTATTACAATAAAAAGC
261 CACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGC
* * * * * *
42042417 ACAAATGACGGTTTGTCACGTCGTTGCCTTTAATACTTCTCAAACTTTCACTTAATGTATTTTAT
326 ACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATG--------
* *
42042482 TTTTATTTTTTTTGTATCTATCCACTTGCT
383 TTTTATTTTTGTTGTATTTATCCACTTGCT
* *
42042512 TCTTGTTCTAAACCAATAAGGAATCTAAAACTACTTGAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
42042577 TTTT-AATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAACGATGGCTT
66 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* **
42042641 GTCACGTGGTTGTCTTTAATAGTTCTCAAACTTTCACTT-AATTTTTTTTTTAATTTTTGTTGTA
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAATTTTTTTTTCGATTTTTGTTGTA
* * * *
42042705 TTTATCCACTCACTTATTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAA
196 TTTATCCACTCGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAA
* * * *
42042770 CACTTGGTAGCTATTTTTGAATGCCACAGTTTAATGTCAGATGCATCTTTGTTACAATAGAAAGC
261 CACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGC
* ** * *
42042835 ACAAAAGGTGGCTTCCCATGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTT-TTT
326 ACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTATTT
* *
42042899 TTGTTGCATTTATCCACTTGTT
391 TTGTTGTATTTATCCACTTGCT
* *
42042921 TCTTGTACTAAACCAATAAGGAATCTAAAGCTAATTGAAAGAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * * * * * * *
42042986 TTCTGAATTCCACGGGTTAATTTTAGACGCATCCCTATTACAATAAAAAACACAAAAGATGGCTT
66 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
**
42043051 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAATTTTTTTTTAAATTTTTGTTGTA
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAATTTTTTTTTCGATTTTTGTTGTA
*
42043116 TTTATCCACTCGCTTCTTGTTCTAAACCAATAAGGAATCT-AAACTAATTGAAACAAACACCAAA
196 TTTATCCACTCGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAA
* * * *
42043180 CACTTAGTGGCTATTTTTGAATGCCACAGTTTAATATCAGAGGCATCTCTGTTATAATAAAAAGT
261 CACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGC
** *
42043245 ACAAAAGATGGCTTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTA
326 ACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTT-A-A------TG
*
42043310 TTTTATTTTTGTTGTATTTATCCACTTGTT
383 TTTTATTTTTGTTGTATTTATCCACTTGCT
* * *
42043340 TCTTGTACTAAACCAATAAGGAACCTAAAACTAATTGAAACAGACACCAAAAACTTGGTGACTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * * *
42043405 TTTTGAATGCCACAGTTTAATGTCAGAGGTATCTCTATTATAGTAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * * *
42043470 GTTACGTGGTTGTCTTTAATAATTCTCAAACTTTCA-TCT-AATGTTTTTTT--ATTTTTGTTAT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACT-TAAATTTTTTTTTCGATTTTTGTTGT
*
42043531 ATTTATCCA-------CTTGTACTAAACCAATAAGGAATCTAAAATTAATTGAAACAAACACCAA
195 ATTTATCCACTCGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAA
* * *
42043589 ACACTTGGTGGCTGTTTTTGAATGCCACAGTTTAATGACAGAGGCATCTCTTTTACAA-AAAAAC
260 ACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAA-
* *
42043653 GCACAAAAGATGGCTTGTCACGTGACTATCTTTAATACTTCTCAAACTTTCACTTAATGGTTTTT
324 GCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAAT-G-----
*
42043718 TTCTTCGATTTTTGTTGTGTTTATCCACCTGCTTGTCCCCTTCTT
383 TT-TT--ATTTTTGTTGTATTTATCCA----CTTG-------C-T
* * *
42043763 CCCTCTTGTACTAAACCAATAATGAATCTAAAACTAATTGAAACAAACACCAAACACTTGATGG-
1 ---TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGC
* * * * *
42043827 TCAGTTTTGAATGCTACGGTTTAATGTCAGAGGTATTTCTGTTACAGTAAAAAGCACAAAAGATG
63 T-ATTTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATG
* ** * *
42043892 GCTTATCACGTGACTGTCTTTAATACTTCTCAAACTTTCAATTAATGTTTTTTTTTTCGATTTTT
127 GCTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA--ATTTTTTTTTCGATTTTT
* *
42043957 GTTGTGTTTATCCACCTGCTTGCCCCCTCATTACCTCTTGGACTAAACCAATAAGGAATCTAAAA
190 GTTGTATTTATCCA-CT-C--G------C--T---TCTTGTACTAAACCAATAAGGAATCTAAAA
* * *
42044022 CTAATTGCAACAAACATCAAACACTTGGTGGCTATTTTTGAATGTCACAGTTTAATGTCAGAGGC
240 CTAATTGAAACAAACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGC
* * *
42044087 ATCTCTGTT--AATATAAAAGTACAAAAGATGGCTTATCACGTGGCTGTCTTTAATATTTCTCAA
305 ATCTCTGTTACAATA-AAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAA
*** ** * * ** * **** * * *
42044150 AAGGTGGC--CAT-TTATCCACCTGT-TTGCCCCT-T-C-CGTCCC
369 ACTTTCACTTAATGTT-T-TATTTTTGTTGTATTTATCCACTTGCT
* * *
42044189 TCTTGTACTAAACCAATAAGAAATTTAAAACTAATTAAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
42044254 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTATAATAAAAAAGCACAAAAGATGACT
66 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAAT-AAAAAGCACAAAAGATGGCT
* * *
42044319 TGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTCCGGTTTTTGTT
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA-ATTTTTTTTT-CGATTTTTGTT
* * * * *
42044384 GTGTTTATCCTCCTGCTTGCCTCCTCCTTCCCTCTTGTACTGACCCAATAAGGAATTTAAAACTA
193 GTATTTATCC-ACT-C--G-------C-T---TCTTGTACTAAACCAATAAGGAATCTAAAACTA
* * * * * * *
42044449 ATTGCAATAGACACCAAACACTTTGTGGCTATTTTTGAATGCCACGGGTTAATGTCAGAAGCATC
243 ATTGAAACAAACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATC
* * * * * *
42044514 TCTGTTATAATAAAAAGCACAAAAGATGGCTTTTTACGTGACTGTCTTTAATACTCCTCAAATTT
308 TCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTT
* *
42044579 TTACTTAATTTTTTTTGCGATTTTTGTTGTATTTATC
373 TCACTTAA--TGTTTT---ATTTTTGTTGTATTTATC
42044616 TGCTTACTGA
Statistics
Matches: 2155, Mismatches: 265, Indels: 192
0.83 0.10 0.07
Matches are distributed among these distances:
402 1 0.00
408 3 0.00
409 117 0.05
410 345 0.16
411 82 0.04
412 58 0.03
413 284 0.13
414 3 0.00
415 13 0.01
416 25 0.01
417 12 0.01
418 180 0.08
419 172 0.08
422 1 0.00
423 105 0.05
424 183 0.08
425 52 0.02
426 152 0.07
427 15 0.01
429 17 0.01
430 3 0.00
431 21 0.01
432 52 0.02
433 90 0.04
434 10 0.00
439 1 0.00
440 1 0.00
441 4 0.00
442 3 0.00
443 3 0.00
450 2 0.00
451 2 0.00
452 44 0.02
453 99 0.05
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (412 bp):
TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAATTTTTTTTTCGATTTTTGTTGTA
TTTATCCACTCGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAA
CACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGC
ACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTATTT
TTGTTGTATTTATCCACTTGCT
Found at i:42044063 original size:226 final size:226
Alignment explanation
Indices: 42043540--42044150 Score: 917
Period size: 227 Copynumber: 2.7 Consensus size: 226
42043530 TATTTATCCA
* *
42043540 CTTGTACTAAACCAATAAGGAATCTAAAATTAATTGAAACAAACACCAAACACTTGGTGGCTGTT
1 CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGCTATT
* * * * *
42043605 TTTGAATGCCACAGTTTAATGACAGAGGCATCTCTTTTACAAAAAAACGCACAAAAGATGGCTTG
66 TTTGAATGCTACAGTTTAATGTCAGAGGCATCTCTGTTACATAAAAA-GCACAAAAGATGGCTTA
* *
42043670 TCACGTGACTATCTTTAATACTTCTCAAACTTTCACTTAATGGTTTTTTTCTTCGATTTTTGTTG
130 TCACGTGACTGTCTTTAATACTTCTCAAACTTTCAATTAATGGTTTTTTTCTTCGATTTTTGTTG
* *
42043735 TGTTTATCCACCTGCTTGTCCCCTTCTTCCCT
195 TGTTTATCCACCTGCTTGTCCCCCTCTTACCT
* * *
42043767 CTTGTACTAAACCAATAATGAATCTAAAACTAATTGAAACAAACACCAAACACTTGATGG-TCAG
1 CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGCT-AT
* * *
42043831 TTTTGAATGCTACGGTTTAATGTCAGAGGTATTTCTGTTACAGTAAAAAGCACAAAAGATGGCTT
65 TTTTGAATGCTACAGTTTAATGTCAGAGGCATCTCTGTTACA-TAAAAAGCACAAAAGATGGCTT
*
42043896 ATCACGTGACTGTCTTTAATACTTCTCAAACTTTCAATTAAT-GTTTTTTTTTTCGATTTTTGTT
129 ATCACGTGACTGTCTTTAATACTTCTCAAACTTTCAATTAATGGTTTTTTTCTTCGATTTTTGTT
42043960 GTGTTTATCCACCTGCTTG-CCCCCTCATTACCT
194 GTGTTTATCCACCTGCTTGTCCCCCTC-TTACCT
* * *
42043993 CTTGGACTAAACCAATAAGGAATCTAAAACTAATTGCAACAAACATCAAACACTTGGTGGCTATT
1 CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGCTATT
*
42044058 TTTGAATG-TCACAGTTTAATGTCAGAGGCATCTCTGTTA-ATATAAAAGTACAAAAGATGGCTT
66 TTTGAATGCT-ACAGTTTAATGTCAGAGGCATCTCTGTTACATA-AAAAGCACAAAAGATGGCTT
* *
42044121 ATCACGTGGCTGTCTTTAATATTTCTCAAA
129 ATCACGTGACTGTCTTTAATACTTCTCAAA
42044151 AGGTGGCCAT
Statistics
Matches: 348, Mismatches: 30, Indels: 14
0.89 0.08 0.04
Matches are distributed among these distances:
224 2 0.01
225 55 0.16
226 137 0.39
227 149 0.43
228 5 0.01
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (226 bp):
CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAAACACCAAACACTTGGTGGCTATT
TTTGAATGCTACAGTTTAATGTCAGAGGCATCTCTGTTACATAAAAAGCACAAAAGATGGCTTAT
CACGTGACTGTCTTTAATACTTCTCAAACTTTCAATTAATGGTTTTTTTCTTCGATTTTTGTTGT
GTTTATCCACCTGCTTGTCCCCCTCTTACCT
Found at i:42045942 original size:22 final size:22
Alignment explanation
Indices: 42045908--42045949 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42045898 ACAAAATTAC
* *
42045908 ATTATCTTTTTTTAACAATAAA
1 ATTATATTATTTTAACAATAAA
*
42045930 ATTATATTATTTTAATAATA
1 ATTATATTATTTTAACAATA
42045950 TATTATCGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTATATTATTTTAACAATAAA
Found at i:42047389 original size:213 final size:211
Alignment explanation
Indices: 42047015--42049094 Score: 2548
Period size: 213 Copynumber: 10.0 Consensus size: 211
42047005 CCTCCTTCCC
* * *
42047015 TCTTGTGCTAAACCAATAAGGAATCTAAAACTAATTGAAATAGACACCAAACACTTTGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * *
42047080 TTTTGAATGTCACGGTTTAATGTCAAAGGCATCTCTCTTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
*
42047145 GTCACGTTGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTATTTTTTTTATTTTTGT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-TTTTT-TTTTTTTTATTTTTGT
42047210 TGTATTTATCCACTTGCT
194 TGTATTTATCCACTTGCT
* * *
42047228 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACTAAACATTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
42047293 TTTTAAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAGTAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * * * * *
42047358 GTCACGTGATTGTCTTTAATACTTCTCAAACTTTCATTTAA--TGTTTTTTTGTTGTTGTTGTTG
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTTTTATTTTTGTTG
42047421 TATTTATCCA------
196 TATTTATCCACTTGCT
* *
42047431 -CTTGTACTAAACCAATAAGGAATCTAAAACTAATTTAAACAGACACCAAACACTTGCTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
42047495 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAAT-AAAAGACACAAAAGATGGCT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAG-CACAAAAGATGGCT
* * ***
42047559 TGTCACGTGGTTGTCTTTAATATTTCTCAAACGTTCACTTAATTTTTTTTTTTATTTA-TCCAG-
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTT-TTTATTTTTGT
*** * * *
42047622 T-TACTTGCCCCTCATTCCC
194 TGTA-TTTATCCAC-TTGCT
*
42047641 TATTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACA-CAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
*
42047705 TTTTGAATGCCCACAGTTTAATGTCAGAGGCATCTCTGTTACAGTAAAAAGCACAAAAGATGGCT
66 TTTTGAATG-CCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCT
* * *
42047770 TGTCACGTGGTTGCCTTTAATACTTCTCAAACTTTCATTTAA----------TTTT-TTGTTGTT
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTTTTATTTTTGTT
42047824 GTATTTATCCA------
195 GTATTTATCCACTTGCT
* **
42047835 -CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGCTGGCTGC
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
42047899 TTTTGAATACTACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAGGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* *
42047964 GTCACGTGGTTGTCTTTAATATTTCTCAAACTTTTACTTAATTTTTTTTTTTTTTTGTATTTATC
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA--TTTTTTTTTTTTT-TATTT-T-
** * ** * * *
42048029 CACTTG-CTTTCCCCTCCTTCCC
191 -TGTTGTATTTATCC-ACTTGCT
* * *
42048051 TATTATACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACA-CAAACACTTTGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * * *
42048115 TTTTGAATGCCACAGTTTAATATCTGAGGCATCTTTGTTACAATAAAAAGCACAAAAAATGACTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * ***
42048180 GTCACGTGGTTGCCTTTAATACTTCTCAAACTTCCACTTAATGTTTTTTTTGAAATTATTTTTGT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-TTTTTTTT-TTTTTATTTTTGT
* *
42048245 TGTATTTATCCATTTGTT
194 TGTATTTATCCACTTGCT
* ** * *
42048263 TCTTGTACTAAACTAATAAGGAATCTAAAACTAATTGAAACAGACAATAAACACTTAGTAGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
42048328 TTTTGAATGCCACAGTTTAATGTCAGATGTATCTTTGTTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* *
42048393 GTCACGTGGTTGCCTTTAATACTTCTCAAATTTTCACTTAA-----TTTTTTTTTATTTTTGTTG
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTTTTATTTTTGTTG
*
42048453 TATTTATCCACTTGTT
196 TATTTATCCACTTGCT
* * * ** *
42048469 TATTGTACTAAACTATTAAAAAAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTTA
1 TCTTGTACTAAACCAAT-AAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTA
* * * *
42048534 TTTTTGAATACCACAGTTTAATGTCAGAGGCATCTCTGTTACAAAAAAAAAAACACAAAAGATGA
65 TTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTAC--AATAAAAAGCACAAAAGATGG
* * *
42048599 CTTGTCACGTGGTTATCTTTAATACTTCTTAAACTTTCACTT-A------TTTTTTTTATTTCTG
128 CTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTTTTATTTTTG
*
42048657 TTGTATTTATCCACTCGCT
193 TTGTATTTATCCACTTGCT
* * * *
42048676 TATTGTTCTAAACCAATAAGGAATCTAAAACAAATTGAAATAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
*
42048741 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * * *
42048806 ATCACGTGGTTGACTTTAATGCTTCTCAAACTTTCACTTAATGTTTTTTTTATTTTATTTTTGTT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-TTTTTTTTTTTTTATTTTTGTT
*
42048871 GTATTTATCCACTTGTT
195 GTATTTATCCACTTGCT
* * * *
42048888 TCTTGTACTAAACCAATAAGGAATTTAAAACTAATTG-AATAGACACCAAGCACTTGGTGGCCAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * * ** *
42048952 TTTTGAATTCCAC-GATTTAATGTTAGAGGCATCTTTATTACAATAAAAAATACAAAAGATGACT
66 TTTTGAATGCCACAG-TTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCT
* * *
42049016 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATACTTTTTTTCTTCTGA-TTTTG
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT--TTTTTTTTTTTTTATTTTTG
42049080 TTGTATTTATCCACT
193 TTGTATTTATCCACT
42049095 CACTGAAAGA
Statistics
Matches: 1621, Mismatches: 185, Indels: 124
0.84 0.10 0.06
Matches are distributed among these distances:
193 134 0.08
194 23 0.01
200 5 0.00
201 11 0.01
202 156 0.10
203 5 0.00
204 66 0.04
205 6 0.00
206 126 0.08
207 129 0.08
208 2 0.00
209 86 0.05
210 33 0.02
211 270 0.17
212 126 0.08
213 276 0.17
214 2 0.00
215 13 0.01
216 109 0.07
217 43 0.03
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (211 bp):
TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTTTTATTTTTGTTG
TATTTATCCACTTGCT
Found at i:42048788 original size:413 final size:403
Alignment explanation
Indices: 42047016--42049056 Score: 2544
Period size: 413 Copynumber: 4.9 Consensus size: 403
42047006 CTCCTTCCCT
* * *
42047016 CTTGTGCTAAACCAATAAGGAATCTAAAACTAATTGAAATAGACACCAAACACTTTGTGGCTATT
1 CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATT
* * * *
42047081 TTTGAATGTCACGGTTTAATGTCAAAGGCATCTCTCTTACAATAAAAAGCACAAAAGATGGCTTG
66 TTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTG
*
42047146 TCACGTTGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTATTTTTTTTATTTTTGTT
131 TCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA------T-TTTTTTTTATTTTTGTT
* * *
42047211 GTATTTATCCACTTGCTTCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACT
189 GTATTTATCCACTTGTTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACC
* * * *
42047276 AAACATTTGGTGGCTATTTTTAAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAGTAAAA
254 AAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAA
* * *
42047341 AGCACAAAAGATGGCTTGTCACGTGATTGTCTTTAATACTTCTCAAACTTTCATTTAATGTTTTT
319 AGCACAAAAGATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTT-AT-TTTTT
*
42047406 TTGTTGTTGTTGTTGTATTTATCCA
382 TT-AT-TT-TTGTTGTATTTATCCA
* *
42047431 CTTGTACTAAACCAATAAGGAATCTAAAACTAATTTAAACAGACACCAAACACTTGCTGGCTATT
1 CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATT
42047496 TTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAAT-AAAAGACACAAAAGATGGCTT
66 TTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAG-CACAAAAGATGGCTT
* * * *
42047560 GTCACGTGGTTGTCTTTAATATTTCTCAAACGTTCACTTAATTTTTTTTT-TTATTTATCCAGTT
130 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTATT-TTTGT--TG-T
* * * ** *
42047624 ACTT-GCCCCTCATTCCCTATTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACA-
191 ATTTATCCACTTGTT---TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACAC
*
42047687 CAAACACTTGGTGGCTATTTTTGAATGCCCACAGTTTAATGTCAGAGGCATCTCTGTTACAGTAA
253 CAAACACTTGGTGGCTATTTTTGAATG-CCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAA
* * **
42047752 AAAGCACAAAAGATGGCTTGTCACGTGGTTGCCTTTAATACTTCTCAAACTTTCA--T-TTAATT
317 AAAGCACAAAAGATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTATTTTTT
*
42047814 TT-TTGTTGTTGTATTTATCCA
382 TTATTTTTGTTGTATTTATCCA
* **
42047835 CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGCTGGCTGCT
1 CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATT
* * *
42047900 TTTGAATACTACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAGGCACAAAAGATGGCTTG
66 TTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTG
* *
42047965 TCACGTGGTTGTCTTTAATATTTCTCAAACTTTTACTTAA-TTTTTTTT-TTTTT-TTGTATTTA
131 TCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTATTTTTGTTGTATTTA
*
42048027 TCCACTTGCTTTCCCCTCCTTCCCTATTATACTAAACCAATAAGGAATCTAAAACTAATTGAAAC
196 TCCACTTG--------T--TT--C--TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAAC
* * * *
42048092 AGACA-CAAACACTTTGTGGCTATTTTTGAATGCCACAGTTTAATATCTGAGGCATCTTTGTTAC
247 AGACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTAC
* * *
42048156 AATAAAAAGCACAAAAAATGACTTGTCACGTGGTTGCCTTTAATACTTCTCAAACTTCCACTTAA
312 AATAAAAAGCACAAAAGATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTT-A
42048221 TGTTTTTTTTGAAATTATTTTTGTTGTATTTATCCA
376 ----TTTTTT----TTATTTTTGTTGTATTTATCCA
* ** *
42048257 TTTGTTTCTTGTACTAAACTAATAAGGAATCTAAAACTAATTGAAACAGACAATAAACACTTAGT
1 -------CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGT
* * * *
42048322 AGCTATTTTTGAATGCCACAGTTTAATGTCAGATGTATCTTTGTTACAATAAAAAGCACAAAAGA
59 GGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGA
* *
42048387 TGGCTTGTCACGTGGTTGCCTTTAATACTTCTCAAATTTTCACTTAATTTTTTTTTATTTTTGTT
124 TGGCTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTATTTTTGTT
* * * **
42048452 GTATTTATCCACTTGTTTATTGTACTAAACTATTAAAAAAATCTAAAACTAATTGAAACAGACAC
189 GTATTTATCCACTTGTTTCTTGTACTAAACCAAT-AAGGAATCTAAAACTAATTGAAACAGACAC
* * *
42048517 CAAACACTTGGTGGTTATTTTTGAATACCACAGTTTAATGTCAGAGGCATCTCTGTTACAAAAAA
253 CAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTAC--AATA
* * *
42048582 AAAAACACAAAAGATGACTTGTCACGTGGTTATCTTTAATACTTCTTAAACTTTCACTTATTTTT
316 AAAAGCACAAAAGATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTATTTTT
*
42048647 TTTATTTCTGTTGTATTTATCCA
381 TTTATTTTTGTTGTATTTATCCA
* * *
42048670 CTCGCTTATTGTTCTAAACCAATAAGGAATCTAAAACAAATTGAAATAGACACCAAACACTTGGT
1 ----C---TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGT
42048735 GGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGA
59 GGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGA
* * * *
42048800 TGACTTATCACGTGGTTGACTTTAATGCTTCTCAAACTTTCACTTAATGTTTTTTTTATTTTATT
124 TGGCTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA-----TTTTT-TTTTATT
* *
42048865 TTTGTTGTATTTATCCACTTGTTTCTTGTACTAAACCAATAAGGAATTTAAAACTAATTG-AATA
183 TTTGTTGTATTTATCCACTTGTTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACA
* * * * * *
42048929 GACACCAAGCACTTGGTGGCCATTTTTGAATTCCAC-GATTTAATGTTAGAGGCATCTTTATTAC
248 GACACCAAACACTTGGTGGCTATTTTTGAATGCCACAG-TTTAATGTCAGAGGCATCTCTGTTAC
**
42048993 AATAAAAAATACAAAAGATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTA
312 AATAAAAAGCACAAAAGATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTA
42049057 ATACTTTTTT
Statistics
Matches: 1431, Mismatches: 133, Indels: 124
0.85 0.08 0.07
Matches are distributed among these distances:
398 4 0.00
399 5 0.00
401 1 0.00
402 3 0.00
403 10 0.01
404 173 0.12
405 5 0.00
406 2 0.00
407 3 0.00
408 17 0.01
409 88 0.06
410 77 0.05
411 6 0.00
412 24 0.02
413 307 0.21
414 5 0.00
415 212 0.15
416 1 0.00
417 68 0.05
418 34 0.02
419 71 0.05
420 53 0.04
421 3 0.00
422 76 0.05
424 1 0.00
429 152 0.11
430 8 0.01
431 5 0.00
432 17 0.01
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (403 bp):
CTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATT
TTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTG
TCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTATTTTTGTTGTATTTA
TCCACTTGTTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACT
TGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAA
AAGATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTATTTTTTTTATTTTTG
TTGTATTTATCCA
Found at i:42049081 original size:211 final size:209
Alignment explanation
Indices: 42047017--42049094 Score: 2514
Period size: 211 Copynumber: 10.0 Consensus size: 209
42047007 TCCTTCCCTC
* * *
42047017 TTGTGCTAAACCAATAAGGAATCTAAAACTAATTGAAATAGACACCAAACACTTTGTGGCTATTT
1 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
* * * * *
42047082 TTGAATGTCACGGTTTAATGTCAAAGGCATCTCTCTTACAATAAAAAGCACAAAAGATGGCTTGT
66 TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGT
* *
42047147 CACGTTGTTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTATTTTTTTTATTTTTGTTG
131 CACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA--TATTT-TTTTTTTTA-TTTTGTTG
* *
42047212 TATTTATCCACTTGCTTC
192 TATTTATCCACTTGTTTA
* * *
42047230 TTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACTAAACATTTGGTGGCTATTT
1 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
* * * *
42047295 TTAAATGCCACGGTTTAATGTCAGAGGCATCTCTGTTACAGTAAAAAGCACAAAAGATGGCTTGT
66 TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGT
* * * * *
42047360 CACGTGATTGTCTTTAATACTTCTCAAACTTTCATTTAATGTTTTTTTGTTGT-TGTTGTTGTAT
131 CACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTT-TTTTATTTTGTTGTAT
42047424 TTATCCAC-------
195 TTATCCACTTGTTTA
* *
42047432 TTGTACTAAACCAATAAGGAATCTAAAACTAATTTAAACAGACACCAAACACTTGCTGGCTATTT
1 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
*
42047497 TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAAT-AAAAGACACAAAAGATGGCTTG
66 TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAG-CACAAAAGATGACTTG
* * ***
42047561 TCACGTGGTTGTCTTTAATATTTCTCAAACGTTCACTT-A-ATTTTTTTTTTTATTTATCCAGTT
130 TCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTTTTTATTT-TGTTG-T
* * * **
42047624 ACTT-GCCCCTCATTCCCTA
193 ATTTATCCACTTGTT---TA
42047643 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACA-CAAACACTTGGTGGCTATTT
1 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
* *
42047707 TTGAATGCCCACAGTTTAATGTCAGAGGCATCTCTGTTACAGTAAAAAGCACAAAAGATGGCTTG
66 TTGAATG-CCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTG
* * *
42047772 TCACGTGGTTGCCTTTAATACTTCTCAAACTTTCA-TT--TA-----ATTTTT-TGTTGTTGTAT
130 TCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTTTTTATTTTGTTGTAT
42047828 TTATCCAC-------
195 TTATCCACTTGTTTA
* **
42047836 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGCTGGCTGCTT
1 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
* * * *
42047901 TTGAATACTACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAGGCACAAAAGATGGCTTGT
66 TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGT
* * * *
42047966 CACGTGGTTGTCTTTAATATTTCTCAAACTTTTACTTAAT-TTTTTTTTTTT-TTTGTATTTATC
131 CACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTTTTTATTT-T-GTTGT-
* * **
42048029 CACTTGCTTTCCCCTCCTTCCCTA
193 -A-TT--TATCCACTTGTT---TA
* *
42048053 TTATACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACA-CAAACACTTTGTGGCTATTT
1 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
* * * *
42048117 TTGAATGCCACAGTTTAATATCTGAGGCATCTTTGTTACAATAAAAAGCACAAAAAATGACTTGT
66 TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGT
* * * *
42048182 CACGTGGTTGCCTTTAATACTTCTCAAACTTCCACTTAATGTTTTTTTTGAAATTATTTTTGTTG
131 CACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTT---TTTA-TTTTGTTG
* *
42048247 TATTTATCCATTTGTTTC
192 TATTTATCCACTTGTTTA
* ** * *
42048265 TTGTACTAAACTAATAAGGAATCTAAAACTAATTGAAACAGACAATAAACACTTAGTAGCTATTT
1 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
* * * *
42048330 TTGAATGCCACAGTTTAATGTCAGATGTATCTTTGTTACAATAAAAAGCACAAAAGATGGCTTGT
66 TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGT
* * *
42048395 CACGTGGTTGCCTTTAATACTTCTCAAATTTTCACTT-A-ATTTTTTTTTAT-TTTTGTTGTATT
131 CACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTTTTTATTTTGTTGTATT
42048457 TATCCACTTGTTTA
196 TATCCACTTGTTTA
* * ** *
42048471 TTGTACTAAACTATTAAAAAAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTTATT
1 TTGTACTAAACCAAT-AAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATT
* * *
42048536 TTTGAATACCACAGTTTAATGTCAGAGGCATCTCTGTTACAAAAAAAAAAACACAAAAGATGACT
65 TTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTAC--AATAAAAAGCACAAAAGATGACT
* *
42048601 TGTCACGTGGTTATCTTTAATACTTCTTAAACTTTCAC-T--TA---TTTTTTTTATTTCTGTTG
128 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTTTTTATTT-TGTTG
* *
42048660 TATTTATCCACTCGCTTA
192 TATTTATCCACTTGTTTA
* * *
42048678 TTGTTCTAAACCAATAAGGAATCTAAAACAAATTGAAATAGACACCAAACACTTGGTGGCTATTT
1 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
*
42048743 TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTAT
66 TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGT
* * *
42048808 CACGTGGTTGACTTTAATGCTTCTCAAACTTTCACTTAATGTTTTTTTTATTTTATTTTTGTTGT
131 CACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-ATTTTTTT-TTTTA-TTTTGTTGT
*
42048873 ATTTATCCACTTGTTTC
193 ATTTATCCACTTGTTTA
* * * *
42048890 TTGTACTAAACCAATAAGGAATTTAAAACTAATTG-AATAGACACCAAGCACTTGGTGGCCATTT
1 TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
* * * * **
42048954 TTGAATTCCAC-GATTTAATGTTAGAGGCATCTTTATTACAATAAAAAATACAAAAGATGACTTG
66 TTGAATGCCACAG-TTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTG
*
42049018 TCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATACTTTTTTTCTTCTGATTTTGTTG
130 TCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATA-TTTTTTT-TT-TTATTTTGTTG
42049083 TATTTATCCACT
192 TATTTATCCACT
42049095 CACTGAAAGA
Statistics
Matches: 1625, Mismatches: 170, Indels: 142
0.84 0.09 0.07
Matches are distributed among these distances:
193 130 0.08
194 25 0.02
196 1 0.00
199 3 0.00
200 16 0.01
201 12 0.01
202 160 0.10
203 5 0.00
204 57 0.04
205 15 0.01
206 124 0.08
207 117 0.07
208 3 0.00
209 72 0.04
210 34 0.02
211 294 0.18
212 108 0.07
213 270 0.17
215 7 0.00
216 109 0.07
217 53 0.03
218 1 0.00
220 5 0.00
221 1 0.00
222 3 0.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (209 bp):
TTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTATTT
TTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGT
CACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTTTTTATTTTGTTGTATT
TATCCACTTGTTTA
Found at i:42049950 original size:19 final size:19
Alignment explanation
Indices: 42049928--42049966 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42049918 TATTTCTTAT
*
42049928 AAATATTAT-TTATATATAA
1 AAAT-TTATATTATAAATAA
42049947 AAATTTATATTATAAATAA
1 AAATTTATATTATAAATAA
42049966 A
1 A
42049967 GTAAACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTATATTATAAATAA
Found at i:42050171 original size:22 final size:21
Alignment explanation
Indices: 42050128--42050171 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
42050118 GTTTTACACA
*
42050128 ATATATTTAATATATTTTTTT
1 ATATATTTAATATATTTGTTT
* *
42050149 ATATATGTTAATGTGTTTGTTT
1 ATATAT-TTAATATATTTGTTT
42050171 A
1 A
42050172 GAAAAAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (21 bp):
ATATATTTAATATATTTGTTT
Found at i:42051370 original size:20 final size:21
Alignment explanation
Indices: 42051345--42051389 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
42051335 AAAATGACCA
42051345 AAAAAAATA-AAATAATTTTC
1 AAAAAAATATAAATAATTTTC
* * *
42051365 AAAAAATTATAATTAATTTTT
1 AAAAAAATATAAATAATTTTC
42051386 AAAA
1 AAAA
42051390 TTTATTTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAAATATAAATAATTTTC
Found at i:42064697 original size:37 final size:35
Alignment explanation
Indices: 42064636--42064706 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 35
42064626 ACTAAAAGAA
42064636 TTAATAATATAAATAGTACAAAAT-AAATTTTTAT
1 TTAATAATATAAATAGTACAAAATAAAATTTTTAT
*
42064670 TTAATAATATAAATAGTAGATATAAATAAAATTTTTA
1 TTAATAATATAAATAGT--ACA-AAATAAAATTTTTA
42064707 CTATTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 17 0.53
36 2 0.06
37 4 0.12
38 9 0.28
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (35 bp):
TTAATAATATAAATAGTACAAAATAAAATTTTTAT
Found at i:42064965 original size:30 final size:31
Alignment explanation
Indices: 42064923--42064982 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
42064913 GAGGGTGGGA
42064923 TGGGAGGGGAGTAAAAGTTTTAAGGGAAAAG
1 TGGGAGGGGAGTAAAAGTTTTAAGGGAAAAG
**
42064954 TGGGA-GGGAGTAAAAGTTTTGGGGGAAAA
1 TGGGAGGGGAGTAAAAGTTTTAAGGGAAAA
42064983 TAAAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.43, T:0.20
Consensus pattern (31 bp):
TGGGAGGGGAGTAAAAGTTTTAAGGGAAAAG
Found at i:42065163 original size:22 final size:22
Alignment explanation
Indices: 42065135--42065181 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
42065125 GGGAAGGAGT
*
42065135 AAAAGTTTTTGGG-AAAAAGTAA
1 AAAAG-TTTGGGGAAAAAAGTAA
42065157 AAAAGTTTGGGGTAAAAAAGTAA
1 AAAAGTTTGGGG-AAAAAAGTAA
42065180 AA
1 AA
42065182 TATTGTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 5 0.23
23 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (22 bp):
AAAAGTTTGGGGAAAAAAGTAA
Found at i:42070221 original size:14 final size:14
Alignment explanation
Indices: 42070202--42070235 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
42070192 AATCCTATAC
42070202 ATATATTTATTAAT
1 ATATATTTATTAAT
*
42070216 ATATATTTATTTAT
1 ATATATTTATTAAT
42070230 -TATATT
1 ATATATT
42070236 ACCATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATATTTATTAAT
Found at i:42070681 original size:21 final size:21
Alignment explanation
Indices: 42070639--42070681 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42070629 AAAGATTTCG
*
42070639 TTTTTAAAGATTGAGACTCGA
1 TTTTTAAAGATTGAGACCCGA
*
42070660 TTTTTATAGATTTGAG-CCCGA
1 TTTTTAAAGA-TTGAGACCCGA
42070681 T
1 T
42070682 CTATGCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (21 bp):
TTTTTAAAGATTGAGACCCGA
Found at i:42071462 original size:29 final size:29
Alignment explanation
Indices: 42071408--42071724 Score: 187
Period size: 29 Copynumber: 11.0 Consensus size: 29
42071398 ATCCCATTAA
* *
42071408 GACCTCTAAACTTCTTAAAAATTACATTTT
1 GACCCCTAAACTTC-CAAAAATTACATTTT
*
42071438 GACCCCTAAACTTCCCAAAATTACATTTT
1 GACCCCTAAACTTCCAAAAATTACATTTT
* *
42071467 GATCCCTGAACTTCCAAAAATTACATTTT
1 GACCCCTAAACTTCCAAAAATTACATTTT
* ** *
42071496 GACCCCTAAACTTCTCCAAAATCCCATTTC
1 GACCCCTAAACTTC-CAAAAATTACATTTT
* * *
42071526 GA-CCC-GAACTTCTCCAAAATTATGATTTT
1 GACCCCTAAACTTC-CAAAAATTA-CATTTT
*
42071555 G-CCCC-AAA-TATCCAAAAAATTACAATATT
1 GACCCCTAAACT-TCC-AAAAATTAC-ATTTT
* *
42071584 -ACCCCTGAACATCCAAAAATTACTATTTT
1 GACCCCTAAACTTCCAAAAATTAC-ATTTT
*
42071613 G-CCCCTGAA-TATCCAAAAA-TACCA-TTT
1 GACCCCTAAACT-TCCAAAAATTA-CATTTT
* * *
42071640 --CCCCTCGAACATCAAAAAATTACCATTTT
1 GACCCCT-AAACTTCCAAAAATTA-CATTTT
** * *
42071669 -ACCCCCGAACATCCAAAAATTACCAATTT
1 GACCCCTAAACTTCCAAAAATTA-CATTTT
* *
42071698 G-CCCC-AAATTTCCAAAAATCACATTTT
1 GACCCCTAAACTTCCAAAAATTACATTTT
42071725 CAACCTCAAA
Statistics
Matches: 233, Mismatches: 36, Indels: 39
0.76 0.12 0.13
Matches are distributed among these distances:
26 5 0.02
27 18 0.08
28 36 0.15
29 139 0.60
30 35 0.15
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.30
Consensus pattern (29 bp):
GACCCCTAAACTTCCAAAAATTACATTTT
Found at i:42071668 original size:56 final size:56
Alignment explanation
Indices: 42071541--42071702 Score: 175
Period size: 56 Copynumber: 2.8 Consensus size: 56
42071531 GAACTTCTCC
** * * *
42071541 AAAATTATGATTTTGCCCCAAATATCCAAAAAATTACAATATTACCCCTGAACATCCA
1 AAAATTACCATTTTGCCCCGAATATCC-AAAAATTACCAT-TTACCCCTGAACATCAA
*
42071599 AAAATTACTATTTTGCCCCTGAATATCCAAAAA-TACCATTT-CCCCTCGAACATCAA
1 AAAATTACCATTTTGCCCC-GAATATCCAAAAATTACCATTTACCCCT-GAACATCAA
* * *
42071655 AAAATTACCATTTTACCCCCGAACATCCAAAAATTACCAATTTGCCCC
1 AAAATTACCATTTT-GCCCCGAATATCCAAAAATTACC-ATTTACCCC
42071703 AAATTTCCAA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
55 5 0.06
56 35 0.39
57 13 0.14
58 26 0.29
59 11 0.12
ACGTcount: A:0.40, C:0.28, G:0.05, T:0.27
Consensus pattern (56 bp):
AAAATTACCATTTTGCCCCGAATATCCAAAAATTACCATTTACCCCTGAACATCAA
Found at i:42071723 original size:56 final size:55
Alignment explanation
Indices: 42071591--42071724 Score: 144
Period size: 56 Copynumber: 2.4 Consensus size: 55
42071581 ATTACCCCTG
* * * *
42071591 AACATCCAAAAATTACTATTTTGCCCCTGAATATCCAAAAATACCATTTCCCCTCG
1 AACATCCAAAAATTAC-ATTTTACCCCCGAACATCCAAAAATACCATTTCCCCTCA
* *
42071647 AACATCAAAAAATTACCATTTTACCCCCGAACATCCAAAAATTACCAATTTGCCC-CA
1 AACATCCAAAAATTA-CATTTTACCCCCGAACATCCAAAAA-TACC-ATTTCCCCTCA
** *
42071704 AATTTCCAAAAATCACATTTT
1 AACATCCAAAAATTACATTTT
42071725 CAACCTCAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
56 41 0.63
57 17 0.26
58 7 0.11
ACGTcount: A:0.40, C:0.29, G:0.04, T:0.28
Consensus pattern (55 bp):
AACATCCAAAAATTACATTTTACCCCCGAACATCCAAAAATACCATTTCCCCTCA
Found at i:42073691 original size:24 final size:24
Alignment explanation
Indices: 42073654--42073770 Score: 180
Period size: 24 Copynumber: 4.9 Consensus size: 24
42073644 GCAAGTTCAT
* *
42073654 TACGTTTACGCTCGTCATCTAATG
1 TACGTTTACACTCGTCAACTAATG
* **
42073678 TACATTTACACTCGTCAGTTAATG
1 TACGTTTACACTCGTCAACTAATG
*
42073702 TACGTTTACGCTCGTCAACTAATG
1 TACGTTTACACTCGTCAACTAATG
42073726 TACGTTTACACTCGTCAACTAATG
1 TACGTTTACACTCGTCAACTAATG
42073750 TACGTTTACACTCGTCAACTA
1 TACGTTTACACTCGTCAACTA
42073771 TTCAGATATA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (24 bp):
TACGTTTACACTCGTCAACTAATG
Found at i:42080763 original size:360 final size:359
Alignment explanation
Indices: 42080060--42080912 Score: 1065
Period size: 360 Copynumber: 2.3 Consensus size: 359
42080050 TATGACTTTT
* * *
42080060 AATATTTTGTACAATATCTTAAAAAAACTTAATAATCTTTTAGAAAAAAAAACTTCATCTTAAAA
1 AATATTTTATACAATATCTTAAAAGAACTTAATAATCTTTTAG---AAAAAACTTCATCCTAAAA
* * *
42080125 TTTTTTCAATTTTTAAAATAACCATCCACTCCCATAAAAACAATTTCACTCAAAATAAATAAATA
63 ATTTTACTATTTTTAAAATAACCATCCACTCCCATAAAAACAATTTCACTC---A-AAATAAATA
* ** * *
42080190 AAACCATCAATAGTTTAAAACAACTTATATACTATCAATTCTATCACACACATGTGCATGTGAAA
124 AAACCATCAATAATTTAAAACAACTTATATACTAGAAATTCTAT-ACACACATATGCATCTGAAA
** * * * * *
42080255 ATTACATATTTAAAATATAAGGTATGTTTAAAAATAACATACAATAAATACTATAACGTATGATT
188 ACAACATATTTAAAATAAAAGGTATATTTAAAAATAACATACAATAAATAATAAAACGCATGATT
* * * * * *
42080320 TGAAACTAATTAATAATAACACATGCAATATGTACAATATTAAAATGAAAAAGTTAGATTGAATT
253 TAAAACTAATTAATAATAACACATGCAATATATACAATATTAAAATAAAAAAATTAAATTAAATT
42080385 ATGAATAAAACAAAATTTAAACACATAAAAACA-T-ATTAAA
318 ATGAATAAAACAAAATTTAAACACATAAAAACATTAATTAAA
**
42080425 AATATTTTATAGGATATCTTAAAAGAACTTAATAATCTTTTAGAAAGAAACTTCATCCTAAAAAT
1 AATATTTTATACAATATCTTAAAAGAACTTAATAATCTTTTAGAAA-AAACTTCATCCTAAAAAT
* * *
42080490 TTTACTATTTTTAAAAATAACTATCCACTACCATGAAAACAATTTCACTCAAAATAAATAAAACC
65 TTTACTATTTTT-AAAATAACCATCCACTCCCATAAAAACAATTTCACTCAAAATAAATAAAACC
* * ** *
42080555 ATCAATAATTT-AAA-AACTTAATGTGTATTAGAAATTCTAT-CATGCATATGCATCTGGAAACA
129 ATCAATAATTTAAAACAACTT-A--TATACTAGAAATTCTATACACACATATGCATCTGAAAACA
* * *
42080617 ACATATTTAGAATACAAAGGTATATTTGAAAATAACATACAATAAATAATAAAACGCATGGTTTA
191 ACATATTTAAAATA-AAAGGTATATTTAAAAATAACATACAATAAATAATAAAACGCATGATTTA
* * * *
42080682 AAATTGATTAATAATAACATATGCAATATATA-TATA-TAATAATAAAATTAAATTAAATTAAAT
255 AAACTAATTAATAATAACACATGCAATATATACAATATTAA-AATAAAA--AAATTAAATTAAAT
* * * *
42080745 TGTGAGTAAAAC-AAATTTAAACACGTAAACACATTAAATTAAA
317 TATGAATAAAACAAAATTTAAACACATAAAAACATT-AATTAAA
42080788 AATATTTTATACAATATCTTAAAAGAACTTAATAATCTTTTAGAAAAAACTTCATCCTAAAAATT
1 AATATTTTATACAATATCTTAAAAGAACTTAATAATCTTTTAGAAAAAACTTCATCCTAAAAATT
* *
42080853 TTACTATTTTTAAAATAACCATCCACTCCCATTACAACAATTTCACTCAAAATAAATAAA
66 TTACTATTTTTAAAATAACCATCCACTCCCATAAAAACAATTTCACTCAAAATAAATAAA
42080913 TAAAACTAGG
Statistics
Matches: 425, Mismatches: 51, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
358 8 0.02
359 41 0.10
360 113 0.27
361 81 0.19
362 33 0.08
363 76 0.18
364 34 0.08
365 39 0.09
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (359 bp):
AATATTTTATACAATATCTTAAAAGAACTTAATAATCTTTTAGAAAAAACTTCATCCTAAAAATT
TTACTATTTTTAAAATAACCATCCACTCCCATAAAAACAATTTCACTCAAAATAAATAAAACCAT
CAATAATTTAAAACAACTTATATACTAGAAATTCTATACACACATATGCATCTGAAAACAACATA
TTTAAAATAAAAGGTATATTTAAAAATAACATACAATAAATAATAAAACGCATGATTTAAAACTA
ATTAATAATAACACATGCAATATATACAATATTAAAATAAAAAAATTAAATTAAATTATGAATAA
AACAAAATTTAAACACATAAAAACATTAATTAAA
Found at i:42081273 original size:21 final size:21
Alignment explanation
Indices: 42081228--42081312 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 21
42081218 GAAAATTTTA
* *
42081228 ATTTTTTAACTTTCTTTAT-AT
1 ATTTTTTAAATTTATTT-TGAT
42081249 ATTTTTTAGAATTTATTTTGA-
1 ATTTTTTA-AATTTATTTTGAT
*
42081270 ATTTTTTAAAATTATTTTGATT
1 ATTTTTTAAATTTATTTTGA-T
*
42081292 ATTTTTTAAATTT-TGTTGAT
1 ATTTTTTAAATTTATTTTGAT
42081312 A
1 A
42081313 GAGACCAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
20 13 0.24
21 22 0.40
22 20 0.36
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (21 bp):
ATTTTTTAAATTTATTTTGAT
Found at i:42081284 original size:20 final size:21
Alignment explanation
Indices: 42081247--42081301 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
42081237 CTTTCTTTAT
*
42081247 ATATTTTTTAGAATTTATTTTG
1 ATATTTTTTA-AAATTATTTTG
42081269 A-ATTTTTTAAAATTATTTTG
1 ATATTTTTTAAAATTATTTTG
42081289 ATTATTTTTTAAA
1 A-TATTTTTTAAA
42081302 TTTTGTTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 11 0.37
21 8 0.27
22 11 0.37
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
ATATTTTTTAAAATTATTTTG
Found at i:42086474 original size:2 final size:2
Alignment explanation
Indices: 42086403--42086458 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
42086393 TATATTAGAG
42086403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42086445 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
42086459 CACACTAATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42088740 original size:47 final size:47
Alignment explanation
Indices: 42088546--42088730 Score: 244
Period size: 47 Copynumber: 3.9 Consensus size: 47
42088536 TTGCACTATC
* * *
42088546 TAGTGGTTCGACCACATATATCTGTTTTGGCAGCTTAACTACAAATA
1 TAGTGGCTCGACCACATATATCTGTTCTGGCAGCTTAACTGCAAATA
* * *
42088593 TAGTGGCTCGACCACATATATTTGTTCTGGTAGCTTGACTGCAAATA
1 TAGTGGCTCGACCACATATATCTGTTCTGGCAGCTTAACTGCAAATA
* * * *
42088640 TAGTGGCTCGACCACATATATTTGTTCTGGTAGCTTGACTGAAAATA
1 TAGTGGCTCGACCACATATATCTGTTCTGGCAGCTTAACTGCAAATA
* * * *
42088687 TTGTGGCTCGACCATATATATCTGATCTGGCAGTTTAACTGCAA
1 TAGTGGCTCGACCACATATATCTGTTCTGGCAGCTTAACTGCAA
42088731 CTCTGGTGGC
Statistics
Matches: 123, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 123 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (47 bp):
TAGTGGCTCGACCACATATATCTGTTCTGGCAGCTTAACTGCAAATA
Found at i:42092265 original size:21 final size:21
Alignment explanation
Indices: 42092239--42092280 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
42092229 CTGTGGAATC
*
42092239 GTCATGGTTTGGAAGAAACAA
1 GTCATGGTTTGAAAGAAACAA
42092260 GTCATGGTTTGAAAGAAACAA
1 GTCATGGTTTGAAAGAAACAA
42092281 CTTGGAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (21 bp):
GTCATGGTTTGAAAGAAACAA
Found at i:42095173 original size:19 final size:19
Alignment explanation
Indices: 42095146--42095183 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42095136 CCCCTCTTAT
42095146 CATAACTGGTATATATAGG
1 CATAACTGGTATATATAGG
*
42095165 CATATCTGGTATATATAGG
1 CATAACTGGTATATATAGG
42095184 TATTAGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (19 bp):
CATAACTGGTATATATAGG
Found at i:42096694 original size:16 final size:16
Alignment explanation
Indices: 42096653--42096707 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
42096643 TAATCACTTT
*
42096653 AATATTAAATTAATA-A
1 AATATT-AATTAAAATA
*
42096669 AATACT-ATTAAAATA
1 AATATTAATTAAAATA
* *
42096684 AATATTAATTAAATTT
1 AATATTAATTAAAATA
42096700 AATATTAA
1 AATATTAA
42096708 ACTATTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 6 0.19
15 6 0.19
16 20 0.62
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATTAATTAAAATA
Found at i:42096702 original size:36 final size:34
Alignment explanation
Indices: 42096619--42096725 Score: 94
Period size: 36 Copynumber: 3.0 Consensus size: 34
42096609 TAAGATAAAC
*
42096619 ATTAAATTAA-ATTAAA-TATTAAAATAATCACTTTAA
1 ATTAAATTAATATAAAACTATTAAAATAAT-A--TT-A
42096655 TATTAAATTAATA-AAATACTATTAAAATAAATATTA
1 -ATTAAATTAATATAAA-ACTATTAAAAT-AATATTA
* *
42096691 ATTAAATTTAATATTAAACTATTATAATAATATTA
1 ATTAAA-TTAATATAAAACTATTAAAATAATATTA
42096726 TTTTTGGAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
35 13 0.21
36 17 0.28
37 16 0.26
38 2 0.03
39 10 0.16
40 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (34 bp):
ATTAAATTAATATAAAACTATTAAAATAATATTA
Found at i:42101465 original size:22 final size:21
Alignment explanation
Indices: 42101440--42101480 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
42101430 TATATTTAAA
42101440 TATATATTAGATTAGGATTTCG
1 TATATATTAGATT-GGATTTCG
42101462 TATATATTAGATTGGATTT
1 TATATATTAGATTGGATTT
42101481 TTATGCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (21 bp):
TATATATTAGATTGGATTTCG
Found at i:42102778 original size:18 final size:18
Alignment explanation
Indices: 42102755--42102789 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42102745 GAGTTAAACG
*
42102755 AATCGAGTTATTCGAGTT
1 AATCGAATTATTCGAGTT
*
42102773 AATCGAATTATTTGAGT
1 AATCGAATTATTCGAGT
42102790 CAACTCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (18 bp):
AATCGAATTATTCGAGTT
Found at i:42103171 original size:145 final size:135
Alignment explanation
Indices: 42102923--42103229 Score: 363
Period size: 145 Copynumber: 2.2 Consensus size: 135
42102913 CTTTTACTCA
* *
42102923 TTTTTACTTTCCCCCAAAACTTTTAC-T-CCCATCCCACCCGCATATACCCAAACCCATTTCCCT
1 TTTTTATTTTCCCCCAAAACTTTTACTTCCCCATCCCACCCGCATATACCCAAACCCATTCCCCT
*
42102986 CCAATTTTTTTTAATATTTTCCCTCCAAAAATTTACTCCCCCATTTACTTT-CCTCAAAAACCCT
66 CCAATTTTTTTTAATATTTTCCCTCCAAAAATTTACTCCCCCATTAACTTTCCCTC-AAAACCCT
42103050 CAAAAC
130 CAAAAC
* * *
42103056 TTTTTATTTTCCCCCAAAACTTTTACTTCCCTCTCATTCCACCC-CATCTATCCTAAACCCATTC
1 TTTTTATTTTCCCCCAAAACTTTTACTT-CC-C-CATCCCACCCGCATATA-CCCAAACCCATT-
* *
42103120 CCCCCCTCCCAATTTTTTTTAAAAATATTTTCTCTCC-AAAATTTAACTCCCCTATTAACTTTCC
61 --CCCCT-CCAATTTTTTTT---AATATTTTCCCTCCAAAAATTT-ACTCCCCCATTAACTTTCC
*
42103184 CTCAAAACCCTTAAAAC
119 CTCAAAACCCTCAAAAC
* *
42103201 TTTTTATTTTTCCCCTAAACTTTTACTTC
1 TTTTTATTTTCCCCCAAAACTTTTACTTC
42103230 TCACCCTTTA
Statistics
Matches: 148, Mismatches: 11, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
133 25 0.17
134 1 0.01
136 1 0.01
137 6 0.04
138 20 0.14
141 4 0.03
142 12 0.08
144 8 0.05
145 67 0.45
146 4 0.03
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.38
Consensus pattern (135 bp):
TTTTTATTTTCCCCCAAAACTTTTACTTCCCCATCCCACCCGCATATACCCAAACCCATTCCCCT
CCAATTTTTTTTAATATTTTCCCTCCAAAAATTTACTCCCCCATTAACTTTCCCTCAAAACCCTC
AAAAC
Found at i:42104681 original size:22 final size:23
Alignment explanation
Indices: 42104624--42104681 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
42104614 TAACACTTGA
*
42104624 GAATTTAACACTTCAGTGCTCCT
1 GAATTTAGCACTTCAGTGCTCCT
**
42104647 GAATCCAGCACTTC-GATGCTCCT
1 GAATTTAGCACTTCAG-TGCTCCT
42104670 G-ATTTAGCACTT
1 GAATTTAGCACTT
42104682 ATGTGTTCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.33
Consensus pattern (23 bp):
GAATTTAGCACTTCAGTGCTCCT
Found at i:42106300 original size:22 final size:21
Alignment explanation
Indices: 42106241--42106304 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 21
42106231 ATAGTCATTA
42106241 TTATTAATTATATTATAAATAT
1 TTATTAATT-TATTATAAATAT
* *
42106263 TT-TT--TTTAGTAAAAATAT
1 TTATTAATTTATTATAAATAT
42106281 TTATGTAATTTATTATAAATAT
1 TTAT-TAATTTATTATAAATAT
42106303 TT
1 TT
42106305 TAATAATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 12 0.35
19 3 0.09
20 1 0.03
21 2 0.06
22 16 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TTATTAATTTATTATAAATAT
Found at i:42106311 original size:22 final size:21
Alignment explanation
Indices: 42106245--42106312 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
42106235 TCATTATTAT
42106245 TAATTATATTATAAATATTTT-
1 TAATT-TATTATAAATATTTTA
* * *
42106266 T--TTTAGTAAAAATATTTATG
1 TAATTTATTATAAATATTT-TA
42106286 TAATTTATTATAAATATTTTAA
1 TAATTTATTATAAATATTTT-A
42106308 TAATT
1 TAATT
42106313 CTTAATAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 1 0.03
21 2 0.05
22 19 0.51
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
TAATTTATTATAAATATTTTA
Found at i:42119592 original size:18 final size:17
Alignment explanation
Indices: 42119552--42119592 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
42119542 TTTAAGTCTA
*
42119552 TAATTTTTTATATTATT
1 TAATTTTTTATATTATG
*
42119569 TTATTTTTATATATTATG
1 TAATTTTT-TATATTATG
42119587 TAATTT
1 TAATTT
42119593 ACAACATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TAATTTTTTATATTATG
Found at i:42123463 original size:12 final size:12
Alignment explanation
Indices: 42123424--42123466 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
42123414 TAATTTTTTT
42123424 TAAATAAAGAAAA
1 TAAAT-AAGAAAA
* *
42123437 TAAAAATATAAAA
1 TAAATA-AGAAAA
42123450 TAAATAAGAAAA
1 TAAATAAGAAAA
42123462 TAAAT
1 TAAAT
42123467 TTTATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (12 bp):
TAAATAAGAAAA
Found at i:42130860 original size:6 final size:6
Alignment explanation
Indices: 42130840--42130898 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
42130830 TTAAATGGGT
* * *
42130840 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTTA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
42130888 TTTAAG TTTAA
1 TTTAAA TTTAA
42130899 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:42130875 original size:14 final size:14
Alignment explanation
Indices: 42130856--42130883 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42130846 TTTATTTTAA
42130856 ATTTAAATTTACTT
1 ATTTAAATTTACTT
42130870 ATTTAAATTTACTT
1 ATTTAAATTTACTT
42130884 TAAATTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTACTT
Found at i:42133028 original size:29 final size:30
Alignment explanation
Indices: 42132996--42133566 Score: 258
Period size: 30 Copynumber: 19.5 Consensus size: 30
42132986 TATACTTTCC
* *
42132996 AAAATT-CCATTTTTAACCCCGGTGTCATCA
1 AAAATTACCA-TTTTAACCCCGATTTCATCA
42133026 AAAATTACCATTTT-ACCCTCGAACTTTC--C-
1 AAAATTACCATTTTAACCC-CG-A-TTTCATCA
42133055 AAAATT-CCATTTTAACCCCGATTTCATCA
1 AAAATTACCATTTTAACCCCGATTTCATCA
*
42133084 AAAATTACCATTTT-ACCCTCAAGCTTTC--C-
1 AAAATTACCATTTTAACCC-C--GATTTCATCA
** * *
42133113 AAAA-T-CTCATTTTTAACCCTAATTTTACCA
1 AAAATTAC-CA-TTTTAACCCCGATTTCATCA
* *
42133143 AAAATTACCATTTTACCCCCTAAACTTTC--C-
1 AAAATTACCATTTTAACCCC--GA-TTTCATCA
*
42133173 AAAATT-CCATTTTTAACCCCGGTTTCATCA
1 AAAATTACCA-TTTTAACCCCGATTTCATCA
* *
42133203 AAAATTACCATTTTACCCCCAAACTTTC--C-
1 AAAATTACCATTTTAACCCC-GA-TTTCATCA
*
42133232 -AAATTTCCATTTTTAACCCCGATTTCATCA
1 AAAATTACCA-TTTTAACCCCGATTTCATCA
42133262 AAAATTACCATTTT-ACCCTCGAACTTTC--C-
1 AAAATTACCATTTTAACCC-CG-A-TTTCATCA
* *
42133291 AAAA-TCCCATTTTTAACCCCGATTTTATCA
1 AAAATTACCA-TTTTAACCCCGATTTCATCA
* **
42133321 AAAATTATCATTTT-ACCCTTAACTTTC-T--
1 AAAATTACCATTTTAACCC-CGA-TTTCATCA
* * *
42133349 AAAATT-CCATTTTTACCCCGGTTTCACCA
1 AAAATTACCATTTTAACCCCGATTTCATCA
* * *
42133378 AAATTTACCATTTTACCCCCAAACTTTC--C-
1 AAAATTACCATTTTAACCCC-GA-TTTCATCA
* * * * **
42133407 AAAA-TCCCATTTTTAACCCTGGTATCATTT
1 AAAATTACCA-TTTTAACCCCGATTTCATCA
42133437 AAAATTACCATTTT-ACCCCTGAACTTTC--C-
1 AAAATTACCATTTTAACCCC-G-A-TTTCATCA
*
42133466 AAAATT-CCATTTTAACCCCGATTTCATAA
1 AAAATTACCATTTTAACCCCGATTTCATCA
*
42133495 AAAAATACCATTTT-ACCCTCGAACTTTC--C-
1 AAAATTACCATTTTAACCC-CG-A-TTTCATCA
*
42133524 AAAATT-CCATTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTAACCCCGATTTCATCA
42133553 AAAATTACCATTTT
1 AAAATTACCATTTT
42133567 GCTCCCGGGT
Statistics
Matches: 413, Mismatches: 54, Indels: 148
0.67 0.09 0.24
Matches are distributed among these distances:
26 16 0.04
27 27 0.07
28 59 0.14
29 121 0.29
30 127 0.31
31 30 0.07
32 30 0.07
33 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGATTTCATCA
Found at i:42133095 original size:58 final size:59
Alignment explanation
Indices: 42132965--42133566 Score: 790
Period size: 59 Copynumber: 10.3 Consensus size: 59
42132955 CTGGGTGGTC
* * * * *
42132965 CAAACATTACCATATTACCC-CTATACTTTCCAAAATTCCATTTTTAACCCCGGTGTCAT
1 CAAAAATTACCATTTTACCCTCGA-ACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
42133024 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
** * *
42133082 CAAAAATTACCATTTTACCCTC-AAGCTTTCCAAAA-TCTCATTTTTAACCCTAATTTTAC
1 CAAAAATTACCATTTTACCCTCGAA-CTTTCCAAAATTC-CATTTTTAACCCCGATTTCAT
* * *
42133141 CAAAAATTACCATTTTACCCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCAT
1 CAAAAATTACCATTTTACCCTC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * *
42133201 CAAAAATTACCATTTTACCCCCAAACTTTCCAAATTTCCATTTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* *
42133260 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTTAT
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * * * *
42133319 CAAAAATTATCATTTTACCCT-TAACTTTCTAAAATTCCATTTTT-ACCCCGGTTTCAC
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * * * * * *
42133376 CAAAATTTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCTGGTATCAT
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
**
42133435 TTAAAATTACCATTTTACCC-CTGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCTC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * *
42133493 AAAAAAATACCATTTTACCCTCGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
42133551 CAAAAATTACCATTTT
1 CAAAAATTACCATTTT
42133567 GCTCCCGGGT
Statistics
Matches: 480, Mismatches: 52, Indels: 23
0.86 0.09 0.04
Matches are distributed among these distances:
57 32 0.07
58 172 0.36
59 222 0.46
60 50 0.10
61 4 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.36
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
Found at i:42133520 original size:117 final size:117
Alignment explanation
Indices: 42132965--42133566 Score: 811
Period size: 117 Copynumber: 5.1 Consensus size: 117
42132955 CTGGGTGGTC
* * * *
42132965 CAAACATTACCATATTACCCCTATACTTTCCAAAATTCCATTTTTAACCCCGGTGTCATCAAAAA
1 CAAAAATTACCATTTTACCCCTA-ACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAA
42133030 TTACCATTTTACCCTCGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCAT
65 TTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
** * *
42133082 CAAAAATTACCATTTTA-CCCTCAAGCTTTCCAAAA-TCTCATTTTTAACCCTAATTTTACCAAA
1 CAAAAATTACCATTTTACCCCT-AA-CTTTCCAAAATTC-CATTTTTAACCCCGATTTCATCAAA
* * *
42133145 AATTACCATTTTACCCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCAT
63 AATTACCATTTTACCCTC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* *
42133201 CAAAAATTACCATTTTACCCCCAAACTTTCCAAATTTCCATTTTTAACCCCGATTTCATCAAAAA
1 CAAAAATTACCATTTTA-CCCCTAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAA
* *
42133266 TTACCATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTTAT
65 TTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
* * * * * *
42133319 CAAAAATTATCATTTTACCCTTAACTTTCTAAAATTCCATTTTT-ACCCCGGTTTCACCAAAATT
1 CAAAAATTACCATTTTACCCCTAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAAT
* * * * * *
42133383 TACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCTGGTATCAT
66 TACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
** *
42133435 TTAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCATAAAAAA
1 CAAAAATTACCATTTTACCCCT-AACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAA
* *
42133499 ATACCATTTTACCCTCGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCAC
65 TTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
42133551 CAAAAATTACCATTTT
1 CAAAAATTACCATTTT
42133567 GCTCCCGGGT
Statistics
Matches: 420, Mismatches: 55, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
116 120 0.29
117 146 0.35
118 66 0.16
119 81 0.19
120 4 0.01
121 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.36
Consensus pattern (117 bp):
CAAAAATTACCATTTTACCCCTAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAAT
TACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT
Found at i:42148255 original size:98 final size:98
Alignment explanation
Indices: 42148134--42148326 Score: 264
Period size: 98 Copynumber: 2.0 Consensus size: 98
42148124 TTGAGTAGGG
* * * * * *
42148134 TTGGATTGATTCGGTTTTAATTTAGGGAAATTGTTTTTGTTTGTTCGTGATGATTATCAAAATAC
1 TTGGATTGATTCGGTTTGAATTTAGGAAAATTGTTTCTGCTTGTTCATGATAATTATCAAAATAC
**
42148199 -CTTTATAGAATATTATTTTTGAATATATAATAA
66 AC-TTATAGAATATTATTTTAAAATATATAATAA
*
42148232 TTGGATTTGATT-GGTTTGGATTTAGGAAAATTGTTTCTGCTTGTTCATGATAATTATCAAAATA
1 TTGGA-TTGATTCGGTTTGAATTTAGGAAAATTGTTTCTGCTTGTTCATGATAATTATCAAAATA
*
42148296 CACTTATATAATATTATTTTAAAATATATAA
65 CACTTATAGAATATTATTTTAAAATATATAA
42148327 CAATAAAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
98 76 0.92
99 7 0.08
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.47
Consensus pattern (98 bp):
TTGGATTGATTCGGTTTGAATTTAGGAAAATTGTTTCTGCTTGTTCATGATAATTATCAAAATAC
ACTTATAGAATATTATTTTAAAATATATAATAA
Found at i:42157781 original size:23 final size:21
Alignment explanation
Indices: 42157744--42157795 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
42157734 AAAATACCCT
42157744 TATATAAT-ATTATTTTTAAA
1 TATATAATAATTATTTTTAAA
42157764 TATATAATAATTAGATTTTTAAA
1 TATATAATAATT--ATTTTTAAA
*
42157787 TATAAAATA
1 TATATAATA
42157796 CATTTATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 8 0.29
21 3 0.11
23 17 0.61
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATAATAATTATTTTTAAA
Found at i:42166686 original size:39 final size:40
Alignment explanation
Indices: 42166627--42166706 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
42166617 AAGAGGTATG
* *
42166627 TCCAATATGAAAAGGGTTGTGACTTTTCAAATGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
*
42166667 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
42166706 T
1 T
42166707 TGATTGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
Found at i:42171544 original size:39 final size:39
Alignment explanation
Indices: 42171500--42171590 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 39
42171490 TGAGACAAGT
* *
42171500 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGGTTGTGA
1 CTCTTCCAAAAGGTATCATCCAATATG-AAAGGGTTGTGA
* * *
42171539 CTCTT-CAAAAGGTGTCCATCCAATTTGAACGGGTTGTGA
1 CTCTTCCAAAAGGTAT-CATCCAATATGAAAGGGTTGTGA
42171578 CTCTT-CAAAAGGT
1 CTCTTCCAAAAGGT
42171591 GTCCATTGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 8 0.18
39 29 0.64
40 8 0.18
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (39 bp):
CTCTTCCAAAAGGTATCATCCAATATGAAAGGGTTGTGA
Found at i:42171562 original size:40 final size:39
Alignment explanation
Indices: 42171517--42171596 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 39
42171507 AAGAGGTATG
42171517 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
* *
42171557 TCCAATTTGAACGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
42171596 T
1 T
42171597 TGATTGCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (39 bp):
TCCAATATGAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
Found at i:42177187 original size:3 final size:3
Alignment explanation
Indices: 42177181--42177210 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42177171 GAACGTTTGA
42177181 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42177211 AGTTTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42177546 original size:14 final size:14
Alignment explanation
Indices: 42177529--42177558 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42177519 CCCAAACCCT
42177529 AAATCCAAAATATA
1 AAATCCAAAATATA
*
42177543 AAATCCAAAATCTA
1 AAATCCAAAATATA
42177557 AA
1 AA
42177559 CCCCAAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATCCAAAATATA
Found at i:42177630 original size:36 final size:36
Alignment explanation
Indices: 42177583--42177656 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
42177573 ATTCATAGTC
42177583 TAATCTATTACCTCATAACCTCAAACTCTTAAACTT
1 TAATCTATTACCTCATAACCTCAAACTCTTAAACTT
42177619 TAATCTATTACCTCATAACCTCAAACTCTTAAACTT
1 TAATCTATTACCTCATAACCTCAAACTCTTAAACTT
42177655 TA
1 TA
42177657 GACCTAAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (36 bp):
TAATCTATTACCTCATAACCTCAAACTCTTAAACTT
Found at i:42192251 original size:31 final size:31
Alignment explanation
Indices: 42192215--42192275 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
42192205 GTCTAATGAC
*
42192215 TTAAAT-AAAATATTTTGAATAGTTCAGTGAA
1 TTAAATGAAAA-ATTTAGAATAGTTCAGTGAA
* *
42192246 TTAAATGAAAACTTTAGAATAGTTTAGTGA
1 TTAAATGAAAAATTTAGAATAGTTCAGTGA
42192276 TAAATTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (31 bp):
TTAAATGAAAAATTTAGAATAGTTCAGTGAA
Found at i:42195492 original size:32 final size:32
Alignment explanation
Indices: 42195452--42195522 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
42195442 ATGTCTTTTA
*
42195452 CTGTTTTGGTAAT-TTTTTTATTGTTTTGGTTG
1 CTGTTTTGGTAATATTTTTTACTGTTTTGG-TG
**
42195484 CTGTTTTGGTGCTATTTTTTACTGTTTTGGTG
1 CTGTTTTGGTAATATTTTTTACTGTTTTGGTG
*
42195516 TTGTTTT
1 CTGTTTT
42195523 ATTGTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.07, C:0.06, G:0.23, T:0.65
Consensus pattern (32 bp):
CTGTTTTGGTAATATTTTTTACTGTTTTGGTG
Found at i:42195532 original size:32 final size:33
Alignment explanation
Indices: 42195465--42195534 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 33
42195455 TTTTGGTAAT
* *
42195465 TTTTTTATTGTTTTGGTTGCTGTTTTGGTGCTA
1 TTTTTTACTGTTTTGGTTGCTGTTTTAGTGCTA
* * *
42195498 TTTTTTACTGTTTTGG-TGTTGTTTTATTGTTA
1 TTTTTTACTGTTTTGGTTGCTGTTTTAGTGCTA
42195530 TTTTT
1 TTTTT
42195535 GTTGCTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.69
Consensus pattern (33 bp):
TTTTTTACTGTTTTGGTTGCTGTTTTAGTGCTA
Found at i:42195537 original size:20 final size:20
Alignment explanation
Indices: 42195514--42195613 Score: 52
Period size: 20 Copynumber: 5.0 Consensus size: 20
42195504 ACTGTTTTGG
42195514 TGTTGTTTTATTGTTATTTT
1 TGTTGTTTTATTGTTATTTT
* *
42195534 TGTTG--CTA-T-TT-TTGT
1 TGTTGTTTTATTGTTATTTT
*
42195549 TGTTGCTTTGCTATTATT-TTTGT
1 TGTTG-TTT--TATTGTTATTT-T
*
42195572 TGCTGTTTTGATTGTTATTTT
1 TGTTGTTTT-ATTGTTATTTT
*
42195593 TGTTGTTTGGA-TGTTATTTT
1 TGTTGTTT-TATTGTTATTTT
42195613 T
1 T
42195614 TTATGCATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
15 8 0.13
16 2 0.03
17 1 0.02
18 2 0.03
20 18 0.30
21 15 0.25
22 10 0.16
23 5 0.08
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.68
Consensus pattern (20 bp):
TGTTGTTTTATTGTTATTTT
Found at i:42195558 original size:23 final size:23
Alignment explanation
Indices: 42195532--42195599 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
42195522 TATTGTTATT
*
42195532 TTTGTTGCTATTTTTGTTGTTGC
1 TTTGTTGTTATTTTTGTTGTTGC
* * * *
42195555 TTTGCTATTATTTTTGTTGCTGT
1 TTTGTTGTTATTTTTGTTGTTGC
42195578 TTTGATTGTTATTTTTGTTGTT
1 TTTG-TTGTTATTTTTGTTGTT
42195600 TGGATGTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 22 0.61
24 14 0.39
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.68
Consensus pattern (23 bp):
TTTGTTGTTATTTTTGTTGTTGC
Found at i:42195598 original size:12 final size:12
Alignment explanation
Indices: 42195519--42195599 Score: 67
Period size: 12 Copynumber: 6.8 Consensus size: 12
42195509 TTTGGTGTTG
*
42195519 TTTTATTGTTAT
1 TTTTGTTGTTAT
*
42195531 TTTTGTTGCTAT
1 TTTTGTTGTTAT
*
42195543 TTTTGTTGTT-G
1 TTTTGTTGTTAT
* * *
42195554 CTTTGCTATTAT
1 TTTTGTTGTTAT
* *
42195566 TTTTGTTGCT-G
1 TTTTGTTGTTAT
42195577 TTTTGATTGTTAT
1 TTTTG-TTGTTAT
42195590 TTTTGTTGTT
1 TTTTGTTGTT
42195600 TGGATGTTAT
Statistics
Matches: 51, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
11 12 0.24
12 34 0.67
13 5 0.10
ACGTcount: A:0.09, C:0.05, G:0.17, T:0.69
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:42195613 original size:21 final size:22
Alignment explanation
Indices: 42195566--42195614 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
42195556 TTGCTATTAT
*
42195566 TTTTGTTGCTGTTTTGATTGTTA
1 TTTT-TTGCTGTTTGGATTGTTA
*
42195589 -TTTTTGTTGTTTGGA-TGTTA
1 TTTTTTGCTGTTTGGATTGTTA
42195609 TTTTTT
1 TTTTTT
42195615 TATGCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 15 0.65
22 3 0.13
ACGTcount: A:0.08, C:0.02, G:0.20, T:0.69
Consensus pattern (22 bp):
TTTTTTGCTGTTTGGATTGTTA
Found at i:42196324 original size:192 final size:192
Alignment explanation
Indices: 42195997--42196556 Score: 1057
Period size: 192 Copynumber: 2.9 Consensus size: 192
42195987 CTGATCTGAG
*
42195997 TCACGATCAATTCTACTTGCACCTTGTTTTCATCTCTTCAAGATAGAATTATAAGTGACAATCTT
1 TCACGATCAGTTCTACTTGCACCTTGTTTTCATCTCTTCAAGATAGAATTATAAGTGACAATCTT
*
42196062 CGCAAATAAGAATCATGCTACTTTTTTTCCTTTTTAACATTTCTTTGTTTGGTAGTTATATAAGA
66 CGCATATAAGAATCATGCTACTTTTTTTCCTTTTTAACATTTCTTTGTTTGGTAGTTATATAAGA
42196127 TTTTGATTGAATTTGGAATTTAGTCGTATCATAATAGGGAGATAATGTCTTTCACTATTATT
131 TTTTGATTGAATTTGGAATTTAGTCGTATCATAATAGGGAGATAATGTCTTTCACTATTATT
42196189 TCACGATCAGTTCTACTTGCACCTTGTTTTCATCTCTTCAAGATAGAATTATAAGTGACAATCTT
1 TCACGATCAGTTCTACTTGCACCTTGTTTTCATCTCTTCAAGATAGAATTATAAGTGACAATCTT
42196254 CGCATATAAGAATCATGCTACTTTTTTTCCTTTTTAACATTTCTTTGTTTGGTAGTTATATAAGA
66 CGCATATAAGAATCATGCTACTTTTTTTCCTTTTTAACATTTCTTTGTTTGGTAGTTATATAAGA
42196319 TTTTGATTGAATTTGGAATTTAGTCGTATCATAATAGGGAGATAATGTCTTTCACTATTATT
131 TTTTGATTGAATTTGGAATTTAGTCGTATCATAATAGGGAGATAATGTCTTTCACTATTATT
42196381 TCACGATCAGTTCTACTTGCACCTTGTTTTCATCTCTTCAAGATAGAATTATAAGTGACAATCTT
1 TCACGATCAGTTCTACTTGCACCTTGTTTTCATCTCTTCAAGATAGAATTATAAGTGACAATCTT
* *
42196446 CGCATATAAGAATCATGCTACTTTTTTTCCTTTTTAATATTTCTTTGTTTGGTAGTTATATTAGA
66 CGCATATAAGAATCATGCTACTTTTTTTCCTTTTTAACATTTCTTTGTTTGGTAGTTATATAAGA
* * *
42196511 TTTTGATTGAATTTGGAACTTAGTTGTATCATAATAGGGTGATAAT
131 TTTTGATTGAATTTGGAATTTAGTCGTATCATAATAGGGAGATAAT
42196557 ATCATTCATT
Statistics
Matches: 361, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
192 361 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (192 bp):
TCACGATCAGTTCTACTTGCACCTTGTTTTCATCTCTTCAAGATAGAATTATAAGTGACAATCTT
CGCATATAAGAATCATGCTACTTTTTTTCCTTTTTAACATTTCTTTGTTTGGTAGTTATATAAGA
TTTTGATTGAATTTGGAATTTAGTCGTATCATAATAGGGAGATAATGTCTTTCACTATTATT
Found at i:42202702 original size:22 final size:21
Alignment explanation
Indices: 42202674--42202714 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
42202664 GTGGATATTC
*
42202674 ATTTAAATTTAATTATAAAAAA
1 ATTTAAAATTAA-TATAAAAAA
42202696 ATTTAAAATTAATATAAAA
1 ATTTAAAATTAATATAAAA
42202715 TTAAACTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTAAAATTAATATAAAAAA
Found at i:42219019 original size:21 final size:20
Alignment explanation
Indices: 42218995--42219037 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
42218985 AAATAAATAA
*
42218995 AAAATTTAAATATAATTGAAT
1 AAAATTTAAAT-TAATTAAAT
*
42219016 AAAACTTGAAATTAATTAAAT
1 AAAA-TTTAAATTAATTAAAT
42219037 A
1 A
42219038 CATATTTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (20 bp):
AAAATTTAAATTAATTAAAT
Found at i:42219833 original size:3 final size:3
Alignment explanation
Indices: 42219825--42219863 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
42219815 TTTGAATGCT
*
42219825 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA ACA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
42219864 ACTTCCTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:42221227 original size:18 final size:19
Alignment explanation
Indices: 42221198--42221293 Score: 112
Period size: 18 Copynumber: 5.3 Consensus size: 19
42221188 GAAAGAGGAA
42221198 CCAAAGAAAGAAGGTGAAG
1 CCAAAGAAAGAAGGTGAAG
*
42221217 CCAAA-AAAGAAGATGAA-
1 CCAAAGAAAGAAGGTGAAG
*
42221234 CAAAAGAAAGAAGGTGAAG
1 CCAAAGAAAGAAGGTGAAG
* *
42221253 CC-AAGAAGGAAGATGAA-
1 CCAAAGAAAGAAGGTGAAG
42221270 -CAGAAGAAAGAAGGTGAAG
1 CCA-AAGAAAGAAGGTGAAG
42221289 CCAAA
1 CCAAA
42221294 AAGGAAGAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
16 1 0.02
17 4 0.06
18 48 0.76
19 8 0.13
20 2 0.03
ACGTcount: A:0.56, C:0.10, G:0.28, T:0.05
Consensus pattern (19 bp):
CCAAAGAAAGAAGGTGAAG
Found at i:42221241 original size:36 final size:36
Alignment explanation
Indices: 42221190--42221301 Score: 179
Period size: 36 Copynumber: 3.1 Consensus size: 36
42221180 CCAGAGAAGA
* * *
42221190 AAGAGGAACCAAAGAAAGAAGGTGAAGCCAAAAAAG
1 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
*
42221226 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAGAAGG
1 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
*
42221262 AAGATGAACAGAAGAAAGAAGGTGAAGCCAAAAAGG
1 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
42221298 AAGA
1 AAGA
42221302 AGAAGGTAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.57, C:0.09, G:0.29, T:0.04
Consensus pattern (36 bp):
AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
Found at i:42221313 original size:36 final size:35
Alignment explanation
Indices: 42221201--42221318 Score: 164
Period size: 36 Copynumber: 3.3 Consensus size: 35
42221191 AGAGGAACCA
* *
42221201 AAGAAAGAAGGTGAAGCCAAAAAAGAAGATGAACAA
1 AAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAA-AG
*
42221237 AAGAAAGAAGGTGAAGCCAAGAAGGAAGATGAACAG
1 AAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAA-AG
* *
42221273 AAGAAAGAAGGTGAAGCCAAAAAGGAAGAAGAAGG
1 AAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAAAG
42221308 TAAGAAAGAAG
1 -AAGAAAGAAG
42221319 AGGAAACCAA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
35 1 0.01
36 74 0.99
ACGTcount: A:0.58, C:0.07, G:0.31, T:0.05
Consensus pattern (35 bp):
AAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAAAG
Found at i:42221313 original size:72 final size:72
Alignment explanation
Indices: 42221178--42221331 Score: 195
Period size: 72 Copynumber: 2.1 Consensus size: 72
42221168 CCAGCAAAAG
*
42221178 AACCAGAGAAGAAAGAGGAACCAAAGAAAGAAGGTGAAGCCAAAAAAGAAGATGAACAAAAGAAA
1 AACCA-AGAAGAAAGAGGAACCAAAGAAAGAAGGTGAAGCCAAAAAAGAAGAAGAACAAAAGAAA
42221243 GAAG-GTGA
65 GAAGAG-GA
* * * * ***
42221251 AGCCAAGAAGGAAGATGAA-CAGAAGAAAGAAGGTGAAGCCAAAAAGGAAGAAGAAGGTAAGAAA
1 AACCAAGAAGAAAGAGGAACCA-AAGAAAGAAGGTGAAGCCAAAAAAGAAGAAGAACAAAAGAAA
42221315 GAAGAGGA
65 GAAGAGGA
42221323 AACCAAGAA
1 AACCAAGAA
42221332 AGATGGTGAG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
71 2 0.03
72 63 0.90
73 5 0.07
ACGTcount: A:0.58, C:0.09, G:0.29, T:0.04
Consensus pattern (72 bp):
AACCAAGAAGAAAGAGGAACCAAAGAAAGAAGGTGAAGCCAAAAAAGAAGAAGAACAAAAGAAAG
AAGAGGA
Found at i:42221330 original size:18 final size:18
Alignment explanation
Indices: 42221190--42221334 Score: 61
Period size: 18 Copynumber: 8.1 Consensus size: 18
42221180 CCAGAGAAGA
42221190 AAGAGG-AACCAAAGAAAG
1 AAGAGGAAACC-AAGAAAG
* *
42221208 AAG-GTGAAGCCAAAAAAG
1 AAGAG-GAAACCAAGAAAG
* *
42221226 AAGATG-AACAAAAGAAAG
1 AAGAGGAAAC-CAAGAAAG
* *
42221244 AAG-GTGAAGCCAAGAAGG
1 AAGAG-GAAACCAAGAAAG
* *
42221262 AAGATG-AACAGAAGAAAG
1 AAGAGGAAAC-CAAGAAAG
*
42221280 AAG-GTGAAGCCAA-AAAGG
1 AAGAG-GAAACCAAGAAA-G
* ***
42221298 AAGAAGAAGGTAAGAAAG
1 AAGAGGAAACCAAGAAAG
42221316 AAGAGGAAACCAAGAAAG
1 AAGAGGAAACCAAGAAAG
42221334 A
1 A
42221335 TGGTGAGAAG
Statistics
Matches: 90, Mismatches: 24, Indels: 26
0.64 0.17 0.19
Matches are distributed among these distances:
17 8 0.09
18 72 0.80
19 10 0.11
ACGTcount: A:0.58, C:0.08, G:0.30, T:0.04
Consensus pattern (18 bp):
AAGAGGAAACCAAGAAAG
Found at i:42227431 original size:28 final size:28
Alignment explanation
Indices: 42227353--42227481 Score: 97
Period size: 27 Copynumber: 4.6 Consensus size: 28
42227343 TTTTAAATCT
* *
42227353 TTTAAAAGTTGATAAAAAAAATTTGGGCCC
1 TTTAAAAGTT-A-AAAAATATTTTGGGCCC
42227383 -TTAAAA-TCTAAAAAA-AGTTTTGGGCCC
1 TTTAAAAGT-TAAAAAATA-TTTTGGGCCC
* * *
42227410 TTTAAAAGTTAATAAATTTTTTTTGG-CC
1 TTTAAAAGTTAA-AAAATATTTTGGGCCC
*
42227438 TTTAAAAAG-AAAAAAATATTTTGGGCCC
1 TTT-AAAAGTTAAAAAATATTTTGGGCCC
* *
42227466 CTTAAAAATTAAAAAA
1 TTTAAAAGTTAAAAAA
42227482 ATAAAATTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
26 1 0.01
27 28 0.35
28 28 0.35
29 22 0.28
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (28 bp):
TTTAAAAGTTAAAAAATATTTTGGGCCC
Done.