Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_pilon, whole genome shotgun sequence
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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 28
Found at i:4073231 original size:251 final size:249
Alignment explanation
Indices: 4072658--4073393 Score: 1176
Period size: 251 Copynumber: 2.9 Consensus size: 249
4072648 AAGTCGTTTC
* * * *
4072658 GAAAAATGAGAAGGCGATTTTCAAAGTTTCTCATTTAATCTTTTCTA-AAAATGAAAATTTTGAA
1 GAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAA--TGTTCAAGAAAATGAAATTTTTGAA
* * *
4072722 AAGTAAGAAGTTTCTTA-CCGGTAAATTATTTCCCACAAATTTGTAAATCCTTAAGGTCATATGT
64 AAGTAAGAAGTTTCTTACCCAGTAAATTAATTCCCACAAATTTGTAAATCCTTAGGGTCATATGT
*
4072786 CAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGCAGTCTTTTGAGCAAGATGATAAG
129 CAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTTCAGTCTTTTGAGCAAGATGATAAG
*
4072851 TCCTTAGGGCCATCCGTTAGACCTTTGGGTAGGATGTTTACACATGATTTTCACAT
194 TCCTTAGGGCCATCCGTAAGACCTTTGGGTAGGATGTTTACACATGATTTTCACAT
*
4072907 G--AAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTTTTGAAAA
1 GAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTTTTGAAAA
* * *
4072970 GTAAGAAGTTTCTTACCCAGTAAATTAATTCCCACAAATATGTAAAACCTTCGGGTCATCA-GTC
66 GTAAGAAGTTTCTTACCCAGTAAATTAATTCCCACAAATTTGTAAATCCTTAGGGTCAT-ATGTC
* * * *
4073034 AATCTTTTGAGCATAATGCTTAAATCCTTAGGGTCATCTTCCAATCTTTTGAGCAAGATGATAAG
130 AGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTT-CAGTCTTTTGAGCAAGATGATAAG
*
4073099 TCCTTAGGGCCATCCGTCAGACCTTTGGGTAGGATGTTTACACATGATTTTTCACAT
194 TCCTTAGGGCCATCCGTAAGACCTTTGGGTAGGATGTTTACACATGA-TTTTCACAT
*
4073156 GAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTTTTGAAAA
1 GAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTTTTGAAAA
4073221 GTAAGAAGTTTCTTACCCAGTAAATTAATTCCCACAAATTTGTAAATCCTTAGGGTCATATGTCA
66 GTAAGAAGTTTCTTACCCAGTAAATTAATTCCCACAAATTTGTAAATCCTTAGGGTCATATGTCA
* * *
4073286 GTCTCTCGAGCATGATGTTTAAATCCTTAGGGTCATCTGTTAGTCTTTTGGAGCAAGATGATAAG
131 GTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCT-TCAGTCTTTT-GAGCAAGATGATAAG
4073351 TCCTTAGGGCCATCCGTAAGACCTTTGGGTAGGATGTTTACAC
194 TCCTTAGGGCCATCCGTAAGACCTTTGGGTAGGATGTTTACAC
4073394 TCTTTATTGA
Statistics
Matches: 447, Mismatches: 30, Indels: 17
0.90 0.06 0.03
Matches are distributed among these distances:
245 5 0.01
246 33 0.07
247 109 0.24
248 70 0.16
249 11 0.02
250 1 0.00
251 160 0.36
252 58 0.13
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (249 bp):
GAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTTTTGAAAA
GTAAGAAGTTTCTTACCCAGTAAATTAATTCCCACAAATTTGTAAATCCTTAGGGTCATATGTCA
GTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTTCAGTCTTTTGAGCAAGATGATAAGTC
CTTAGGGCCATCCGTAAGACCTTTGGGTAGGATGTTTACACATGATTTTCACAT
Found at i:4073355 original size:42 final size:42
Alignment explanation
Indices: 4073263--4073364 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
4073253 CACAAATTTG
* * *
4073263 TAAATCCTTAGGGTCATATGTCAGTCTCTCGAGCATGATGTT
1 TAAATCCTTAGGGTCATCTGTCAGTCTCTCGAGCAAGATGTA
* * *
4073305 TAAATCCTTAGGGTCATCTGTTAGTCTTTTGGAGCAAGATG-A
1 TAAATCCTTAGGGTCATCTGTCAGTC-TCTCGAGCAAGATGTA
* *
4073347 TAAGTCCTTAGGGCCATC
1 TAAATCCTTAGGGTCATC
4073365 CGTAAGACCT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 40 0.78
43 11 0.22
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (42 bp):
TAAATCCTTAGGGTCATCTGTCAGTCTCTCGAGCAAGATGTA
Found at i:4073439 original size:29 final size:29
Alignment explanation
Indices: 4073400--4073455 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
4073390 ACACTCTTTA
*
4073400 TTGACTTCCTAGTAAAAAGAAGTCAATCT
1 TTGACTTCCTAATAAAAAGAAGTCAATCT
* *
4073429 TTGATTTCCTAATAAAGAGAAGTCAAT
1 TTGACTTCCTAATAAAAAGAAGTCAAT
4073456 TGGACAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (29 bp):
TTGACTTCCTAATAAAAAGAAGTCAATCT
Found at i:4073742 original size:43 final size:43
Alignment explanation
Indices: 4073694--4073788 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
4073684 AACAAAAAAT
*
4073694 TAGATCCAGGCCCAGACCCGGTCCAAACCCGGAAGCCCAACAA
1 TAGATCCAGGCCCAGACCCGATCCAAACCCGGAAGCCCAACAA
* ** * * *
4073737 TAGATCCAGGTCCAGACTTGATCTAGACCCGGAAGCCCAACAG
1 TAGATCCAGGCCCAGACCCGATCCAAACCCGGAAGCCCAACAA
4073780 TAGATCCAG
1 TAGATCCAG
4073789 ACTCATATGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.32, C:0.34, G:0.22, T:0.13
Consensus pattern (43 bp):
TAGATCCAGGCCCAGACCCGATCCAAACCCGGAAGCCCAACAA
Found at i:4078470 original size:41 final size:40
Alignment explanation
Indices: 4078408--4078512 Score: 111
Period size: 41 Copynumber: 2.6 Consensus size: 40
4078398 TAGAACAAAC
* * *
4078408 TATAGCGGCGTTTGAACAAAAATGCCACTAAAGTACAAGTA
1 TATAGTGGCGTTTGTA-AAAAATGCCACTAAAATACAAGTA
* * ** *
4078449 TATAGTGGTGTTTGTATAAAAACGCCACTAAAATATGAGTC
1 TATAGTGGCGTTTGTA-AAAAATGCCACTAAAATACAAGTA
*
4078490 TATTGTGGCGTTTGTAAAAAATG
1 TATAGTGGCGTTTGTAAAAAATG
4078513 ATGCTAAAGT
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (40 bp):
TATAGTGGCGTTTGTAAAAAATGCCACTAAAATACAAGTA
Found at i:4078624 original size:41 final size:41
Alignment explanation
Indices: 4078516--4078676 Score: 114
Period size: 41 Copynumber: 3.9 Consensus size: 41
4078506 AAAAATGATG
* * ** *
4078516 CTAAAGTACTACTCTATTGTGGCGTTTGTTAAAAAACGCAA
1 CTAAAGTACTACTCTATTGCGACGTTTGTTAAAAAATACCA
* * * * * *
4078557 CTATAG-A-TGAACCCTACTACGGCGTTTG-TATAAAAATACCG
1 CTAAAGTACT--ACTCTATTGCGACGTTTGTTA-AAAAATACCA
*
4078598 CTAAAGTACTACTCTATTGCGACGTTTGTTGAAAAAATATCA
1 CTAAAGTACTACTCTATTGCGACGTTTGTT-AAAAAATACCA
* *
4078640 CTAAAGTACTACTCTGTTGC-AGCGTTTATTGAAAAAA
1 CTAAAGTACTACTCTATTGCGA-CGTTTGTT-AAAAAA
4078677 CACAACTACA
Statistics
Matches: 94, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 45 0.48
42 43 0.46
43 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (41 bp):
CTAAAGTACTACTCTATTGCGACGTTTGTTAAAAAATACCA
Found at i:4078644 original size:42 final size:42
Alignment explanation
Indices: 4078588--4078676 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
4078578 GCGTTTGTAT
* *
4078588 AAAAATACCGCTAAAGTACTACTCTATTGC-GACGTTTGTTGA
1 AAAAATACCACTAAAGTACTACTCTATTGCAG-CGTTTATTGA
* *
4078630 AAAAATATCACTAAAGTACTACTCTGTTGCAGCGTTTATTGA
1 AAAAATACCACTAAAGTACTACTCTATTGCAGCGTTTATTGA
4078672 AAAAA
1 AAAAA
4078677 CACAACTACA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (42 bp):
AAAAATACCACTAAAGTACTACTCTATTGCAGCGTTTATTGA
Found at i:4078994 original size:20 final size:20
Alignment explanation
Indices: 4078952--4078997 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
4078942 CGTAAAATCT
*
4078952 AATAAATTAAAAACTTGAAA
1 AATAAATTAAAAACTAGAAA
*
4078972 AATAGATTAAAAA-TAGAATA
1 AATAAATTAAAAACTAGAA-A
4078992 AATAAA
1 AATAAA
4078998 AATTAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (20 bp):
AATAAATTAAAAACTAGAAA
Found at i:4086305 original size:13 final size:14
Alignment explanation
Indices: 4086287--4086318 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
4086277 GGTCAAAGGA
4086287 GGTCAACGGTC-AC
1 GGTCAACGGTCAAC
4086300 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
4086314 GGTCA
1 GGTCA
4086319 GGTTGGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.25, C:0.28, G:0.31, T:0.16
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:4086308 original size:7 final size:7
Alignment explanation
Indices: 4086287--4086318 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
4086277 GGTCAAAGGA
4086287 GGTCAAC
1 GGTCAAC
4086294 GGTC-AC
1 GGTCAAC
4086300 GGTCAAC
1 GGTCAAC
4086307 GGTCAAC
1 GGTCAAC
4086314 GGTCA
1 GGTCA
4086319 GGTTGGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.25, C:0.28, G:0.31, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:4086329 original size:17 final size:17
Alignment explanation
Indices: 4086287--4086344 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
4086277 GGTCAAAGGA
*
4086287 GGTCAACGGTCACGGTCAAC
1 GGTCAACGGTCA-GGTC--G
*
4086307 GGTCAACGGTCAGGTTG
1 GGTCAACGGTCAGGTCG
* *
4086324 GGTCAATGGTCGGGTCG
1 GGTCAACGGTCAGGTCG
4086341 GGTC
1 GGTC
4086345 GGTCGGGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 18 0.55
19 3 0.09
20 12 0.36
ACGTcount: A:0.17, C:0.22, G:0.40, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCAGGTCG
Found at i:4086383 original size:10 final size:10
Alignment explanation
Indices: 4086356--4086457 Score: 61
Period size: 10 Copynumber: 10.3 Consensus size: 10
4086346 GTCGGGTTAG
4086356 ACCGG-TCAA
1 ACCGGTTCAA
* *
4086365 ACCGATTCAG
1 ACCGGTTCAA
4086375 ACCGGTTCAA
1 ACCGGTTCAA
4086385 ACCGG-TCGAA
1 ACCGGTTC-AA
* *
4086395 AACGGTTCGA
1 ACCGGTTCAA
4086405 ACCGG-TCGAA
1 ACCGGTTC-AA
*
4086415 AACGG-TCAA
1 ACCGGTTCAA
* * *
4086424 AACTGATCAA
1 ACCGGTTCAA
4086434 TACCGGTTCAAA
1 -ACCGGTTC-AA
4086446 ACCGG-TCAA
1 ACCGGTTCAA
4086455 ACC
1 ACC
4086458 AGTTTTCCAG
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
9 19 0.26
10 40 0.55
11 12 0.16
12 2 0.03
ACGTcount: A:0.34, C:0.28, G:0.22, T:0.16
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:4086400 original size:20 final size:20
Alignment explanation
Indices: 4086377--4086424 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
4086367 CGATTCAGAC
4086377 CGGTTCAAACCGGTCGAAAA
1 CGGTTCAAACCGGTCGAAAA
*
4086397 CGGTTCGAACCGGTCGAAAA
1 CGGTTCAAACCGGTCGAAAA
4086417 CGG-TCAAA
1 CGGTTCAAA
4086425 ACTGATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (20 bp):
CGGTTCAAACCGGTCGAAAA
Found at i:4094529 original size:12 final size:11
Alignment explanation
Indices: 4094498--4094550 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
4094488 GTCACTGCCC
4094498 TAATTCTTATTCT
1 TAATT-TTATT-T
*
4094511 TATTTTTATGTT
1 TAATTTTAT-TT
4094523 TAATTTTAATTT
1 TAATTTT-ATTT
4094535 TAA-TTTATTT
1 TAATTTTATTT
4094545 TAATTT
1 TAATTT
4094551 GATCATTGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 7 0.20
11 5 0.14
12 16 0.46
13 7 0.20
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (11 bp):
TAATTTTATTT
Found at i:4094673 original size:19 final size:20
Alignment explanation
Indices: 4094644--4094683 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4094634 TTAATTAGCC
4094644 TTAATATTAATTAAATTAAA
1 TTAATATTAATTAAATTAAA
*
4094664 TTAA-ATTAATTTAATTAAA
1 TTAATATTAATTAAATTAAA
4094683 T
1 T
4094684 ATATTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATATTAATTAAATTAAA
Found at i:4095258 original size:87 final size:88
Alignment explanation
Indices: 4095058--4095243 Score: 245
Period size: 88 Copynumber: 2.1 Consensus size: 88
4095048 AATTGATTAG
* * *
4095058 GGTT-ATAATTAGAGCCATAACTTTAGACTTTTCACAATTTAGTCCTTCAAATTTTTAAATTAGA
1 GGTTAATAATTAGAGCCTTAATTTTAGACTTTTCACAATTTAGTCCTTCAAATCTTTAAATTAGA
** *
4095122 TATTCTTCTGACATAATTAACTA
66 TATTCTTCAAACATAAATAACTA
* *
4095145 GGTTAATAATTAGAGCCTTAATTTTAGA-TTATTCACAATTTAGTCCTTTAGATCTTT-AATTAG
1 GGTTAATAATTAGAGCCTTAATTTTAGACTT-TTCACAATTTAGTCCTTCAAATCTTTAAATTAG
*
4095208 ATATTCCTT-AAACATAAATAATTA
65 ATATT-CTTCAAACATAAATAACTA
4095232 GGTTAATAATTA
1 GGTTAATAATTA
4095244 TTGCCTCTAT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
87 40 0.46
88 47 0.54
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (88 bp):
GGTTAATAATTAGAGCCTTAATTTTAGACTTTTCACAATTTAGTCCTTCAAATCTTTAAATTAGA
TATTCTTCAAACATAAATAACTA
Found at i:4105572 original size:22 final size:23
Alignment explanation
Indices: 4105547--4105592 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
4105537 TGACCGGTCT
4105547 GACCCGTTGACC-GACCCGACCC
1 GACCCGTTGACCTGACCCGACCC
4105569 GACCCGTTGACCTGACCCGACCC
1 GACCCGTTGACCTGACCCGACCC
4105592 G
1 G
4105593 GTGACATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.17, C:0.48, G:0.24, T:0.11
Consensus pattern (23 bp):
GACCCGTTGACCTGACCCGACCC
Found at i:4105585 original size:18 final size:18
Alignment explanation
Indices: 4105559--4105597 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4105549 CCCGTTGACC
*
4105559 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGGT
*
4105577 GACCTGACCCGACCCGGT
1 GACCCGACCCGACCCGGT
4105595 GAC
1 GAC
4105598 ATTTTGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.46, G:0.26, T:0.10
Consensus pattern (18 bp):
GACCCGACCCGACCCGGT
Found at i:4105626 original size:29 final size:28
Alignment explanation
Indices: 4105593--4105782 Score: 218
Period size: 29 Copynumber: 6.6 Consensus size: 28
4105583 ACCCGACCCG
* *
4105593 GTGACATTTTGAGAATTATTTTGAAAATA
1 GTGACATTCTGGGAATTATTTTGAAAA-A
** * *
4105622 GTGACATTCAAGGAAATATTTTGATAAAG
1 GTGACATTCTGGGAATTATTTTGA-AAAA
* *
4105651 GTGACATTCTGGGAAATATTTTAAAAAAA
1 GTGACATTCTGGGAATTATTTT-GAAAAA
* *
4105680 GTAACATTCTGGGAAATATTTTGAAAAA
1 GTGACATTCTGGGAATTATTTTGAAAAA
4105708 GGTGACATTCTGGGAATTATTTTGAAAAA
1 -GTGACATTCTGGGAATTATTTTGAAAAA
*
4105737 TTGACATTCTGGGAATTATTTTGAAAAA
1 GTGACATTCTGGGAATTATTTTGAAAAA
* *
4105765 TATGACATTTTGGGAATT
1 -GTGACATTCTGGGAATT
4105783 TTTGAATATG
Statistics
Matches: 140, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
28 32 0.23
29 104 0.74
30 4 0.03
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.36
Consensus pattern (28 bp):
GTGACATTCTGGGAATTATTTTGAAAAA
Found at i:4105763 original size:57 final size:57
Alignment explanation
Indices: 4105592--4105782 Score: 247
Period size: 58 Copynumber: 3.3 Consensus size: 57
4105582 GACCCGACCC
* * ** *
4105592 GGTGACATTTTGAGAATTATTTTGAAAATAGTGACATTCAAGGAAATATTTTGATAAA
1 GGTGACATTCTGGGAATTATTTTGAAAA-AGTGACATTCTGGGAAATATTTTGAAAAA
* * *
4105650 GGTGACATTCTGGGAAATATTTTAAAAAAAGTAACATTCTGGGAAATATTTTGAAAAA
1 GGTGACATTCTGGGAATTATTTT-GAAAAAGTGACATTCTGGGAAATATTTTGAAAAA
* *
4105708 GGTGACATTCTGGGAATTATTTTGAAAAATTGACATTCTGGGAATTATTTTGAAAAA
1 GGTGACATTCTGGGAATTATTTTGAAAAAGTGACATTCTGGGAAATATTTTGAAAAA
** *
4105765 TATGACATTTTGGGAATT
1 GGTGACATTCTGGGAATT
4105783 TTTGAATATG
Statistics
Matches: 116, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
57 45 0.39
58 67 0.58
59 4 0.03
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (57 bp):
GGTGACATTCTGGGAATTATTTTGAAAAAGTGACATTCTGGGAAATATTTTGAAAAA
Found at i:4106430 original size:63 final size:63
Alignment explanation
Indices: 4106361--4106484 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
4106351 CTAATGTGAC
** *
4106361 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCCACGGCCCTGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
4106424 TCTTAGGTAGGCTCCACGGCCCTGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCTCCACGGCCCTGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
4106485 TCCCTTAGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
62 1 0.02
63 52 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCTCCACGGCCCTGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:4106444 original size:32 final size:32
Alignment explanation
Indices: 4106361--4106484 Score: 89
Period size: 31 Copynumber: 4.0 Consensus size: 32
4106351 CTAATGTGAC
* * *
4106361 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
4106391 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
*
4106424 TCTTAGGTAGGCTC-CACGGCCCTGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGGCCCT-AAGATGTA
*
4106455 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
4106485 TCCCTTAGGA
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
30 2 0.03
31 46 0.63
32 23 0.32
33 2 0.03
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:4106555 original size:27 final size:27
Alignment explanation
Indices: 4106501--4106560 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
4106491 AGGATAACTC
*
4106501 TTTTATGAGATTTACTGCAGTATAATT
1 TTTTATGAGATTTACTGCACTATAATT
* *
4106528 TTTTATGAGATTTACTGGACTATGATT
1 TTTTATGAGATTTACTGCACTATAATT
4106555 TGTTTA
1 T-TTTA
4106561 GTGTACCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (27 bp):
TTTTATGAGATTTACTGCACTATAATT
Found at i:4112714 original size:29 final size:29
Alignment explanation
Indices: 4112672--4112892 Score: 239
Period size: 29 Copynumber: 7.6 Consensus size: 29
4112662 ACCCGACCCG
* * *
4112672 GTGATATTTTGGGAATTATTTTGAAAATT
1 GTGACATTCTGGGAATTATTTTGAAAATA
* *
4112701 GTGATATTTTGGGAATTATTTTGAAAATA
1 GTGACATTCTGGGAATTATTTTGAAAATA
* * * *
4112730 GTAACATTCTAGGAAATATTTTGATAAA-G
1 GTGACATTCTGGGAATTATTTTGA-AAATA
* *
4112759 GTGACATTCTGGGAAATATTTTGAAAAAAA
1 GTGACATTCTGGGAATTATTTTG-AAAATA
* * *
4112789 GTGACATTCTAGGAAATATTTTGAAAATT
1 GTGACATTCTGGGAATTATTTTGAAAATA
* * *
4112818 TTGATATTCTGGGAATTATTTTGAAAAAA
1 GTGACATTCTGGGAATTATTTTGAAAATA
4112847 GTGACATTCTGGGAATTATTTTGAAAA-A
1 GTGACATTCTGGGAATTATTTTGAAAATA
*
4112875 GATGACATTTTGGGAATT
1 G-TGACATTCTGGGAATT
4112893 TTCCAATTTG
Statistics
Matches: 166, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
28 2 0.01
29 138 0.83
30 26 0.16
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (29 bp):
GTGACATTCTGGGAATTATTTTGAAAATA
Found at i:4123088 original size:22 final size:21
Alignment explanation
Indices: 4123063--4123114 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
4123053 TTATTTTTAA
4123063 TATATATACTTTTAATAAAATT
1 TATATATACTTTTAATAAAA-T
* *
4123085 TATATATAATTTTTCATAAAAT
1 TATATAT-ACTTTTAATAAAAT
4123107 TATATATA
1 TATATATA
4123115 AATTGGTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 15 0.56
23 11 0.41
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATATACTTTTAATAAAAT
Found at i:4123115 original size:22 final size:23
Alignment explanation
Indices: 4123062--4123115 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
4123052 ATTATTTTTA
4123062 ATATATATACTTTTAATAAAATTT
1 ATATATA-ACTTTTAATAAAATTT
* *
4123086 ATATATAATTTTTCATAAAA-TT
1 ATATATAACTTTTAATAAAATTT
4123108 ATATATAA
1 ATATATAA
4123116 ATTGGTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.36
23 11 0.39
24 7 0.25
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATAACTTTTAATAAAATTT
Found at i:4123228 original size:34 final size:31
Alignment explanation
Indices: 4123167--4123228 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
4123157 ATTTTAATTA
* *
4123167 ATATTAAATTTTATATAATTTATCTAAAAAT
1 ATATTAAATTTTACATAATTTAACTAAAAAT
4123198 ATATTAAATTTTACATCAACATTTAACTAAA
1 ATATTAAATTTTACAT--A-ATTTAACTAAA
4123229 TAAGCATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 15 0.58
33 1 0.04
34 10 0.38
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATTAAATTTTACATAATTTAACTAAAAAT
Found at i:4124339 original size:21 final size:19
Alignment explanation
Indices: 4124314--4124352 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
4124304 ATGCAATCAC
4124314 CAAAAGCTTGAAACTGAAAAT
1 CAAAAGCTT-AAA-TGAAAAT
*
4124335 CAAAATCTTAAATGAAAA
1 CAAAAGCTTAAATGAAAA
4124353 CTATAGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (19 bp):
CAAAAGCTTAAATGAAAAT
Found at i:4125589 original size:32 final size:32
Alignment explanation
Indices: 4125548--4125612 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
4125538 CTTTTGCTTC
4125548 GTAAAGTGGAAAGGATGATAAAATGAAAAGTT
1 GTAAAGTGGAAAGGATGATAAAATGAAAAGTT
4125580 GTAAAGTGGAAAGGATGATAAAATGAAAAGTT
1 GTAAAGTGGAAAGGATGATAAAATGAAAAGTT
4125612 G
1 G
4125613 AAATAGGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (32 bp):
GTAAAGTGGAAAGGATGATAAAATGAAAAGTT
Found at i:4125607 original size:16 final size:16
Alignment explanation
Indices: 4125556--4125607 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
4125546 TCGTAAAGTG
4125556 GAAAGGATGATAAAAT
1 GAAAGGATGATAAAAT
* * *
4125572 GAAAAGTTG-TAAAGT
1 GAAAGGATGATAAAAT
4125587 GGAAAGGATGATAAAAT
1 -GAAAGGATGATAAAAT
4125604 GAAA
1 GAAA
4125608 AGTTGAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (16 bp):
GAAAGGATGATAAAAT
Found at i:4125623 original size:32 final size:32
Alignment explanation
Indices: 4125550--4125623 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
4125540 TTTGCTTCGT
*
4125550 AAAGTGGAAAGGATGATAAAATGAAAAGTTGT
1 AAAGTGGAAAGGATGATAAAATGAAAAGTTGA
4125582 AAAGTGGAAAGGATGATAAAATGAAAAGTTGA
1 AAAGTGGAAAGGATGATAAAATGAAAAGTTGA
4125614 AATAG-GGAAA
1 AA-AGTGGAAA
4125624 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 38 0.95
33 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (32 bp):
AAAGTGGAAAGGATGATAAAATGAAAAGTTGA
Found at i:4128988 original size:197 final size:197
Alignment explanation
Indices: 4128653--4129040 Score: 776
Period size: 197 Copynumber: 2.0 Consensus size: 197
4128643 AGATCAGAGC
4128653 ATTTCAAACTAAATGTGTAGTACATGCCAACAGTTTACAAATTAACAAAAACCTACATTTATTTG
1 ATTTCAAACTAAATGTGTAGTACATGCCAACAGTTTACAAATTAACAAAAACCTACATTTATTTG
4128718 TCTTGATCTGATCCTCACGGGATATGCTATCCTCAACGAATCAACCTTCAGATTTCTTCAAACCT
66 TCTTGATCTGATCCTCACGGGATATGCTATCCTCAACGAATCAACCTTCAGATTTCTTCAAACCT
4128783 AATCGTGAGGAAATCACACGCTAAGTCGATGACTTTGTGAGGCAAAACTAAAGAGTACTAATTAT
131 AATCGTGAGGAAATCACACGCTAAGTCGATGACTTTGTGAGGCAAAACTAAAGAGTACTAATTAT
4128848 AG
196 AG
4128850 ATTTCAAACTAAATGTGTAGTACATGCCAACAGTTTACAAATTAACAAAAACCTACATTTATTTG
1 ATTTCAAACTAAATGTGTAGTACATGCCAACAGTTTACAAATTAACAAAAACCTACATTTATTTG
4128915 TCTTGATCTGATCCTCACGGGATATGCTATCCTCAACGAATCAACCTTCAGATTTCTTCAAACCT
66 TCTTGATCTGATCCTCACGGGATATGCTATCCTCAACGAATCAACCTTCAGATTTCTTCAAACCT
4128980 AATCGTGAGGAAATCACACGCTAAGTCGATGACTTTGTGAGGCAAAACTAAAGAGTACTAA
131 AATCGTGAGGAAATCACACGCTAAGTCGATGACTTTGTGAGGCAAAACTAAAGAGTACTAA
4129041 ACTTTATAGA
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 191 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (197 bp):
ATTTCAAACTAAATGTGTAGTACATGCCAACAGTTTACAAATTAACAAAAACCTACATTTATTTG
TCTTGATCTGATCCTCACGGGATATGCTATCCTCAACGAATCAACCTTCAGATTTCTTCAAACCT
AATCGTGAGGAAATCACACGCTAAGTCGATGACTTTGTGAGGCAAAACTAAAGAGTACTAATTAT
AG
Found at i:4129282 original size:21 final size:21
Alignment explanation
Indices: 4129258--4129329 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
4129248 CACTGAAGTG
*
4129258 CCACATAATTGTCCAGAATGA
1 CCACATAATTGTCCCGAATGA
*
4129279 CCACATAGGTT-TGCACCGAAGTG-
1 CCACATA-ATTGT-C-CCGAA-TGA
4129302 CCACATAATTGTCCCGAATGA
1 CCACATAATTGTCCCGAATGA
4129323 CCACATA
1 CCACATA
4129330 GACCCTTGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 2 0.05
21 20 0.48
22 6 0.14
23 12 0.29
24 2 0.05
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (21 bp):
CCACATAATTGTCCCGAATGA
Found at i:4129294 original size:44 final size:44
Alignment explanation
Indices: 4129245--4129330 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
4129235 AACTCGTAAA
*
4129245 TTGCACTGAAGTGCCACATAATTGTCCAGAATGACCACATAGGT
1 TTGCACCGAAGTGCCACATAATTGTCCAGAATGACCACATAGGT
*
4129289 TTGCACCGAAGTGCCACATAATTGTCCCGAATGACCACATAG
1 TTGCACCGAAGTGCCACATAATTGTCCAGAATGACCACATAG
4129331 ACCCTTGACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (44 bp):
TTGCACCGAAGTGCCACATAATTGTCCAGAATGACCACATAGGT
Found at i:4131301 original size:329 final size:328
Alignment explanation
Indices: 4130681--4131340 Score: 1275
Period size: 329 Copynumber: 2.0 Consensus size: 328
4130671 GCAATTCCAC
*
4130681 TATAAAACCTTAAAATTTTCAAACTATTCTAATTCAACCACTGAGTTTAAAATTCTTACATTTTG
1 TATAAAACCTTAAAATTTTCAAACTATTCTAATTCAACCACTAAGTTTAAAATTCTTACATTTTG
4130746 GTCACTGACTCAATGATTGGGATATTACAAATCTCCCCCTTAAGAAAATTCATCCTCAAATTTTC
66 GTCACTGACTCAATGATTGGGATATTACAAATCTCCCCCTTAAGAAAATTCATCCTCAAATTTTC
* *
4130811 ATTGCACAAAGAGGCGGGGTATTGTTTCCTCATATCTTCTTCACGCTCCCACGTAGCGTCTTCTA
131 ATTACACAAAGAGGCGGGGTATTGTTTCCTCATATCTTCTTCACGCTCCCACGTAGCATCTTCTA
4130876 CTTTATGGTTTCTCCAAAGAAGCTTAACTAGTGGAATCGTCTTATTCCGTAATTGCTTGATTTCA
196 CTTTATGGTTTCTCCAAAGAAGCTTAACTAGTGGAATCGTCTTATTCCGTAATTGCTTGATTTCA
4130941 AATGCTAGAATTTGTACTGGTTCTTCCTCATAGGTCAAGTTAGACTGAACTTCTATCACATCTGG
261 AATGCTAGAATTTGTACTGGTTCTTCCTCATAGGTCAAGTTAGACTGAACTTCTATCACATCTGG
4131006 AGT
326 AGT
*
4131009 TATAAAACCTTAAATTTTTCAAACTATTCTAATTCAACCACTAAGTTTAAAATTCTTACATTTTG
1 TATAAAACCTTAAAATTTTCAAACTATTCTAATTCAACCACTAAGTTTAAAATTCTTACATTTTG
4131074 GTCACTGACTCAATGATTGGGATATTACAAATCTCCCCCTTAAGAAAATTCATCCTCAAATTTTC
66 GTCACTGACTCAATGATTGGGATATTACAAATCTCCCCCTTAAGAAAATTCATCCTCAAATTTTC
4131139 ATTACACAAAGAGGCGGGGGTATTGTTTCCTCATATCTTCTTCACGCTCCCACGTAGCATCTTCT
131 ATTACACAAAGAGGC-GGGGTATTGTTTCCTCATATCTTCTTCACGCTCCCACGTAGCATCTTCT
4131204 ACTTTATGGTTTCTCCAAAGAAGCTTAACTAGTGGAATCGTCTTATTCCGTAATTGCTTGATTTC
195 ACTTTATGGTTTCTCCAAAGAAGCTTAACTAGTGGAATCGTCTTATTCCGTAATTGCTTGATTTC
4131269 AAATGCTAGAATTTGTACTGGTTCTTCCTCATAGGTCAAGTTAGACTGAACTTCTATCACATCTG
260 AAATGCTAGAATTTGTACTGGTTCTTCCTCATAGGTCAAGTTAGACTGAACTTCTATCACATCTG
4131334 GAGT
325 GAGT
4131338 TAT
1 TAT
4131341 GATATATGCA
Statistics
Matches: 327, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
328 142 0.43
329 185 0.57
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (328 bp):
TATAAAACCTTAAAATTTTCAAACTATTCTAATTCAACCACTAAGTTTAAAATTCTTACATTTTG
GTCACTGACTCAATGATTGGGATATTACAAATCTCCCCCTTAAGAAAATTCATCCTCAAATTTTC
ATTACACAAAGAGGCGGGGTATTGTTTCCTCATATCTTCTTCACGCTCCCACGTAGCATCTTCTA
CTTTATGGTTTCTCCAAAGAAGCTTAACTAGTGGAATCGTCTTATTCCGTAATTGCTTGATTTCA
AATGCTAGAATTTGTACTGGTTCTTCCTCATAGGTCAAGTTAGACTGAACTTCTATCACATCTGG
AGT
Found at i:4135137 original size:23 final size:24
Alignment explanation
Indices: 4135111--4135164 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
4135101 TCCCGAAGAA
4135111 CCACATAGG-TTTACACCGAAGTG
1 CCACATAGGTTTTACACCGAAGTG
* *
4135134 CCACATAGGTTTTGCATCGAAGTG
1 CCACATAGGTTTTACACCGAAGTG
4135158 CCACATA
1 CCACATA
4135165 ATTGTCCCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (24 bp):
CCACATAGGTTTTACACCGAAGTG
Found at i:4136248 original size:13 final size:13
Alignment explanation
Indices: 4136221--4136267 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
4136211 ATCAAATATT
*
4136221 CATTTC-AAAACC
1 CATTTCTAAAATC
4136233 CATTT-TACAAATC
1 CATTTCTA-AAATC
4136246 CATTTCTAAAATC
1 CATTTCTAAAATC
4136259 CATTTCTAA
1 CATTTCTAA
4136268 TTCACTCCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 6 0.19
13 23 0.74
14 2 0.06
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (13 bp):
CATTTCTAAAATC
Found at i:4136728 original size:44 final size:44
Alignment explanation
Indices: 4136680--4136832 Score: 137
Period size: 44 Copynumber: 3.5 Consensus size: 44
4136670 GATGATGTCA
* * * *
4136680 ATCCAACTCTTTATGTGATGGATTCGAGCGAGAGGGTGATGTTG
1 ATCCAACTCTTTATGTGATGGAATCGAGCGAAAGGGTAATGATG
* * *
4136724 ATCCAA-TTTCTTATGTGATAGAATCGAGCGAAATGGTAATGATG
1 ATCCAACTCT-TTATGTGATGGAATCGAGCGAAAGGGTAATGATG
* * * * ** *
4136768 ATCCAGCTCCTTATGTGATGGAATCAAGCGAAAAGAAAAGTGTTG
1 ATCCAACTCTTTATGTGATGGAATCGAGCGAAAGGGTAA-TGATG
* *
4136813 GTCCAACTCCTTATGTGATG
1 ATCCAACTCTTTATGTGATG
4136833 AGCGAGCCAG
Statistics
Matches: 88, Mismatches: 18, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
43 2 0.02
44 63 0.72
45 23 0.26
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (44 bp):
ATCCAACTCTTTATGTGATGGAATCGAGCGAAAGGGTAATGATG
Found at i:4144197 original size:15 final size:15
Alignment explanation
Indices: 4144156--4144197 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4144146 ATGAAAGAGG
4144156 TGGAATCTGAAAGAAT
1 TGGAATCTG-AAGAAT
* *
4144172 TGAAATATGAAGAAT
1 TGGAATCTGAAGAAT
4144187 TGGAATCTGAA
1 TGGAATCTGAA
4144198 TCTGAAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (15 bp):
TGGAATCTGAAGAAT
Found at i:4144857 original size:34 final size:34
Alignment explanation
Indices: 4144776--4144858 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 34
4144766 TTTTCACCCT
* * * * *
4144776 AAACTCGAACCCAACCTGAATATTACACTTTAAA
1 AAACTCGAACCCGACCTAAATATCAAACTTAAAA
*
4144810 AAACTC-AATCCGACCTAAATATCAAACTTAAAA
1 AAACTCGAACCCGACCTAAATATCAAACTTAAAA
*
4144843 AAACCCGAACCCGACC
1 AAACTCGAACCCGACC
4144859 CGAACACTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 26 0.65
34 14 0.35
ACGTcount: A:0.46, C:0.30, G:0.06, T:0.18
Consensus pattern (34 bp):
AAACTCGAACCCGACCTAAATATCAAACTTAAAA
Found at i:4146243 original size:32 final size:31
Alignment explanation
Indices: 4146203--4146271 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
4146193 TCAATTTTTT
* *
4146203 ATTTTGAATTCGATTCG-AGCTTAATTTTAAA
1 ATTTTGAA-TCAATTCGAAGCTTAATTTAAAA
*
4146234 ATTTGTGAATCAATTCGAAGTTTAATTTAAAAA
1 ATTT-TGAATCAATTCGAAGCTTAATTT-AAAA
4146267 ATTTT
1 ATTTT
4146272 TATTCGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
31 11 0.34
32 14 0.44
33 7 0.22
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTTGAATCAATTCGAAGCTTAATTTAAAA
Found at i:4151972 original size:182 final size:184
Alignment explanation
Indices: 4151472--4152274 Score: 851
Period size: 186 Copynumber: 4.3 Consensus size: 184
4151462 CCTTACACTA
** * **
4151472 GGGCACAACATTATTTTTTATATATATTTTTAACATTTTCAACTTTTAACTTATTTTTTTATCGT
1 GGGCACAACCGTATTTCTTATATATATTCATAACATTTTCAACTTTTAACTTATTTTTTTA-CGT
* * ** * *
4151537 GGGAATGTCTAAGTTCCCATCAACTTAAACTTTGATAACATTTTAGGGGCAAACTATTTTATTTA
65 GGGAATGTCTAAG-GCCCATCAACTTAAACTCTGATAACATTTTAGGCACAACCTATTTTATTAA
* * * * *
4151602 TGAAAATGTTAACATTACATATCACAATTTATTTCTTAATGAACCATGACATTCTT
129 TAAAAATATTAACATTACAGATCACAATCTATTTATTAATGAACCATGACATTCTT
* *
4151658 GGG-AGCAACCATATTTCTTATATATATTCATAACATTTTCAGCTTTTAACTTATTTTTTTATCG
1 GGGCA-CAACCGTATTTCTTATATATATTCATAACATTTTCAACTTTTAACTTATTTTTTTA-CG
* * * * *
4151722 TGGGAATGTCGAAAGCCCTACCAACTTAAACTCTGGTAACATTTTAGGCACAACCTATTTTGTTA
64 TGGGAATGTCTAAGGCCC-ATCAACTTAAACTCTGATAACATTTTAGGCACAACCTATTTTATTA
* * * * *
4151787 ATAAAAATATTAACTTTGCAGATCACAACCTATTTATTAATGACCCATGACATTTTT
128 ATAAAAATATTAACATTACAGATCACAATCTATTTATTAATGAACCATGACATTCTT
4151844 GGGCACAACCGTATTTCTTATATATA-TCATAACATTTTCAACTTTTAACTTA-TTTTTTA-GTG
1 GGGCACAACCGTATTTCTTATATATATTCATAACATTTTCAACTTTTAACTTATTTTTTTACGTG
* * * * * *
4151906 GGAATATCTAAGGCCTCATTAGCTTAAACTCTGATAACATTTTAGGCGCAACCTAATTCATTAAT
66 GGAATGTCTAAGGCC-CATCAACTTAAACTCTGATAACATTTTAGGCACAACCTATTTTATTAAT
* * * *
4151971 AAAAACATTAACATTACAGATCGCAATCTATTTATCAGTGAACCATGACATTCTT
130 AAAAATATTAACATTACAGATCACAATCTATTTATTAATGAACCATGACATTCTT
* ** * * *
4152026 GGGCGCAATTGTATTTCTTATACATATTCATTACATTTTCAACTTTTAAATTATTTTTTTATCGT
1 GGGCACAACCGTATTTCTTATATATATTCATAACATTTTCAACTTTTAACTTATTTTTTTA-CGT
* * * * * * *
4152091 GAGAATGTCCAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCAAAACTTATTTTATTAA
65 GGGAATGTCTAAGGC-CCATCAACTTAAACTCTGATAACATTTTAGGCACAACCTATTTTATTAA
* * * * * * * *
4152156 TAAAAATAGTAACATTACATATCGCGACCTATTTCTTACTAAACCATGACATTCTT
129 TAAAAATATTAACATTACAGATCACAATCTATTTATTAATGAACCATGACATTCTT
* ** ** * * *
4152212 AGGTGCAATTGTATTTATTATATATATATATTGATAACATTTTC-AGTTCTTAACTTATTTTTT
1 GGGCACAACCGTA--T-TTCT-TATATATATTCATAACATTTTCAACTT-TTAACTTATTTTTT
4152275 CTCGTAGGAA
Statistics
Matches: 520, Mismatches: 83, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
182 123 0.24
183 25 0.05
184 14 0.03
185 29 0.06
186 288 0.55
187 2 0.00
188 1 0.00
189 6 0.01
190 32 0.06
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (184 bp):
GGGCACAACCGTATTTCTTATATATATTCATAACATTTTCAACTTTTAACTTATTTTTTTACGTG
GGAATGTCTAAGGCCCATCAACTTAAACTCTGATAACATTTTAGGCACAACCTATTTTATTAATA
AAAATATTAACATTACAGATCACAATCTATTTATTAATGAACCATGACATTCTT
Found at i:4152235 original size:368 final size:370
Alignment explanation
Indices: 4151473--4152238 Score: 946
Period size: 368 Copynumber: 2.1 Consensus size: 370
4151463 CTTACACTAG
** * **
4151473 GGCACAACATTATTTTTTATATATATTTTTAACATTTTCAACTTTTAACTTATTTTTTTATCGTG
1 GGCACAACCGTATTTATTATATATA-TCATAACATTTTCAACTTTTAACTTATTTTTTTA-CGTG
* * * * * * *
4151538 GGAATGTCTAAGTTCCCATCAACTTAAACTTTGATAACATTTTAGGGGCAAACTATTTTATTTAT
64 GGAATATCTAAGTGCCCATCAACTTAAACTCTGATAACATTTTAGGCGCAAACTAATTCATTAAT
* ** * * * *
4151603 GAAAATGTTAACATTACATATCACAATTTATTTCTTAATGAACCATGACATTCTTGGGAGCAACC
129 AAAAACATTAACATTACAGATCACAATCTATTTATCAATGAACCATGACATTCTTGGGAGCAACC
* * * * *
4151668 ATATTTCTTATATATATTCATAACATTTTCAGCTTTTAACTTATTTTTTTATCGTGGGAATGTCG
194 ATATTTCTTATACATATTCATAACATTTTCAACTTTTAAATTATTTTTTTATCGTGAGAATGTCC
* * *
4151733 AAAGCCCTACCAACTTAAACTCTGGTAACATTTTAGGCACAACCTATTTTGTTAATAAAAATATT
259 AAAGCCCTACCAACTTAAACTCTGGTAACATTTTAGGCAAAACCTATTTTATTAATAAAAATAGT
* * * * * *
4151798 AACTTTGCAGATCACAACCTATTTATTAATGACCCATGACATTTTTG
324 AACATTACAGATCACAACCTATTTATTAATAAACCATGACATTCTTA
*
4151845 GGCACAACCGTATTTCTTATATATATCATAACATTTTCAACTTTTAACTTA-TTTTTTA-GTGGG
1 GGCACAACCGTATTTATTATATATATCATAACATTTTCAACTTTTAACTTATTTTTTTACGTGGG
* * *
4151908 AATATCTAAG-GCCTCATTAGCTTAAACTCTGATAACATTTTAGGCGCAACCTAATTCATTAATA
66 AATATCTAAGTGCC-CATCAACTTAAACTCTGATAACATTTTAGGCGCAAACTAATTCATTAATA
* * * ***
4151972 AAAACATTAACATTACAGATCGCAATCTATTTATCAGTGAACCATGACATTCTTGGGCGCAATTG
130 AAAACATTAACATTACAGATCACAATCTATTTATCAATGAACCATGACATTCTTGGGAGCAACCA
*
4152037 TATTTCTTATACATATTCATTACATTTTCAACTTTTAAATTATTTTTTTATCGTGAGAATGTCCA
195 TATTTCTTATACATATTCATAACATTTTCAACTTTTAAATTATTTTTTTATCGTGAGAATGTCCA
* * * * *
4152102 AGGCTCC-ATCAGCTTAAACTTTGGTAACATTTTAGGCAAAACTTATTTTATTAATAAAAATAGT
260 AAGC-CCTACCAACTTAAACTCTGGTAACATTTTAGGCAAAACCTATTTTATTAATAAAAATAGT
* * * * *
4152166 AACATTACATATCGCGACCTATTTCTTACTAAACCATGACATTCTTA
324 AACATTACAGATCACAACCTATTTATTAATAAACCATGACATTCTTA
** **
4152213 GGTGCAATTGTATTTATTATATATAT
1 GGCACAACCGTATTTATTATATATAT
4152239 ATATTGATAA
Statistics
Matches: 334, Mismatches: 58, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
367 2 0.01
368 277 0.83
369 2 0.01
370 7 0.02
371 24 0.07
372 22 0.07
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (370 bp):
GGCACAACCGTATTTATTATATATATCATAACATTTTCAACTTTTAACTTATTTTTTTACGTGGG
AATATCTAAGTGCCCATCAACTTAAACTCTGATAACATTTTAGGCGCAAACTAATTCATTAATAA
AAACATTAACATTACAGATCACAATCTATTTATCAATGAACCATGACATTCTTGGGAGCAACCAT
ATTTCTTATACATATTCATAACATTTTCAACTTTTAAATTATTTTTTTATCGTGAGAATGTCCAA
AGCCCTACCAACTTAAACTCTGGTAACATTTTAGGCAAAACCTATTTTATTAATAAAAATAGTAA
CATTACAGATCACAACCTATTTATTAATAAACCATGACATTCTTA
Found at i:4152297 original size:368 final size:367
Alignment explanation
Indices: 4151473--4152339 Score: 870
Period size: 368 Copynumber: 2.3 Consensus size: 367
4151463 CTTACACTAG
** * **
4151473 GGCACAACATTATTTTTTATATATATTTTTAACATTTTCAACTTTTAACTTATTTTTTTATCGTG
1 GGCACAACCGTATTTATTATATATA-TCATAACATTTTCAACTTTTAACTTA-TTTTTTA-C-TG
* * ** * * * * * * * * *
4151538 GGA-ATGTCTAAGTTCCCATCAACTTAAACTTTGATAACATTTTAGGGGCAAACTATTTTATTTA
62 CGATA-G-CAAAGGACTCATTAGCTTAAACTCTGATAACATTTTAGGCGCAACCTAATTCATTAA
* ** * * * *
4151602 TGAAAATGTTAACATTACATATCACAATTTATTTCTTAATGAACCATGACATTCTTGGGAGCAAC
125 TAAAAACATTAACATTACAGATCACAATCTATTTATCAATGAACCATGACATTCTTGGGAGCAAC
* * * *
4151667 CATATTTCTTATATATATTCATAACATTTTCAGCTTTTAACTTATTTTTTTATCGTGGGAATGTC
190 CATATTTCTTATACATATTCATAACATTTTCAACTTTTAAATTATTTTTTTATCGTGAGAATGTC
* * * *
4151732 GAAAGCCCTACCAACTTAAACTCTGGTAACATTTTAGGCACAACCTATTTTGTTAATAAAAATAT
255 CAAAGCCCTACCAACTTAAACTCTGGTAACATTTTAGGCAAAACCTATTTTATTAATAAAAATAG
* * * * * *
4151797 TAACTTTGCAGATCACAACCTATTTATTAATGACCCATGACATTTTTG
320 TAACATTACAGATCACAACCTATTTATTAATAAACCATGACATTCTTA
* * *
4151845 GGCACAACCGTATTTCTTATATATATCATAACATTTTCAACTTTTAACTTATTTTTTAGTGGGAA
1 GGCACAACCGTATTTATTATATATATCATAACATTTTCAACTTTTAACTTATTTTTTACTGCG-A
* * *
4151910 TATCTAAGGCCTCATTAGCTTAAACTCTGATAACATTTTAGGCGCAACCTAATTCATTAATAAAA
65 TAGCAAAGGACTCATTAGCTTAAACTCTGATAACATTTTAGGCGCAACCTAATTCATTAATAAAA
* * * ***
4151975 ACATTAACATTACAGATCGCAATCTATTTATCAGTGAACCATGACATTCTTGGGCGCAATTGTAT
130 ACATTAACATTACAGATCACAATCTATTTATCAATGAACCATGACATTCTTGGGAGCAACCATAT
* *
4152040 TTCTTATACATATTCATTACATTTTCAACTTTTAAATTATTTTTTTATCGTGAGAATGTCCAAGG
195 TTCTTATACATATTCATAACATTTTCAACTTTTAAATTATTTTTTTATCGTGAGAATGTCCAAAG
* * * *
4152105 CTCC-ATCAGCTTAAACTTTGGTAACATTTTAGGCAAAACTTATTTTATTAATAAAAATAGTAAC
260 C-CCTACCAACTTAAACTCTGGTAACATTTTAGGCAAAACCTATTTTATTAATAAAAATAGTAAC
* * * * *
4152169 ATTACATATCGCGACCTATTTCTTACTAAACCATGACATTCTTA
324 ATTACAGATCACAACCTATTTATTAATAAACCATGACATTCTTA
** ** * *
4152213 GGTGCAATTGTATTTATTATATATATATATTGATAACATTTTC-AGTTCTTAACTTATTTTTT-C
1 GGCACAACCGTA--T-TTAT-TATATATA-TCATAACATTTTCAACTT-TTAACTTATTTTTTAC
* * * **
4152276 T-CG-TAGGAAAGGACT-ATTAGCTTAAACTCTCG-TAATC-TTTTAGACGTAACCTAACACATT
60 TGCGATAGCAAAGGACTCATTAGCTTAAACTCT-GATAA-CATTTTAGGCGCAACCTAATTCATT
4152336 AATA
123 AATA
4152340 GTATTCATAA
Statistics
Matches: 411, Mismatches: 73, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
368 301 0.73
369 13 0.03
370 9 0.02
371 28 0.07
372 34 0.08
373 26 0.06
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (367 bp):
GGCACAACCGTATTTATTATATATATCATAACATTTTCAACTTTTAACTTATTTTTTACTGCGAT
AGCAAAGGACTCATTAGCTTAAACTCTGATAACATTTTAGGCGCAACCTAATTCATTAATAAAAA
CATTAACATTACAGATCACAATCTATTTATCAATGAACCATGACATTCTTGGGAGCAACCATATT
TCTTATACATATTCATAACATTTTCAACTTTTAAATTATTTTTTTATCGTGAGAATGTCCAAAGC
CCTACCAACTTAAACTCTGGTAACATTTTAGGCAAAACCTATTTTATTAATAAAAATAGTAACAT
TACAGATCACAACCTATTTATTAATAAACCATGACATTCTTA
Found at i:4152782 original size:158 final size:157
Alignment explanation
Indices: 4152573--4153265 Score: 740
Period size: 158 Copynumber: 4.5 Consensus size: 157
4152563 TTAAGTTTAT
** * * * * *
4152573 TTTTTTACCAAATTTGAATTACATGCTCTTACACCATTGTAGAATATATATGTACTTTCAATTTC
1 TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCGTAGAATACATATGTACTTTCAATTCC
4152638 TCTTTTTGATAACAAATTTTTTATATTTT-AATTTAGTCCCTCAATTTTTTATAATTTCCTTATT
66 TCTTTTTGATAACAAATTTTTTAT-TTTTCAATTTAGTCCCTCAATTTTTTATAATTTCCTTATT
*
4152702 TCTTCAATTCATCATTTGTTTTAAGTCCG
130 TCTTCAATTCATCATTTATTTT-AGTCCG
* *
4152731 TTTTTTACCAAATTTGAACCATATGCTCCTAAATCATCGTAGAATACATATGTACTTTCAATTCC
1 TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCGTAGAATACATATGTACTTTCAATTCC
* * * *
4152796 TCTTTTTGATAACAAATTTTCTATTTTTCAATTTAGTTCATCAACTTTTTATAATTTCCTTATTT
66 TCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCCTCAATTTTTTATAATTTCCTTATTT
*
4152861 CTTCAATTCATCCTTTAATTTTAGTCAC-
131 CTTCAATTCATCATTT-ATTTTAGTC-CG
* **
4152889 -TTTTTACCAAATTTGAACCACATGCTCCTAAAACATTTTAGAATACATATGTACTTTCAATTCC
1 TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCGTAGAATACATATGTACTTTCAATTCC
*
4152953 TCTTTTTGAT---AAATTTTTTATACTTTTTAATTTAGTCCCTC-A-TTTTT-TAATATT-C--A
66 TCTTTTTGATAACAAATTTTTTAT--TTTTCAATTTAGTCCCTCAATTTTTTATAAT-TTCCTTA
* * * * ** * **
4153009 ATTCATC-CTTTAT--TTTA-GGT-CTCTT
128 TTTCTTCAATTCATCATTTATTTTAGTCCG
* ** *
4153034 TTTTTTATCAAATTTGAATTACATGCTCCTAAACCATCATAGAATACATATGTACTTTCAATTCC
1 TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCGTAGAATACATATGTACTTTCAATTCC
* * *
4153099 TCTTTTTTATAACAATTTTTTTATTTTTCAATTTAGTCCCTCATTTTTTTTTATAATTTCCTTAT
66 TCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCCTCA--ATTTTTTATAATTTCCTTAT
*
4153164 TTCTTGAATTCATCATTTATTTTGAGTCCG
129 TTCTTCAATTCATCATTTATTTT-AGTCCG
* * * * * ***
4153194 -TTTTAACCTAATTTGAACCACATGCTCATATACTAAAATAGAATACATATGTAAC-TTCAATTC
1 TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCGTAGAATACATATGT-ACTTTCAATTC
*
4153257 TTACTTTTT
65 CT-CTTTTT
4153266 TACTAAAAAT
Statistics
Matches: 446, Mismatches: 62, Indels: 52
0.80 0.11 0.09
Matches are distributed among these distances:
145 2 0.00
146 68 0.15
147 18 0.04
148 3 0.01
149 10 0.02
150 4 0.01
151 13 0.03
152 5 0.01
153 5 0.01
154 22 0.05
155 5 0.01
156 15 0.03
157 78 0.17
158 132 0.30
159 56 0.13
160 10 0.02
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (157 bp):
TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCGTAGAATACATATGTACTTTCAATTCC
TCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCCTCAATTTTTTATAATTTCCTTATTT
CTTCAATTCATCATTTATTTTAGTCCG
Found at i:4153126 original size:146 final size:144
Alignment explanation
Indices: 4152862--4153147 Score: 418
Period size: 146 Copynumber: 2.0 Consensus size: 144
4152852 TCCTTATTTC
**
4152862 TTCAATTCATCCTTTAATTTTAGTCACTTTTTACCAAATTTGAACCACATGCTCCTAAAACATTT
1 TTCAATTCATCCTTTAATTTTAGTCACTTTTTACCAAATTTGAACCACATGCTCCTAAAACATCA
4152927 TAGAATACATATGTACTTTCAATTCCTCTTTTTGATAAATTTTTTATACTTTTT-AATTTAGTCC
66 TAGAATACATATGTACTTTCAATTCCTCTTTTTGATAAATTTTTTATACTTTTTCAATTTAGTCC
4152991 CTCATTTTTTAATA
131 CTCATTTTTTAATA
* * ** *
4153005 TTCAATTCATCCTTT-ATTTTAGGTCTCTTTTTTTTATCAAATTTGAATTACATGCTCCTAAACC
1 TTCAATTCATCCTTTAATTTTA-GTCAC---TTTTTACCAAATTTGAACCACATGCTCCTAAAAC
*
4153069 ATCATAGAATACATATGTACTTTCAATTCCTCTTTTTTATAACAATTTTTT-TA-TTTTTCAATT
62 ATCATAGAATACATATGTACTTTCAATTCCTCTTTTTGAT-A-AATTTTTTATACTTTTTCAATT
4153132 TAGTCCCTCATTTTTT
125 TAGTCCCTCATTTTTT
4153148 TTTATAATTT
Statistics
Matches: 128, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
142 6 0.05
143 19 0.15
146 72 0.56
147 23 0.18
148 8 0.06
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (144 bp):
TTCAATTCATCCTTTAATTTTAGTCACTTTTTACCAAATTTGAACCACATGCTCCTAAAACATCA
TAGAATACATATGTACTTTCAATTCCTCTTTTTGATAAATTTTTTATACTTTTTCAATTTAGTCC
CTCATTTTTTAATA
Found at i:4153922 original size:28 final size:27
Alignment explanation
Indices: 4153871--4153934 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
4153861 TTAAAATAAT
4153871 TAATAAATTAAATATAAATAATTACAAAA
1 TAATAAA-TAAATATAAATAATTA-AAAA
* * * *
4153900 TAATAAATGAATATAGATGATTATAAA
1 TAATAAATAAATATAAATAATTAAAAA
4153927 TAATAAAT
1 TAATAAAT
4153935 TTAAATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 11 0.35
28 13 0.42
29 7 0.23
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (27 bp):
TAATAAATAAATATAAATAATTAAAAA
Found at i:4154283 original size:4 final size:4
Alignment explanation
Indices: 4154276--4154379 Score: 80
Period size: 4 Copynumber: 28.0 Consensus size: 4
4154266 AATAATTATT
* * * *
4154276 TATA TATA TATA TATA TA-A TAT- TA-A TAAA TTTA -ATT TAAA T-TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
4154319 -ATA TATA TATA TATA TATA TATA TATA -ATA TTTA TATA TTTA -ATT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
4154364 TAAA TATA TATA TATA
1 TATA TATA TATA TATA
4154380 CCCTGCCTGA
Statistics
Matches: 77, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
3 15 0.19
4 62 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:4154287 original size:6 final size:6
Alignment explanation
Indices: 4154276--4154379 Score: 80
Period size: 6 Copynumber: 18.7 Consensus size: 6
4154266 AATAATTATT
* * * *
4154276 TATATA TATATA TATATA -ATAT- TA-ATA AATTTA -ATTTA AAT-TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * *
4154319 -ATATA TATATA TATATA TATATA TATA-A TATTTA TATATT TA-ATT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
4154364 TAAATA TATATA TATA
1 TATATA TATATA TATA
4154380 CCCTGCCTGA
Statistics
Matches: 83, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
4 4 0.05
5 24 0.29
6 55 0.66
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:4154350 original size:52 final size:50
Alignment explanation
Indices: 4154276--4154379 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 50
4154266 AATAATTATT
4154276 TATATATATATATATATAATATTAATAAATTTAATTTAAATTAATATATATA
1 TATATATATATATATATAATATTAATAAATTTAATTTAAA-T-ATATATATA
* *
4154328 TATATATATATATATATAATATTTATATATTTAATTTAAATATATATATA
1 TATATATATATATATATAATATTAATAAATTTAATTTAAATATATATATA
4154378 TA
1 TA
4154380 CCCTGCCTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
50 11 0.22
51 1 0.02
52 38 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (50 bp):
TATATATATATATATATAATATTAATAAATTTAATTTAAATATATATATA
Found at i:4154921 original size:19 final size:19
Alignment explanation
Indices: 4154897--4154940 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
4154887 ACGAACGTTC
4154897 AATTATAAATTTATCCTTA
1 AATTATAAATTTATCCTTA
*
4154916 AATTATATATTTATCCTTA
1 AATTATAAATTTATCCTTA
4154935 AATTAT
1 AATTAT
4154941 TTTAGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTATAAATTTATCCTTA
Found at i:4166226 original size:43 final size:43
Alignment explanation
Indices: 4166165--4166287 Score: 228
Period size: 43 Copynumber: 2.9 Consensus size: 43
4166155 ATTCTCTGTG
4166165 GACCTCGTTAAATTGGTTAAATGCTTTTTTAGAATTGCACAGA
1 GACCTCGTTAAATTGGTTAAATGCTTTTTTAGAATTGCACAGA
4166208 GACCTCGTTAAATTGGTTAAATGCTTTTTTAGAATTGCACAGA
1 GACCTCGTTAAATTGGTTAAATGCTTTTTTAGAATTGCACAGA
* *
4166251 GACCTCGTTAAATTGGTTAAATGCTTCTTCAGAATTG
1 GACCTCGTTAAATTGGTTAAATGCTTTTTTAGAATTG
4166288 TTGAGCCACT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (43 bp):
GACCTCGTTAAATTGGTTAAATGCTTTTTTAGAATTGCACAGA
Found at i:4170108 original size:16 final size:17
Alignment explanation
Indices: 4170077--4170119 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
4170067 TGACCGGTCT
*
4170077 GACCCGATCAGTTGA-CC
1 GACCCGA-CCGTTGACCC
*
4170094 GACTCGACCGTTGACCC
1 GACCCGACCGTTGACCC
4170111 GACCCGACC
1 GACCCGACC
4170120 CAGTGACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.21, C:0.42, G:0.23, T:0.14
Consensus pattern (17 bp):
GACCCGACCGTTGACCC
Found at i:4170166 original size:29 final size:29
Alignment explanation
Indices: 4170122--4170255 Score: 196
Period size: 29 Copynumber: 4.6 Consensus size: 29
4170112 ACCCGACCCA
* *
4170122 GTGACATTCTGAGAATTATTTTGAAAAAT
1 GTGACATTCTGGGAATTATTTTGAAAAAG
*
4170151 GTGATATTCTGGGAATTATTTTGAAAAAG
1 GTGACATTCTGGGAATTATTTTGAAAAAG
*
4170180 GTGACATTCTGGGAATTATTTTAAAAAAG
1 GTGACATTCTGGGAATTATTTTGAAAAAG
* *
4170209 ATGACATTTTGGGAATTATTTTGAAAAAAG
1 GTGACATTCTGGGAATTATTTTG-AAAAAG
*
4170239 GTGACATTTTGGGAATT
1 GTGACATTCTGGGAATT
4170256 TTTGAGTGTG
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
29 73 0.77
30 22 0.23
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (29 bp):
GTGACATTCTGGGAATTATTTTGAAAAAG
Found at i:4177585 original size:22 final size:22
Alignment explanation
Indices: 4177560--4177608 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
4177550 TGACCGGTCT
4177560 GACCCGACCCGTTGAC-CGACCC
1 GACCCG-CCCGTTGACTCGACCC
* *
4177582 GACCCGGCTGTTGACTCGACCC
1 GACCCGCCCGTTGACTCGACCC
4177604 GACCC
1 GACCC
4177609 AGTGATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.16, C:0.47, G:0.24, T:0.12
Consensus pattern (22 bp):
GACCCGCCCGTTGACTCGACCC
Found at i:4177665 original size:29 final size:29
Alignment explanation
Indices: 4177610--4177742 Score: 214
Period size: 29 Copynumber: 4.6 Consensus size: 29
4177600 ACCCGACCCA
* *
4177610 GTGATATTCTGAGAATTATTTTGAAAAAG
1 GTGACATTCTGGGAATTATTTTGAAAAAG
4177639 GTGACATTCT-GGAATTATTTTGAAAAAAG
1 GTGACATTCTGGGAATTATTTTG-AAAAAG
4177668 GTGACATTCTGGGAATTATTTTGAAAAAG
1 GTGACATTCTGGGAATTATTTTGAAAAAG
4177697 GTGACATTCTGGGAATTATTTTGAAAAAG
1 GTGACATTCTGGGAATTATTTTGAAAAAG
* *
4177726 GTGAAATTTTGGGAATT
1 GTGACATTCTGGGAATT
4177743 TTTGAATATG
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
28 11 0.11
29 75 0.77
30 12 0.12
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (29 bp):
GTGACATTCTGGGAATTATTTTGAAAAAG
Found at i:4179931 original size:37 final size:37
Alignment explanation
Indices: 4179876--4179948 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
4179866 AAACAAACGT
**
4179876 TAGAGTTTTAGTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACAAGGATTCAAACTCCTAAAAATAGGA
*
4179913 TAGAGTTTTACAATGATTCAAACTCCTAAAAATAGG
1 TAGAGTTTTACAAGGATTCAAACTCCTAAAAATAGG
4179949 TTCCACAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (37 bp):
TAGAGTTTTACAAGGATTCAAACTCCTAAAAATAGGA
Found at i:4180502 original size:25 final size:26
Alignment explanation
Indices: 4180438--4180503 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
4180428 CATTTTATGC
*
4180438 ATTTTTTTACTT-TAGTATATATTTTT
1 ATTTTTTTA-TTATAGTATATATTGTT
4180464 ATTTTTTTAGATTATA-TATATATATGTT
1 ATTTTTTT--ATTATAGTATATAT-TGTT
4180492 A-TTTTTTATTAT
1 ATTTTTTTATTAT
4180504 CCGTTTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 5 0.14
26 8 0.23
27 15 0.43
28 7 0.20
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (26 bp):
ATTTTTTTATTATAGTATATATTGTT
Found at i:4180549 original size:8 final size:7
Alignment explanation
Indices: 4180533--4180618 Score: 50
Period size: 8 Copynumber: 11.1 Consensus size: 7
4180523 ATATATTTAC
4180533 TATTTTT
1 TATTTTT
4180540 TATGTTTT
1 TAT-TTTT
4180548 TATTTTT
1 TATTTTT
4180555 TATATATATAT
1 TAT-T-T-T-T
4180566 TA-TTTT
1 TATTTTT
4180572 TACTTTTT
1 TA-TTTTT
*
4180580 TA-TTAT
1 TATTTTT
4180586 TATTTTAT
1 TATTTT-T
4180594 TATTTGTTT
1 TA-TT-TTT
*
4180603 TATTTATA
1 TATTT-TT
4180611 TATTTTT
1 TATTTTT
4180618 T
1 T
4180619 CTTCTTTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 24
0.69 0.04 0.26
Matches are distributed among these distances:
6 8 0.13
7 16 0.25
8 26 0.41
9 7 0.11
10 3 0.05
11 3 0.05
ACGTcount: A:0.22, C:0.01, G:0.02, T:0.74
Consensus pattern (7 bp):
TATTTTT
Found at i:4180572 original size:25 final size:26
Alignment explanation
Indices: 4180537--4180645 Score: 75
Period size: 27 Copynumber: 4.2 Consensus size: 26
4180527 ATTTACTATT
*
4180537 TTTTATGTTTTTATTTTTTATATATA
1 TTTTATCTTTTTATTTTTTATATATA
*
4180563 TATTA--TTTTTACTTTTTTAT-TATTA
1 TTTTATCTTTTTA-TTTTTTATATA-TA
*
4180588 TTTTAT-TATTTGT-TTTATTTATATATT
1 TTTTATCT-TTT-TATTT-TTTATATATA
* * *
4180615 TTTTCTTCTTTTTCTTTTTTATATATT
1 TTTT-ATCTTTTTATTTTTTATATATA
4180642 TTTT
1 TTTT
4180646 TATATTACTT
Statistics
Matches: 69, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
24 8 0.12
25 14 0.20
26 8 0.12
27 28 0.41
28 10 0.14
29 1 0.01
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTATCTTTTTATTTTTTATATATA
Found at i:4180579 original size:39 final size:39
Alignment explanation
Indices: 4180474--4180596 Score: 96
Period size: 40 Copynumber: 3.1 Consensus size: 39
4180464 ATTTTTTTAG
* **
4180474 ATTATATATATATATGT--TA-TTTTTTATTATCCGTTTT
1 ATTATATATATATATTTACTACTTTTTTATTAT-TATTTT
*
4180511 ATTAATTTATATATATATTTACTA-TTTTTTATGTTTTTATTTT
1 ATT-A--TATATATATATTTACTACTTTTTTA--TTATTATTTT
*
4180554 -TTATATATATATTATTT-TTACTTTTTTATTATTATTTT
1 ATTATATATATA-TATTTACTACTTTTTTATTATTATTTT
4180592 ATTAT
1 ATTAT
4180597 TTGTTTTATT
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
37 3 0.04
38 10 0.14
39 14 0.20
40 24 0.34
41 1 0.01
42 11 0.16
43 4 0.06
44 3 0.04
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (39 bp):
ATTATATATATATATTTACTACTTTTTTATTATTATTTT
Found at i:4180583 original size:17 final size:16
Alignment explanation
Indices: 4180536--4180644 Score: 60
Period size: 17 Copynumber: 6.3 Consensus size: 16
4180526 TATTTACTAT
4180536 TTTTTATGTTTTTA-T-
1 TTTTTAT-TTTTTATTA
* *
4180551 TTTTTATATATATATTA
1 TTTTTAT-TTTTTATTA
4180568 TTTTTACTTTTTTATTA
1 TTTTTA-TTTTTTATTA
*
4180585 TTATTTTATTATTTGTTTTA
1 -T-TTTTATT-TTT-TATTA
* *
4180605 TTTATATATTTTTTCTTC
1 TTT-T-TATTTTTTATTA
*
4180623 TTTTTCTTTTTTATATA
1 TTTTTATTTTTTAT-TA
4180640 TTTTT
1 TTTTT
4180645 TTATATTACT
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
15 11 0.15
16 9 0.12
17 20 0.27
18 12 0.16
19 13 0.18
20 8 0.11
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTTATTTTTTATTA
Found at i:4180607 original size:77 final size:85
Alignment explanation
Indices: 4180459--4180640 Score: 193
Period size: 79 Copynumber: 2.2 Consensus size: 85
4180449 TTAGTATATA
* *
4180459 TTTTTATTTTTTTAGATTATATATATATATGTTATTTTTTATTATCCGTTTTATTAATTTATATA
1 TTTTTA-TTTTTTATA-TATATATATATATGTTATTTTTTATTATCCATTTTATTAATTTATATA
* *
4180524 TATATTTA-CTATTTTTT-ATG
64 TATATTTATATATTTTTTCATC
* * *
4180544 TTTTTATTTTTTATATATATAT-TAT-TTTTACTTTTTTATTAT-TATTTTATT-ATTTGT-T-T
1 TTTTTATTTTTTATATATATATATATATGTTA-TTTTTTATTATCCATTTTATTAATTTATATAT
*
4180603 -TATTTATATATTTTTTCTTC
65 ATATTTATATATTTTTTCATC
*
4180623 TTTTTCTTTTTTATATAT
1 TTTTTATTTTTTATATAT
4180641 TTTTTTATAT
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
77 6 0.07
78 9 0.11
79 19 0.22
80 5 0.06
81 11 0.13
82 14 0.16
83 7 0.08
84 8 0.09
85 6 0.07
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.70
Consensus pattern (85 bp):
TTTTTATTTTTTATATATATATATATATGTTATTTTTTATTATCCATTTTATTAATTTATATATA
TATTTATATATTTTTTCATC
Found at i:4183707 original size:8 final size:8
Alignment explanation
Indices: 4183684--4183731 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
4183674 AGATTCGATC
4183684 AGAATAAAA
1 AGAA-AAAA
4183693 AGAAAAAA
1 AGAAAAAA
4183701 ATGAAAAAA
1 A-GAAAAAA
4183710 AGAAAAAA
1 AGAAAAAA
*
4183718 A-AACAAAG
1 AGAA-AAAA
4183726 AGAAAA
1 AGAAAA
4183732 TAAAAAAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
7 2 0.06
8 19 0.54
9 14 0.40
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (8 bp):
AGAAAAAA
Found at i:4183730 original size:24 final size:24
Alignment explanation
Indices: 4183703--4183748 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4183693 AGAAAAAAAT
4183703 GAAAA-AAAGAAAAAAAAACAAAGA
1 GAAAATAAA-AAAAAAAAACAAAGA
* *
4183727 GAAAATAAAAAAGAGAAACAAA
1 GAAAATAAAAAAAAAAAACAAA
4183749 AACAAAGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.02
Consensus pattern (24 bp):
GAAAATAAAAAAAAAAAACAAAGA
Found at i:4183738 original size:30 final size:29
Alignment explanation
Indices: 4183698--4183760 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
4183688 TAAAAAGAAA
*
4183698 AAAATGAAAAAAAGAAAAAAAAACAAAGAG
1 AAAATAAAAAAAAGAAAAAAAAACAAAG-G
* *
4183728 AAAATAAAAAAGAGAAACAAAAACAAAGG
1 AAAATAAAAAAAAGAAAAAAAAACAAAGG
4183757 AAAA
1 AAAA
4183761 AGTGAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (29 bp):
AAAATAAAAAAAAGAAAAAAAAACAAAGG
Found at i:4183750 original size:14 final size:13
Alignment explanation
Indices: 4183704--4183750 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
4183694 GAAAAAAATG
*
4183704 AAAAAAAGAAAAA
1 AAAAAAAGAGAAA
4183717 AAAACAAAGAGAAA
1 AAAA-AAAGAGAAA
4183731 ATAAAAAAGAGAAA
1 A-AAAAAAGAGAAA
*
4183745 CAAAAA
1 AAAAAA
4183751 CAAAGGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 9 0.30
14 18 0.60
15 3 0.10
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:4185651 original size:21 final size:21
Alignment explanation
Indices: 4185626--4185691 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4185616 TGATACAATT
4185626 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
4185647 TCTCTTGAGAC-AA--TT-TC
1 TCTCTTGAAACAAATTTTGTC
4185664 -C-CTTGAAACAAAGTTTTGTC
1 TCTCTTGAAACAAA-TTTTGTC
4185684 TCTCTTGA
1 TCTCTTGA
4185692 GATAGTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 7 0.19
16 3 0.08
17 2 0.06
18 2 0.06
19 2 0.06
20 4 0.11
21 11 0.31
22 5 0.14
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:4185652 original size:36 final size:36
Alignment explanation
Indices: 4185552--4185710 Score: 194
Period size: 37 Copynumber: 4.4 Consensus size: 36
4185542 TTGAATATGT
* *
4185552 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* * ** * *
4185587 TTTCTTTTGGAACTAGGTTTTGTCACTCTTGATACAA
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAA
4185624 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* * *
4185660 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAA
4185697 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
4185711 CCTATCTTTG
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
35 4 0.04
36 40 0.39
37 59 0.57
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
Found at i:4185680 original size:73 final size:73
Alignment explanation
Indices: 4185552--4185710 Score: 212
Period size: 73 Copynumber: 2.2 Consensus size: 73
4185542 TTGAATATGT
* ** * * *
4185552 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAGGTTTTGTCACTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCACTCT
*
4185616 TGATACAA
66 TGAGACAA
* *
4185624 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCACTCT
* *
4185689 TGAGATAG
66 TGAGACAA
4185697 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
4185711 CCTATCTTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 4 0.05
73 71 0.95
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCACTCT
TGAGACAA
Found at i:4185804 original size:175 final size:175
Alignment explanation
Indices: 4185469--4185812 Score: 385
Period size: 175 Copynumber: 2.0 Consensus size: 175
4185459 ACAAGGGGTC
4185469 GTCTCGCTTGAGACTAATTTACCCAAAACAAAGTTTTATCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTCTCGCTTGAGACTAATTTACCCAAAACAAAGTTTTATCTCTCTTGAGACAGTTTCCCTTGAAA
* * * *
4185534 CAAAATATTTGAATATGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAA
66 CAAAATATTTGAATATGTTTTCCTTGAAACAAATTTTGCCTCCCTTGAGACAGTTTATCTTGAAA
******** *
4185599 CTAGGTTTTGTCACTCTTGATACAATTTCTCTTGAAACAAATTTT
131 CTAAAAAAAAACACTCTTGAAACAATTTCTCTTGAAACAAATTTT
* * * * *
4185644 GTCTCTCTTGAGAC-AATTT-CCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGA
1 GTCTCGCTTGAGACTAATTTACCC--AAAACAAAGTTTTATCTCTCTTGAGACAGTTTCCCTTGA
** *
4185707 AACACCTATCTTTGAATATG-TTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTATCT
64 AACA-AAATATTTGAATATGTTTTC-CTTGAAAC-AAATTTTGCCTCCCTTGAGACAGTTTATCT
**
4185771 TGAAAC-ACAAAAAAAAC-CT-TTGAAATTATTTCTCTTGAAACA
126 TGAAACTA-AAAAAAAACACTCTTGAAACAATTTCTCTTGAAACA
4185813 CAAAAACAAA
Statistics
Matches: 140, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
173 3 0.02
174 5 0.04
175 76 0.54
176 23 0.16
177 33 0.24
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (175 bp):
GTCTCGCTTGAGACTAATTTACCCAAAACAAAGTTTTATCTCTCTTGAGACAGTTTCCCTTGAAA
CAAAATATTTGAATATGTTTTCCTTGAAACAAATTTTGCCTCCCTTGAGACAGTTTATCTTGAAA
CTAAAAAAAAACACTCTTGAAACAATTTCTCTTGAAACAAATTTT
Found at i:4185812 original size:35 final size:36
Alignment explanation
Indices: 4185768--4185847 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
4185758 AGACAGTTTA
*
4185768 TCTTGAAACACAAAAA-AAACCTTTGAAATTATTTC
1 TCTTGAAACACAAAAACAAACCTTTGAAAATATTTC
*
4185803 TCTTGAAACACAAAAACAAACCTTTGAAAATGTTTC
1 TCTTGAAACACAAAAACAAACCTTTGAAAATATTTC
4185839 TCTTGAAAC
1 TCTTGAAAC
4185848 CCAAGCCTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 16 0.38
36 26 0.62
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (36 bp):
TCTTGAAACACAAAAACAAACCTTTGAAAATATTTC
Found at i:4186493 original size:37 final size:37
Alignment explanation
Indices: 4186452--4186598 Score: 249
Period size: 37 Copynumber: 4.0 Consensus size: 37
4186442 AAAAAAACGT
*
4186452 TAGAGTTTTAGTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
4186489 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
4186526 TAGAGTTTTACTAGGATTCAAACTCATAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* * *
4186563 TAGAGTTTTACTATGATTTAAACTCTTAAAAATAGG
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGG
4186599 TTCCACAAGC
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:4187244 original size:40 final size:42
Alignment explanation
Indices: 4187149--4187275 Score: 119
Period size: 42 Copynumber: 3.2 Consensus size: 42
4187139 TAGATTACAC
* **
4187149 ATATATATATATATGTTA-TTTTTTA-TTATCCGTTTTATTA-
1 ATATATATATATAT-TTACTTATTTATTTATGTGTTTTATTAT
4187189 AT-T-TATATATATTTAC-TATTT-TTTATGT-TTTTATTAT
1 ATATATATATATATTTACTTATTTATTTATGTGTTTTATTAT
* * *
4187226 ATATATATATTATTTTTACTTTTTTATTTATTTGTTTTATT-T
1 ATATATATA-TATATTTACTTATTTATTTATGTGTTTTATTAT
4187268 ATATATAT
1 ATATATAT
4187276 TTTCTTCTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
36 8 0.11
37 13 0.18
38 10 0.14
39 5 0.07
40 10 0.14
41 4 0.06
42 15 0.21
43 7 0.10
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (42 bp):
ATATATATATATATTTACTTATTTATTTATGTGTTTTATTAT
Found at i:4187276 original size:40 final size:40
Alignment explanation
Indices: 4187149--4187276 Score: 104
Period size: 40 Copynumber: 3.2 Consensus size: 40
4187139 TAGATTACAC
* ** *
4187149 ATATATATATATATGTTA-TTTTTTA-TTATCCGTTTTATTA
1 ATATATAT-TAT-TTTTACTTTTTTATTTATTTGTTTTATTT
* * * * *
4187189 ATTTATA-TATATTTACTATTTTTTATGT-TTT-TATTATAT
1 ATATATATTATTTTTAC--TTTTTTATTTATTTGTTTTATTT
4187228 ATATATATTATTTTTACTTTTTTATTTATTTGTTTTATTT
1 ATATATATTATTTTTACTTTTTTATTTATTTGTTTTATTT
4187268 ATATATATT
1 ATATATATT
4187277 TTCTTCTTTT
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
37 3 0.04
38 12 0.18
39 14 0.21
40 37 0.55
41 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (40 bp):
ATATATATTATTTTTACTTTTTTATTTATTTGTTTTATTT
Found at i:4187286 original size:38 final size:38
Alignment explanation
Indices: 4187181--4187304 Score: 116
Period size: 38 Copynumber: 3.3 Consensus size: 38
4187171 TTATTATCCG
* *
4187181 TTTTATTA-ATTTATATATATTTAC-TATTTTTTATGT
1 TTTTATTATATTTATATATATTTTCTTCTTTTTTATGT
* *
4187217 TTTTATTATATATATATATTATTTT-TACTTTTTTAT-T
1 TTTTATTATATTTATATA-TATTTTCTTCTTTTTTATGT
* * *
4187254 TATTTGTTTTATTTATATATATTTTCTTCTTTTTCT-TCT
1 T-TTTATTATATTTATATATATTTTCTTCTTTTT-TATGT
4187293 TTTTA-TATATTT
1 TTTTATTATATTT
4187305 TTTAGATTAC
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
36 8 0.11
37 22 0.31
38 38 0.54
39 3 0.04
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (38 bp):
TTTTATTATATTTATATATATTTTCTTCTTTTTTATGT
Found at i:4187370 original size:21 final size:22
Alignment explanation
Indices: 4187337--4187397 Score: 52
Period size: 26 Copynumber: 2.6 Consensus size: 22
4187327 CTTTGCTTTC
* *
4187337 TTTATCTTATCTTTT-ATTTAA
1 TTTATTTTTTCTTTTAATTTAA
4187358 TTTATTTTTTCTTCATTTTAATTTAA
1 TTTA--TTTT-TTC-TTTTAATTTAA
4187384 TTTATTTATTTCTT
1 TTTATTT-TTTCTT
4187398 ACATTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
21 4 0.12
23 5 0.16
24 8 0.25
25 5 0.16
26 10 0.31
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTATTTTTTCTTTTAATTTAA
Found at i:4187381 original size:26 final size:27
Alignment explanation
Indices: 4187348--4187404 Score: 91
Period size: 26 Copynumber: 2.1 Consensus size: 27
4187338 TTATCTTATC
4187348 TTTTATTTAATTTATTT-TTTCTT-CA
1 TTTTATTTAATTTATTTATTTCTTACA
4187373 TTTTAATTTAATTTATTTATTTCTTACA
1 TTTT-ATTTAATTTATTTATTTCTTACA
4187401 TTTT
1 TTTT
4187405 TATCTAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 4 0.14
26 13 0.45
27 6 0.21
28 6 0.21
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTATTTAATTTATTTATTTCTTACA
Found at i:4188652 original size:41 final size:40
Alignment explanation
Indices: 4188597--4188766 Score: 171
Period size: 41 Copynumber: 4.2 Consensus size: 40
4188587 TCGATCTTGG
* * *
4188597 CAGCATGCACTAATTCACAATTCGATTATATTCAATCATAT
1 CAGCATGCAATAATTCACAATTCAATTA-ATTCAATCATGT
* * * * * *
4188638 CAACATCCAATAATTCACCATTCAACTAAATTCGATCATGG
1 CAGCATGCAATAATTCACAATTCAA-TTAATTCAATCATGT
*
4188679 CAGCATGCAATAATTCACAATAT-TATTCAATTCAATCATGT
1 CAGCATGCAATAATTCACAAT-TCAATT-AATTCAATCATGT
* * *
4188720 CAGCATGCAATAATCCACAATTCAACTTAATTCGATCATGG
1 CAGCATGCAATAATTCACAATTCAA-TTAATTCAATCATGT
4188761 CAGCAT
1 CAGCAT
4188767 TAAAAATATT
Statistics
Matches: 104, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.02
41 97 0.93
42 5 0.05
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.30
Consensus pattern (40 bp):
CAGCATGCAATAATTCACAATTCAATTAATTCAATCATGT
Found at i:4188712 original size:82 final size:82
Alignment explanation
Indices: 4188586--4188766 Score: 249
Period size: 82 Copynumber: 2.2 Consensus size: 82
4188576 TTCAATCGAG
* *
4188586 TTCGATCTTGGCAGCATGCACTAATTCACAATTCGATTATATTCAATCATATCAACATCCAATAA
1 TTCGATCATGGCAGCATGCAATAATTCACAATTCGATTATATTCAATCATATCAACATCCAATAA
* *
4188651 TTCACCATTCAACTAAA
66 TCCACAATTCAACTAAA
* * * *
4188668 TTCGATCATGGCAGCATGCAATAATTCACAATAT-TATTCA-ATTCAATCATGTCAGCATGCAAT
1 TTCGATCATGGCAGCATGCAATAATTCACAAT-TCGATT-ATATTCAATCATATCAACATCCAAT
*
4188731 AATCCACAATTCAACTTAA
64 AATCCACAATTCAACTAAA
4188750 TTCGATCATGGCAGCAT
1 TTCGATCATGGCAGCAT
4188767 TAAAAATATT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
82 86 0.98
83 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (82 bp):
TTCGATCATGGCAGCATGCAATAATTCACAATTCGATTATATTCAATCATATCAACATCCAATAA
TCCACAATTCAACTAAA
Found at i:4195098 original size:16 final size:16
Alignment explanation
Indices: 4195077--4195109 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4195067 TTCTTCCACC
4195077 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
*
4195093 TATGTTAGAATGGAAA
1 TATGTTAGAATGCAAA
4195109 T
1 T
4195110 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:4198643 original size:16 final size:16
Alignment explanation
Indices: 4198622--4198654 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4198612 TTCTTCCACC
4198622 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
4198638 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
4198654 T
1 T
4198655 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:4199544 original size:27 final size:27
Alignment explanation
Indices: 4199463--4199726 Score: 223
Period size: 27 Copynumber: 9.3 Consensus size: 27
4199453 AATATTTTTG
* *
4199463 AAACTATATTATATATAATAACAGTTTTAAA
1 AAACTATACTATATATAAT---A-TTTTCAA
*
4199494 AAACTATATTATATAATAACTATTTTCAA
1 AAACTATACTATAT-ATAA-TATTTTCAA
4199523 AAAGC-ATACTATATATAATATTTTTC-A
1 AAA-CTATACTATATATAATA-TTTTCAA
* * *
4199550 AAACCATATTATATAACAATTATTTTCAA
1 AAACTATACTATAT-ATAA-TATTTTCAA
*
4199579 AAACTATACTATATACAATAGTTTTC-A
1 AAACTATACTATATATAATA-TTTTCAA
4199606 AAACTATACTATATATAATAGTTTTC-A
1 AAACTATACTATATATAATA-TTTTCAA
* * *
4199633 AAACCATATTATATAATAATTATTTTTAA
1 AAACTATACTATAT-ATAA-TATTTTCAA
4199662 AAACTATACTATATATAATAATTTTC-A
1 AAACTATACTATATATAAT-ATTTTCAA
* *
4199689 AAACTATATTATATAATAACTAGTTTCAAA
1 AAACTATACTATAT-ATAA-TATTTTC-AA
4199719 AAACTATA
1 AAACTATA
4199727 GTTTTCAAAA
Statistics
Matches: 201, Mismatches: 15, Indels: 35
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.00
27 70 0.35
28 52 0.26
29 48 0.24
30 11 0.05
31 14 0.07
32 4 0.02
33 1 0.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (27 bp):
AAACTATACTATATATAATATTTTCAA
Found at i:4199640 original size:83 final size:82
Alignment explanation
Indices: 4199487--4199719 Score: 317
Period size: 83 Copynumber: 2.8 Consensus size: 82
4199477 ATAATAACAG
* *
4199487 TTTTAAAAAACTATATTATATAATAACTATTTTCAAAAAGC-ATACTATATATAATATTTTTCAA
1 TTTTAAAAAACTATACTATAT-ATAA-TATTTTC-AAAA-CTATACTATATATAATAGTTTTCAA
4199551 AACCATATTATATAACAATTA
62 AACCATATTATATAACAATTA
* *
4199572 TTTTCAAAAACTATACTATATACAATAGTTTTCAAAACTATACTATATATAATAGTTTTCAAAAC
1 TTTTAAAAAACTATACTATATATAATA-TTTTCAAAACTATACTATATATAATAGTTTTCAAAAC
*
4199637 CATATTATATAATAATTA
65 CATATTATATAACAATTA
* *
4199655 TTTTTAAAAACTATACTATATATAATAATTTTCAAAACTATATTATATAATAACTAG-TTTCAAA
1 TTTTAAAAAACTATACTATATATAAT-ATTTTCAAAACTATACTATAT-ATAA-TAGTTTTCAAA
4199719 A
63 A
4199720 AACTATAGTT
Statistics
Matches: 135, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
82 1 0.01
83 91 0.67
84 21 0.16
85 22 0.16
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (82 bp):
TTTTAAAAAACTATACTATATATAATATTTTCAAAACTATACTATATATAATAGTTTTCAAAACC
ATATTATATAACAATTA
Found at i:4199707 original size:56 final size:56
Alignment explanation
Indices: 4199474--4199826 Score: 272
Period size: 56 Copynumber: 6.5 Consensus size: 56
4199464 AACTATATTA
* * * * *
4199474 TATATAATAA-CAGTTTTAAAAAACTATATTATATAATAACT-ATTTTCAAAAAGCATAC
1 TATATAATAATTA-TTTTTAAAAACTATACTATAT-ATAA-TAATTTTC-AAAACCATAT
* * * * * * *
4199532 TATAT-ATAA-TATTTTTCAAAACCATATTATATAACAATTATTTTCAAAAACTATAC
1 TATATAATAATTATTTTTAAAAACTATACTATAT-ATAATAATTTTC-AAAACCATAT
* * * *
4199588 TATAT-ACAA-TAGTTTTCAAAACTATACTATATATAATAGTTTTCAAAACCATAT
1 TATATAATAATTATTTTTAAAAACTATACTATATATAATAATTTTCAAAACCATAT
*
4199642 TATATAATAATTATTTTTAAAAACTATACTATATATAATAATTTTCAAAACTATAT
1 TATATAATAATTATTTTTAAAAACTATACTATATATAATAATTTTCAAAACCATAT
* * * *
4199698 TATATAATAACTA-GTTTCAAAA--A-AC------T-ATAGTTTTCAAAACCATAT
1 TATATAATAATTATTTTTAAAAACTATACTATATATAATAATTTTCAAAACCATAT
* * * * *
4199743 TATATAATAATTATTTTAAAAAATTATATTATATATAATAGTTATCAAAACCATTAT
1 TATATAATAATTATTTTTAAAAACTATACTATATATAATAATTTTCAAAACCA-TAT
* *
4199800 TATATAATAACTATTTTCAAAAACTAT
1 TATATAATAATTATTTTTAAAAACTAT
4199827 TCTCCATATA
Statistics
Matches: 245, Mismatches: 35, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
45 29 0.12
46 7 0.03
48 1 0.00
49 1 0.00
52 2 0.01
53 1 0.00
54 13 0.05
55 21 0.09
56 133 0.54
57 32 0.13
58 5 0.02
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (56 bp):
TATATAATAATTATTTTTAAAAACTATACTATATATAATAATTTTCAAAACCATAT
Found at i:4199732 original size:45 final size:44
Alignment explanation
Indices: 4199683--4199770 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
4199673 TATATAATAA
*
4199683 TTTTCAAAACTATATTATATAATAACTAGTTTCAAAAAACTATAG
1 TTTTCAAAACCATATTATATAATAACTA-TTTCAAAAAACTATAG
* * *
4199728 TTTTCAAAACCATATTATATAATAATTATTTTAAAAAATTATA
1 TTTTCAAAACCATATTATATAATAACTATTTCAAAAAACTATA
4199771 TTATATATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 13 0.33
45 26 0.67
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (44 bp):
TTTTCAAAACCATATTATATAATAACTATTTCAAAAAACTATAG
Found at i:4199740 original size:101 final size:101
Alignment explanation
Indices: 4199623--4199826 Score: 329
Period size: 101 Copynumber: 2.0 Consensus size: 101
4199613 ACTATATATA
* *
4199623 ATAGTTTTCAAAACCATATTATATAATAATTATTTTTAAAAACTATACTATATATAATAATTTTC
1 ATAGTTTTCAAAACCATATTATATAATAATTATTTTAAAAAACTATACTATATATAATAATTATC
*
4199688 AAAACTA-TATTATATAATAACTAGTTTCAAAAAACT
66 AAAACCATTATTATATAATAACTAGTTTC-AAAAACT
* * *
4199724 ATAGTTTTCAAAACCATATTATATAATAATTATTTTAAAAAATTATATTATATATAATAGTTATC
1 ATAGTTTTCAAAACCATATTATATAATAATTATTTTAAAAAACTATACTATATATAATAATTATC
*
4199789 AAAACCATTATTATATAATAACTATTTTCAAAAACT
66 AAAACCATTATTATATAATAACTAGTTTCAAAAACT
4199825 AT
1 AT
4199827 TCTCCATATA
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 75 0.79
102 20 0.21
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (101 bp):
ATAGTTTTCAAAACCATATTATATAATAATTATTTTAAAAAACTATACTATATATAATAATTATC
AAAACCATTATTATATAATAACTAGTTTCAAAAACT
Found at i:4199785 original size:72 final size:73
Alignment explanation
Indices: 4199656--4199792 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 73
4199646 TAATAATTAT
* *
4199656 TTTTAAAAACTATACTATATATAATAATTTTCAAAACTATATTATATAATAACTAGTT-TCAAAA
1 TTTTAAAAACCATACTATATATAATAATTTTAAAAACTATATTATATAATAACTAGTTATCAAAA
4199720 AACTATAG
66 AACTATAG
* * * *
4199728 TTTTCAAAACCATATTATATAATAATTATTTTAAAAAATTATATTATAT-ATAA-TAGTTATCAA
1 TTTTAAAAACCATACTATAT-ATAATAATTTT-AAAAACTATATTATATAATAACTAGTTATCAA
4199791 AA
64 AA
4199793 CCATTATTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
72 22 0.39
73 20 0.36
74 14 0.25
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (73 bp):
TTTTAAAAACCATACTATATATAATAATTTTAAAAACTATATTATATAATAACTAGTTATCAAAA
AACTATAG
Found at i:4199819 original size:29 final size:28
Alignment explanation
Indices: 4199728--4199821 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 28
4199718 AAAACTATAG
4199728 TTTTCAAAACCA-TATTATATAATAATTA
1 TTTTCAAAACCATTATTATATAATAA-TA
*
4199756 TTTT-AAAA-AATTA-TATTATATATAATA
1 TTTTCAAAACCATTATTA-TATA-ATAATA
*
4199783 GTTATCAAAACCATTATTATATAATAACTA
1 -TTTTCAAAACCATTATTATATAATAA-TA
4199813 TTTTCAAAA
1 TTTTCAAAA
4199822 ACTATTCTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
26 3 0.06
27 12 0.22
28 11 0.20
29 16 0.30
30 10 0.19
31 2 0.04
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.43
Consensus pattern (28 bp):
TTTTCAAAACCATTATTATATAATAATA
Found at i:4199836 original size:57 final size:56
Alignment explanation
Indices: 4199724--4199839 Score: 153
Period size: 57 Copynumber: 2.1 Consensus size: 56
4199714 TCAAAAAACT
* * * *
4199724 ATAGTTTTCAAAACCATATTATATAATAATTATTTTAAAAAATTATATTATATATA
1 ATAGTTATCAAAACCATATTATATAATAACTATTTTAAAAAACTATATTACATATA
* *
4199780 ATAGTTATCAAAACCATTATTATATAATAACTATTTTCAAAAACTAT-TCTCCATATA
1 ATAGTTATCAAAACCA-TATTATATAATAACTATTTTAAAAAACTATAT-TACATATA
4199837 ATA
1 ATA
4199840 TACCTATCCA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 16 0.31
57 36 0.69
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (56 bp):
ATAGTTATCAAAACCATATTATATAATAACTATTTTAAAAAACTATATTACATATA
Found at i:4200083 original size:41 final size:41
Alignment explanation
Indices: 4200026--4200351 Score: 194
Period size: 41 Copynumber: 7.7 Consensus size: 41
4200016 AAGAATAATA
*
4200026 TGCTCCACTGCTCTTCAGGGTAGGTCAGATCAAGATAGATT
1 TGCTCCACTGCTCTTCAGGGTAGGTCAAATCAAGATAGATT
* * *
4200067 TGCTCCGCTGCTCTTCAGGGTAGGTCAAATCTA-ATGGAATCT
1 TGCTCCACTGCTCTTCAGGGTAGGTCAAATCAAGATAG-AT-T
* * * * *
4200109 T-CTCTACTGCCCTTTAGGGTAAGTCAAATTCAAAGAGAAAGGGATAT
1 TGCTCCACTGCTCTTCAGGGTAGGTCAAA-TC--A-AGATA--GAT-T
* * *
4200156 T-CTCCACTGCTCTTCAGGGTAGGTTAAATCAGGAAAGATT
1 TGCTCCACTGCTCTTCAGGGTAGGTCAAATCAAGATAGATT
* * * * *
4200196 TGCTCCACTACTCTTCAGGATAGGTCAAATCTA-ATGGAATA
1 TGCTCCACTGCTCTTCAGGGTAGGTCAAATCAAGATAG-ATT
* * * * * * *
4200237 TGCTGCTCTACTCTTCAGGGTAGGTCAGATTAAAAAAAGGGATT
1 TGCTCCACTGCTCTTCAGGGTAGGTCA-AATCAAGATA--GATT
** * **
4200281 TGCTCTGCTACTCTTCAACGTAGGT-AAGATCAAGATAGATT
1 TGCTCCACTGCTCTTCAGGGTAGGTCAA-ATCAAGATAGATT
* * * *
4200322 TTCTCCATTGCTCTTTAAGGTAGGTCAAAT
1 TGCTCCACTGCTCTTCAGGGTAGGTCAAAT
4200352 ATAATGGAAT
Statistics
Matches: 216, Mismatches: 52, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
40 7 0.03
41 133 0.62
42 10 0.05
43 11 0.05
44 23 0.11
45 2 0.01
46 3 0.01
47 26 0.12
48 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (41 bp):
TGCTCCACTGCTCTTCAGGGTAGGTCAAATCAAGATAGATT
Found at i:4200258 original size:129 final size:124
Alignment explanation
Indices: 4200023--4200689 Score: 416
Period size: 129 Copynumber: 5.3 Consensus size: 124
4200013 TTAAAGAATA
* * * *
4200023 ATATGCTCCACTGCTCTTCAGGGTAGGTCAGATCAAGATAGATTTGCTCCGCTGCTCTTCAGGGT
1 ATATTCTCCACTGCTCTTCAGGGTAGGTTAAATCAAGATAGATTTGCTCCACTGCTCTTCA-GGT
* * * * * *
4200088 AGGTCAAATCTAATGGAATCTTCTCTACTGCCCTTTAGGGTAAGTCAAATTCAAAGAGAAAGGG
65 AGGTCAAATCTAATGGAATATCCTCT-CTACTCTTCAGGGTAGGTCAAATT-AAA-A-AAAGGG
* * *
4200152 ATATTCTCCACTGCTCTTCAGGGTAGGTTAAATCAGGAAAGATTTGCTCCACTACTCTTCAGGAT
1 ATATTCTCCACTGCTCTTCAGGGTAGGTTAAATCAAGATAGATTTGCTCCACTGCTCTTCAGG-T
* *
4200217 AGGTCAAATCTAATGGAATATGCTGCTCTACTCTTCAGGGTAGGTCAGATTAAAAAAAGGG
65 AGGTCAAATCTAATGGAATATCCT-CTCTACTCTTCAGGGTAGGTCAAATTAAAAAAAGGG
** * ** * * *
4200278 AT-TTGCTCTGCTACTCTTCAACGTAGG-TAAGATCAAGATAGATTTTCTCCATTGCTCTTTAAG
1 ATATT-CTCCACTGCTCTTCAGGGTAGGTTAA-ATCAAGATAGATTTGCTCCACTGCTC-TTCAG
* * * **
4200341 GTAGGTCAAATATAATGGAATATCCTCTTTTCCTCTTCAGGGTAGGTCAAATTAAAAAAAAAG
63 GTAGGTCAAATCTAATGGAATATCCTC-TCTACTCTTCAGGGTAGGTCAAATTAAAAAAAGGG
* * ** * * * * **
4200404 ATTTTCTTCGTTTCTCTTCAGGGTAGG-----TC-AGAT-G--TTG---CATTGCTATTTACTAT
1 ATATTCTCCACTGCTCTTCAGGGTAGGTTAAATCAAGATAGATTTGCTCCACTGCTCTTCA-GGT
* * * * * * *
4200457 AGGTCAAATCTAATGAAATCTGCTCTGTTACTCTTTAGGGTAGGTCAGATTCAAAGAAAAAAGG
65 AGGTCAAATCTAATGGAATATCCTCT-CTACTCTTCAGGGTAGGTCAAATT--AA-AAAAAGGG
* * * * * * *
4200521 --A-TCTACTCTGTTTCTTCAGGGTAGGTCAGATCAAAATAGATTTGCTCCACTGCTCTTAAGGG
1 ATATTCTCCACTG-CTCTTCAGGGTAGGTTAAATCAAGATAGATTTGCTCCACTGCTCTTCA-GG
* * * * * * * *
4200583 TAGGTAAAATCTAATGGAATTTGCTC-CGTTGCTCTTCAGGGTAGGTTAGACTCAAAGAAAAATG
64 TAGGTCAAATCTAATGGAATATCCTCTC--TACTCTTCAGGGTAGGTCA-AAT-TAA-AAAAAGG
4200647 G
124 G
* * * * *
4200648 ATCTGCTCCGCTGCTCTTTAGGGTAGGTTAGATCAAGATAGA
1 ATATTCTCCACTGCTCTTCAGGGTAGGTTAAATCAAGATAGA
4200690 ATGGAATTTA
Statistics
Matches: 423, Mismatches: 83, Indels: 64
0.74 0.15 0.11
Matches are distributed among these distances:
113 4 0.01
114 55 0.13
115 13 0.03
116 2 0.00
117 9 0.02
119 1 0.00
120 6 0.01
121 5 0.01
122 1 0.00
124 3 0.01
125 6 0.01
126 117 0.28
127 66 0.16
128 6 0.01
129 121 0.29
130 8 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (124 bp):
ATATTCTCCACTGCTCTTCAGGGTAGGTTAAATCAAGATAGATTTGCTCCACTGCTCTTCAGGTA
GGTCAAATCTAATGGAATATCCTCTCTACTCTTCAGGGTAGGTCAAATTAAAAAAAGGG
Found at i:4200336 original size:126 final size:125
Alignment explanation
Indices: 4200033--4200689 Score: 497
Period size: 126 Copynumber: 5.3 Consensus size: 125
4200023 ATATGCTCCA
* * * *
4200033 CTGCTCTTCAGGGTAGGTCAGATCAAGATAGATTTGCTCCGCTGCTCTTCAGGGTAGGTCAAATC
1 CTGCTCTTCAGGGTAGGTAAGATCAAGATAGATTTGCTCCACTGCTCTTAAGGATAGGTCAAATC
* * * * * * * * **
4200098 TAATGGAATCTTCTCTACTGCCCTTTAGGGTAAGTCAAATTCAAAGAGAAAGGGATATT-CTCCA
66 TAATGGAATATGCTCT-CTACTCTTCAGGGTAGGTCAGATT-AAA-A-AAAAGGAT-TTGCTCTG
* * * *
4200162 CTGCTCTTCAGGGTAGGTTAA-ATCAGGAAAGATTTGCTCCACTACTCTTCAGGATAGGTCAAAT
1 CTGCTCTTCAGGGTAGG-TAAGATCAAGATAGATTTGCTCCACTGCTCTTAAGGATAGGTCAAAT
*
4200226 CTAATGGAATATGCTGCTCTACTCTTCAGGGTAGGTCAGATTAAAAAAAGGGATTTGCTCTG
65 CTAATGGAATATGCT-CTCTACTCTTCAGGGTAGGTCAGATTAAAAAAAAGGATTTGCTCTG
* ** * *
4200288 CTACTCTTCAACGTAGGTAAGATCAAGATAGATTTTCTCCATTGCTCTTTAAGG-TAGGTCAAAT
1 CTGCTCTTCAGGGTAGGTAAGATCAAGATAGATTTGCTCCACTGCTC-TTAAGGATAGGTCAAAT
* * * * * * *
4200352 ATAATGGAATATCCTCTTTTCCTCTTCAGGGTAGGTCAAATTAAAAAAAAAGATTTTCT-TCG
65 CTAATGGAATATGCTC-TCTACTCTTCAGGGTAGGTCAGATTAAAAAAAAGGATTTGCTCT-G
* * * * * **
4200414 TTTCTCTTCAGGGTA-G---G-TC-AGAT-G--TTG---CATTGCTATTTACTATAGGTCAAATC
1 CTGCTCTTCAGGGTAGGTAAGATCAAGATAGATTTGCTCCACTGCTCTTAAGGATAGGTCAAATC
* * * * * *
4200467 TAATGAAATCTGCTCTGTTACTCTTTAGGGTAGGTCAGATTCAAAGAAAAAAGGATCTACTCTG
66 TAATGGAATATGCTCT-CTACTCTTCAGGGTAGGTCAGATT--AA-AAAAAAGGATTTGCTCTG
* * * * *
4200531 -T-TTCTTCAGGGTAGGTCAGATCAAAATAGATTTGCTCCACTGCTCTTAAGGGTAGGTAAAATC
1 CTGCTCTTCAGGGTAGGTAAGATCAAGATAGATTTGCTCCACTGCTCTTAAGGATAGGTCAAATC
* * * * * *
4200594 TAATGGAATTTGCTC-CGTTGCTCTTCAGGGTAGGTTAGACTCAAAGAAAAATGGATCTGCTCCG
66 TAATGGAATATGCTCTC--TACTCTTCAGGGTAGGTCAGA-TTAAA-AAAAA-GGATTTGCTCTG
* *
4200658 CTGCTCTTTAGGGTAGGTTAGATCAAGATAGA
1 CTGCTCTTCAGGGTAGGTAAGATCAAGATAGA
4200690 ATGGAATTTA
Statistics
Matches: 423, Mismatches: 73, Indels: 64
0.76 0.13 0.11
Matches are distributed among these distances:
113 4 0.01
114 50 0.12
115 11 0.03
116 4 0.01
117 15 0.04
118 1 0.00
119 2 0.00
120 6 0.01
121 5 0.01
122 2 0.00
124 3 0.01
125 9 0.02
126 124 0.29
127 66 0.16
128 5 0.01
129 112 0.26
130 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (125 bp):
CTGCTCTTCAGGGTAGGTAAGATCAAGATAGATTTGCTCCACTGCTCTTAAGGATAGGTCAAATC
TAATGGAATATGCTCTCTACTCTTCAGGGTAGGTCAGATTAAAAAAAAGGATTTGCTCTG
Found at i:4200656 original size:47 final size:47
Alignment explanation
Indices: 4200595--4200726 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 47
4200585 GGTAAAATCT
4200595 AATGGAATTTGCTCCGTTGCTCTTCAGGGTAGGTTAGACTCAAAGA-AA
1 AATGGAATTTGCTCCGTTGCTCTTCAGGGTAGGTTAGA-TC-AAGATAA
* * * *
4200643 AATGG-ATCTGCTCCGCTGCTCTTTAGGGTAGGTTAGATCAAGATAG
1 AATGGAATTTGCTCCGTTGCTCTTCAGGGTAGGTTAGATCAAGATAA
* * *
4200689 AATGGAATTTACTCC-TATACTCTTCAGGGTAAGTTAGA
1 AATGGAATTTGCTCCGT-TGCTCTTCAGGGTAGGTTAGA
4200727 ATTAGGGAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
45 4 0.06
46 8 0.11
47 54 0.76
48 5 0.07
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (47 bp):
AATGGAATTTGCTCCGTTGCTCTTCAGGGTAGGTTAGATCAAGATAA
Found at i:4215019 original size:448 final size:448
Alignment explanation
Indices: 4214184--4215078 Score: 1648
Period size: 448 Copynumber: 2.0 Consensus size: 448
4214174 TCATTAGGAC
*
4214184 GCTATAATGTTTTCAACATATTAGTTATGGTAGAAAGTTGAGCAGCTATTGAATCATTACCCTCA
1 GCTATAAAGTTTTCAACATATTAGTTATGGTAGAAAGTTGAGCAGCTATTGAATCATTACCCTCA
4214249 ATTTCATATGATCCAGATACTTTTCTACCGGTTCCCAGCCTTGTAGTCGGGAATTAATAGTCATT
66 ATTTCATATGATCCAGATACTTTTCTACCGGTTCCCAGCCTTGTAGTCGGGAATTAATAGTCATT
* *
4214314 AGTTGCTATCCTGTCGAGGATATCAAAGGCTTCATCGTGTGATTTGTCAAGTAAAGTACCATTTT
131 AGTTGCTATCCTGTCGAGGATATCAAAGGCTTCATCGGGTGATTTGTCAAGTAAAGTACCATTTG
*
4214379 CTGAGGCATCTAACATCATTCGAGTAGGTGTATTAACTCTATTGTAGAACATCACGACTTGAGTC
196 CTGAGGCATCTAACATCATTCGAGTAGGTGTATTAACTCCATTGTAGAACATCACGACTTGAGTC
*
4214444 CATTCATGAAATCTGTGATTCACACACTTACGAAGTAGACTTTTATACCTATCCCAACGCTCGTA
261 CATTCATGAAATCTGTGATTCACACACTTACGAAGTAGACTTTTATACCTATCCCAACACTCGTA
4214509 CATTGATTCAACATCACCTTGGCGAAAACTGGCAATATCATTGCGTAGTTGTGTATTCATATTGG
326 CATTGATTCAACATCACCTTGGCGAAAACTGGCAATATCATTGCGTAGTTGTGTATTCATATTGG
* *
4214574 GTGGATTGTATCAAAGTAGGAAAATCTTGCATAAATCCGCCCAAGATTCTATTGAGCA
391 GTGGATTGTATCAAAGTAGGAAAATCTTGCATAAATCCGCCAAAGATTCCATTGAGCA
4214632 GCTATAAAGTTTTCAACATATTAGTTATGGTAGAAAGTTGAGCAGCTATTGAATTC-TTACCCTC
1 GCTATAAAGTTTTCAACATATTAGTTATGGTAGAAAGTTGAGCAGCTATTGAA-TCATTACCCTC
*
4214696 AATTTCATATGATCCAGATACTTTTCTACCGGTTCCCAGCCTTGTAGTCGGGAATTACTAGTCAT
65 AATTTCATATGATCCAGATACTTTTCTACCGGTTCCCAGCCTTGTAGTCGGGAATTAATAGTCAT
* *
4214761 TAGTTGCTATCCTGTTGAGGATATCAAAGGCTTCCTCGGGTGATTTGTCAAGTAAAGTACCATTT
130 TAGTTGCTATCCTGTCGAGGATATCAAAGGCTTCATCGGGTGATTTGTCAAGTAAAGTACCATTT
*
4214826 GCTGAGGTATCTAACATCATTCGAGTAGGTGTATTAACTCCATTGTAGAACATCACGACTTGAGT
195 GCTGAGGCATCTAACATCATTCGAGTAGGTGTATTAACTCCATTGTAGAACATCACGACTTGAGT
* *
4214891 CCATTCATGAAATCTGTGGTTCACACACTTGCGAAGTAGACTTTTATACCTATCCCAACACTCGT
260 CCATTCATGAAATCTGTGATTCACACACTTACGAAGTAGACTTTTATACCTATCCCAACACTCGT
4214956 ACATTGATTCAACATCACCTTGGCGAAAACTGGCAATATCATTGCGTAGTTGTGTATTCATATTG
325 ACATTGATTCAACATCACCTTGGCGAAAACTGGCAATATCATTGCGTAGTTGTGTATTCATATTG
*
4215021 GGTGGATTGTATCAAAGTAGGAAACTCTTGCATAAATCCGCCAAAGATTCCATTGAGC
390 GGTGGATTGTATCAAAGTAGGAAAATCTTGCATAAATCCGCCAAAGATTCCATTGAGC
4215079 CTGAAAGAAC
Statistics
Matches: 432, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
448 430 1.00
449 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (448 bp):
GCTATAAAGTTTTCAACATATTAGTTATGGTAGAAAGTTGAGCAGCTATTGAATCATTACCCTCA
ATTTCATATGATCCAGATACTTTTCTACCGGTTCCCAGCCTTGTAGTCGGGAATTAATAGTCATT
AGTTGCTATCCTGTCGAGGATATCAAAGGCTTCATCGGGTGATTTGTCAAGTAAAGTACCATTTG
CTGAGGCATCTAACATCATTCGAGTAGGTGTATTAACTCCATTGTAGAACATCACGACTTGAGTC
CATTCATGAAATCTGTGATTCACACACTTACGAAGTAGACTTTTATACCTATCCCAACACTCGTA
CATTGATTCAACATCACCTTGGCGAAAACTGGCAATATCATTGCGTAGTTGTGTATTCATATTGG
GTGGATTGTATCAAAGTAGGAAAATCTTGCATAAATCCGCCAAAGATTCCATTGAGCA
Found at i:4216150 original size:231 final size:231
Alignment explanation
Indices: 4215717--4216178 Score: 908
Period size: 231 Copynumber: 2.0 Consensus size: 231
4215707 AAACTTGATC
4215717 GCTTGGAAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGAATCAAGTAATA
1 GCTTGGAAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGAATCAAGTAATA
4215782 AAGGGTAAGTGAGTTATCGTCTCCTCAGGGATTGGTTGGTTCTTTTTAAGTTTCACCACAACCAG
66 AAGGGTAAGTGAGTTATCGTCTCCTCAGGGATTGGTTGGTTCTTTTTAAGTTTCACCACAACCAG
4215847 AACTAGTTGTCACAAGTAATTCCTGAAGTCTTATCAAACTAGAAAACTATTAGTAATAAAGCAAG
131 AACTAGTTGTCACAAGTAATTCCTGAAGTCTTATCAAACTAGAAAACTATTAGTAATAAAGCAAG
4215912 AAAAATATTATAAAGTATGATTGTAGAAAAGTTTGG
196 AAAAATATTATAAAGTATGATTGTAGAAAAGTTTGG
4215948 GCTTGGAAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGAATCAAGTAATA
1 GCTTGGAAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGAATCAAGTAATA
4216013 AAGGGTAAGTGAGTTATCGTCTCCTCAGGGATTGGTTGGTTCTTTTTAAGTTTCACCACAACCAG
66 AAGGGTAAGTGAGTTATCGTCTCCTCAGGGATTGGTTGGTTCTTTTTAAGTTTCACCACAACCAG
4216078 AACTAGTTGTCACAAGTTAATTCCTGAAGTCTTATCAAACTAGAAAACTATTAGTAATAAAGCAA
131 AACTAGTTGTCACAAG-TAATTCCTGAAGTCTTATCAAACTAGAAAACTATTAGTAATAAAGCAA
4216143 G-AAAATATTATAAAGTATGATTGTAGAAAAGTTTGG
195 GAAAAATATTATAAAGTATGATTGTAGAAAAGTTTGG
4216179 TCGAGGAATT
Statistics
Matches: 230, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
231 181 0.79
232 49 0.21
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (231 bp):
GCTTGGAAATGTATATGCTAAGGCAAGCAATTTTGTGCAAGTATACACAATCGAATCAAGTAATA
AAGGGTAAGTGAGTTATCGTCTCCTCAGGGATTGGTTGGTTCTTTTTAAGTTTCACCACAACCAG
AACTAGTTGTCACAAGTAATTCCTGAAGTCTTATCAAACTAGAAAACTATTAGTAATAAAGCAAG
AAAAATATTATAAAGTATGATTGTAGAAAAGTTTGG
Found at i:4219411 original size:2 final size:2
Alignment explanation
Indices: 4219404--4219437 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4219394 ACTAATTACT
4219404 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
4219438 CAAAAAACAT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4219476 original size:6 final size:6
Alignment explanation
Indices: 4219467--4219493 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4219457 TATAAATTAA
4219467 ATTTAT ATTTAT ATTTAT ATTTAT ATT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATT
4219494 CATAATATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTAT
Found at i:4226605 original size:21 final size:21
Alignment explanation
Indices: 4226581--4226625 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
4226571 TTTGGTATTC
4226581 GAGGTTGATTTATTCATTTTA
1 GAGGTTGATTTATTCATTTTA
4226602 GAGGTTGATTTATTCATTTTA
1 GAGGTTGATTTATTCATTTTA
4226623 GAG
1 GAG
4226626 TTGGAGGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.49
Consensus pattern (21 bp):
GAGGTTGATTTATTCATTTTA
Found at i:4229998 original size:2 final size:2
Alignment explanation
Indices: 4229991--4230034 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4229981 AAACCAATGA
4229991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4230033 AT
1 AT
4230035 TTAAAAATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4230552 original size:31 final size:31
Alignment explanation
Indices: 4230516--4230589 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
4230506 GGCCTGAGAC
* *
4230516 CCTACCCAAGAAAGTTCTCAGGG-CCTCAGGG
1 CCTACCCAAGAAAGTCCT-AGGGTCCTCAGAG
* * * *
4230547 TCTACCCTAGAGAGTCCTTGGGTCCTCAGAG
1 CCTACCCAAGAAAGTCCTAGGGTCCTCAGAG
4230578 CCTACCCAAGAA
1 CCTACCCAAGAA
4230590 TCGTCTTAGG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
30 3 0.09
31 30 0.91
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (31 bp):
CCTACCCAAGAAAGTCCTAGGGTCCTCAGAG
Found at i:4230744 original size:18 final size:18
Alignment explanation
Indices: 4230721--4230764 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
4230711 AGTTCATAAA
4230721 CCAATAAATTCCATGATT
1 CCAATAAATTCCATGATT
4230739 CCAATAAATTCCATGATT
1 CCAATAAATTCCATGATT
4230757 CC-ATAAAT
1 CCAATAAAT
4230765 CAGGAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.32
Consensus pattern (18 bp):
CCAATAAATTCCATGATT
Found at i:4232707 original size:14 final size:14
Alignment explanation
Indices: 4232685--4232741 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
4232675 GGTCAAAGTC
*
4232685 AACGGGTTGACTCA
1 AACGAGTTGACTCA
4232699 AACGAGTTGACTCA
1 AACGAGTTGACTCA
* * *
4232713 GATGAGTTGACTTA
1 AACGAGTTGACTCA
* *
4232727 GACGAGATGACTCA
1 AACGAGTTGACTCA
4232741 A
1 A
4232742 TTCGGGTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (14 bp):
AACGAGTTGACTCA
Found at i:4237098 original size:22 final size:22
Alignment explanation
Indices: 4237060--4237119 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
4237050 TTACAAATAG
*
4237060 GGTACTGA-TACCCTACTACAA
1 GGTACTGATTCCCCTACTACAA
*
4237081 GGTACTGATTCCCCTACTACAG
1 GGTACTGATTCCCCTACTACAA
4237103 GGTACTGATTCCCCTAC
1 GGTACTGATTCCCCTAC
4237120 AATAGTACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 8 0.22
22 28 0.78
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.27
Consensus pattern (22 bp):
GGTACTGATTCCCCTACTACAA
Found at i:4237520 original size:16 final size:17
Alignment explanation
Indices: 4237499--4237531 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4237489 TTATCATGAT
4237499 CTCTATCAT-ATTCATA
1 CTCTATCATCATTCATA
*
4237515 CTCTATTATCATTCATA
1 CTCTATCATCATTCATA
4237532 TTTCTTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
CTCTATCATCATTCATA
Found at i:4237866 original size:22 final size:22
Alignment explanation
Indices: 4237841--4237901 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
4237831 GGCATATGAA
*
4237841 ATTTGTCCCGAAGGACCTA-TGT
1 ATTTGTCCCGAAGGACC-ACTAT
4237863 ATTTGTCCCGAAGGACCACTAT
1 ATTTGTCCCGAAGGACCACTAT
* *
4237885 ATATGTCCCGAATGACC
1 ATTTGTCCCGAAGGACC
4237902 GTGTAGACCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCACTAT
Found at i:4238787 original size:19 final size:20
Alignment explanation
Indices: 4238750--4238788 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4238740 TTTTTCATTT
4238750 AGGGGGTATCGATACCCCCC
1 AGGGGGTATCGATACCCCCC
4238770 AGGGGGTATCTG-TACCCCC
1 AGGGGGTATC-GATACCCCC
4238789 TGCACAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.18, C:0.33, G:0.31, T:0.18
Consensus pattern (20 bp):
AGGGGGTATCGATACCCCCC
Found at i:4238844 original size:20 final size:22
Alignment explanation
Indices: 4238808--4238849 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4238798 TGGAATTTTC
4238808 GTTCAAGCCTAGAAAA-TCACT
1 GTTCAAGCCTAGAAAATTCACT
*
4238829 GTTCATGCCT-GAAAATTCACT
1 GTTCAAGCCTAGAAAATTCACT
4238850 ATAACAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
GTTCAAGCCTAGAAAATTCACT
Found at i:4239069 original size:12 final size:12
Alignment explanation
Indices: 4239052--4239076 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4239042 AGATGACAAG
4239052 TCAAATTCAACT
1 TCAAATTCAACT
4239064 TCAAATTCAACT
1 TCAAATTCAACT
4239076 T
1 T
4239077 ATTAACTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAAATTCAACT
Found at i:4246486 original size:21 final size:21
Alignment explanation
Indices: 4246466--4246504 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4246456 CACTACAAGA
*
4246466 ATTT-ATGGCCTCGACAAAAG
1 ATTTCATGGCCTCAACAAAAG
*
4246486 ATTTCATGGCTTCAACAAA
1 ATTTCATGGCCTCAACAAA
4246505 GGCCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (21 bp):
ATTTCATGGCCTCAACAAAAG
Found at i:4255955 original size:42 final size:42
Alignment explanation
Indices: 4255903--4256015 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
4255893 GCTATAGACT
4255903 TGTACTTTAGTGGCGTTTTTGTTATAAATGTTGCAATAATCA
1 TGTACTTTAGTGGCGTTTTTGTTATAAATGTTGCAATAATCA
* * * * * *
4255945 TGTAATTTAGTGACCTTTTTGTAATAAATGTTGCAATAGTTA
1 TGTACTTTAGTGGCGTTTTTGTTATAAATGTTGCAATAATCA
* * **
4255987 TGTACCTTAGTAGCGTTTTTAATATAAAT
1 TGTACTTTAGTGGCGTTTTTGTTATAAAT
4256016 ACATCTATTG
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (42 bp):
TGTACTTTAGTGGCGTTTTTGTTATAAATGTTGCAATAATCA
Found at i:4264268 original size:22 final size:22
Alignment explanation
Indices: 4264241--4264296 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
4264231 TATTTATTTT
**
4264241 AATTTATTTTTTATACTTTTAA
1 AATTTATTTAATATACTTTTAA
* *
4264263 AATTTAACTTAATATATTTTTAA
1 AATTT-ATTTAATATACTTTTAA
4264286 AATTATATTTA
1 AATT-TATTTA
4264297 TATGTGATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 5 0.19
23 21 0.78
24 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTATTTAATATACTTTTAA
Found at i:4272046 original size:20 final size:20
Alignment explanation
Indices: 4271984--4272072 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
4271974 TCAGTCACAT
4271984 GTGTATGGATACACATGCAGG
1 GTGTATGGATACAC-TGCAGG
*
4272005 GTGTATCGATACAC--CA--
1 GTGTATGGATACACTGCAGG
*
4272021 GTGTATGGATACACTACAGG
1 GTGTATGGATACACTGCAGG
* *
4272041 GTGTATCGATACATTGCAGG
1 GTGTATGGATACACTGCAGG
4272061 GTGTATGGATAC
1 GTGTATGGATAC
4272073 CCTTTAACAC
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
16 13 0.22
18 4 0.07
20 28 0.48
21 13 0.22
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (20 bp):
GTGTATGGATACACTGCAGG
Found at i:4272048 original size:36 final size:37
Alignment explanation
Indices: 4271984--4272053 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
4271974 TCAGTCACAT
*
4271984 GTGTATGGATACACATGCAGGGTGTATCGATACACCA
1 GTGTATGGATACACATACAGGGTGTATCGATACACCA
4272021 GTGTATGGATACAC-TACAGGGTGTATCGATACA
1 GTGTATGGATACACATACAGGGTGTATCGATACA
4272054 TTGCAGGGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (37 bp):
GTGTATGGATACACATACAGGGTGTATCGATACACCA
Found at i:4272320 original size:21 final size:20
Alignment explanation
Indices: 4272296--4272352 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
4272286 ATGTTTAATG
4272296 AAAAAGGTACCAATTGTTAA
1 AAAAAGGTACCAATTGTTAA
* *
4272316 CAAAAGGATATCAATTGTTAA
1 AAAAAGG-TACCAATTGTTAA
4272337 AAAAA--TACCAATTGTT
1 AAAAAGGTACCAATTGTT
4272353 GGAAAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 10 0.31
20 6 0.19
21 16 0.50
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (20 bp):
AAAAAGGTACCAATTGTTAA
Found at i:4275458 original size:20 final size:18
Alignment explanation
Indices: 4275432--4275485 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 18
4275422 CATTACAGCC
4275432 AGGGTGTATGGATACACT
1 AGGGTGTATGGATACACT
*
4275450 ACTGGGTGTATCGATACACT
1 A--GGGTGTATGGATACACT
4275470 A--GTGTATGGATACACT
1 AGGGTGTATGGATACACT
4275486 CATAGGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 14 0.44
18 1 0.03
20 17 0.53
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (18 bp):
AGGGTGTATGGATACACT
Found at i:4275476 original size:16 final size:16
Alignment explanation
Indices: 4275455--4275485 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4275445 ACACTACTGG
4275455 GTGTATCGATACACTA
1 GTGTATCGATACACTA
*
4275471 GTGTATGGATACACT
1 GTGTATCGATACACT
4275486 CATAGGTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (16 bp):
GTGTATCGATACACTA
Found at i:4275498 original size:36 final size:36
Alignment explanation
Indices: 4275435--4275506 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
4275425 TACAGCCAGG
* *
4275435 GTGTATGGATACACTACTGGGTGTATCGATACACTA
1 GTGTATGGATACACTACTAGGTATATCGATACACTA
*
4275471 GTGTATGGATACACT-CATAGGTATATCGGTACACTA
1 GTGTATGGATACACTAC-TAGGTATATCGATACACTA
4275507 TTTGCATTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 31 0.97
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (36 bp):
GTGTATGGATACACTACTAGGTATATCGATACACTA
Found at i:4275560 original size:21 final size:21
Alignment explanation
Indices: 4275534--4275644 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 21
4275524 AGCATTCACA
**
4275534 GGTGTATAAATACACCTATAG
1 GGTGTATCGATACACCTATAG
4275555 GGTGTATCGATACACCTATAG
1 GGTGTATCGATACACCTATAG
4275576 GGTGTATCGATACACC---A-
1 GGTGTATCGATACACCTATAG
* **
4275593 -GTGTATGGATACA-CTGCAG
1 GGTGTATCGATACACCTATAG
* *
4275612 GGTGTATGGATACA-CTGTAG
1 GGTGTATCGATACACCTATAG
*
4275632 GGTGTATGGATAC
1 GGTGTATCGATAC
4275645 CCTTTGACAC
Statistics
Matches: 81, Mismatches: 4, Indels: 11
0.84 0.04 0.11
Matches are distributed among these distances:
15 1 0.01
16 12 0.15
18 2 0.02
20 31 0.38
21 35 0.43
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (21 bp):
GGTGTATCGATACACCTATAG
Found at i:4275618 original size:20 final size:20
Alignment explanation
Indices: 4275553--4275644 Score: 102
Period size: 20 Copynumber: 4.8 Consensus size: 20
4275543 ATACACCTAT
* **
4275553 AGGGTGTATCGATACACCTAT
1 AGGGTGTATGGATACA-CTGC
*
4275574 AGGGTGTATCGATACAC--C
1 AGGGTGTATGGATACACTGC
4275592 A--GTGTATGGATACACTGC
1 AGGGTGTATGGATACACTGC
*
4275610 AGGGTGTATGGATACACTGT
1 AGGGTGTATGGATACACTGC
4275630 AGGGTGTATGGATAC
1 AGGGTGTATGGATAC
4275645 CCTTTGACAC
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
16 13 0.20
18 3 0.05
20 32 0.50
21 16 0.25
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (20 bp):
AGGGTGTATGGATACACTGC
Done.