Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 19 of 255
Found at i:5082277 original size:19 final size:21
Alignment explanation
Indices: 5082249--5082296 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
5082239 TAATTATTTA
5082249 TTTTAGTTTTGATTCTAA-AT
1 TTTTAGTTTTGATTCTAATAT
* *
5082269 TTTTA-TTTTTATTTTAATAT
1 TTTTAGTTTTGATTCTAATAT
5082289 TTTTAGTT
1 TTTTAGTT
5082297 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTTGATTCTAATAT
Found at i:5082395 original size:27 final size:28
Alignment explanation
Indices: 5082360--5082413 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5082350 TATTTTGATA
*
5082360 ATGAATTTTA-AATTTTTTATATTTTTC
1 ATGAATTTTATAATATTTTATATTTTTC
* *
5082387 ATGACTTTTATAATATTTTATTTTTTT
1 ATGAATTTTATAATATTTTATATTTTT
5082414 TAAAATTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (28 bp):
ATGAATTTTATAATATTTTATATTTTTC
Found at i:5083569 original size:10 final size:10
Alignment explanation
Indices: 5083537--5083570 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
5083527 TAAAACATGT
5083537 AAAAAATTTA
1 AAAAAATTTA
5083547 AAATAATATTTA
1 AAA-AA-ATTTA
5083559 AAAAAATTTA
1 AAAAAATTTA
5083569 AA
1 AA
5083571 TCTTTTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.45
11 4 0.18
12 8 0.36
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:5087386 original size:5 final size:5
Alignment explanation
Indices: 5087376--5087419 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
5087366 ATATATGTCA
5087376 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
5087420 AAACACAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:5088036 original size:18 final size:18
Alignment explanation
Indices: 5088013--5088047 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5088003 TCAAATACAT
5088013 TTAAAAACA-TAAAAAATA
1 TTAAAAA-ATTAAAAAATA
5088031 TTAAAAAATTAAAAAAT
1 TTAAAAAATTAAAAAAT
5088048 GATACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TTAAAAAATTAAAAAATA
Found at i:5092024 original size:3 final size:3
Alignment explanation
Indices: 5092011--5092085 Score: 50
Period size: 3 Copynumber: 24.3 Consensus size: 3
5092001 GAGGGCATAT
5092011 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
5092055 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA A
5092086 AAAAATAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
2 7 0.12
3 40 0.69
4 9 0.16
5 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5092037 original size:18 final size:18
Alignment explanation
Indices: 5092007--5092093 Score: 88
Period size: 18 Copynumber: 4.7 Consensus size: 18
5091997 TGGAGAGGGC
5092007 ATATATAAT-ATAATAATA
1 ATATA-AATAATAATAATA
5092025 ATATAAATAATAATATATA
1 ATATAAATAATAATA-ATA
*
5092044 CATGAGAAATAATAATAATA
1 -AT-ATAAATAATAATAATA
* *
5092064 ATATAAATAATAGTAAAA
1 ATATAAATAATAATAATA
*
5092082 ATA-AAAAAATAA
1 ATATAAATAATAA
5092094 AAAAATAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.17
18 27 0.46
19 5 0.08
20 5 0.08
21 12 0.20
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (18 bp):
ATATAAATAATAATAATA
Found at i:5092095 original size:7 final size:8
Alignment explanation
Indices: 5092078--5092103 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5092068 AAATAATAGT
5092078 AAAAATAA
1 AAAAATAA
5092086 AAAAATAA
1 AAAAATAA
5092094 AAAAATAA
1 AAAAATAA
5092102 AA
1 AA
5092104 CAAAGCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:5092553 original size:38 final size:38
Alignment explanation
Indices: 5092511--5092593 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
5092501 TGGGGTGGTT
*
5092511 TAGGTGGCTAAGGTAGGTGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTAGGTGGCCAACAAGGGTGGTGGAG
*
5092549 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTAGGTGGCCAACAAGGGTGGTGGAG
5092587 TAGGTGG
1 TAGGTGG
5092594 GATTAGGGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.22, C:0.11, G:0.49, T:0.18
Consensus pattern (38 bp):
TAGGTGGCCAAGGTAGGTGGCCAACAAGGGTGGTGGAG
Found at i:5093119 original size:68 final size:68
Alignment explanation
Indices: 5093002--5093272 Score: 418
Period size: 68 Copynumber: 4.0 Consensus size: 68
5092992 GCTTCGATTA
* * * *
5093002 ATCCACTAAAACTTCAAGGAAATCTGTTGTGGCTTTTAGCTGCTCCAACGCCATTTCAGGAAGAA
1 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAA
5093067 GAG
66 GAG
* * * *
5093070 ATTCACTGAAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCGCTCCAACGCCATATCAGGGAGAA
1 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAA
5093135 GAG
66 GAG
*
5093138 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACACCATTTCAGGGAA-A
1 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCA-GGAAGA
5093202 AGAG
65 AGAG
* * *
5093206 ATCCACTGAAACTTCAAGGAGATCTACTGTGGCTTTTAGCCGCTCTAACGCCATTTCAGGGAGAA
1 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAA
5093271 GA
66 GA
5093273 TATTTGATTT
Statistics
Matches: 186, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
67 3 0.02
68 180 0.97
69 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (68 bp):
ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAA
GAG
Found at i:5101490 original size:19 final size:19
Alignment explanation
Indices: 5101448--5101494 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5101438 AGTGAAAGTT
*
5101448 TAATGCAAATGTTTCAATG
1 TAATGCAAATGTTGCAATG
*
5101467 TAATGCAAATGTATGGAATG
1 TAATGCAAATGT-TGCAATG
5101487 -AATGCAAA
1 TAATGCAAA
5101495 AGAAAGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (19 bp):
TAATGCAAATGTTGCAATG
Found at i:5105221 original size:26 final size:26
Alignment explanation
Indices: 5105191--5105285 Score: 124
Period size: 26 Copynumber: 3.8 Consensus size: 26
5105181 GGACTCACCA
*
5105191 CAGCTCGTATGAGCTTACCGATATAT
1 CAGCTCGTAAGAGCTTACCGATATAT
*
5105217 CAGCTCATAAGAGCTTACCGATATAT
1 CAGCTCGTAAGAGCTTACCGATATAT
*
5105243 TAGCTCGTAAGAGCTTACC-AT-T-T
1 CAGCTCGTAAGAGCTTACCGATATAT
* *
5105266 CAACTCGAAAGAGCTTACCG
1 CAGCTCGTAAGAGCTTACCG
5105286 TTTCAACTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
23 17 0.28
24 1 0.02
25 2 0.03
26 41 0.67
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (26 bp):
CAGCTCGTAAGAGCTTACCGATATAT
Found at i:5105277 original size:23 final size:23
Alignment explanation
Indices: 5105246--5105332 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
5105236 GATATATTAG
*
5105246 CTCGTAAGAGCTTACCATTTCAA
1 CTCGAAAGAGCTTACCATTTCAA
*
5105269 CTCGAAAGAGCTTACCGTTTCAA
1 CTCGAAAGAGCTTACCATTTCAA
* * *
5105292 CTCAAAAGAGCTTACTATTTCAG
1 CTCGAAAGAGCTTACCATTTCAA
*
5105315 CTTGAAAAAGAGCTTACC
1 CTCG--AAAGAGCTTACC
5105333 GATCATGGCT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 42 0.79
25 11 0.21
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (23 bp):
CTCGAAAGAGCTTACCATTTCAA
Found at i:5111997 original size:60 final size:60
Alignment explanation
Indices: 5111924--5112050 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
5111914 ATTGAATAGT
* **
5111924 TTGAGTG-TCCATTTTGTAATTTTTCATAGTTAGATGAGTAAAAGAAAATTTTACTAATAC
1 TTGAGTGATCCATTTTGTAACTTTTCATAGTTAGATGAAAAAAAGAAAA-TTTACTAATAC
* * * *
5111984 TTGAGTGAT-CATTTTGTAACTTTTCCTAGTTGGATGAAAAAAATAAAATTTACTAATAG
1 TTGAGTGATCCATTTTGTAACTTTTCATAGTTAGATGAAAAAAAGAAAATTTACTAATAC
5112043 TTGAGTGA
1 TTGAGTGA
5112051 CTATTAGTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 18 0.31
60 40 0.68
61 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (60 bp):
TTGAGTGATCCATTTTGTAACTTTTCATAGTTAGATGAAAAAAAGAAAATTTACTAATAC
Found at i:5112604 original size:36 final size:37
Alignment explanation
Indices: 5112534--5112606 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
5112524 AAAAAGTTAA
*
5112534 TGTTTTAGCCAATATTCCATTAAAAAACATTAATTTG
1 TGTTTTAGCCAATATTCCATTAAAAAACAATAATTTG
*
5112571 TGTTTTAGCCCATATTCCATTAAAAAA-AATAATTTG
1 TGTTTTAGCCAATATTCCATTAAAAAACAATAATTTG
5112607 ACTCTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 8 0.24
37 26 0.76
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (37 bp):
TGTTTTAGCCAATATTCCATTAAAAAACAATAATTTG
Found at i:5113083 original size:3 final size:3
Alignment explanation
Indices: 5113075--5113129 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
5113065 GAAGTGAGAC
5113075 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5113123 ATA ATA A
1 ATA ATA A
5113130 AGATAAAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5113193 original size:25 final size:27
Alignment explanation
Indices: 5113136--5113185 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
5113126 ATAAAGATAA
* *
5113136 AATTATACTTTGATCTTTCTAAAAAAT
1 AATTATACTTTAATCTCTCTAAAAAAT
5113163 AATTATA-TTTAATCTCTC-AAAAA
1 AATTATACTTTAATCTCTCTAAAAA
5113186 TTTATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 9 0.43
27 7 0.33
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (27 bp):
AATTATACTTTAATCTCTCTAAAAAAT
Found at i:5117332 original size:26 final size:26
Alignment explanation
Indices: 5117296--5117379 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5117286 CATGAAATTC
5117296 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5117322 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5117348 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5117374 TTATCA
1 TTATCA
5117380 ATTTGTATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5122776 original size:26 final size:26
Alignment explanation
Indices: 5122740--5122823 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5122730 CATGAAATTC
5122740 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5122766 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5122792 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5122818 TTATCA
1 TTATCA
5122824 ATTTGTAGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5127499 original size:34 final size:34
Alignment explanation
Indices: 5127456--5127524 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 34
5127446 ACAATGTGTC
5127456 TACTTTGTATAATAACCTTAATTTGGG-CCTTGAT
1 TACTTTGTATAATAACCTTAATTTGGGTCC-TGAT
5127490 TACTTTGTATAATAACCTTAATTTGGGTCCTGAT
1 TACTTTGTATAATAACCTTAATTTGGGTCCTGAT
5127524 T
1 T
5127525 TTGAGATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (34 bp):
TACTTTGTATAATAACCTTAATTTGGGTCCTGAT
Found at i:5129060 original size:27 final size:27
Alignment explanation
Indices: 5129030--5129082 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5129020 ACTTGTGAAA
5129030 TTAA-TTTAATTTATTATTTTT-ATTTTT
1 TTAAGTTT-ATTT-TTATTTTTCATTTTT
*
5129057 TTAAGTTTATTTTTGTTTTTCATTTT
1 TTAAGTTTATTTTTATTTTTCATTTT
5129083 AGTTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 7 0.30
27 13 0.57
28 3 0.13
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.74
Consensus pattern (27 bp):
TTAAGTTTATTTTTATTTTTCATTTTT
Found at i:5130526 original size:45 final size:45
Alignment explanation
Indices: 5130427--5130527 Score: 125
Period size: 45 Copynumber: 2.2 Consensus size: 45
5130417 AAAGGATACT
* *
5130427 ATAACGTCTTTCAACTATGATCTTAATCATTTATATCATGATGTC
1 ATAACATCTTTCAACTATGATCTTAATCATCTATATCATGATGTC
* *
5130472 ATAGCATCTTTCAACTATTG-TCTTACTCATCCT-TATCATGATGTC
1 ATAACATCTTTCAACTA-TGATCTTAATCAT-CTATATCATGATGTC
*
5130517 ATAATATCTTT
1 ATAACATCTTT
5130528 TAGTTATGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
45 45 0.94
46 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.44
Consensus pattern (45 bp):
ATAACATCTTTCAACTATGATCTTAATCATCTATATCATGATGTC
Found at i:5131489 original size:26 final size:26
Alignment explanation
Indices: 5131450--5131501 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5131440 TTTAACCATG
5131450 TCTAAATCAACCATTATATTTCTCTA
1 TCTAAATCAACCATTATATTTCTCTA
* * *
5131476 TCTAAATTAGCCATTATTTTTCTCTA
1 TCTAAATCAACCATTATATTTCTCTA
5131502 ACTCTTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.02, T:0.46
Consensus pattern (26 bp):
TCTAAATCAACCATTATATTTCTCTA
Found at i:5131671 original size:17 final size:18
Alignment explanation
Indices: 5131649--5131683 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5131639 GTAAGATCCC
5131649 AAAAA-TAGGGTTAGAAA
1 AAAAATTAGGGTTAGAAA
*
5131666 AAAAATTAGGGTTTGAAA
1 AAAAATTAGGGTTAGAAA
5131684 CTAAGAGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (18 bp):
AAAAATTAGGGTTAGAAA
Found at i:5132618 original size:104 final size:106
Alignment explanation
Indices: 5132508--5132709 Score: 255
Period size: 106 Copynumber: 1.9 Consensus size: 106
5132498 TGTCTAGGCT
* * * * * *
5132508 GTGTAACTCACTGTTTATGATTTAGGACCACACGGCCAGGGACAT-CG-GCGTGTGCCCAGGCCG
1 GTGTAACTCACTATTTATAATTTAAGACCACACAGACAGGGAAATGCGTGCGTGTGCCCAGGCCG
* * *
5132571 TGTGAGCTACACGGGTAAGGACATGGGCATGTATCCAAGTC
66 TGTAAGCCACACGGGCAAGGACATGGGCATGTATCCAAGTC
* * * * *
5132612 GTGTAACTCACTATTTATAATTTAAGATCACACAGATAGGGAAATGGGTGTGTGTGCCCAGGTCG
1 GTGTAACTCACTATTTATAATTTAAGACCACACAGACAGGGAAATGCGTGCGTGTGCCCAGGCCG
*
5132677 TGTAAGCCACACGGGCAAGGATATGGGCATGTA
66 TGTAAGCCACACGGGCAAGGACATGGGCATGTA
5132710 CCTAGGCCGT
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 37 0.46
105 1 0.01
106 43 0.53
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (106 bp):
GTGTAACTCACTATTTATAATTTAAGACCACACAGACAGGGAAATGCGTGCGTGTGCCCAGGCCG
TGTAAGCCACACGGGCAAGGACATGGGCATGTATCCAAGTC
Found at i:5132736 original size:42 final size:42
Alignment explanation
Indices: 5132675--5132807 Score: 124
Period size: 42 Copynumber: 3.2 Consensus size: 42
5132665 GTGCCCAGGT
* * *
5132675 CGTGTAAGCCACACGGGCAAGGATATGGGCATGTACCTAGGC
1 CGTGTGAGCCAAACAGGCAAGGATATGGGCATGTACCTAGGC
* * * *
5132717 CGTGTGAGCTAAACAGGCAAGGATATGAGCGTGTACCTAGGT
1 CGTGTGAGCCAAACAGGCAAGGATATGGGCATGTACCTAGGC
* * * * * * *
5132759 CTTGTAAGCCACACAGGCAAGAACATGGACATGTGTCC-AGGC
1 CGTGTGAGCCAAACAGGCAAGGATATGGGCATGT-ACCTAGGC
5132801 CGTGTGA
1 CGTGTGA
5132808 CTCACTGTTT
Statistics
Matches: 70, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
42 68 0.97
43 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.32, T:0.19
Consensus pattern (42 bp):
CGTGTGAGCCAAACAGGCAAGGATATGGGCATGTACCTAGGC
Found at i:5134272 original size:21 final size:20
Alignment explanation
Indices: 5134238--5134291 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
5134228 GTTATAACTT
*
5134238 TATTCATTTATATAAATATTTTA
1 TATT-ATTT-TATAAA-ATTATA
*
5134261 TATTTTTTTAT-AAATTATA
1 TATTATTTTATAAAATTATA
5134280 TATTATTTTATA
1 TATTATTTTATA
5134292 TATGATAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 15 0.56
20 2 0.07
21 3 0.11
22 3 0.11
23 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTATTTTATAAAATTATA
Found at i:5134293 original size:21 final size:21
Alignment explanation
Indices: 5134244--5134293 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
5134234 ACTTTATTCA
*
5134244 TTTATATAAATATTTTATATTT
1 TTTATAT-AATATTATATATTT
5134266 TTT-TATAA-ATTATATATTAT
1 TTTATATAATATTATATATT-T
5134286 TTTATATA
1 TTTATATA
5134294 TGATAATCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 9 0.36
20 6 0.24
21 7 0.28
22 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATATAATATTATATATTT
Found at i:5140687 original size:18 final size:18
Alignment explanation
Indices: 5140661--5140725 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
5140651 TAAAAAATTT
*
5140661 AAATGAAATGCAAGTAAA
1 AAATTAAATGCAAGTAAA
5140679 AAATTAAATGAGCAA-T-AA
1 AAATTAAAT--GCAAGTAAA
*
5140697 AAATATAGCAT-CAAGTAAA
1 AAAT-TA-AATGCAAGTAAA
5140716 AAATTAAATG
1 AAATTAAATG
5140726 AAACATAGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
17 5 0.14
18 17 0.46
19 9 0.24
20 6 0.16
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (18 bp):
AAATTAAATGCAAGTAAA
Found at i:5144694 original size:18 final size:18
Alignment explanation
Indices: 5144671--5144773 Score: 80
Period size: 18 Copynumber: 5.4 Consensus size: 18
5144661 ACATCGCGAT
*
5144671 CTGAAGCCCGAAGTCTAG
1 CTGAAGCCCGAAGTCTAA
**
5144689 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
* *
5144710 CAGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
**
5144728 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
*
5144749 CGGAAGCCCGAAGTCTAA
1 CTGAAGCCCGAAGTCTAA
5144767 CTGAAGC
1 CTGAAGC
5144774 TCATCAGAGC
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
18 23 0.36
19 13 0.20
20 13 0.20
21 15 0.23
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (18 bp):
CTGAAGCCCGAAGTCTAA
Found at i:5144715 original size:21 final size:21
Alignment explanation
Indices: 5144691--5144755 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
5144681 AAGTCTAGCT
5144691 GAAGCACATAAGTGCTAAACA
1 GAAGCACATAAGTGCTAAACA
** *
5144712 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACA
*
5144730 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACA
5144751 GAAGC
1 GAAGC
5144756 CCGAAGTCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACA
Found at i:5144732 original size:39 final size:39
Alignment explanation
Indices: 5144673--5144773 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
5144663 ATCGCGATCT
*
5144673 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACA
1 GAAGCCCGAAGTCTAACTGAAGCACATAAGTGCTAAACA
* *
5144712 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGTCTAACTGAAGCACATAAGTGCTAAACA
5144751 GAAGCCCGAAGTCTAACTGAAGC
1 GAAGCCCGAAGTCTAACTGAAGC
5144774 TCATCAGAGC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.38, C:0.24, G:0.25, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGTCTAACTGAAGCACATAAGTGCTAAACA
Found at i:5148666 original size:53 final size:53
Alignment explanation
Indices: 5148604--5148712 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
5148594 AGCTTTACTT
5148604 AAAATTTAAAAAACTAAAATATTTACTTAAGACCTAACACGGGTACAACCGTC
1 AAAATTTAAAAAACTAAAATATTTACTTAAGACCTAACACGGGTACAACCGTC
* *
5148657 AAAATTTAAAAGACTAAAATATTTACTTAAGACCTAACACGGGTACAACTGTC
1 AAAATTTAAAAAACTAAAATATTTACTTAAGACCTAACACGGGTACAACCGTC
5148710 AAA
1 AAA
5148713 TGGGCAAGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (53 bp):
AAAATTTAAAAAACTAAAATATTTACTTAAGACCTAACACGGGTACAACCGTC
Found at i:5154616 original size:19 final size:19
Alignment explanation
Indices: 5154588--5154624 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5154578 AGTTTTTTTT
5154588 TTTTAAGAAAATCTTAAAA
1 TTTTAAGAAAATCTTAAAA
* *
5154607 TTTTATGAAAATTTTAAA
1 TTTTAAGAAAATCTTAAA
5154625 TAATTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (19 bp):
TTTTAAGAAAATCTTAAAA
Found at i:5155298 original size:20 final size:21
Alignment explanation
Indices: 5155275--5155318 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5155265 TTTTAAAATT
5155275 AAAA-AAAATTTAAATTTAAA
1 AAAATAAAATTTAAATTTAAA
***
5155295 AAAATATTTTTTAAATTTAAA
1 AAAATAAAATTTAAATTTAAA
5155316 AAA
1 AAA
5155319 TTAATTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATAAAATTTAAATTTAAA
Found at i:5155309 original size:21 final size:20
Alignment explanation
Indices: 5155261--5155318 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 20
5155251 TTAATTAATT
*
5155261 AATTTTTTAAAATTAAAAAA
1 AATTTTTTAAATTTAAAAAA
5155281 AA---TTTAAATTTAAAAAA
1 AATTTTTTAAATTTAAAAAA
5155298 ATATTTTTTAAATTTAAAAAA
1 A-ATTTTTTAAATTTAAAAAA
5155319 TTAATTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
17 15 0.45
18 1 0.03
20 2 0.06
21 15 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTTTTAAATTTAAAAAA
Found at i:5158931 original size:25 final size:25
Alignment explanation
Indices: 5158901--5158948 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
5158891 TATTTTACGA
5158901 TTGAGAATGCTTATTATTGTACTAT
1 TTGAGAATGCTTATTATTGTACTAT
5158926 TTGAGAATGCTTATTATTGTACT
1 TTGAGAATGCTTATTATTGTACT
5158949 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (25 bp):
TTGAGAATGCTTATTATTGTACTAT
Found at i:5160022 original size:101 final size:101
Alignment explanation
Indices: 5159847--5160045 Score: 371
Period size: 101 Copynumber: 2.0 Consensus size: 101
5159837 TCAAGCATCT
* *
5159847 TTTAAAGAGAAGGGAAAGAATATGGAGACAAATTTTATATGTCAAGATGATGAAATGGAGGCAAA
1 TTTAAAGAGAAGGGAAAGAATATGGAGACAAATTTTATATGCCAAGATGATGAAATGGACGCAAA
5159912 AGATGAAAATATTCACTATGATACTAAAACTGATCC
66 AGATGAAAATATTCACTATGATACTAAAACTGATCC
*
5159948 TTTAAAGAGAATGGAAAGAATATGGAGACAAATTTTATATGCCAAGATGATGAAATGGACGCAAA
1 TTTAAAGAGAAGGGAAAGAATATGGAGACAAATTTTATATGCCAAGATGATGAAATGGACGCAAA
5160013 AGATGAAAATATTCACTATGATACTAAAACTGA
66 AGATGAAAATATTCACTATGATACTAAAACTGA
5160046 CCATGCCTAC
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (101 bp):
TTTAAAGAGAAGGGAAAGAATATGGAGACAAATTTTATATGCCAAGATGATGAAATGGACGCAAA
AGATGAAAATATTCACTATGATACTAAAACTGATCC
Found at i:5178877 original size:6 final size:6
Alignment explanation
Indices: 5178861--5178890 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
5178851 TAAACTAAAA
5178861 TATAGTT TATATT TATATT TATATT TATAT
1 TATA-TT TATATT TATATT TATATT TATAT
5178891 AATCAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:5180278 original size:11 final size:11
Alignment explanation
Indices: 5180198--5180279 Score: 64
Period size: 11 Copynumber: 7.3 Consensus size: 11
5180188 AAAATGTAAT
5180198 ATAAATATATA
1 ATAAATATATA
*
5180209 AGAAATATAATA
1 ATAAATAT-ATA
*
5180221 GATATAATATAAA
1 -ATA-AATATATA
5180234 ATAACATATA-A
1 ATAA-ATATATA
5180245 A-ACAATATAT-
1 ATA-AATATATA
5180255 ATAAATA-ATTA
1 ATAAATATA-TA
5180266 ATAAATATATA
1 ATAAATATATA
5180277 ATA
1 ATA
5180280 TATGTGAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
9 1 0.02
10 12 0.21
11 24 0.41
12 12 0.21
13 4 0.07
14 5 0.09
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAAATATATA
Found at i:5181964 original size:26 final size:26
Alignment explanation
Indices: 5181928--5181983 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
5181918 AAATAGTACT
5181928 ACTTAGTTCCTAGACAATTGTATTTG
1 ACTTAGTTCCTAGACAATTGTATTTG
5181954 ACTTAGTTCCTAGACAATTGTATTTG
1 ACTTAGTTCCTAGACAATTGTATTTG
5181980 ACTT
1 ACTT
5181984 TGGATCACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (26 bp):
ACTTAGTTCCTAGACAATTGTATTTG
Found at i:5183508 original size:17 final size:17
Alignment explanation
Indices: 5183486--5183522 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5183476 TTGTTTTTAT
*
5183486 TTTTTACAGTGAATTAA
1 TTTTTACAGTAAATTAA
*
5183503 TTTTTAGAGTAAATTAA
1 TTTTTACAGTAAATTAA
5183520 TTT
1 TTT
5183523 GTTTCACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (17 bp):
TTTTTACAGTAAATTAA
Found at i:5183580 original size:15 final size:15
Alignment explanation
Indices: 5183553--5183600 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
5183543 ATTTAAAAGG
*
5183553 TAAATTAATTTTTTA
1 TAAATTAAATTTTTA
*
5183568 TACATTAAATTTTTGAA
1 TAAATTAAATTTTT--A
5183585 TAAATTAAATTATTTA
1 TAAATTAAATT-TTTA
5183601 GTTGAGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
17 11 0.41
18 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
TAAATTAAATTTTTA
Found at i:5183581 original size:17 final size:17
Alignment explanation
Indices: 5183553--5183595 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
5183543 ATTTAAAAGG
*
5183553 TAAATT-AATTTTT-TA
1 TAAATTAAATTTTTGAA
*
5183568 TACATTAAATTTTTGAA
1 TAAATTAAATTTTTGAA
5183585 TAAATTAAATT
1 TAAATTAAATT
5183596 ATTTAGTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 5 0.22
16 7 0.30
17 11 0.48
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TAAATTAAATTTTTGAA
Found at i:5183723 original size:24 final size:20
Alignment explanation
Indices: 5183704--5183743 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5183694 ATTTTTGACA
5183704 ATAAAAATAAATAATTTTTT
1 ATAAAAATAAATAATTTTTT
*
5183724 ATTAAAATAAATAATTTTTT
1 ATAAAAATAAATAATTTTTT
5183744 TAATTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAAATAAATAATTTTTT
Found at i:5188269 original size:21 final size:20
Alignment explanation
Indices: 5188244--5188300 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
5188234 GTTGGGGTCT
*
5188244 ACACGCCCATGTGAGGGTCAC
1 ACACGCCCGTGTGAGGG-CAC
* *
5188265 ACACGCTCGTGTGGAGGGGAC
1 ACACGCCCGTGT-GAGGGCAC
5188286 ACACGCCCGTGTGAG
1 ACACGCCCGTGTGAG
5188301 CAGCCCGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 23 0.74
22 5 0.16
ACGTcount: A:0.21, C:0.30, G:0.35, T:0.14
Consensus pattern (20 bp):
ACACGCCCGTGTGAGGGCAC
Found at i:5195356 original size:25 final size:25
Alignment explanation
Indices: 5195324--5195386 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
5195314 TCTTATAAAC
*
5195324 ATATTTAATTTTTTTATTAATTATT
1 ATATTTAATTTTATTATTAATTATT
* *
5195349 ATATTTAATTTTATTATTAGTTGTT
1 ATATTTAATTTTATTATTAATTATT
* *
5195374 TTATTTTATTTTA
1 ATATTTAATTTTA
5195387 GAAATCATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (25 bp):
ATATTTAATTTTATTATTAATTATT
Found at i:5195366 original size:13 final size:13
Alignment explanation
Indices: 5195325--5195366 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5195315 CTTATAAACA
*
5195325 TATTTAATTTTTT
1 TATTTAATTTTAT
5195338 TA-TTAATTATTA-
1 TATTTAATT-TTAT
5195350 TATTTAATTTTAT
1 TATTTAATTTTAT
5195363 TATT
1 TATT
5195367 AGTTGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTAATTTTAT
Found at i:5196546 original size:9 final size:9
Alignment explanation
Indices: 5196532--5196556 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5196522 ATAGACTAAT
5196532 AAAAATTTA
1 AAAAATTTA
5196541 AAAAATTTA
1 AAAAATTTA
5196550 AAAAATT
1 AAAAATT
5196557 AGAAATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAATTTA
Found at i:5197431 original size:33 final size:33
Alignment explanation
Indices: 5197368--5197433 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
5197358 GCCCATGTCG
**
5197368 ATTCAAGTTCGAGAAAGCTCGAGCTTGAGAAAA
1 ATTCAAGTTCGAGAAAGCTCGAGCCCGAGAAAA
5197401 ATTCAAGTT-GAGAAAAGC-CTGAGCCCGAGAAAA
1 ATTCAAGTTCGAG-AAAGCTC-GAGCCCGAGAAAA
5197434 TCTAAGCTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (33 bp):
ATTCAAGTTCGAGAAAGCTCGAGCCCGAGAAAA
Found at i:5204604 original size:26 final size:26
Alignment explanation
Indices: 5204568--5204624 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
5204558 ATGAAATTCC
*
5204568 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCAAT
5204594 TATCATGGAACATTTACCTAACCAAT
1 TATCATGGAACATTTACCTAACCAAT
5204620 TATCA
1 TATCA
5204625 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCAAT
Found at i:5206560 original size:10 final size:10
Alignment explanation
Indices: 5206541--5206590 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
5206531 TTAAATTCTA
5206541 AAAGATAAAT
1 AAAGATAAAT
5206551 ACAA-ATAAAT
1 A-AAGATAAAT
5206561 AAAGATAAAT
1 AAAGATAAAT
5206571 AAAGATAAAT
1 AAAGATAAAT
5206581 GAAA-ATAAAT
1 -AAAGATAAAT
5206591 CCTAAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.05
10 30 0.81
11 5 0.14
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5206807 original size:17 final size:18
Alignment explanation
Indices: 5206776--5206809 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5206766 ATTTCACGCT
5206776 TTTTGCCCTTAAATTTAC
1 TTTTGCCCTTAAATTTAC
*
5206794 TTTTG-CCTTCAATTTA
1 TTTTGCCCTTAAATTTA
5206810 GTCCCTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTTGCCCTTAAATTTAC
Found at i:5207411 original size:96 final size:96
Alignment explanation
Indices: 5207250--5207426 Score: 246
Period size: 96 Copynumber: 1.8 Consensus size: 96
5207240 TTTACTTTCA
* * * *
5207250 CTTAGGAAAATATTGAACCTTTTGATGCGAAGAGAGATGACAGCCAAGCACCCCACCCCCATTAC
1 CTTAAGAAAATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGAACCCCACCCCCATTAC
5207315 TCAGCCCAACACATTCCTAATTTTTATTTTT
66 TCAGCCCAACACATTCCTAATTTTTATTTTT
* * * ***
5207346 CTTAAGAACATATCGAACCTTTTGACGTGAAGAGAGATGACAGCCAAGAACCTCACCCTGGTTAC
1 CTTAAGAAAATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGAACCCCACCCCCATTAC
* *
5207411 TCAGTCCAACTCATTC
66 TCAGCCCAACACATTC
5207427 TTAAAAATTA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 69 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (96 bp):
CTTAAGAAAATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGAACCCCACCCCCATTAC
TCAGCCCAACACATTCCTAATTTTTATTTTT
Found at i:5211236 original size:17 final size:18
Alignment explanation
Indices: 5211214--5211247 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5211204 AATCGAATTG
5211214 AAATTGTG-AAATTAAAT
1 AAATTGTGAAAATTAAAT
5211231 AAATTGTGAAAATTAAA
1 AAATTGTGAAAATTAAA
5211248 ATGGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (18 bp):
AAATTGTGAAAATTAAAT
Found at i:5217643 original size:42 final size:41
Alignment explanation
Indices: 5217593--5217719 Score: 134
Period size: 42 Copynumber: 3.0 Consensus size: 41
5217583 CTTCATTTTC
* *
5217593 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAG-CCAACTATGGTCTTACACATATTCACAT-A
* * *
5217636 T-GATGCCATAGCGCAGCTATGGTTTTACACATATTCATATA
1 TCGATGCCATAGC-CAACTATGGTCTTACACATATTCACATA
*
5217677 TCGATGCCATAGCCGACCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCC-AACTATGGTCTTACAC-ATATTCACATA
5217718 TC
1 TC
5217720 TCACTGATGC
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
41 11 0.15
42 59 0.82
43 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (41 bp):
TCGATGCCATAGCCAACTATGGTCTTACACATATTCACATA
Found at i:5217870 original size:31 final size:31
Alignment explanation
Indices: 5217834--5217943 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
5217824 TTGTAACTGA
* *
5217834 AGCTACCACTATTCACTGATCAGGTAGTCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
*
5217865 TGCTACCACTTTTCACTGATCAGGTAGCCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
* *
5217896 AGCTACCACTTTTCACTGATCAGGTAGCAGA
1 AGCTACCACTTTTCACTGATCAGGTAGCCGG
5217927 AGCTACCACTTTTCACT
1 AGCTACCACTTTTCACT
5217944 TGTCATTTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (31 bp):
AGCTACCACTTTTCACTGATCAGGTAGCCGG
Found at i:5218030 original size:50 final size:51
Alignment explanation
Indices: 5217919--5218047 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
5217909 CACTGATCAG
* *
5217919 GTAGCAGAAGCTACCACTTTTCACTTGTCATTTATCATTGATCAGATAAGT
1 GTAGCAGAAGCTATCACTTATCACTTGTCATTTATCATTGATCAGATAAGT
* *
5217970 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCAGAAGCTATCACTTATCACTTGTCA-TTTATCATTGATCAGATAAGT
*
5218020 GTAGCTGAAGCTATCACTTATCACTTGT
1 GTAGCAGAAGCTATCACTTATCACTTGT
5218048 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 44 0.62
51 27 0.38
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCAGAAGCTATCACTTATCACTTGTCATTTATCATTGATCAGATAAGT
Found at i:5232444 original size:18 final size:18
Alignment explanation
Indices: 5232421--5232464 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5232411 TTTTTTCTTT
5232421 AATTT-AATATTAATATAA
1 AATTTAAAT-TTAATATAA
* *
5232439 AATTTAAATTTATTATTA
1 AATTTAAATTTAATATAA
5232457 AATTTAAA
1 AATTTAAA
5232465 AAATCATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTAAATTTAATATAA
Found at i:5235105 original size:35 final size:35
Alignment explanation
Indices: 5235066--5235136 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
5235056 TCTAGGATTA
*
5235066 CATATCTTTGAAGATCCCATTCCATATTTGCCAAG
1 CATATCTTTGAAGATCACATTCCATATTTGCCAAG
* * *
5235101 CATATCTTTGAAGATTACTTTCCATATTTTCCAAG
1 CATATCTTTGAAGATCACATTCCATATTTGCCAAG
5235136 C
1 C
5235137 TCTAGAGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (35 bp):
CATATCTTTGAAGATCACATTCCATATTTGCCAAG
Found at i:5240290 original size:35 final size:35
Alignment explanation
Indices: 5240248--5240316 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
5240238 TCGAGGATCG
*
5240248 CATATCTTTGAAGATCCCCTTCCATATTTGCCAAC
1 CATATCTTTGAAGATCACCTTCCATATTTGCCAAC
* *
5240283 CATATCTTTGAAGATTACTTTCCATATTTGCCAA
1 CATATCTTTGAAGATCACCTTCCATATTTGCCAA
5240317 GCTTCGGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (35 bp):
CATATCTTTGAAGATCACCTTCCATATTTGCCAAC
Found at i:5244792 original size:85 final size:85
Alignment explanation
Indices: 5244646--5244816 Score: 225
Period size: 85 Copynumber: 2.0 Consensus size: 85
5244636 TAAGATTCAC
* * * *
5244646 TTTCACAATAGATAAGACAATGTAAAAAATAAGGTCAAAATCCAGTTTCGGATGATCTTGTGACA
1 TTTCACAATAGATAAGACAATGTAAAAAATAAGATCAAAATCCAATTTCAGATAATCTTGTGACA
5244711 TACCTACAACAACACAAGTA
66 TACCTACAACAACACAAGTA
* * * * * * * *
5244731 TTTCACCATAGGTAATACAATGTCAAAGATAAGATCAACATCCAATTTCAGATAATTTTGTGACG
1 TTTCACAATAGATAAGACAATGTAAAAAATAAGATCAAAATCCAATTTCAGATAATCTTGTGACA
*
5244796 TACCTGCAACAACACAAGTA
66 TACCTACAACAACACAAGTA
5244816 T
1 T
5244817 GTGGAACGTC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (85 bp):
TTTCACAATAGATAAGACAATGTAAAAAATAAGATCAAAATCCAATTTCAGATAATCTTGTGACA
TACCTACAACAACACAAGTA
Found at i:5245568 original size:13 final size:13
Alignment explanation
Indices: 5245550--5245586 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
5245540 ATATGCCAAA
5245550 GTTGAAACCGAGG
1 GTTGAAACCGAGG
5245563 GTTGAAACCGAGG
1 GTTGAAACCGAGG
5245576 GTTGAAACCGA
1 GTTGAAACCGA
5245587 AGAATGCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (13 bp):
GTTGAAACCGAGG
Found at i:5250046 original size:10 final size:11
Alignment explanation
Indices: 5250024--5250062 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
5250014 AAATTAGTTG
5250024 TTAAATTTTAAA
1 TTAAA-TTTAAA
5250036 TTAAA-TTAAA
1 TTAAATTTAAA
5250046 TTAAATTTCAAA
1 TTAAATTT-AAA
5250058 TTAAA
1 TTAAA
5250063 ATATTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.40
11 2 0.08
12 13 0.52
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:5251690 original size:22 final size:23
Alignment explanation
Indices: 5251658--5251714 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5251648 AAAGGGGGGG
*
5251658 ATCGATGGTATTTTGAGGA-AGA
1 ATCGATTGTATTTTGAGGAGAGA
*
5251680 ATCGATTGTATTTTGGGGAGAGA
1 ATCGATTGTATTTTGAGGAGAGA
**
5251703 AGAGATTGTATT
1 ATCGATTGTATT
5251715 AGAGGGGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.35
Consensus pattern (23 bp):
ATCGATTGTATTTTGAGGAGAGA
Found at i:5251709 original size:23 final size:22
Alignment explanation
Indices: 5251665--5251714 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
5251655 GGGATCGATG
**
5251665 GTATTTTGAGGAAGAATCGATT
1 GTATTTTGAGGAAGAAGAGATT
*
5251687 GTATTTTGGGGAGAGAAGAGATT
1 GTATTTTGAGGA-AGAAGAGATT
5251710 GTATT
1 GTATT
5251715 AGAGGGGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (22 bp):
GTATTTTGAGGAAGAAGAGATT
Found at i:5252419 original size:38 final size:39
Alignment explanation
Indices: 5252313--5252462 Score: 250
Period size: 38 Copynumber: 3.9 Consensus size: 39
5252303 ATAAAGTATG
*
5252313 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATG
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATA
5252352 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATA
*
5252391 GTTTTAATTAATAAT-AAAACAAAATAGTATGGGGAGTA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATA
* *
5252429 GTTTTAATTAATAAT-AAAACAAAGTAGCATGGGG
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGG
5252463 GAGTGGAATC
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
38 54 0.50
39 53 0.50
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.31
Consensus pattern (39 bp):
GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATA
Found at i:5252464 original size:77 final size:78
Alignment explanation
Indices: 5252313--5252462 Score: 250
Period size: 77 Copynumber: 1.9 Consensus size: 78
5252303 ATAAAGTATG
*
5252313 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATGGTTTTAATTAATAATAAAAACAAAAT
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATAGTTTTAATTAATAATAAAAACAAAAT
*
5252378 AGTATGGGGAATA
66 AGCATGGGGAATA
* *
5252391 GTTTTAATTAATAAT-AAAACAAAATAGTATGGGGAGTAGTTTTAATTAATAAT-AAAACAAAGT
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATAGTTTTAATTAATAATAAAAACAAAAT
5252454 AGCATGGGG
66 AGCATGGGG
5252463 GAGTGGAATC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
76 17 0.25
77 36 0.53
78 15 0.22
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.31
Consensus pattern (78 bp):
GTTTTAATTAATAATAAAAACAAAATAGTATGGGGAATAGTTTTAATTAATAATAAAAACAAAAT
AGCATGGGGAATA
Found at i:5265209 original size:205 final size:203
Alignment explanation
Indices: 5264829--5265409 Score: 842
Period size: 205 Copynumber: 2.8 Consensus size: 203
5264819 TAGGTCGCAG
* * * *
5264829 CATAACAGATCTGGCCTTCAGATGTTATACTGAAGCAGATCCAAGATGGCTTGGTATCCTTGTGT
1 CATAGCAGATCTCGCCTTCAGATGTT-TACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGT
5264894 TTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATG-AAGCAAATCT
65 TTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGA-GAAAGCAAATCT
5264958 AAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGG
129 AAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGG
*
5265023 AGAGCAGACA
194 AGAGCAAACA
*
5265033 CATAGTAGATCTCGCCTTCAGATGATTTCACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
1 CATAGCAGATCTCGCCTTCAGATG-TTT-ACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
* *
5265098 TTTACAAGAAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGAGAAAGCAAATCT
64 TTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGAGAAAGCAAATCT
* * *
5265163 AAGATAATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCATTTTGATGG
129 AAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGG
5265228 AGAGCAAACA
194 AGAGCAAACA
* * * *
5265238 CATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCTAAGATGGTTTGGCATCCTTATG
1 CATAGCAGATCTCGCCTTCAGATGTTTA--CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG
* * * * * ** *
5265303 CTTACAAGGAGCAAATCGAA-TCATAGTTGATTTAGCTTTCACGTGCTTACGTTAAAGCAAATTT
64 TTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGAGAAAGCAAATCT
* * * * *
5265367 AAGATGATTTGGCATCTCTGTATTGTTAGGGAACAAATCGAAG
129 AAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAG
5265410 AAATAGATTT
Statistics
Matches: 339, Mismatches: 33, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
203 1 0.00
204 99 0.29
205 239 0.71
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (203 bp):
CATAGCAGATCTCGCCTTCAGATGTTTACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGTT
TACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGAGAAAGCAAATCTAA
GATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAG
AGCAAACA
Found at i:5265597 original size:133 final size:133
Alignment explanation
Indices: 5265444--5265860 Score: 739
Period size: 133 Copynumber: 3.2 Consensus size: 133
5265434 AGACGGGGGG
5265444 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
1 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
*
5265509 GGCATCCCTGTGCTTATAGGGAACAAGTTGAAAAACAGCAGATTTGGCATCCCTGTGCTTATAGG
66 GGCATCCCTGTGCTTATAGGGAACAAGTTGAAAAATAGCAGATTTGGCATCCCTGTGCTTATAGG
5265574 GAA
131 GAA
* *
5265577 CAGATTGAAGATAGCAGATCTGACATTCCTTTGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
1 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
5265642 GGCATCCCTGTGCTTATAGGGAACAAGTTGAAAAATAGCAGATTTGGCATCCCTGTGCTTATAGG
66 GGCATCCCTGTGCTTATAGGGAACAAGTTGAAAAATAGCAGATTTGGCATCCCTGTGCTTATAGG
5265707 GAA
131 GAA
* *
5265710 CAGATCGAATATAGCAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAGCAT
1 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
* * *
5265775 GGCATCCCTGTGTTTATAGGGAACAAGTTG-AAGATAGCAGATTTGGCATCCCTGTGTTTATAGG
66 GGCATCCCTGTGCTTATAGGGAACAAGTTGAAAAATAGCAGATTTGGCATCCCTGTGCTTATAGG
5265839 GAA
131 GAA
*
5265842 CAAATCGAAGA-AGCAGATC
1 CAGATCGAAGATAGCAGATC
5265861 AAAGAACTCA
Statistics
Matches: 272, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
131 8 0.03
132 44 0.16
133 220 0.81
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (133 bp):
CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTAAAGCAGATCGAAGATTTCAGCAT
GGCATCCCTGTGCTTATAGGGAACAAGTTGAAAAATAGCAGATTTGGCATCCCTGTGCTTATAGG
GAA
Found at i:5265612 original size:44 final size:44
Alignment explanation
Indices: 5265444--5265860 Score: 350
Period size: 44 Copynumber: 9.5 Consensus size: 44
5265434 AGACGGGGGG
* * * **
5265444 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTAAA
1 CAGATCGAAGATAGCAGATCTGGCATCCCTGTGCTTATAGGGAA
**
5265488 GCAGATCGAAGATTTCAG--CATGGCATCCCTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAGATC-TGGCATCCCTGTGCTTATAGGGAA
* * * *
5265532 CA-AGTTGAAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
1 CAGA-TCG-AAGATAGCAGATCTGGCATCCCTGTGCTTATAGGGAA
* * * * * **
5265577 CAGATTGAAGATAGCAGATCTGACATTCCTTTGCTTACAGTAAA
1 CAGATCGAAGATAGCAGATCTGGCATCCCTGTGCTTATAGGGAA
**
5265621 GCAGATCGAAGATTTCAG--CATGGCATCCCTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAGATC-TGGCATCCCTGTGCTTATAGGGAA
* * *
5265665 CA-AGTTGAAAAATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
1 CAGA-TCG-AAGATAGCAGATCTGGCATCCCTGTGCTTATAGGGAA
* * * * *
5265710 CAGATCGAATATAGCAGATCTGACATTCCTGTGCTTACAGTGAA
1 CAGATCGAAGATAGCAGATCTGGCATCCCTGTGCTTATAGGGAA
** *
5265754 GCAGATCGAAGATTTCAG--CATGGCATCCCTGTGTTTATAGGGAA
1 -CAGATCGAAGATAGCAGATC-TGGCATCCCTGTGCTTATAGGGAA
* * *
5265798 CA-AGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATCTGGCATCCCTGTGCTTATAGGGAA
*
5265842 CAAATCGAAGA-AGCAGATC
1 CAGATCGAAGATAGCAGATC
5265861 AAAGAACTCA
Statistics
Matches: 296, Mismatches: 57, Indels: 40
0.75 0.15 0.10
Matches are distributed among these distances:
42 3 0.01
43 30 0.10
44 160 0.54
45 101 0.34
46 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (44 bp):
CAGATCGAAGATAGCAGATCTGGCATCCCTGTGCTTATAGGGAA
Found at i:5267034 original size:40 final size:38
Alignment explanation
Indices: 5266982--5267123 Score: 180
Period size: 40 Copynumber: 3.6 Consensus size: 38
5266972 ATAAAGTATG
*
5266982 GTTTTAATTAATAATAGAAACAAAATAGTATTGAGGAATG
1 GTTTTAATTAATAATA-AAACAAAATAGTATTG-GGAATA
* *
5267022 GTTTTAATTAATAATAAAAACATAATAGTATGGGGGAATA
1 GTTTTAATTAATAAT-AAAACAAAATAGTAT-TGGGAATA
5267062 GTTTT-ATTGAATAATAAAACAAAATAGTA-TGGGAGAGTA
1 GTTTTAATT-AATAATAAAACAAAATAGTATTGGGA-A-TA
5267101 GTTTTAATTAATAATAAAACAAA
1 GTTTTAATTAATAATAAAACAAA
5267124 GTAGCATGGG
Statistics
Matches: 91, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
37 4 0.04
38 1 0.01
39 37 0.41
40 47 0.52
41 2 0.02
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (38 bp):
GTTTTAATTAATAATAAAACAAAATAGTATTGGGAATA
Found at i:5267090 original size:79 final size:79
Alignment explanation
Indices: 5266982--5267136 Score: 212
Period size: 79 Copynumber: 2.0 Consensus size: 79
5266972 ATAAAGTATG
*
5266982 GTTTTAATTAATAATAGAAACAAAATAGTATTGAGGA-A-TGGTTTTAATTAATAATAAAAACAT
1 GTTTTAATTAATAATAGAAACAAAATAGTA-TG-GGAGAGTAGTTTTAATTAATAAT-AAAACA-
*
5267045 AA-TAGTATGGGGGAATA
62 AAGTAGCATGGGGGAATA
5267062 GTTTT-ATTGAATAATA-AAACAAAATAGTATGGGAGAGTAGTTTTAATTAATAATAAAACAAAG
1 GTTTTAATT-AATAATAGAAACAAAATAGTATGGGAGAGTAGTTTTAATTAATAATAAAACAAAG
5267125 TAGCATGGGGGA
65 TAGCATGGGGGA
5267137 GTGGAATCAA
Statistics
Matches: 69, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
77 5 0.07
78 20 0.29
79 32 0.46
80 12 0.17
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.31
Consensus pattern (79 bp):
GTTTTAATTAATAATAGAAACAAAATAGTATGGGAGAGTAGTTTTAATTAATAATAAAACAAAGT
AGCATGGGGGAATA
Found at i:5267092 original size:39 final size:39
Alignment explanation
Indices: 5266982--5267136 Score: 204
Period size: 39 Copynumber: 3.9 Consensus size: 39
5266972 ATAAAGTATG
* * *
5266982 GTTTTAATTAATAATAGAAACAAAATAGTATTGAGGAATG
1 GTTTTAATTAATAATA-AAACAAAATAGTATGGGGGAATA
*
5267022 GTTTTAATTAATAATAAAAACATAATAGTATGGGGGAATA
1 GTTTTAATTAATAAT-AAAACAAAATAGTATGGGGGAATA
* *
5267062 GTTTT-ATTGAATAATAAAACAAAATAGTATGGGAGAGTA
1 GTTTTAATT-AATAATAAAACAAAATAGTATGGGGGAATA
* *
5267101 GTTTTAATTAATAATAAAACAAAGTAGCATGGGGGA
1 GTTTTAATTAATAATAAAACAAAATAGTATGGGGGA
5267137 GTGGAATCAA
Statistics
Matches: 102, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
39 53 0.52
40 48 0.47
41 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.31
Consensus pattern (39 bp):
GTTTTAATTAATAATAAAACAAAATAGTATGGGGGAATA
Found at i:5277491 original size:25 final size:26
Alignment explanation
Indices: 5277449--5277497 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
5277439 ATTATTATTA
*
5277449 AAAGTAAAGTAAATAG-AAAGAAAAT
1 AAAGTAAAGTAAAAAGAAAAGAAAAT
5277474 AAAGTAAAG-AACAAAGAAAAGAAA
1 AAAGTAAAGTAA-AAAGAAAAGAAA
5277498 CAGAATAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.10
25 12 0.57
26 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.10
Consensus pattern (26 bp):
AAAGTAAAGTAAAAAGAAAAGAAAAT
Found at i:5279052 original size:21 final size:20
Alignment explanation
Indices: 5279004--5279077 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
5278994 AGGCACTTTA
5279004 TGTGTCGTATTTCAGGCACCTC
1 TGTGTCGTA--TCAGGCACCTC
5279026 TGTGTCGTATCAGGCACCTC
1 TGTGTCGTATCAGGCACCTC
* * * *
5279046 GTGTGTCGTTTTAGGCACTTTA
1 -TGTGTCGTATCAGGCAC-CTC
5279068 TGTGTCGTAT
1 TGTGTCGTAT
5279078 ACTGATCAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.24
21 24 0.53
22 10 0.22
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.39
Consensus pattern (20 bp):
TGTGTCGTATCAGGCACCTC
Found at i:5285310 original size:25 final size:26
Alignment explanation
Indices: 5285268--5285316 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
5285258 ATTATTATTA
*
5285268 AAAGTAAAGTAAATAG-AAAGAAAAT
1 AAAGTAAAGTAAAAAGAAAAGAAAAT
5285293 AAAGTAAAG-AACAAAGAAAAGAAA
1 AAAGTAAAGTAA-AAAGAAAAGAAA
5285317 CAGAATAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.10
25 12 0.57
26 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.10
Consensus pattern (26 bp):
AAAGTAAAGTAAAAAGAAAAGAAAAT
Found at i:5286841 original size:23 final size:22
Alignment explanation
Indices: 5286813--5286897 Score: 84
Period size: 21 Copynumber: 3.9 Consensus size: 22
5286803 TTTATCGATC
* *
5286813 AGGCACTTTATGTGTCGTATTT
1 AGGCACCTCATGTGTCGTATTT
* *
5286835 CAGGCACCTCGTGTGTCATA-TT
1 -AGGCACCTCATGTGTCGTATTT
*
5286857 AGGCACCTCGTGTGTCGT-TTT
1 AGGCACCTCATGTGTCGTATTT
* *
5286878 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCATGTGTCGTAT
5286898 ACTGATCAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 34 0.65
22 3 0.06
23 15 0.29
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (22 bp):
AGGCACCTCATGTGTCGTATTT
Found at i:5294378 original size:21 final size:22
Alignment explanation
Indices: 5294354--5294394 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5294344 AATAAAGAAT
5294354 AAATTAATTTA-TTTTATTAAA
1 AAATTAATTTATTTTTATTAAA
*
5294375 AAATTTATTTATTTTTATTA
1 AAATTAATTTATTTTTATTA
5294395 CTTAGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AAATTAATTTATTTTTATTAAA
Found at i:5295422 original size:14 final size:15
Alignment explanation
Indices: 5295400--5295433 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5295390 TTTGATAAAC
* *
5295400 TGAAAAATTAAGTGT
1 TGAAAATTTAAGTAT
5295415 TGAAAATTTAAGTAT
1 TGAAAATTTAAGTAT
5295430 TGAA
1 TGAA
5295434 TTTTTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAAAATTTAAGTAT
Found at i:5298279 original size:15 final size:15
Alignment explanation
Indices: 5298261--5298289 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5298251 ATATATAAAA
5298261 AATAAATATTTATCT
1 AATAAATATTTATCT
5298276 AATAAATATTTATC
1 AATAAATATTTATC
5298290 AAAGCTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATATTTATCT
Found at i:5298479 original size:21 final size:21
Alignment explanation
Indices: 5298455--5298499 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5298445 CCTAAATCCC
*
5298455 GAACCCTAAATCAT-GAACCTT
1 GAACCCAAAAT-ATCGAACCTT
*
5298476 GAACGCAAAATATCGAACCTT
1 GAACCCAAAATATCGAACCTT
5298497 GAA
1 GAA
5298500 TATCAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.20
Consensus pattern (21 bp):
GAACCCAAAATATCGAACCTT
Found at i:5298599 original size:21 final size:21
Alignment explanation
Indices: 5298575--5298625 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5298565 TCAAACCTCA
* *
5298575 AACCTTGAACACC-AAATCATG
1 AACCTTAAAC-CCTAAACCATG
5298596 AACCTTAAACCCTAAACCATG
1 AACCTTAAACCCTAAACCATG
5298617 AACC-TAAAC
1 AACCTTAAAC
5298626 TCAGAACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.45, C:0.31, G:0.06, T:0.18
Consensus pattern (21 bp):
AACCTTAAACCCTAAACCATG
Found at i:5298797 original size:21 final size:21
Alignment explanation
Indices: 5298773--5298822 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5298763 TTGAGGTTCG
5298773 AGATTTAAGGTTCTAAATTCA
1 AGATTTAAGGTTCTAAATTCA
* **
5298794 AGATTTGAGGTTCTTGATTCA
1 AGATTTAAGGTTCTAAATTCA
5298815 AGATTTAA
1 AGATTTAA
5298823 AGTAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (21 bp):
AGATTTAAGGTTCTAAATTCA
Found at i:5299008 original size:20 final size:20
Alignment explanation
Indices: 5298992--5299038 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
5298982 AAGCCCCCCC
*
5298992 AAAAAACCTAACCCCCCAAA
1 AAAAAACCTAACCCCCCCAA
*
5299012 AAAAAACCTAACTCCCCCTAA
1 AAAAAACCTAAC-CCCCCCAA
5299033 AAAAAA
1 AAAAAA
5299039 ACCAAGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.57, C:0.34, G:0.00, T:0.09
Consensus pattern (20 bp):
AAAAAACCTAACCCCCCCAA
Found at i:5299040 original size:22 final size:20
Alignment explanation
Indices: 5298992--5299041 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 20
5298982 AAGCCCCCCC
5298992 AAAAAACCTAACCCCCCAAA
1 AAAAAACCTAACCCCCCAAA
5299012 AAAAAACCTAACTCCCCCTAAA
1 AAAAAACCTAAC-CCCCC-AAA
5299034 AAAAAACC
1 AAAAAACC
5299042 AAGAAACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 12 0.43
21 5 0.18
22 11 0.39
ACGTcount: A:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (20 bp):
AAAAAACCTAACCCCCCAAA
Found at i:5301149 original size:29 final size:29
Alignment explanation
Indices: 5301111--5301170 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
5301101 ATAGTACAAA
*
5301111 CGATTTGAGTACCCATCTAGAACCAAAAC
1 CGATTCGAGTACCCATCTAGAACCAAAAC
5301140 CGATTCGAGTACCCATCTAGAACCAAAAC
1 CGATTCGAGTACCCATCTAGAACCAAAAC
5301169 CG
1 CG
5301171 CATATAGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.18
Consensus pattern (29 bp):
CGATTCGAGTACCCATCTAGAACCAAAAC
Found at i:5301635 original size:12 final size:12
Alignment explanation
Indices: 5301618--5301653 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5301608 ATTCATTTGA
5301618 CATTCATGCATT
1 CATTCATGCATT
*
5301630 CATTCATGCATC
1 CATTCATGCATT
*
5301642 CATTCATTCATT
1 CATTCATGCATT
5301654 GCATATCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:5301647 original size:16 final size:17
Alignment explanation
Indices: 5301626--5301657 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5301616 GACATTCATG
5301626 CATTCATTCA-TGCATC
1 CATTCATTCATTGCATC
5301642 CATTCATTCATTGCAT
1 CATTCATTCATTGCAT
5301658 ATCCCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (17 bp):
CATTCATTCATTGCATC
Found at i:5310282 original size:72 final size:71
Alignment explanation
Indices: 5310161--5310355 Score: 248
Period size: 72 Copynumber: 2.7 Consensus size: 71
5310151 GAGTTAAGCC
* * * *
5310161 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTGTTTTT-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGA
5310225 TGAGGTA
65 TGAGGTA
**
5310232 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGA
1 TTTTCAATTTTTGT-TTTTAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGA
5310297 TGAGGTA
65 TGAGGTA
* * * * *
5310304 ATTTCAATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 TTTTCAATTTTTGTTT-TTAA-AATCAACTCATATTGCAAGAGGTGAGTTGA
5310356 ACCTTTTAAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 6 0.06
72 71 0.66
73 30 0.28
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGAT
GAGGTA
Found at i:5310450 original size:253 final size:253
Alignment explanation
Indices: 5310134--5310920 Score: 1493
Period size: 253 Copynumber: 3.1 Consensus size: 253
5310124 TTTAAATTGA
*
5310134 CTCATATTGCAAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTA
1 CTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTA
5310199 GAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCAT
66 GAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCAT
*
5310264 ATTGCAAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAAT
131 ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAAT
*
5310329 CAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTTCAAAATTAG
196 CAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTTCAAAATCAG
*
5310387 CTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTTAAAATCAACTCATATTGCTA
1 CTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTA
5310452 GAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCAT
66 GAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCAT
*
5310517 ATTGCGAGAGATGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAAT
131 ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAAT
*
5310582 CAACTCATATTGCGAGAGGTGGGTTTAACCTTTTAATTTCTACTTTTTTCAAAATCAG
196 CAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTTCAAAATCAG
5310640 CTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTA
1 CTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTA
*
5310705 GAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAATTTTTGTGTTTTAATTTCAACTCAT
66 GAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCAT
5310770 ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAAT
131 ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAAT
*
5310835 CAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCGACTTTTTTCAAAATCAG
196 CAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTTCAAAATCAG
*
5310893 CTCATATTGCGAGAGGTGAGTTGAGCCT
1 CTCATATTGCGAGAGGTGAGTTAAGCCT
5310921 CAGGTCACGC
Statistics
Matches: 522, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
253 522 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (253 bp):
CTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTA
GAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCAT
ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGTTTGTCAAGAAT
CAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTTCAAAATCAG
Found at i:5310455 original size:53 final size:55
Alignment explanation
Indices: 5310321--5310467 Score: 192
Period size: 55 Copynumber: 2.7 Consensus size: 55
5310311 TTTCTGTTTG
*
5310321 TCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAA-CCTTTTAATTTCTACTTTTT
1 TCAA-AATCAACTCATATTGCGAGAGGTGAGTT-AAGCCTTTTAATTTCTACTTTTT
* * **
5310377 TCAAAATTAGCTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTT-TTGTTTTT
1 TCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTACTTTTT
* *
5310431 T-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCT
1 TCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCT
5310468 CGGGGCACGC
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
53 32 0.40
54 9 0.11
55 36 0.44
56 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (55 bp):
TCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTACTTTTT
Found at i:5310535 original size:72 final size:71
Alignment explanation
Indices: 5310414--5310599 Score: 239
Period size: 72 Copynumber: 2.6 Consensus size: 71
5310404 GAGTTAAGCC
* * * * *
5310414 TTTT-AATTTTTGTTTTTTAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTG-TTTTTAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGA
5310478 TGAGGTA
65 TGAGGTA
**
5310485 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGA
1 TTTTCAATTTTTGT-TTTTAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGA
5310550 TGAGGTA
65 TGAGGTA
* * *
5310557 ATTTCAATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGAG
1 TTTTCAATTTTTGTTT-TTAA-AATCAACTCATATTGCGAGAG
5310600 GTGGGTTTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 7 0.07
72 73 0.74
73 19 0.19
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGAT
GAGGTA
Found at i:5310708 original size:53 final size:53
Alignment explanation
Indices: 5310562--5310720 Score: 205
Period size: 53 Copynumber: 2.9 Consensus size: 53
5310552 AGGTAATTTC
* * *
5310562 AATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTTAA-CCTTTT
1 AATTTTTGTTTTTCAA-AATCAACTCATATTGCGAGAGGTGAG-TTAAGCCTTTT
*
5310616 AATTTCTACT-TTTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTTAAGCCTTTT
1 AATTT-T--TGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTT
* *
5310671 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCT
1 AATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCT
5310721 CGGGGCACGC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
52 1 0.01
53 39 0.42
54 10 0.11
55 35 0.38
56 7 0.08
57 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (53 bp):
AATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTT
Found at i:5310784 original size:72 final size:71
Alignment explanation
Indices: 5310667--5310861 Score: 255
Period size: 72 Copynumber: 2.7 Consensus size: 71
5310657 GAGTTAAGCC
* * * *
5310667 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTGTTTTT-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGAT
*
5310732 GAGGTAT
65 GAGGTAA
**
5310739 TTTTAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGAT
1 TTTTAATTTTTGT-TTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGAT
5310804 GAGGTAA
65 GAGGTAA
* * * *
5310811 TTTCAATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 TTTTAATTTTTGTTT-TTAA-AATCAACTCATATTGCGAGAGGTGAGTTGA
5310862 ACCTTTTAAT
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
71 2 0.02
72 74 0.69
73 31 0.29
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (71 bp):
TTTTAATTTTTGTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATG
AGGTAA
Found at i:5311070 original size:88 final size:85
Alignment explanation
Indices: 5310865--5311092 Score: 240
Period size: 88 Copynumber: 2.6 Consensus size: 85
5310855 GGGTTGAACC
** * *
5310865 TTTTAATTTCGACTTTTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG
1 TTTTAATTTTTAC-TTTTCCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG
* *
5310930 CCGAAGTATTTTCAATTTTTG
65 CCGAAGTATTTTCAAATTCTG
* ** ** * *
5310951 TTTTCATTATTATGTTTTTGAAAGAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCA
1 TTTTAATT-TT-TACTTTTCCAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
* *
5311016 CATGTCGAGGTATTTTCAAATTCTG
63 C--GCCGAAGTATTTTCAAATTCTG
* *
5311041 TTTTTAATTTTTACTTTTCCAAAACCAACTCATATTGCGAGAGGTGGGTTGA
1 -TTTTAATTTTTACTTTTCCAAAATCAACTCATATTGCGAGAGGTGAGTTGA
5311093 ACCTTTTAAT
Statistics
Matches: 114, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
86 7 0.06
87 7 0.06
88 66 0.58
89 7 0.06
90 20 0.18
91 7 0.06
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (85 bp):
TTTTAATTTTTACTTTTCCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
CGAAGTATTTTCAAATTCTG
Found at i:5311134 original size:55 final size:53
Alignment explanation
Indices: 5311042--5311201 Score: 239
Period size: 55 Copynumber: 2.9 Consensus size: 53
5311032 CAAATTCTGT
* *
5311042 TTTTAATTTTTACTTTTCCAAAACCAACTCATATTGCGAGAGGTGGGTTGAACC
1 TTTTAATTTCTACTTTT-CAAAATCAACTCATATTGCGAGAGGTGGGTTGAACC
5311096 TTTTAATTTCTACTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACC
1 TTTTAATTTCTACTT-TTCAA-AATCAACTCATATTGCGAGAGGTGGGTTGAACC
* * *
5311151 TTTTAATTTCTACTTTTTCAAAATCAGCTCATATTGTGAGAGGTGAGTTGA
1 TTTTAATTTCTAC-TTTTCAAAATCAACTCATATTGCGAGAGGTGGGTTGA
5311202 GCCTCGGGTC
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
54 44 0.45
55 52 0.53
56 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (53 bp):
TTTTAATTTCTACTTTTCAAAATCAACTCATATTGCGAGAGGTGGGTTGAACC
Found at i:5311246 original size:14 final size:14
Alignment explanation
Indices: 5311227--5311253 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5311217 TCGAGGTATT
5311227 TTCAAATTCTGTTA
1 TTCAAATTCTGTTA
5311241 TTCAAATTCTGTT
1 TTCAAATTCTGTT
5311254 TTTAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (14 bp):
TTCAAATTCTGTTA
Found at i:5311285 original size:102 final size:100
Alignment explanation
Indices: 5311151--5311433 Score: 294
Period size: 89 Copynumber: 2.9 Consensus size: 100
5311141 GGGTTGAACC
* * * *
5311151 TTTTAATTTCTACTTTTTCAAAATCAGCTCATATTGTGAGAGGTGAGTTGAGCCTC-GGGTCACA
1 TTTTAATTTCTACTTTTCCAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG-CAC-
5311215 TG-TCGAGGTATTTTCAAATTCTG-TTATTCAAATTCTGT
64 -GCT-GAGGTATTTTCAAATTCTGCTT-TTCAAATTCTGT
*
5311253 TTTTAATTTTTACTTTTCCAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTTTAATTTCTACTTTTCCAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
*
5311318 TGAGGTATTTTCAATTTCTGCTTTTC-AATTC---
66 TGAGGTATTTTCAAATTCTGCTTTTCAAATTCTGT
* * *
5311349 ---------CTACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC
1 TTTTAATTTCTACTTTTC--CAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
*
5311405 GCTGAGGTATTTTCAATTTCTG-TTTTCAA
64 GCTGAGGTATTTTCAAATTCTGCTTTTCAA
5311434 TTTATGTTGT
Statistics
Matches: 165, Mismatches: 10, Indels: 25
0.82 0.05 0.12
Matches are distributed among these distances:
87 8 0.05
88 5 0.03
89 65 0.39
99 5 0.03
100 22 0.13
101 3 0.02
102 54 0.33
103 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (100 bp):
TTTTAATTTCTACTTTTCCAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
TGAGGTATTTTCAAATTCTGCTTTTCAAATTCTGT
Found at i:5311344 original size:14 final size:14
Alignment explanation
Indices: 5311325--5311359 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5311315 CGCTGAGGTA
* *
5311325 TTTTCAATTTCTGC
1 TTTTCAATTCCTAC
5311339 TTTTCAATTCCTAC
1 TTTTCAATTCCTAC
5311353 TTTTCAA
1 TTTTCAA
5311360 AAAAATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (14 bp):
TTTTCAATTCCTAC
Found at i:5311389 original size:89 final size:86
Alignment explanation
Indices: 5311241--5311478 Score: 320
Period size: 89 Copynumber: 2.7 Consensus size: 86
5311231 AATTCTGTTA
* * * * *
5311241 TTCAAATTCTGTTTTTAATTTTTACTT-TTCCAAAACCAACTCATATTGCGAGAGGTGAGTTGAG
1 TTCAATTTCTGTTTTCAATTTAT-CTTGTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
5311305 CCTCAGGGCACGCTGAGGTATT
65 CCTCAGGGCACGCTGAGGTATT
5311327 TTCAATTTCTGCTTTTCAATTCCTA-CTT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
1 TTCAATTTCTG-TTTTCAATT--TATCTTGTTC--AAAAATCAACTCATATTGCGAGAGGTGAGT
*
5311390 TGAGCCTCAGGTCACGCTGAGGTATT
61 TGAGCCTCAGGGCACGCTGAGGTATT
* * *
5311416 TTCAATTTCTGTTTTCAATTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 TTCAATTTCTGTTTTCAATTTATCTTGTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
5311479 ACCTTTTAAT
Statistics
Matches: 136, Mismatches: 9, Indels: 14
0.86 0.06 0.09
Matches are distributed among these distances:
86 43 0.32
87 16 0.12
88 12 0.09
89 65 0.48
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (86 bp):
TTCAATTTCTGTTTTCAATTTATCTTGTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
CTCAGGGCACGCTGAGGTATT
Found at i:5311432 original size:13 final size:13
Alignment explanation
Indices: 5311414--5311447 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5311404 CGCTGAGGTA
*
5311414 TTTTCAATTTCTG
1 TTTTCAATTTATG
5311427 TTTTCAATTTATG
1 TTTTCAATTTATG
5311440 TTGTTCAA
1 TT-TTCAA
5311448 GAATCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:5311694 original size:72 final size:72
Alignment explanation
Indices: 5311496--5311721 Score: 276
Period size: 72 Copynumber: 3.0 Consensus size: 72
5311486 AATTTCTACT
* ** * * *
5311496 TTTTCAAAA-TCAGCTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTT
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACAT--TGAGGTAATT
5311559 TCAATTTCTG
63 TCAATTTCTG
*
5311569 TCTTTCAAAAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACATTGAGGT
1 T-TTTC------AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGT
5311634 AATTTCAATTTCTG
59 AATTTCAATTTCTG
*
5311648 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCA
5311713 ATTTCTG
66 ATTTCTG
5311720 TT
1 TT
5311722 CAAAATGAAT
Statistics
Matches: 135, Mismatches: 9, Indels: 19
0.83 0.06 0.12
Matches are distributed among these distances:
72 67 0.50
73 1 0.01
74 4 0.03
78 4 0.03
79 20 0.15
80 4 0.03
81 34 0.25
82 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (72 bp):
TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCA
ATTTCTG
Found at i:5311735 original size:49 final size:49
Alignment explanation
Indices: 5311675--5311770 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
5311665 ATATTGCGAG
*
5311675 AAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTCA
1 AAATGAATTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTCA
5311724 AAATGAATTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTT
1 AAATGAATTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTT
5311771 TTCAAAATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (49 bp):
AAATGAATTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTCA
Found at i:5311817 original size:121 final size:121
Alignment explanation
Indices: 5311603--5311842 Score: 408
Period size: 121 Copynumber: 2.0 Consensus size: 121
5311593 ATATTGCGAG
*
5311603 AAATGAGTTGAACCTCAAGACACATTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
1 AAATGAATTGAACCTCAAGACACATTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
*
5311668 TTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTCA
66 TTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTCA
* *
5311724 AAATGAATTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
1 AAATGAATTGAACCTCAAGACACATTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
* * * *
5311789 TTGCGAGAAATTAGTTGATCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTT
66 TTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTT
5311843 TTTCAAAAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 111 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (121 bp):
AAATGAATTGAACCTCAAGACACATTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
TTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTCA
Found at i:5311894 original size:79 final size:75
Alignment explanation
Indices: 5311724--5312078 Score: 412
Period size: 79 Copynumber: 4.7 Consensus size: 75
5311714 TTTCTGTTCA
* * * *
5311724 AAATGAATTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TTTTC--AAAATTCAACTC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
5311786 ATATTGCGAG
66 ATATTGCGAG
* * *
5311796 AAATTAGTTGATCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAAAAATCA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTC----AAAAAAATCA
*
5311861 ACTCATATTGTGAG
62 ACTCATATTGCGAG
*
5311875 AAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
5311940 ATATTGCGAG
66 ATATTGCGAG
** * * * * *
5311950 AGGTGAGTTGAGCCTCAGGACACGCAGAGGTAATTTCAATTTCT-ATTGTCAAAAAAATCAACTC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
* *
5312014 GTATTGTGAG
66 ATATTGCGAG
*** * * *
5312024 AGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTTTTTCAA
1 AAATGAGTTGAGCCTCAAG--ACACGCTGAGGTATTTTCAATTTCTGTTTTTCAA
5312079 TTTCTGCCTT
Statistics
Matches: 246, Mismatches: 27, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
72 39 0.16
73 5 0.02
74 44 0.18
75 61 0.25
76 22 0.09
77 6 0.02
79 69 0.28
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (75 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
ATATTGCGAG
Found at i:5312004 original size:151 final size:150
Alignment explanation
Indices: 5311724--5312288 Score: 476
Period size: 151 Copynumber: 3.6 Consensus size: 150
5311714 TTTCTGTTCA
* * * *
5311724 AAATGAATTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TTTTC--AAAATTCAACTC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
** * * * * *
5311786 ATATTGCGAGAAATTAGTTGATCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAA
66 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-ATTTTC---A
5311851 AAAAAAATCAACTCATATTGTGAG
127 AAAAAAATCAACTCATATTGTGAG
*
5311875 AAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
* * *
5311940 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCAGAGGTAATTTCAATTTCTATTGTC-AAAA
66 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTATTTTCAAAAA
*
5312004 AAATCAACTCGTATTGTGAG
131 AAATCAACTCATATTGTGAG
*** * * *
5312024 AGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTTTTTCAATTTCTGCCTT
1 AAATGAGTTGAGCCTCAAG--ACACGCTGAGGTATTTTCAA--------TTTC--TGT-T---TT
* * *
5312089 TCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGCGCTGAGCTATT
50 TC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATT
* * *
5312153 TTCAATTT-TGTCTTTCAAAAAAAATAAACTCATATTGCGAG
110 TTCAATTTCTAT-TTTCAAAAAAAATCAACTCATATTGTGAG
** * * * * *
5312194 AGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCA
1 AAATGAGTTGAGCCTCA-A-GACACGCTGAGGTA--TTTTCAATTTCTGTTTTTCAAAAAAATCA
* **
5312259 ACTCACATTGCGAGATTTGAGTTGAGCCTC
62 ACTCATATTGCGAGAGGTGAGTTGAGCCTC
5312289 GGGTCACATG
Statistics
Matches: 339, Mismatches: 44, Indels: 56
0.77 0.10 0.13
Matches are distributed among these distances:
149 38 0.11
151 59 0.17
152 5 0.01
153 4 0.01
154 57 0.17
156 36 0.11
158 4 0.01
159 4 0.01
161 3 0.01
162 3 0.01
164 3 0.01
165 4 0.01
166 2 0.01
167 39 0.12
168 2 0.01
169 22 0.06
170 47 0.14
172 7 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (150 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTATTTTCAAAAA
AAATCAACTCATATTGTGAG
Found at i:5312201 original size:77 final size:78
Alignment explanation
Indices: 5312072--5312667 Score: 357
Period size: 88 Copynumber: 7.2 Consensus size: 78
5312062 CAATTTCCGT
**
5312072 TTTTCAATTTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT
1 TTTTCAATTTCTGTTTTTC-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT
*
5312137 CACGCGCTGAGCTA
65 CACACGCTGAGCTA
* * * *
5312151 TTTTCAATTT-TGTCTTTCAAAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAGAT
1 TTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGCT
* *
5312214 CACACACTGAGGTA
65 CACACGCTGAGCTA
* * * ** * *
5312228 TTTTTTCAATTTATATTTTTC-AAAAAAATCAACTCACATTGCGAGATTTGAGTTGAGCCTCGGG
1 --TTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC
* *
5312292 TCACATG-TCGAGGTA
64 TCACACGCT-GAGCTA
** * *
5312307 TTTTCAAAATCTGTTTTTCAAATTCTGTTTTCAAAAATCAACTTATATTGCGAGAAGTGAGTTGA
1 TTTTCAATTTCTGTTTTTCAAA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
**
5312372 GCCTTGGCTCACGTGCTGAGCTA
56 GCCTTGGCTCACACGCTGAGCTA
* *
5312395 TTTTCAATTTCTGTTTTTTTTTTCAAAAAAATTCAACTCATATTACGAGAGGTGAGTTGAGCTTT
1 TTTTCAATTTCTG-----TTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC---
* ** * * *
5312460 TTAATTTCTGCGAGA-GTTGAGTTGA
58 CT--TGGCT-C-ACACGCTGAGCT-A
* * **
5312485 GTCTTTTAATTTCTGTTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCCAG
1 -T-TTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGG
** *
5312547 -TCACA-TATCGAGGTA
63 CTCACACGCT-GAGCTA
** * *
5312562 TTTTCAAAATCTGCTTTTCAAGTTAAGTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGA
1 TTTTCAATTTCTG-TTTT----TCAA-----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
5312627 GCCTTGGCTCACACGCTGAGCTA
56 GCCTTGGCTCACACGCTGAGCTA
5312650 TTTTCAATTTCTGTTTTT
1 TTTTCAATTTCTGTTTTT
5312668 AATGTCTGTT
Statistics
Matches: 399, Mismatches: 69, Indels: 94
0.71 0.12 0.17
Matches are distributed among these distances:
75 9 0.02
76 8 0.02
77 68 0.17
78 15 0.04
79 65 0.16
80 9 0.02
81 1 0.00
83 32 0.08
84 32 0.08
86 1 0.00
87 11 0.03
88 116 0.29
89 9 0.02
90 2 0.01
91 1 0.00
92 11 0.03
93 9 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (78 bp):
TTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTC
ACACGCTGAGCTA
Found at i:5312296 original size:79 final size:77
Alignment explanation
Indices: 5312072--5312296 Score: 254
Period size: 79 Copynumber: 2.9 Consensus size: 77
5312062 CAATTTCCGT
** * *
5312072 TTTTCAATTTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT
1 TTTTCAATTT-TATCTTTC-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAT
* *
5312137 CACGCGCTGAGCTA
64 CACACACTGAGCTA
* * * *
5312151 TTTTCAATTTTGTCTTTCAAAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCA
1 TTTTCAATTTTATCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCA
*
5312216 CACACTGAGGTA
66 CACACTGAGCTA
* * ** *
5312228 TTTTTTCAATTTATATTTTTC-AAAAAAATCAACTCACATTGCGAGATTTGAGTTGAGCCTCGGG
1 --TTTTCAATTT-TATCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA
5312292 TCACA
63 TCACA
5312297 TGTCGAGGTA
Statistics
Matches: 125, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
77 51 0.41
78 7 0.06
79 61 0.49
80 6 0.05
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (77 bp):
TTTTCAATTTTATCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCA
CACACTGAGCTA
Found at i:5312326 original size:14 final size:13
Alignment explanation
Indices: 5312307--5312342 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
5312297 TGTCGAGGTA
5312307 TTTTCAAAATCTG
1 TTTTCAAAATCTG
*
5312320 TTTTTCAAATTCTG
1 -TTTTCAAAATCTG
5312334 TTTTCAAAA
1 TTTTCAAAA
5312343 ATCAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTTCAAAATCTG
Found at i:5312481 original size:30 final size:30
Alignment explanation
Indices: 5312440--5312499 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5312430 ACTCATATTA
5312440 CGAGAGGTGAGTTGAG-CTTTTTAATTTCTG
1 CGAGAGGTGAGTTGAGTC-TTTTAATTTCTG
*
5312470 CGAGAGTTGAGTTGAGTCTTTTAATTTCTG
1 CGAGAGGTGAGTTGAGTCTTTTAATTTCTG
5312500 TTTTTCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (30 bp):
CGAGAGGTGAGTTGAGTCTTTTAATTTCTG
Found at i:5312582 original size:255 final size:249
Alignment explanation
Indices: 5311898--5312667 Score: 803
Period size: 255 Copynumber: 3.1 Consensus size: 249
5311888 CTCAAGACAT
* * *
5311898 GCTGAGGTATTTTCAATTTCTG----TT-TTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAG
1 GCTGAGCTATTTTCAATTTCTGTTTTTTCTTTCAAAAAAAATAAACTCATATTACGAGAGGTGAG
* * * * * *
5311957 TTGAGCCTCAGGA-CACGCA--GAGGTA--ATTTCAATTTCTA-TTGTCAAAAAAATCAACTCGT
66 TTGAGCTTCA-GATCACACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCAT
* * * * ** * *
5312016 ATTGTGAGAGGCGAGTTGAGCCT-CAGGTCACACGCCGAGGTATTTTCAATTTCCGTTTTTCAAT
129 ATTGCGAGAGGTGAGTTGAGCCTCCA-GTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAA
5312080 TTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
193 TTCTG--TTTC---AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
*
5312142 GCTGAGCTATTTTCAATTT-TG-----TCTTTCAAAAAAAATAAACTCATATTGCGAGAGGTGAG
1 GCTGAGCTATTTTCAATTTCTGTTTTTTCTTTCAAAAAAAATAAACTCATATTACGAGAGGTGAG
* *
5312201 TTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACA
66 TTGAGCTTCAGATCACACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCATA
** **
5312266 TTGCGAGATTTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATT
130 TTGCGAGAGGTGAGTTGAGCCTCCAGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATT
* * *
5312331 CTGTTTTC-AAAAATCAACTTATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGT
195 CTG-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
* * *
5312386 GCTGAGCTATTTTCAATTTCTGTTTTTTTTTTCAAAAAAATTCAACTCATATTACGAGAGGTGAG
1 GCTGAGCTATTTTCAATTTCTGTTTTTTCTTTCAAAAAAAATAAACTCATATTACGAGAGGTGAG
* * * * * * *
5312451 TTGAGCTTTTTA-ATTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATC
66 TTGAGC--TTCAGA--TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATC
* * *
5312513 AACTCATATTGCGAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTT
122 AACTCATATTGCGAGAGGTGAGTTGAGCCTCCAGTCACATGTCGAGGTATTTTCAAAATCTGTTT
* ** * *
5312578 TTCAAGTTAAGTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTTGGCTCACAC
187 TTCAAATTCTGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
5312641 GCTGAGCTATTTTCAATTTCTGTTTTT
1 GCTGAGCTATTTTCAATTTCTGTTTTT
5312668 AATGTCTGTT
Statistics
Matches: 448, Mismatches: 53, Indels: 39
0.83 0.10 0.07
Matches are distributed among these distances:
242 1 0.00
243 8 0.02
244 125 0.28
245 2 0.00
246 6 0.01
248 15 0.03
249 74 0.17
250 40 0.09
251 1 0.00
252 3 0.01
253 2 0.00
254 5 0.01
255 143 0.32
256 5 0.01
257 13 0.03
258 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (249 bp):
GCTGAGCTATTTTCAATTTCTGTTTTTTCTTTCAAAAAAAATAAACTCATATTACGAGAGGTGAG
TTGAGCTTCAGATCACACACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCATAT
TGCGAGAGGTGAGTTGAGCCTCCAGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATTC
TGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGC
Found at i:5313356 original size:19 final size:19
Alignment explanation
Indices: 5313317--5313356 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5313307 GCCTATTAAG
**
5313317 CCCCCCCAAAAAAACCTAA
1 CCCCCCCAAAAAAACAAAA
*
5313336 CCCCCCCAAAAAAAGAAAA
1 CCCCCCCAAAAAAACAAAA
5313355 CC
1 CC
5313357 TAACTCCCCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.45, G:0.03, T:0.03
Consensus pattern (19 bp):
CCCCCCCAAAAAAACAAAA
Found at i:5313359 original size:24 final size:25
Alignment explanation
Indices: 5313327--5313375 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
5313317 CCCCCCCAAA
5313327 AAAACCTAA-CCCCCCCAAAAAAAG
1 AAAACCTAACCCCCCCCAAAAAAAG
5313351 AAAACCTAACTCCCCCCCAAAAAAA
1 AAAACCTAAC-CCCCCCCAAAAAAA
5313376 CCAAGAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 9 0.39
26 14 0.61
ACGTcount: A:0.53, C:0.39, G:0.02, T:0.06
Consensus pattern (25 bp):
AAAACCTAACCCCCCCCAAAAAAAG
Found at i:5314141 original size:37 final size:37
Alignment explanation
Indices: 5314100--5314201 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 37
5314090 CTAATATTTT
5314100 CTTTTATTGTAGATATTATTATTATTATTAT-TACATA
1 CTTTTATT-TAGATATTATTATTATTATTATGTACATA
*
5314137 CTTTTATTATATGCATATATATATATGTATTTTTATGTACATA
1 CTTTTATT-TA-G-ATAT-TAT-TAT-TATTATTATGTACATA
*
5314180 -TTATTATTT-TATATTATTATTA
1 CTT-TTATTTAGATATTATTATTA
5314202 CCAAATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 8 0.15
40 3 0.05
41 3 0.05
42 11 0.20
43 11 0.20
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (37 bp):
CTTTTATTTAGATATTATTATTATTATTATGTACATA
Found at i:5333465 original size:5 final size:5
Alignment explanation
Indices: 5333455--5333485 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
5333445 AAACAAATGT
5333455 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
5333486 ATTCCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:5338384 original size:12 final size:12
Alignment explanation
Indices: 5338367--5338392 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5338357 TATAATTTGC
5338367 AAAACACCATTA
1 AAAACACCATTA
5338379 AAAACACCATTA
1 AAAACACCATTA
5338391 AA
1 AA
5338393 TATATTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAACACCATTA
Found at i:5345812 original size:17 final size:17
Alignment explanation
Indices: 5345783--5345820 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
5345773 ATTCTTTCGA
5345783 TATTGTATAAATTTATTT
1 TATTGTATAAATTT-TTT
5345801 TATTGT-TAAATTTTTT
1 TATTGTATAAATTTTTT
5345817 TATT
1 TATT
5345821 ATTTTAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 7 0.35
18 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (17 bp):
TATTGTATAAATTTTTT
Found at i:5345850 original size:30 final size:31
Alignment explanation
Indices: 5345803--5345866 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
5345793 ATTTATTTTA
*
5345803 TTGTTAAATTTTTTTATTATTTTAAAGACAT
1 TTGTTAAATTTTATTATTATTTTAAAGACAT
*
5345834 TTGTT-AATTTTATTATTATTTTAGAGACAT
1 TTGTTAAATTTTATTATTATTTTAAAGACAT
5345864 TTG
1 TTG
5345867 ATTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (31 bp):
TTGTTAAATTTTATTATTATTTTAAAGACAT
Found at i:5346559 original size:47 final size:47
Alignment explanation
Indices: 5346490--5346584 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
5346480 TGTGATTGTG
5346490 AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAAACTAATAGT
1 AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAAACTAATAGT
*
5346537 AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAGACTAATAGT
1 AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAAACTAATAGT
5346584 A
1 A
5346585 GCATATGAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.29
Consensus pattern (47 bp):
AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAAACTAATAGT
Done.