Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 15 of 18
Found at i:6097907 original size:39 final size:40
Alignment explanation
Indices: 6097844--6097951 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 40
6097834 CTTTATTAAA
* * **
6097844 ATATAA-TTTTTTAATAGTTGTATTATGAAAGGTTTTTAG
1 ATATAACTTTTTTAATAATTATATTATGAAAGGTTGCTAG
*
6097883 ATATAACTTTTTT-ATAATTATATTATGTAAGGTTGCTAG
1 ATATAACTTTTTTAATAATTATATTATGAAAGGTTGCTAG
* * * *
6097922 ATATAAC-TATTGAATAGTTGTATTATGAAA
1 ATATAACTTTTTTAATAATTATATTATGAAA
6097952 AGAAACAAGT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
38 3 0.05
39 48 0.84
40 6 0.11
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (40 bp):
ATATAACTTTTTTAATAATTATATTATGAAAGGTTGCTAG
Found at i:6098161 original size:21 final size:21
Alignment explanation
Indices: 6098121--6098161 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6098111 AGTCATACCT
*
6098121 TTCTTTCTTTTAAAAAATTTC
1 TTCTTTCTTCTAAAAAATTTC
* *
6098142 TTCTTTCTTCTCAAATATTT
1 TTCTTTCTTCTAAAAAATTT
6098162 GTAACAATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (21 bp):
TTCTTTCTTCTAAAAAATTTC
Found at i:6101532 original size:21 final size:22
Alignment explanation
Indices: 6101504--6101555 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
6101494 CATAAAAACT
*
6101504 AATAAATAATA-ATCAAATTAA
1 AATAAATAATACATAAAATTAA
*
6101525 AGTAAATAA-ACATAAAATTAA
1 AATAAATAATACATAAAATTAA
*
6101546 AATAACTAAT
1 AATAAATAAT
6101556 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (22 bp):
AATAAATAATACATAAAATTAA
Found at i:6101570 original size:16 final size:16
Alignment explanation
Indices: 6101544--6101586 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
6101534 ACATAAAATT
*
6101544 AAAATAACTAATTA-A
1 AAAATAACTAACTATA
6101559 AAAATAAACTAACTATA
1 AAAAT-AACTAACTATA
6101576 AAAATAACTAA
1 AAAATAACTAA
6101587 GTTGTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 14 0.56
17 6 0.24
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:6101580 original size:32 final size:34
Alignment explanation
Indices: 6101500--6101586 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 34
6101490 AAAACATAAA
*
6101500 AACTAATAAATAATAATCAAATTAAAGTAAATAAACAT
1 AACT-ATAAA-AATAA-CTAATTAAAG-AAATAAACAT
* *
6101538 AA-AATTAAAATAACTAATTAAA-AAATAAAC-T
1 AACTATAAAAATAACTAATTAAAGAAATAAACAT
6101569 AACTATAAAAATAACTAA
1 AACTATAAAAATAACTAA
6101587 GTTGTAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
31 3 0.07
32 21 0.49
34 8 0.19
35 5 0.12
36 4 0.09
38 2 0.05
ACGTcount: A:0.66, C:0.08, G:0.01, T:0.25
Consensus pattern (34 bp):
AACTATAAAAATAACTAATTAAAGAAATAAACAT
Found at i:6104388 original size:39 final size:39
Alignment explanation
Indices: 6104304--6104393 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
6104294 TTAATAATTA
* * **
6104304 TATTAAGAAAGGTTATTAGATATAACTTTTTTATAGTTG
1 TATTATGAAAGGTTATTAGATATAACTATTGAATAGTTG
**
6104343 CGTTATGAAAGGTTATTAGATATAACTATTGAAT-GCTTG
1 TATTATGAAAGGTTATTAGATATAACTATTGAATAG-TTG
6104382 TATTATGAAAGG
1 TATTATGAAAGG
6104394 AAACACCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.02
39 41 0.98
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (39 bp):
TATTATGAAAGGTTATTAGATATAACTATTGAATAGTTG
Found at i:6104621 original size:21 final size:21
Alignment explanation
Indices: 6104592--6104636 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6104582 AAAGTCATAC
*
6104592 TCTTTTTTCTTCTT-AAAAATT
1 TCTTATTTCTT-TTCAAAAATT
*
6104613 TCTTATTTCTTTTCAAATATT
1 TCTTATTTCTTTTCAAAAATT
6104634 TCT
1 TCT
6104637 AACATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (21 bp):
TCTTATTTCTTTTCAAAAATT
Found at i:6109850 original size:16 final size:16
Alignment explanation
Indices: 6109822--6109854 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6109812 GGAAAATTTG
6109822 ATGCAAAAGGTGATGA
1 ATGCAAAAGGTGATGA
6109838 ATGCGAAAA-GTGATGA
1 ATGC-AAAAGGTGATGA
6109854 A
1 A
6109855 GAAATCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.45, C:0.06, G:0.30, T:0.18
Consensus pattern (16 bp):
ATGCAAAAGGTGATGA
Found at i:6113809 original size:32 final size:29
Alignment explanation
Indices: 6113762--6113822 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 29
6113752 AAAGAAAAGC
*
6113762 AATCATTTTACCTTATCACATTTTTTAAAAA
1 AATCATTTTACCTTATC-C-TATTTTAAAAA
*
6113793 AATCAATTTTAGCTTATCCTATTTTAAAAA
1 AATC-ATTTTACCTTATCCTATTTTAAAAA
6113823 GAAAAGTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 10 0.37
31 5 0.19
32 12 0.44
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.44
Consensus pattern (29 bp):
AATCATTTTACCTTATCCTATTTTAAAAA
Found at i:6120629 original size:34 final size:34
Alignment explanation
Indices: 6120548--6120631 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
6120538 GTCAAATAAA
* *
6120548 TTATCACGTTTAAAAAGAAAAGCAATCAGTTTTACC
1 TTATCACGTTT--TAAGAAAAGCAATCACTTTTACC
* * * *
6120584 TTATTATGTTTTAAGAAAAGCAATTACTTTTATC
1 TTATCACGTTTTAAGAAAAGCAATCACTTTTACC
*
6120618 TTATCCCGTTTTAA
1 TTATCACGTTTTAA
6120632 AAAGAAAAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
34 30 0.77
36 9 0.23
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (34 bp):
TTATCACGTTTTAAGAAAAGCAATCACTTTTACC
Found at i:6122454 original size:41 final size:41
Alignment explanation
Indices: 6122409--6122508 Score: 150
Period size: 41 Copynumber: 2.5 Consensus size: 41
6122399 TCAGTTACAG
* *
6122409 ATAGTGGTATTTGTGTTATCTATCACA-TCATTGATTACAAA
1 ATAGTGGTATTTGTGATATCTATCACACT-ATTAATTACAAA
*
6122450 ATAGTGGTATTTGTGATATCTGTCACACTATTAATTACAAA
1 ATAGTGGTATTTGTGATATCTATCACACTATTAATTACAAA
6122491 ATAGTGGTA-TTGTGATAT
1 ATAGTGGTATTTGTGATAT
6122509 TTGCCTACAT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 9 0.16
41 45 0.82
42 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (41 bp):
ATAGTGGTATTTGTGATATCTATCACACTATTAATTACAAA
Found at i:6122535 original size:41 final size:40
Alignment explanation
Indices: 6122409--6122553 Score: 148
Period size: 41 Copynumber: 3.5 Consensus size: 40
6122399 TCAGTTACAG
* * **
6122409 ATAGTGGTATTTGTGTTATCTATCACATCATTGATTACAAA
1 ATAGTGGTATTTGTGATATTTGCCACAT-ATTGATTACAAA
* * *
6122450 ATAGTGGTATTTGTGATATCTGTCACACTATTAATTACAAA
1 ATAGTGGTATTTGTGATATTTGCCACA-TATTGATTACAAA
* *
6122491 ATAGTGGTA-TTGTGATATTTGCCTACATAATTGATTATAGA
1 ATAGTGGTATTTGTGATATTTGCC-ACAT-ATTGATTACAAA
* *
6122532 ATAGTGATATTTATGATATTTG
1 ATAGTGGTATTTGTGATATTTG
6122554 TTCAATGCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
40 13 0.14
41 65 0.72
42 12 0.13
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (40 bp):
ATAGTGGTATTTGTGATATTTGCCACATATTGATTACAAA
Found at i:6126292 original size:17 final size:17
Alignment explanation
Indices: 6126267--6126300 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6126257 ATTAATATTT
6126267 TAATATTTAAATCATAA
1 TAATATTTAAATCATAA
* *
6126284 TAATGTTTAAATTATAA
1 TAATATTTAAATCATAA
6126301 ATAAAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Found at i:6126668 original size:42 final size:41
Alignment explanation
Indices: 6126622--6126726 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 41
6126612 TAATATTTTA
* *
6126622 AATTTGAAAAT-TAATTAAAATTATTAA-CATTTTAATCATAAT
1 AATTTGAAAATATAAATAAAA-TATTAATC-TTTTAA-AATAAT
* *
6126664 AATTTTAAATTATAAATAAAATATTAATCTTTTAAAATAAT
1 AATTTGAAAATATAAATAAAATATTAATCTTTTAAAATAAT
*
6126705 AA-TT-AAATTAT-AATAAAATATT
1 AATTTGAAAATATAAATAAAATATT
6126727 GATATTTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
38 11 0.19
39 7 0.12
40 2 0.04
41 7 0.12
42 21 0.37
43 9 0.16
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (41 bp):
AATTTGAAAATATAAATAAAATATTAATCTTTTAAAATAAT
Found at i:6126674 original size:41 final size:41
Alignment explanation
Indices: 6126637--6126763 Score: 120
Period size: 42 Copynumber: 3.1 Consensus size: 41
6126627 GAAAATTAAT
*
6126637 TAAAATTATTAA-CATTTTAATCATAATAATTTTAAATTATAAA
1 TAAAA-TATTAATC-TTTTAA-AATAATAATTTTAAATTATAAA
6126680 TAAAATATTAATCTTTTAAAATAATAA--TTAAATTAT-AA
1 TAAAATATTAATCTTTTAAAATAATAATTTTAAATTATAAA
* * * * *
6126718 TAAAATATTGAT-ATTTAAATTATTAATTATTAATATTTTAAA
1 TAAAATATTAATCTTTTAAAATAATAATT-TTAA-ATTATAAA
6126760 TAAA
1 TAAA
6126764 TTATAAATTA
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
37 11 0.15
38 13 0.18
39 9 0.12
40 4 0.06
41 11 0.15
42 18 0.25
43 6 0.08
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (41 bp):
TAAAATATTAATCTTTTAAAATAATAATTTTAAATTATAAA
Found at i:6126772 original size:27 final size:25
Alignment explanation
Indices: 6126733--6126788 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 25
6126723 TATTGATATT
*
6126733 TAAATTATTAATTATTAATATTTTAAA
1 TAAATTATAAATTATT-ATA-TTTAAA
6126760 TAAATTATAAATTATTATATTTAAA
1 TAAATTATAAATTATTATATTTAAA
6126785 -AAAT
1 TAAAT
6126789 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 4 0.14
25 6 0.21
26 3 0.11
27 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAAATTATAAATTATTATATTTAAA
Found at i:6127612 original size:17 final size:17
Alignment explanation
Indices: 6127590--6127627 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
6127580 AGAGTTATCT
6127590 TATGGCAAAGAAAAATA
1 TATGGCAAAGAAAAATA
*
6127607 TATGGCAAAGAAAAATC
1 TATGGCAAAGAAAAATA
6127624 TATG
1 TATG
6127628 CCATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.21
Consensus pattern (17 bp):
TATGGCAAAGAAAAATA
Found at i:6131642 original size:23 final size:24
Alignment explanation
Indices: 6131588--6131661 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 24
6131578 TAAAATTTAT
*
6131588 ATTTT-ATTTATAAAACAGTTCACAA
1 ATTTTAATTTATAAAACAATT-A-AA
*
6131613 ATATTAATTTATAAAA-AATTAAA
1 ATTTTAATTTATAAAACAATTAAA
*
6131636 ATTTTAA--TATAAAATATATTAAA
1 ATTTTAATTTATAAAACA-ATTAAA
6131659 ATT
1 ATT
6131662 AAAGCTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
21 7 0.16
22 1 0.02
23 17 0.40
24 1 0.02
25 7 0.16
26 10 0.23
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (24 bp):
ATTTTAATTTATAAAACAATTAAA
Found at i:6132101 original size:15 final size:16
Alignment explanation
Indices: 6132074--6132103 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6132064 ATGGATGTTG
6132074 AAAAATTTATAAAAAT
1 AAAAATTTATAAAAAT
6132090 AAAAATTT-TAAAAA
1 AAAAATTTATAAAAA
6132104 GTTTATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATTTATAAAAAT
Found at i:6133279 original size:25 final size:25
Alignment explanation
Indices: 6133244--6133292 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
6133234 GCTCTTGGGT
*
6133244 CTCCTCTATGCAATTCAGACAAGGC
1 CTCCTCCATGCAATTCAGACAAGGC
* *
6133269 CTCCTCCATGCCATTGAGACAAGG
1 CTCCTCCATGCAATTCAGACAAGG
6133293 ACTCATTGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (25 bp):
CTCCTCCATGCAATTCAGACAAGGC
Found at i:6149118 original size:106 final size:106
Alignment explanation
Indices: 6148928--6149141 Score: 374
Period size: 106 Copynumber: 2.0 Consensus size: 106
6148918 ATCCTGGTAG
* * *
6148928 AACCCTGCTCCTTAATTCTAATCCCATGACATATTAAAGGAAAACGCAAGATTTGCACCTACTAG
1 AACCCTACTCCGTAATTCCAATCCCATGACATATTAAAGGAAAACGCAAGATTTGCACCTACTAG
* *
6148993 AATTCCCTTTTGAAGTGTAAACTTAAAAAACCCACTAATAA
66 AATTCCCTTTTGAAATGTAAACTAAAAAAACCCACTAATAA
*
6149034 AACCCTACTCCGTAATTCCAATCCCATGACATGTTAAAGGAAAACGCAAGATTTGCACCTACTAG
1 AACCCTACTCCGTAATTCCAATCCCATGACATATTAAAGGAAAACGCAAGATTTGCACCTACTAG
6149099 AATTCCCTTTTGAAATGTAAACTAAAAAAACCCACTAATAA
66 AATTCCCTTTTGAAATGTAAACTAAAAAAACCCACTAATAA
6149140 AA
1 AA
6149142 ATTACTTAAT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (106 bp):
AACCCTACTCCGTAATTCCAATCCCATGACATATTAAAGGAAAACGCAAGATTTGCACCTACTAG
AATTCCCTTTTGAAATGTAAACTAAAAAAACCCACTAATAA
Found at i:6152820 original size:15 final size:15
Alignment explanation
Indices: 6152800--6152832 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
6152790 AAAATATATA
6152800 TTTATAA-TTAATAAT
1 TTTATAAGTT-ATAAT
6152815 TTTATAAGTTATAAT
1 TTTATAAGTTATAAT
6152830 TTT
1 TTT
6152833 TGTAACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTATAAGTTATAAT
Found at i:6162326 original size:13 final size:13
Alignment explanation
Indices: 6162308--6162337 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6162298 CACACAAGCC
6162308 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
6162321 AAAAAAGAAAAAG
1 AAAAAAAAAAAAG
6162334 AAAA
1 AAAA
6162338 GACTGATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:6164168 original size:29 final size:29
Alignment explanation
Indices: 6164133--6164204 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
6164123 AATATTAATC
* *
6164133 ATAAAAATTTATTTAATATAAAATAAAAAT
1 ATAAAAATTTAATTAA-ATAAAATAAAAAG
*
6164163 ATAAAAATTTAATTAAATATAATAAAAAG
1 ATAAAAATTTAATTAAATAAAATAAAAAG
*
6164192 ATAACATATTTAA
1 ATAA-AAATTTAA
6164205 ATTTTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 15 0.41
30 22 0.59
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (29 bp):
ATAAAAATTTAATTAAATAAAATAAAAAG
Found at i:6164977 original size:38 final size:38
Alignment explanation
Indices: 6164926--6164998 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
6164916 AGCTATCCTT
*
6164926 CCGTCTAGATCTCCAACGCCATCGAGGTATATATCTCA
1 CCGTCTAGATCTCCAACACCATCGAGGTATATATCTCA
* * *
6164964 CCGTCTAGCTCTCCCACACCATCGAGGTCTATATC
1 CCGTCTAGATCTCCAACACCATCGAGGTATATATC
6164999 GTCATCCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (38 bp):
CCGTCTAGATCTCCAACACCATCGAGGTATATATCTCA
Found at i:6165504 original size:42 final size:42
Alignment explanation
Indices: 6165424--6165504 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
6165414 TCAGCCCCCT
*
6165424 TAATAACAAAGTTTGTAAAATTAAAAGAGAATTAGAAATACG
1 TAATAACAAAGTTTGTAAAATTAAAAGAGAAATAGAAATACG
* *
6165466 TAATAACAAATTTTGTAAAATTAGAAGA-AAATAGGAAAT
1 TAATAACAAAGTTTGTAAAATTAAAAGAGAAATA-GAAAT
6165505 GCTTAACAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 4 0.11
42 31 0.89
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.27
Consensus pattern (42 bp):
TAATAACAAAGTTTGTAAAATTAAAAGAGAAATAGAAATACG
Found at i:6166423 original size:181 final size:182
Alignment explanation
Indices: 6166181--6166547 Score: 468
Period size: 181 Copynumber: 2.0 Consensus size: 182
6166171 TATGTATATA
* * * *
6166181 GTGACTTGTTGTTATGTATTGCGTGACGTTGGGGCAGTATGTGACTAGTTATGTTGGCATAACAT
1 GTGACTTATTGTTATGTATTGCGTGACATTGGGGCAGTACGTAACTAGTTATGTTGGCATAACAT
* * * * * *
6166246 GAGTGGATATTAGGCATCGGGTGACTTATTATTAGGTATTGCGAGACTAGAGGTGTGTGACTTGT
66 GAGTAGATATTACGCATCGAGTGACTTATTATTAGGTATTGCAAGACTAGAGGTGCGTGACTTAT
* * *
6166311 GCAATTCATCT-TTTATTTTGAAGCTTTTGTTCCCTAGTTTGTAAGCATTGT
131 GCAATTCATCTATTTATTTTGAAGCTTTTGTTCACTAGTTTGTAAACACTGT
* * * * **
6166362 GTGACTTATTGTTATGTATTGTGTGACATT-GGGCTGTTACGTAATTGGTTATGTTGGCATAATG
1 GTGACTTATTGTTATGTATTGCGTGACATTGGGGCAG-TACGTAACTAGTTATGTTGGCATAACA
* * * *
6166426 TGAGTAGATATTACGCATTGAGTGACTTATTCTTAGGTATTGCAAGATTGGAGGTGCGTGACTTA
65 TGAGTAGATATTACGCATCGAGTGACTTATTATTAGGTATTGCAAGACTAGAGGTGCGTGACTTA
* * * *
6166491 TGTAATTCATCTATTTGTTTTGAGGCTTTTGTTCATTAGTTTGTAAACACTGT
130 TGCAATTCATCTATTTATTTTGAAGCTTTTGTTCACTAGTTTGTAAACACTGT
6166544 GTGA
1 GTGA
6166548 TTGGTTTTTA
Statistics
Matches: 157, Mismatches: 27, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
180 5 0.03
181 114 0.73
182 38 0.24
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (182 bp):
GTGACTTATTGTTATGTATTGCGTGACATTGGGGCAGTACGTAACTAGTTATGTTGGCATAACAT
GAGTAGATATTACGCATCGAGTGACTTATTATTAGGTATTGCAAGACTAGAGGTGCGTGACTTAT
GCAATTCATCTATTTATTTTGAAGCTTTTGTTCACTAGTTTGTAAACACTGT
Found at i:6166757 original size:22 final size:22
Alignment explanation
Indices: 6166732--6166773 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6166722 TTGTTATCTA
*
6166732 GTTTATATGCATTGTGTGACTT
1 GTTTATATGCATTGAGTGACTT
* *
6166754 GTTTTTATGTATTGAGTGAC
1 GTTTATATGCATTGAGTGAC
6166774 CTGTGATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.50
Consensus pattern (22 bp):
GTTTATATGCATTGAGTGACTT
Found at i:6166860 original size:202 final size:203
Alignment explanation
Indices: 6166370--6166946 Score: 745
Period size: 202 Copynumber: 2.8 Consensus size: 203
6166360 GTGTGACTTA
* * * *
6166370 TTGTTATGTATTGTGTGACATTGGGCTGTTACGTAATTGGTTATGTTGGCATAATGTGAGTAGAT
1 TTGTTATGT-TTGCGTGACATTGGGCTGTTACGTGACTGGTTATGTTGGCATAATGTGAGTGGAT
* * * * * *
6166435 ATTACGCATTGAGTGACTTATTCTTAGGTATTGCAAGATTGG-AGGTGCGTGACTTATGTAATTC
65 ATTACGCATTGAGTGACTTATTATTAGGTATTGCGAGACTGGTA-GTGCATGACTTGTGCAATTC
* * *
6166499 ATCTATTTGTTTTGAGGCTTTTGTTCAT-TAGTTTGTAAACACTGTGTGATTGGTTTTTATATAT
129 ATCTA-TTGTTTTGAGGCTTTTGTTCATCTAGTTTATAAGCATTGTGTGATTGGTTTTTATATAT
*
6166563 TGCATGGCCTG
193 TGCATGACCTG
* * * *
6166574 TTGTTATGTTTTGCATGAGATTAGGCTGTTACGTGACTGGTTATGTTGGTATAATGTGAGTGGAT
1 TTGTTATG-TTTGCGTGACATTGGGCTGTTACGTGACTGGTTATGTTGGCATAATGTGAGTGGAT
*
6166639 ATTACGCATTGAGTGACTTATTATTAGGTATTGCGAGACTGGTAGTGCATGACCTGTGCAATTCA
65 ATTACGCATTGAGTGACTTATTATTAGGTATTGCGAGACTGGTAGTGCATGACTTGTGCAATTCA
* * *
6166704 TCTATTATTTTGAGGCTTTTGTT-ATCTAGTTTATATGCATTGTGTGACTT-GTTTTTATGTATT
130 TCTATTGTTTTGAGGCTTTTGTTCATCTAGTTTATAAGCATTGTGTGA-TTGGTTTTTATATATT
6166767 G-AGTGACCTG
194 GCA-TGACCTG
* *
6166777 -TGATTATGTTTGCGTGACATTGGGCTGTTATGTGACTGGTTATGTTGGCATAATGTGAATGGAT
1 TTG-TTATGTTTGCGTGACATTGGGCTGTTACGTGACTGGTTATGTTGGCATAATGTGAGTGGAT
** * * *
6166841 ATTACATATTGAATGACTTATTATTAGGTATTACGAGACTGGTGGTGCATGACTTGTGCAATTCA
65 ATTACGCATTGAGTGACTTATTATTAGGTATTGCGAGACTGGTAGTGCATGACTTGTGCAATTCA
* * * *
6166906 ACTCTTGTTTTGAGGCTTTTGTTCA-CTAGTTTTTAGGCATT
130 TCTATTGTTTTGAGGCTTTTGTTCATCTAGTTTATAAGCATT
6166947 TCATGAATGT
Statistics
Matches: 327, Mismatches: 39, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
202 148 0.45
203 60 0.18
204 117 0.36
205 2 0.01
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (203 bp):
TTGTTATGTTTGCGTGACATTGGGCTGTTACGTGACTGGTTATGTTGGCATAATGTGAGTGGATA
TTACGCATTGAGTGACTTATTATTAGGTATTGCGAGACTGGTAGTGCATGACTTGTGCAATTCAT
CTATTGTTTTGAGGCTTTTGTTCATCTAGTTTATAAGCATTGTGTGATTGGTTTTTATATATTGC
ATGACCTG
Found at i:6170393 original size:46 final size:46
Alignment explanation
Indices: 6170315--6170545 Score: 153
Period size: 46 Copynumber: 5.1 Consensus size: 46
6170305 TGTATGCTAC
* * ** * *
6170315 TCACGCGTCTCAATATCAACTAATCATACGATTCCATAATAACTAG
1 TCACGCGACTCCATATTTACTACTCATGCGATTCCATAATAACTAG
** * *
6170361 TCACGCGACTCCATATTTACTACTCATGCGATTTTATAATAAATAC
1 TCACGCGACTCCATATTTACTACTCATGCGATTCCATAATAACTAG
* * * * * * * * * *
6170407 TCACGTGATTCTATAATAACTAGTAACGCCATTCCAT-AT-ACTAC
1 TCACGCGACTCCATATTTACTACTCATGCGATTCCATAATAACTAG
* * * * * *
6170451 ACATGCGACTCCATATTTATTACTAATGCGATTCCATATTTACTAG
1 TCACGCGACTCCATATTTACTACTCATGCGATTCCATAATAACTAG
* ** * *
6170497 TCACGCGATTCCA-ATTTGTTTACTCACGCGATTCCATATTAACTAG
1 TCACGCGACTCCATATTT-ACTACTCATGCGATTCCATAATAACTAG
6170543 TCA
1 TCA
6170546 TGTGATTCAA
Statistics
Matches: 140, Mismatches: 42, Indels: 6
0.74 0.22 0.03
Matches are distributed among these distances:
44 30 0.21
45 7 0.05
46 103 0.74
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (46 bp):
TCACGCGACTCCATATTTACTACTCATGCGATTCCATAATAACTAG
Found at i:6170553 original size:23 final size:23
Alignment explanation
Indices: 6170311--6170541 Score: 128
Period size: 23 Copynumber: 10.1 Consensus size: 23
6170301 TCCATGTATG
* *
6170311 CTACTCACGCG-TCTCAATATCAA
1 CTACTCACGCGAT-TCCATATTAA
* ** *
6170334 CTAATCATACGATTCCATAATAA
1 CTACTCACGCGATTCCATATTAA
* * *
6170357 CTAGTCACGCGACTCCATATTTA
1 CTACTCACGCGATTCCATATTAA
* ** *
6170380 CTACTCATGCGATTTTATAATAA
1 CTACTCACGCGATTCCATATTAA
* * * *
6170403 ATACTCACGTGATTCTATAATAA
1 CTACTCACGCGATTCCATATTAA
* * *
6170426 CTAGTAACGCCATTCCATA-T-A
1 CTACTCACGCGATTCCATATTAA
* * * *
6170447 CTACACATGCGACTCCATATTTA
1 CTACTCACGCGATTCCATATTAA
* * * *
6170470 TTACTAATGCGATTCCATATTTA
1 CTACTCACGCGATTCCATATTAA
* **
6170493 CTAGTCACGCGATTCCA-ATTTGT
1 CTACTCACGCGATTCCATA-TTAA
*
6170516 TTACTCACGCGATTCCATATTAA
1 CTACTCACGCGATTCCATATTAA
6170539 CTA
1 CTA
6170542 GTCATGTGAT
Statistics
Matches: 153, Mismatches: 50, Indels: 10
0.72 0.23 0.05
Matches are distributed among these distances:
21 14 0.09
22 3 0.02
23 134 0.88
24 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (23 bp):
CTACTCACGCGATTCCATATTAA
Found at i:6174225 original size:23 final size:23
Alignment explanation
Indices: 6174184--6174227 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6174174 CTAGTCATGC
* *
6174184 TGTCACGCAATGACCTATCAATA
1 TGTCACGCAATCACATATCAATA
*
6174207 TGTCACGCTATCACATATCAA
1 TGTCACGCAATCACATATCAA
6174228 ACACTCACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (23 bp):
TGTCACGCAATCACATATCAATA
Found at i:6178665 original size:2 final size:2
Alignment explanation
Indices: 6178658--6178684 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6178648 TTCAACTTTT
6178658 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6178685 GTATGCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6179618 original size:24 final size:24
Alignment explanation
Indices: 6179591--6179645 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
6179581 AAGTAACCAT
6179591 AATTTTTAAAAATATTTA-TTTTAA
1 AATTTTT-AAAATATTTATTTTTAA
** *
6179615 AATTGTTTTGAATTTTTATTTTTAA
1 AATT-TTTAAAATATTTATTTTTAA
6179640 AATTTT
1 AATTTT
6179646 ATGAAATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTTTAAAATATTTATTTTTAA
Found at i:6179650 original size:24 final size:24
Alignment explanation
Indices: 6179605--6179650 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
6179595 TTTAAAAATA
*
6179605 TTTATTTTAAAATTGTTTTGAATT
1 TTTATTTTAAAATTGTTATGAATT
6179629 TTTATTTTTAAAATT-TTATGAA
1 TTTA-TTTTAAAATTGTTATGAA
6179651 ATAACACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (24 bp):
TTTATTTTAAAATTGTTATGAATT
Found at i:6186044 original size:21 final size:23
Alignment explanation
Indices: 6186009--6186050 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
6185999 ATTTATGATG
*
6186009 TTGGTATAACATTAGCAACTTAT
1 TTGGTATAACATTAGAAACTTAT
6186032 TTGGT-TAA-ATTAGAAACTT
1 TTGGTATAACATTAGAAACTT
6186051 CTATAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 3 0.17
23 5 0.28
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (23 bp):
TTGGTATAACATTAGAAACTTAT
Found at i:6193542 original size:75 final size:75
Alignment explanation
Indices: 6193449--6193599 Score: 259
Period size: 75 Copynumber: 2.0 Consensus size: 75
6193439 CTCAAAATAT
* *
6193449 TCTGATAGACCCTTTTTGATCTCT-GAAAACTATCCCAATCAATGTATTTCCCATAGGAAATGGG
1 TCTGACAGACCCTCTTTGATCTCTAG-AAACTATCCCAATCAATGTATTTCCCATAGGAAATGGG
6193513 TGCATTCTTTA
65 TGCATTCTTTA
*
6193524 TCTGACAGACCCTCTTTGATCTCTAGAAACTATCCCAATCAATGTATTTCCCATAGGAGATGGGT
1 TCTGACAGACCCTCTTTGATCTCTAGAAACTATCCCAATCAATGTATTTCCCATAGGAAATGGGT
6193589 GCATTCTTTA
66 GCATTCTTTA
6193599 T
1 T
6193600 TTTCCTAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
75 71 0.99
76 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (75 bp):
TCTGACAGACCCTCTTTGATCTCTAGAAACTATCCCAATCAATGTATTTCCCATAGGAAATGGGT
GCATTCTTTA
Found at i:6199355 original size:232 final size:232
Alignment explanation
Indices: 6198940--6199378 Score: 605
Period size: 232 Copynumber: 1.9 Consensus size: 232
6198930 ATCAGTGATG
*
6198940 GCATCACACATTTCATAATATATTGCCCTTATGTAAATAGACATTCTAGTACTCTAATAAAAGTA
1 GCATCACACATTTCATAATATATTGCCCTTATGTAAATAGACATTCTAGTACTCCAATAAAAGTA
* * * * *
6199005 GTTTGATCCATCAAACAGAGGCGATCTATTTATAGACTATCCCTCAGTAACAACAGATTTTTGGA
66 GTTGGATCCATCAAACAGAGGAGATCTATTTATAAACTATCCCTCAGCAACAACAAATTTTTGGA
* * *
6199070 AAACCATTTGGATCTTCTTTAGGATGTTAAGTCTTAAGAATGAGGGTTAGGCTCTAATACCACTT
131 AAACCATTTGGATCTCCCTTAGGATGTTAAGTCTTAAAAATGAGGGTTAGGCTCTAATACCACTT
6199135 GTTGATCCCAAAGAAATGTGTTGGAGAGGGGTGAATA
196 GTTGATCCCAAAGAAATGTGTTGGAGAGGGGTGAATA
* * * * * * *
6199172 GCATCTCATATTTCATAATCTATTGCCTTTATGTAAATATACATTCTAGTGCTCCAAT-AGAGTT
1 GCATCACACATTTCATAATATATTGCCCTTATGTAAATAGACATTCTAGTACTCCAATAAAAG-T
* * * * * *
6199236 AGTTGGATCCATCAAACATAGGTAG-TTTTTTTGTAAACTGTCCCTCAGCAACAATAAATTTTT-
65 AGTTGGATCCATCAAACAGAGG-AGATCTATTTATAAACTATCCCTCAGCAACAACAAATTTTTG
* *
6199299 GAAGAGCCATTTGGATCTCCCTTAGGATGTTAAGTCTTAAAAATGAGGGTTAGGCTCTGATACCA
129 GAA-AACCATTTGGATCTCCCTTAGGATGTTAAGTCTTAAAAATGAGGGTTAGGCTCTAATACCA
*
6199364 CTTGTTGGTCCCAAA
193 CTTGTTGATCCCAAA
6199379 TAATATACTA
Statistics
Matches: 179, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
231 6 0.03
232 172 0.96
233 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (232 bp):
GCATCACACATTTCATAATATATTGCCCTTATGTAAATAGACATTCTAGTACTCCAATAAAAGTA
GTTGGATCCATCAAACAGAGGAGATCTATTTATAAACTATCCCTCAGCAACAACAAATTTTTGGA
AAACCATTTGGATCTCCCTTAGGATGTTAAGTCTTAAAAATGAGGGTTAGGCTCTAATACCACTT
GTTGATCCCAAAGAAATGTGTTGGAGAGGGGTGAATA
Found at i:6202724 original size:18 final size:18
Alignment explanation
Indices: 6202703--6202743 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6202693 AAATCATAGA
6202703 TTTTGAGATTTTCTT-TTT
1 TTTTGA-ATTTTCTTATTT
*
6202721 TTTTCAATTTTCTTATTT
1 TTTTGAATTTTCTTATTT
6202739 TTTTG
1 TTTTG
6202744 TACTGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.73
Consensus pattern (18 bp):
TTTTGAATTTTCTTATTT
Found at i:6203311 original size:2 final size:2
Alignment explanation
Indices: 6203306--6203340 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6203296 AATATCGCTG
*
6203306 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6203341 GTGCCCGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:6211379 original size:30 final size:30
Alignment explanation
Indices: 6211344--6211409 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
6211334 GGTTCCCCAC
* *
6211344 ACATTTCCCTCTAAAAGTTTTTCCT-CAAA
1 ACATTTCCCTCCAAAAGTTTTCCCTCCAAA
*
6211373 AGCATTTTCCTCCAAAAGTTTTCCCTCCAAA
1 A-CATTTCCCTCCAAAAGTTTTCCCTCCAAA
6211404 ACATTT
1 ACATTT
6211410 GGGAGGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 26 0.81
31 5 0.16
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (30 bp):
ACATTTCCCTCCAAAAGTTTTCCCTCCAAA
Found at i:6211399 original size:15 final size:15
Alignment explanation
Indices: 6211347--6211404 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
6211337 TCCCCACACA
*
6211347 TTTCCCTCTAAAAGT
1 TTTCCCTCCAAAAGT
*
6211362 TTTTCCT-CAAAAGCAT
1 TTTCCCTCCAAAAG--T
6211378 TTT-CCTCCAAAAGT
1 TTTCCCTCCAAAAGT
6211392 TTTCCCTCCAAAA
1 TTTCCCTCCAAAA
6211405 CATTTGGGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 9 0.24
15 18 0.49
16 10 0.27
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.36
Consensus pattern (15 bp):
TTTCCCTCCAAAAGT
Found at i:6211439 original size:16 final size:16
Alignment explanation
Indices: 6211418--6211454 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6211408 TTGGGAGGGA
*
6211418 AAGCTAAAGTTTCTAG
1 AAGCTAAAATTTCTAG
6211434 AAGCTAAAATTTCTAG
1 AAGCTAAAATTTCTAG
*
6211450 CAGCT
1 AAGCT
6211455 CAACACATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (16 bp):
AAGCTAAAATTTCTAG
Found at i:6211613 original size:15 final size:15
Alignment explanation
Indices: 6211593--6211638 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
6211583 CTGTGTAGGC
6211593 CTGCGTGCTGCGCAT
1 CTGCGTGCTGCGCAT
6211608 CTGCGTGCTGCGCAT
1 CTGCGTGCTGCGCAT
*
6211623 CTGCGTGCCGCGCAT
1 CTGCGTGCTGCGCAT
6211638 C
1 C
6211639 GGCTGTGCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.07, C:0.37, G:0.33, T:0.24
Consensus pattern (15 bp):
CTGCGTGCTGCGCAT
Found at i:6212926 original size:2 final size:2
Alignment explanation
Indices: 6212919--6212955 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
6212909 AAAGCCAGTG
* *
6212919 AT AT AT AT AC AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6212956 AAACAACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6223961 original size:27 final size:27
Alignment explanation
Indices: 6223893--6223948 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
6223883 ATAATTATGA
*
6223893 TAGAATATTAAATAAACATTAATAGTT
1 TAGAAAATTAAATAAACATTAATAGTT
6223920 TAGAAAATTAAATAAACATTAATAGTT
1 TAGAAAATTAAATAAACATTAATAGTT
6223947 TA
1 TA
6223949 CACTTTCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.36
Consensus pattern (27 bp):
TAGAAAATTAAATAAACATTAATAGTT
Found at i:6224192 original size:15 final size:15
Alignment explanation
Indices: 6224153--6224193 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
6224143 CTTATAATGC
6224153 AATGTGATTACAAGT
1 AATGTGATTACAAGT
*
6224168 AATATGATTACAAGT
1 AATGTGATTACAAGT
*
6224183 AATGTAATTAC
1 AATGTGATTAC
6224194 GAACAATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:6224470 original size:30 final size:30
Alignment explanation
Indices: 6224426--6224523 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 30
6224416 TTTAATGTCA
*
6224426 TATATTTTATTTTTATTTTTATTATAATCT
1 TATATTTTATTTTTATTTTTAATATAATCT
*
6224456 TATATCTTTA-TTTTATTTTTAATATAATTT
1 TATAT-TTTATTTTTATTTTTAATATAATCT
*
6224486 TATATATTATATATTTTA-TTTTAATTTAAT-T
1 TATAT-TT-TAT-TTTTATTTTTAATATAATCT
6224517 TAT-TTTT
1 TATATTTT
6224524 CCTTTAAAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
28 1 0.02
29 2 0.03
30 31 0.52
31 10 0.17
32 11 0.18
33 5 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (30 bp):
TATATTTTATTTTTATTTTTAATATAATCT
Found at i:6231798 original size:23 final size:23
Alignment explanation
Indices: 6231768--6231860 Score: 107
Period size: 23 Copynumber: 4.1 Consensus size: 23
6231758 TGAATGGTAT
* *
6231768 ATAT-GAATCGCGTGACTTGTTG
1 ATATGGAATCACGTGACTAGTTG
* * *
6231790 TTATGGAATCAAGTGACTATTTG
1 ATATGGAATCACGTGACTAGTTG
** *
6231813 ATATGGAATTGCGAGACTAGTTG
1 ATATGGAATCACGTGACTAGTTG
6231836 ATATGGAATCACGTGACTAGTTG
1 ATATGGAATCACGTGACTAGTTG
6231859 AT
1 AT
6231861 GTGGTATTAC
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
22 3 0.05
23 53 0.95
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (23 bp):
ATATGGAATCACGTGACTAGTTG
Found at i:6231844 original size:46 final size:45
Alignment explanation
Indices: 6231768--6231860 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 45
6231758 TGAATGGTAT
* * * *
6231768 ATATGAATCGCGTGACTTGTTGTTATGGAATCAAGTGACTATTTG
1 ATATGAATCGCGAGACTAGTTGATATGGAATCAAGTGACTAGTTG
* *
6231813 ATATGGAATTGCGAGACTAGTTGATATGGAATCACGTGACTAGTTG
1 ATAT-GAATCGCGAGACTAGTTGATATGGAATCAAGTGACTAGTTG
6231859 AT
1 AT
6231861 GTGGTATTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
45 4 0.10
46 37 0.90
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (45 bp):
ATATGAATCGCGAGACTAGTTGATATGGAATCAAGTGACTAGTTG
Found at i:6231872 original size:23 final size:23
Alignment explanation
Indices: 6231778--6231873 Score: 102
Period size: 23 Copynumber: 4.2 Consensus size: 23
6231768 ATATGAATCG
* * *
6231778 CGTGACTTGTTGTTATGGAATCA
1 CGTGACTAGTTGATATGGAATTA
* * *
6231801 AGTGACTATTTGATATGGAATTG
1 CGTGACTAGTTGATATGGAATTA
* *
6231824 CGAGACTAGTTGATATGGAATCA
1 CGTGACTAGTTGATATGGAATTA
* *
6231847 CGTGACTAGTTGATGTGGTATTA
1 CGTGACTAGTTGATATGGAATTA
6231870 CGTG
1 CGTG
6231874 GCTTCAAGCA
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.35
Consensus pattern (23 bp):
CGTGACTAGTTGATATGGAATTA
Found at i:6235561 original size:38 final size:39
Alignment explanation
Indices: 6235483--6235564 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 39
6235473 GTTGGATGGG
* * * * *
6235483 GATATAGACCTCGATGGCCATTGGCGAGCTGGACGCCGA
1 GATATAGACCCCAATGGCCATTGGAGAGCTGAACGACGA
6235522 GATATAGACCCCAATGG-CATTGGAGAGCTGAACGACGA
1 GATATAGACCCCAATGGCCATTGGAGAGCTGAACGACGA
6235560 GATAT
1 GATAT
6235565 CTAAATCGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
38 23 0.61
39 15 0.39
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.18
Consensus pattern (39 bp):
GATATAGACCCCAATGGCCATTGGAGAGCTGAACGACGA
Found at i:6240368 original size:23 final size:23
Alignment explanation
Indices: 6240316--6240360 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6240306 AAATGAATGA
* * *
6240316 AAAAATAAAAAAATGGAAATATC
1 AAAAATAAAAAAAAGAAAAAATC
6240339 AAAAATAAAAAAAAGAAAAAAT
1 AAAAATAAAAAAAAGAAAAAAT
6240361 TGAAAATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (23 bp):
AAAAATAAAAAAAAGAAAAAATC
Found at i:6241040 original size:2 final size:2
Alignment explanation
Indices: 6241033--6241064 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6241023 GAAACATACA
6241033 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
6241065 TTGTATGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6241125 original size:3 final size:3
Alignment explanation
Indices: 6241117--6241169 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
6241107 CTAGTTAATA
6241117 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
6241165 AAC AA
1 AAC AA
6241170 TAATAATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:6241226 original size:30 final size:28
Alignment explanation
Indices: 6241192--6241254 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
6241182 TAATAAATAT
*
6241192 AAAATAAAATGGTAATAGGAGTTATGTTTA
1 AAAATAAAATAGT-AT-GGAGTTATGTTTA
* *
6241222 AAAATTAATTAGTATGGAGTTATGTTTA
1 AAAATAAAATAGTATGGAGTTATGTTTA
6241250 AAAAT
1 AAAAT
6241255 TAATTTCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 18 0.60
29 2 0.07
30 10 0.33
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (28 bp):
AAAATAAAATAGTATGGAGTTATGTTTA
Found at i:6249202 original size:9 final size:9
Alignment explanation
Indices: 6249188--6249222 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
6249178 ATATAGTTAC
6249188 TACTACTAT
1 TACTACTAT
6249197 TACTACTAT
1 TACTACTAT
* *
6249206 TACTAGTAC
1 TACTACTAT
6249215 TACTACTA
1 TACTACTA
6249223 GAGATAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (9 bp):
TACTACTAT
Found at i:6251176 original size:35 final size:35
Alignment explanation
Indices: 6251100--6251181 Score: 123
Period size: 35 Copynumber: 2.4 Consensus size: 35
6251090 CCAAGCTTTT
*
6251100 ACAATGACTTTTCACAAGCTCAGCCACAACCTTCA
1 ACAATGGCTTTTCACAAGCTCAGCCACAACCTTCA
*
6251135 ACAATGGCTTTTCA-AAGGCTCAGCCATAACCTTCA
1 ACAATGGCTTTTCACAA-GCTCAGCCACAACCTTCA
6251170 ACAATGG-TTTTC
1 ACAATGGCTTTTC
6251182 CTTAGGATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 7 0.16
35 37 0.84
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (35 bp):
ACAATGGCTTTTCACAAGCTCAGCCACAACCTTCA
Found at i:6251990 original size:14 final size:14
Alignment explanation
Indices: 6251971--6251997 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6251961 CTATTTAATT
6251971 TTAGTTTTAATTTA
1 TTAGTTTTAATTTA
6251985 TTAGTTTTAATTT
1 TTAGTTTTAATTT
6251998 TTCCTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TTAGTTTTAATTTA
Found at i:6253869 original size:27 final size:27
Alignment explanation
Indices: 6253839--6253906 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
6253829 CACCTAAATG
* *
6253839 TTACGCACTTGGGAATGTCCCTATGCA
1 TTACACACTTAGGAATGTCCCTATGCA
*
6253866 TTACACACTTAGGAATGTCCCTATGCG
1 TTACACACTTAGGAATGTCCCTATGCA
*
6253893 GTACACACTT-GGAA
1 TTACACACTTAGGAA
6253907 CGCTCCCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 4 0.11
27 33 0.89
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (27 bp):
TTACACACTTAGGAATGTCCCTATGCA
Found at i:6273444 original size:20 final size:22
Alignment explanation
Indices: 6273421--6273460 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
6273411 GCACACACGG
6273421 ACGCACGCA-G-ACACACGCCC
1 ACGCACGCACGCACACACGCCC
6273441 ACGCACGCACGCACACACGC
1 ACGCACGCACGCACACACGC
6273461 ACATGGACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.30, C:0.50, G:0.20, T:0.00
Consensus pattern (22 bp):
ACGCACGCACGCACACACGCCC
Found at i:6273470 original size:22 final size:22
Alignment explanation
Indices: 6273414--6273483 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
6273404 GACACAAGCA
6273414 CACACGGACGCACGCAGACACACG
1 CACACGGACGCACGC--ACACACG
* *
6273438 CCCACGCACGCACGCACACACG
1 CACACGGACGCACGCACACACG
* * *
6273460 CACATGGACGCACTCACGCACG
1 CACACGGACGCACGCACACACG
6273482 CA
1 CA
6273484 GACAACACAC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 26 0.67
24 13 0.33
ACGTcount: A:0.30, C:0.46, G:0.21, T:0.03
Consensus pattern (22 bp):
CACACGGACGCACGCACACACG
Found at i:6273495 original size:2 final size:2
Alignment explanation
Indices: 6273488--6273512 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6273478 CACGCAGACA
6273488 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
6273513 AAGGACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6278632 original size:24 final size:24
Alignment explanation
Indices: 6278605--6278660 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
6278595 ATCATGGAAA
*
6278605 ATTTAAAT-AATTTTTTATTTTTTT
1 ATTTAAATGAA-TTTTTATATTTTT
*
6278629 ATTTAATTGAATTTTTATATTTTT
1 ATTTAAATGAATTTTTATATTTTT
6278653 ATTTAAAT
1 ATTTAAAT
6278661 TAAATAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
ATTTAAATGAATTTTTATATTTTT
Found at i:6278671 original size:29 final size:25
Alignment explanation
Indices: 6278607--6278676 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 25
6278597 CATGGAAAAT
*
6278607 TTAAATAATTTTT-TATTTTTTTAT
1 TTAAATAATTTTTATATTTTTTTAA
*
6278631 TTAATTGAATTTTTATATTTTTATTTAAA
1 TTAAAT-AATTTTTATA-TTTT-TTT-AA
6278660 TTAAATAAATTTTTATA
1 TTAAAT-AATTTTTATA
6278677 ATTAATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.14
25 7 0.19
26 2 0.05
27 4 0.11
28 3 0.08
29 16 0.43
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (25 bp):
TTAAATAATTTTTATATTTTTTTAA
Found at i:6279107 original size:13 final size:13
Alignment explanation
Indices: 6279089--6279125 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
6279079 CGGCTGTTTC
6279089 TTTATATTTTATT
1 TTTATATTTTATT
6279102 TTTATATTTTATT
1 TTTATATTTTATT
*
6279115 TGTTAGATTTT
1 T-TTATATTTT
6279126 GACAATCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTATATTTTATT
Found at i:6279378 original size:6 final size:6
Alignment explanation
Indices: 6279368--6279411 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
6279358 TATCCAACTA
*
6279368 CTGTGA CTGTGC CTGTGC CTGTGC CTGTGC CTGTGC CTGTGC CT
1 CTGTGC CTGTGC CTGTGC CTGTGC CTGTGC CTGTGC CTGTGC CT
6279412 AATATTCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.02, C:0.32, G:0.32, T:0.34
Consensus pattern (6 bp):
CTGTGC
Found at i:6292218 original size:21 final size:21
Alignment explanation
Indices: 6292194--6292253 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
6292184 TTTCCCTCGA
*
6292194 TTCAGGCATTCGCTCCCTTGG
1 TTCAGGCATTCGCTCCCTAGG
*
6292215 TTCAGGCATTTGCTCCCTAGG
1 TTCAGGCATTCGCTCCCTAGG
* * *
6292236 GTGAGTCATTCGCTCCCT
1 TTCAGGCATTCGCTCCCT
6292254 CAAACCAGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.12, C:0.32, G:0.23, T:0.33
Consensus pattern (21 bp):
TTCAGGCATTCGCTCCCTAGG
Found at i:6296015 original size:21 final size:21
Alignment explanation
Indices: 6295963--6296016 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
6295953 TTTTTTTATA
* *
6295963 CATGATGTATAACAACTTAAC
1 CATGATGTGTAACAACCTAAC
*
6295984 CATGGTGTGTAACAACCTAAC
1 CATGATGTGTAACAACCTAAC
*
6296005 CATGATATGTAA
1 CATGATGTGTAA
6296017 TATATTTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (21 bp):
CATGATGTGTAACAACCTAAC
Found at i:6298625 original size:21 final size:20
Alignment explanation
Indices: 6298580--6298619 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
6298570 GGATAGATTC
6298580 ATTTAATATTTTTTAATTATA
1 ATTTAATATTTTTT-ATTATA
6298601 ATTTAATATTATTTT-TTAT
1 ATTTAATATT-TTTTATTAT
6298620 CTATTTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTAATATTTTTTATTATA
Found at i:6306963 original size:18 final size:16
Alignment explanation
Indices: 6306930--6306977 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 16
6306920 TATTTTTTCC
6306930 TTTTCTTTATTTTTTAT
1 TTTTCTTT-TTTTTTAT
6306947 TTTTCTTTTGTTCTTTAT
1 TTTTCTTTT-TT-TTTAT
6306965 TTTTCATTTTTTT
1 TTTTC-TTTTTTT
6306978 AAAATATCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 12 0.43
19 4 0.14
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTCTTTTTTTTTAT
Found at i:6306967 original size:17 final size:17
Alignment explanation
Indices: 6306919--6306969 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
6306909 CAAAATCCAA
**
6306919 TTATTTTTTCCTTTTCT
1 TTATTTTTTATTTTTCT
6306936 TTATTTTTTATTTTTCT
1 TTATTTTTTATTTTTCT
6306953 TT-TGTTCTTTATTTTTC
1 TTAT-TT-TTTATTTTTC
6306970 ATTTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 1 0.03
17 19 0.63
18 10 0.33
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (17 bp):
TTATTTTTTATTTTTCT
Found at i:6307477 original size:16 final size:17
Alignment explanation
Indices: 6307445--6307486 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
6307435 TTTCTTTCAC
*
6307445 TAAATTAAATTAAATTT
1 TAAATTAAATAAAATTT
6307462 TAAATTAAA-AAAA-TT
1 TAAATTAAATAAAATTT
*
6307477 TAAAATAAAT
1 TAAATTAAAT
6307487 TTAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 10 0.45
16 3 0.14
17 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTAAATAAAATTT
Found at i:6307488 original size:11 final size:11
Alignment explanation
Indices: 6307462--6307496 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
6307452 AATTAAATTT
6307462 TAAA-TTAAAA
1 TAAATTTAAAA
6307472 -AAATTTAAAA
1 TAAATTTAAAA
6307482 TAAATTTAAAA
1 TAAATTTAAAA
6307493 TAAA
1 TAAA
6307497 AAGGTTTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.13
10 6 0.26
11 14 0.61
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:6307617 original size:13 final size:13
Alignment explanation
Indices: 6307593--6307625 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6307583 TTTAATATTT
6307593 TAAAAT-AAATAA
1 TAAAATAAAATAA
*
6307605 TGAAATAAAATAA
1 TAAAATAAAATAA
6307618 TAAAATAA
1 TAAAATAA
6307626 TATTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
TAAAATAAAATAA
Found at i:6307666 original size:27 final size:28
Alignment explanation
Indices: 6307635--6307696 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
6307625 ATATTTTAAT
*
6307635 AATAAATTA-TTA-ATTTTTTAAATGAA
1 AATAAATTATTTATATTTTATAAATGAA
6307661 ATATAAATTATTTATATTTTATAAATGAA
1 A-ATAAATTATTTATATTTTATAAATGAA
6307690 AATAAAT
1 AATAAAT
6307697 AATCATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 1 0.03
27 8 0.25
28 9 0.28
29 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
AATAAATTATTTATATTTTATAAATGAA
Found at i:6307704 original size:27 final size:29
Alignment explanation
Indices: 6307647--6307705 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
6307637 TAAATTATTA
* * *
6307647 ATTTTTTAAATGAAATATAAATTATTTAT
1 ATTTTATAAATGAAATATAAATTAATCAT
6307676 ATTTTATAAATGAAA-ATAAA-TAATCAT
1 ATTTTATAAATGAAATATAAATTAATCAT
6307703 ATT
1 ATT
6307706 AACATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 14 0.52
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (29 bp):
ATTTTATAAATGAAATATAAATTAATCAT
Found at i:6307788 original size:21 final size:22
Alignment explanation
Indices: 6307746--6307788 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
6307736 TAAAAAATTA
* *
6307746 TTAAAATAATAAATATTTTAAT
1 TTAAAATAATAAAAATTATAAT
*
6307768 TTAAAA-ATTAAAAATTATAAT
1 TTAAAATAATAAAAATTATAAT
6307789 AAATAGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAATAATAAAAATTATAAT
Found at i:6308646 original size:26 final size:26
Alignment explanation
Indices: 6308599--6308681 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 26
6308589 TTAATTCCAA
** * *
6308599 GGATAATTTTATTACTAGAAGTGAAT
1 GGATAATTTTACCACCAAAAGTGAAT
*
6308625 GGATAATTTTACCACCAAAAGTGGAT
1 GGATAATTTTACCACCAAAAGTGAAT
* * *
6308651 GGATGATTTTACCATCAAAAGTAAAT
1 GGATAATTTTACCACCAAAAGTGAAT
6308677 GGATA
1 GGATA
6308682 CCTTAACCCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (26 bp):
GGATAATTTTACCACCAAAAGTGAAT
Found at i:6308714 original size:26 final size:26
Alignment explanation
Indices: 6308685--6308742 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
6308675 ATGGATACCT
**
6308685 TAACCCAGTAACTTATTAAAAATGGA
1 TAACCCAGTAACCCATTAAAAATGGA
* * *
6308711 TAACCCATTAACCCATTAGAAGTGGA
1 TAACCCAGTAACCCATTAAAAATGGA
6308737 TAACCC
1 TAACCC
6308743 GCCAGAAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (26 bp):
TAACCCAGTAACCCATTAAAAATGGA
Found at i:6308785 original size:28 final size:28
Alignment explanation
Indices: 6308754--6308812 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
6308744 CCAGAAATGG
* *
6308754 ATGGATACTTATAACCTACCAAAAGTGA
1 ATGGATACTTATAACCCACCAAAAGTAA
* *
6308782 ATGGATACTTTTAACCCACCAGAAGTAA
1 ATGGATACTTATAACCCACCAAAAGTAA
6308810 ATG
1 ATG
6308813 AGTAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (28 bp):
ATGGATACTTATAACCCACCAAAAGTAA
Found at i:6310840 original size:21 final size:22
Alignment explanation
Indices: 6310805--6310848 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6310795 CTCTTAAAGT
6310805 AATTTAAAATAAAATAATATAA
1 AATTTAAAATAAAATAATATAA
* *
6310827 AATTT-AATTAAAATAATTTAA
1 AATTTAAAATAAAATAATATAA
6310848 A
1 A
6310849 TTAACTGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTTAAAATAAAATAATATAA
Found at i:6313281 original size:14 final size:15
Alignment explanation
Indices: 6313243--6313274 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6313233 TAATGTTATA
6313243 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
6313258 ATTAAAATAAAACAT
1 ATTAAAATAAAAAAT
6313273 AT
1 AT
6313275 AATATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:6313306 original size:25 final size:25
Alignment explanation
Indices: 6313289--6313376 Score: 70
Period size: 28 Copynumber: 3.3 Consensus size: 25
6313279 TAAGAATTAG
6313289 AAAATTAAAATAAAATAAAATATAA
1 AAAATTAAAATAAAATAAAATATAA
* * * *
6313314 AAAATTAAATTTTATATAATATGGATAA
1 AAAATTAAA-ATAAAATAAAAT--ATAA
6313342 CAAAATT-AAATCAAAATATATAATATAA
1 -AAAATTAAAAT-AAAATA-A-AATATAA
6313370 AAAATTA
1 AAAATTA
6313377 TATTAAAGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
25 9 0.19
26 8 0.17
27 7 0.15
28 14 0.30
29 7 0.15
30 2 0.04
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAATTAAAATAAAATAAAATATAA
Found at i:6313424 original size:33 final size:34
Alignment explanation
Indices: 6313349--6313436 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 34
6313339 TAACAAAATT
* * *
6313349 AAATCAAAATATATAATATAAAAAATTATATTAAAG
1 AAATGAAAATA-A-AATATATAAAATTATAATAAAG
*
6313385 AAATGAAAATAAAATATATAAGATTATAAT-AAG
1 AAATGAAAATAAAATATATAAAATTATAATAAAG
6313418 AAATGAAAATAAAATATAT
1 AAATGAAAATAAAATATAT
6313437 GACACTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
33 22 0.46
34 15 0.31
35 1 0.02
36 10 0.21
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (34 bp):
AAATGAAAATAAAATATATAAAATTATAATAAAG
Found at i:6326990 original size:91 final size:91
Alignment explanation
Indices: 6326835--6327016 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
6326825 AAGGCGCAAG
6326835 ATAATTTTCTCCAAATACTTAGCTACAGCTGTTAGTGTGATACAACTATAATTCAGGTTTCTAGC
1 ATAATTTTCTCCAAATACTTAGCTACAGCTGTTAGTGTGATACAACTATAATTCAGGTTTCTAGC
6326900 TTAATAATTACTACAATTGTCATCAT
66 TTAATAATTACTACAATTGTCATCAT
6326926 ATAATTTTCTCCAAATACTTAGCTACAGCTGTTAGTGTGATACAACTATAATTCAGGTTTCTAGC
1 ATAATTTTCTCCAAATACTTAGCTACAGCTGTTAGTGTGATACAACTATAATTCAGGTTTCTAGC
6326991 TTAATAATTACTACAATTGTCATCAT
66 TTAATAATTACTACAATTGTCATCAT
6327017 GATACGCAAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (91 bp):
ATAATTTTCTCCAAATACTTAGCTACAGCTGTTAGTGTGATACAACTATAATTCAGGTTTCTAGC
TTAATAATTACTACAATTGTCATCAT
Found at i:6334683 original size:21 final size:20
Alignment explanation
Indices: 6334655--6334693 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6334645 GTGCCCGTAA
**
6334655 TTGCTTAATTGATTAAGAAT
1 TTGCTTAATCCATTAAGAAT
6334675 TTGCATTAATCCATTAAGA
1 TTGC-TTAATCCATTAAGA
6334694 CTAATCTATC
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:0.10, G:0.13, T:0.41
Consensus pattern (20 bp):
TTGCTTAATCCATTAAGAAT
Found at i:6335094 original size:29 final size:29
Alignment explanation
Indices: 6335053--6335109 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
6335043 AAATATTTAT
*
6335053 AACATTCACAGTAGCTAAACAAGATATAC
1 AACATCCACAGTAGCTAAACAAGATATAC
* *
6335082 AACATCCATAGTAGCTAAGCAAGATATA
1 AACATCCACAGTAGCTAAACAAGATATA
6335110 TTGAATATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (29 bp):
AACATCCACAGTAGCTAAACAAGATATAC
Found at i:6339464 original size:21 final size:22
Alignment explanation
Indices: 6339440--6339483 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
6339430 TGTGTTAATC
* *
6339440 TTCAAGGCAAGGTTTTC-CTTT
1 TTCAAGACAAGCTTTTCTCTTT
*
6339461 TTCAATACAAGCTTTTCTCTTT
1 TTCAAGACAAGCTTTTCTCTTT
6339483 T
1 T
6339484 ATTTCTCTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.48
Consensus pattern (22 bp):
TTCAAGACAAGCTTTTCTCTTT
Found at i:6343719 original size:52 final size:50
Alignment explanation
Indices: 6343641--6343745 Score: 124
Period size: 52 Copynumber: 2.1 Consensus size: 50
6343631 AGGAATTTCT
* * * *
6343641 AATCCATTAACAGGATATTTGCTTTTTTAGCATA-AAGTGATAACCCTTACAC
1 AATCCATAAAAAGGATATTTGCTTTTTGA-C-TAGAAGCGAT-ACCCTTACAC
6343693 AATCCATAAAAAGGAT-TCTTGCTTTTTGACTAGAAGCGATACCCTTACAC
1 AATCCATAAAAAGGATAT-TTGCTTTTTGACTAGAAGCGATACCCTTACAC
6343743 AAT
1 AAT
6343746 TCACAAAGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
50 15 0.32
51 8 0.17
52 24 0.51
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.32
Consensus pattern (50 bp):
AATCCATAAAAAGGATATTTGCTTTTTGACTAGAAGCGATACCCTTACAC
Found at i:6347388 original size:14 final size:14
Alignment explanation
Indices: 6347369--6347395 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6347359 CAGTTCTTTA
6347369 GATAGTTCGATTAG
1 GATAGTTCGATTAG
6347383 GATAGTTCGATTA
1 GATAGTTCGATTA
6347396 TTAGAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (14 bp):
GATAGTTCGATTAG
Found at i:6349136 original size:13 final size:13
Alignment explanation
Indices: 6349118--6349142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6349108 TCTACATATG
6349118 AATGATTATATTA
1 AATGATTATATTA
6349131 AATGATTATATT
1 AATGATTATATT
6349143 TGCTAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AATGATTATATTA
Found at i:6351741 original size:64 final size:64
Alignment explanation
Indices: 6351670--6351789 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 64
6351660 GCAATCAAGG
* *
6351670 CTATTTGTTGTTACTTTTATCCATTGTTGAAGACTGTTAATGATTTGTTATTATTTGTTAAAGA
1 CTATTTGTTATTACTTTTATCCATTGTTGAAGACTGCTAATGATTTGTTATTATTTGTTAAAGA
** * * * *
6351734 CTATTTGTTATTGTTTTTATCCATTGTTTAATATTGCTAATGATTTGTTGTTATTT
1 CTATTTGTTATTACTTTTATCCATTGTTGAAGACTGCTAATGATTTGTTATTATTT
6351790 ACTCGTGACT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.23, C:0.07, G:0.14, T:0.56
Consensus pattern (64 bp):
CTATTTGTTATTACTTTTATCCATTGTTGAAGACTGCTAATGATTTGTTATTATTTGTTAAAGA
Found at i:6351800 original size:64 final size:64
Alignment explanation
Indices: 6351670--6351814 Score: 164
Period size: 64 Copynumber: 2.3 Consensus size: 64
6351660 GCAATCAAGG
** * **
6351670 CTATTTGTTGTTACTTTTATCCATTGTTGAAGACTGTTAATGATTTGTTATTATTTGTTAAAGA
1 CTATTTGTTGTTGTTTTTATCCATTGTTGAAGACTGCTAATGATTTGTTATTATTTACTAAAGA
* * * * * ***
6351734 CTATTTGTTATTGTTTTTATCCATTGTTTAATATTGCTAATGATTTGTTGTTATTTACTCGTGA
1 CTATTTGTTGTTGTTTTTATCCATTGTTGAAGACTGCTAATGATTTGTTATTATTTACTAAAGA
*
6351798 CTATTTATTGTTGTTTT
1 CTATTTGTTGTTGTTTT
6351815 CATTTATGTT
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.21, C:0.08, G:0.14, T:0.56
Consensus pattern (64 bp):
CTATTTGTTGTTGTTTTTATCCATTGTTGAAGACTGCTAATGATTTGTTATTATTTACTAAAGA
Found at i:6352684 original size:2 final size:2
Alignment explanation
Indices: 6352677--6352707 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6352667 CAAGACACAA
6352677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6352708 AAAACATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6353450 original size:2 final size:2
Alignment explanation
Indices: 6353445--6353475 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6353435 ATATACATAG
6353445 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
6353476 TATATAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6358753 original size:29 final size:29
Alignment explanation
Indices: 6358677--6358756 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
6358667 GCTGGGGGCC
***
6358677 AAAATTTTTAAAAATTTTGGCTAACATAT
1 AAAATTTTTAAAAATTTTTTATAACATAT
6358706 AAAATTTTTAAAAATTTTTTATAACATAT
1 AAAATTTTTAAAAATTTTTTATAACATAT
6358735 AAAATTTTT-AAAATTTTTTATA
1 AAAATTTTTAAAAATTTTTTATA
6358757 TATTCTTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 13 0.27
29 35 0.73
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (29 bp):
AAAATTTTTAAAAATTTTTTATAACATAT
Found at i:6364103 original size:2 final size:2
Alignment explanation
Indices: 6364096--6364120 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6364086 AAGGAACACA
6364096 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6364121 AAATAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6370000 original size:30 final size:28
Alignment explanation
Indices: 6369965--6370042 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 28
6369955 TTATAAATAA
6369965 AATATAATATAATATAAAAAATTAAAAATT
1 AATATAATATAATATAAAAAATT-AAAA-T
* *
6369995 TATATAATATAGGTA-AAAGAAATTAAAAT
1 AATATAATATA-ATATAAA-AAATTAAAAT
*
6370024 AACAT-ATATAATATAAAAA
1 AATATAATATAATATAAAAA
6370043 TTATATTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 4 0.10
28 8 0.20
29 4 0.10
30 17 0.43
31 7 0.17
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (28 bp):
AATATAATATAATATAAAAAATTAAAAT
Found at i:6370070 original size:33 final size:33
Alignment explanation
Indices: 6370033--6370105 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
6370023 TAACATATAT
*
6370033 AATATA-AAAATTATATTAAAGAAATAAAAATAA
1 AATATATAAAATTATAAT-AAGAAATAAAAATAA
* * *
6370066 AATATATAAGATTATAATAAGAAATGAAAGTAA
1 AATATATAAAATTATAATAAGAAATAAAAATAA
6370099 AATATAT
1 AATATAT
6370106 GACATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (33 bp):
AATATATAAAATTATAATAAGAAATAAAAATAA
Found at i:6370388 original size:15 final size:15
Alignment explanation
Indices: 6370337--6370379 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
6370327 CACATTGCTG
6370337 GCAATCATATTACTT
1 GCAATCATATTACTT
*
6370352 GCAATCATATTATTT
1 GCAATCATATTACTT
*
6370367 ACAATCATATTAC
1 GCAATCATATTAC
6370380 CTGTAATCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (15 bp):
GCAATCATATTACTT
Found at i:6372002 original size:403 final size:404
Alignment explanation
Indices: 6371240--6372044 Score: 1211
Period size: 403 Copynumber: 2.0 Consensus size: 404
6371230 ATCTTACTAA
* * *
6371240 TAATTGTAATAAAAATATTTCAAAGATCATCATTTAATGAATACACATTTTTAAATATAAATTTT
1 TAATTATAATAAAAATATTTCAAAGATCATCACTTAATGAATACACATTTATAAATATAAATTTT
6371305 GGATGTTTTACACAATTGAAAAATATTGATATGTTTATAGTGTCATGGTAAAAAAAAAAATGATG
66 GGATGTTTTACACAATTGAAAAATATTGATATGTTTATAGTGTCATGGT--AAAAAAAAATGATG
* **
6371370 AAATGGAAAATTTTTTGAAAATTAAAGTTAACATTCATCATAGATATATAGTTAAATGCTTTGAA
129 AAATGGAAAATTTTTTGAAAATTAAAATTAACATTCATCATAGATATATAGTTAAATGCTTCAAA
* *
6371435 AAATATTATTATTTATTTTGTCCATTTTCATTTCCATTCTTAATTTTAATCCTAAATTAGTGAGA
194 AAATATTATTATTTATTTTGTCAATTTTCATTTCCATTCTTAATTTTAATCCAAAATTAGTGAGA
* * ** *
6371500 ATCAAATGGCACCGTTATTTTTAATCAACTCCTTGTTGCTATGTGTGGTTCCGAGAACTAGTCCG
259 ATCAAATGGCACCATTATTTTTAATCAACTCCTTGTCGCTATGTGAAGTTCCGAGAACTAGTCCA
* * * *
6371565 CCTTGACATGAAAATTTGGAGTCATCACCAATCTTTTTTATGAGGTACGATTGGCCACTTATTAG
324 CCTCGACATGAAAATTTAGAGTCATCACCAATCTTTTTTATAAGGTACAATTGGCCACTTATTAG
*
6371630 ATTCGTTCTATTATAC
389 ATTCGTACTATTATAC
* **
6371646 TAATTATAATAAAAAATATTTCAAAGATCATTACTTAATGAATACATGTTTATAAATATAAATTT
1 TAATTATAAT-AAAAATATTTCAAAGATCATCACTTAATGAATACACATTTATAAATATAAATTT
* *
6371711 TGGATGTTTTACACAATTGATAAATATTGATATGTTTATAGTGTTATGGT-AAAAAAAATGATGA
65 TGGATGTTTTACACAATTGAAAAATATTGATATGTTTATAGTGTCATGGTAAAAAAAAATGATGA
* * * * * * *
6371775 AATGGAAAATTTTTTGAAAATTAAAATTTACTTTTATTATAGATGTGTGGTTAAAT-CTTCAAAA
130 AATGGAAAATTTTTTGAAAATTAAAATTAACATTCATCATAGATATATAGTTAAATGCTTCAAAA
* *
6371839 AATATTATTATTTATTTTGTCAATTTTCATTTCCATTTTTAATTTTGATCCAAAATTAGTGAGAA
195 AATATTATTATTTATTTTGTCAATTTTCATTTCCATTCTTAATTTTAATCCAAAATTAGTGAGAA
* * * *
6371904 TCAAATGGCACCATTGTTTTTAATCAACTCCTTGTCGCTATGTGCAAG-TCTGAGAACTCGTCTA
260 TCAAATGGCACCATTATTTTTAATCAACTCCTTGTCGCTATGTG-AAGTTCCGAGAACTAGTCCA
* *
6371968 CCTCGACATGAAAATTTAGAGTCATTATCAATCTTTTTTATAAGGTACAATTGGCCACTTATTAG
324 CCTCGACATGAAAATTTAGAGTCATCACCAATCTTTTTTATAAGGTACAATTGGCCACTTATTAG
6372033 ATTCGTACTATT
389 ATTCGTACTATT
6372045 TGCTGATGTC
Statistics
Matches: 359, Mismatches: 38, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
403 190 0.53
404 63 0.18
406 9 0.03
407 97 0.27
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (404 bp):
TAATTATAATAAAAATATTTCAAAGATCATCACTTAATGAATACACATTTATAAATATAAATTTT
GGATGTTTTACACAATTGAAAAATATTGATATGTTTATAGTGTCATGGTAAAAAAAAATGATGAA
ATGGAAAATTTTTTGAAAATTAAAATTAACATTCATCATAGATATATAGTTAAATGCTTCAAAAA
ATATTATTATTTATTTTGTCAATTTTCATTTCCATTCTTAATTTTAATCCAAAATTAGTGAGAAT
CAAATGGCACCATTATTTTTAATCAACTCCTTGTCGCTATGTGAAGTTCCGAGAACTAGTCCACC
TCGACATGAAAATTTAGAGTCATCACCAATCTTTTTTATAAGGTACAATTGGCCACTTATTAGAT
TCGTACTATTATAC
Found at i:6372332 original size:13 final size:13
Alignment explanation
Indices: 6372314--6372367 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
6372304 TCTTTCTCTA
6372314 ATTTATTTATATT
1 ATTTATTTATATT
*
6372327 ATTTATTTATTTT
1 ATTTATTTATATT
*
6372340 ATTCATTATTATCATT
1 ATTTA-T-TTAT-ATT
6372356 ATTTA-TTATATT
1 ATTTATTTATATT
6372368 TTTTCAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
12 3 0.09
13 20 0.59
14 1 0.03
15 4 0.12
16 6 0.18
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTATTTATATT
Found at i:6373720 original size:2 final size:2
Alignment explanation
Indices: 6373713--6373742 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6373703 GTTTTTGTAT
6373713 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
6373743 CCCCTACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6375357 original size:21 final size:21
Alignment explanation
Indices: 6375312--6375366 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
6375302 AAAGTGGTTG
* * *
6375312 GAGGTTTTGGAGAATGTACCTA
1 GAGGTTTTGAAG-AGGTACCCA
6375334 GAGGTTTTGAAGAGGTACCCA
1 GAGGTTTTGAAGAGGTACCCA
6375355 GAGGTTTT-AAGA
1 GAGGTTTTGAAGA
6375367 ATGCTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 4 0.13
21 15 0.50
22 11 0.37
ACGTcount: A:0.29, C:0.09, G:0.33, T:0.29
Consensus pattern (21 bp):
GAGGTTTTGAAGAGGTACCCA
Found at i:6376442 original size:47 final size:46
Alignment explanation
Indices: 6376304--6376478 Score: 165
Period size: 47 Copynumber: 3.7 Consensus size: 46
6376294 GTTAGTTGAA
* ** * * *
6376304 ATGAACAAATAATACATCAAAGGAGAGATATTTTCCTTAGTCAAATA
1 ATGAACAAATAATAAATCAAATAAGA-ATATTTTCCTAAGTCAAGTG
* * * * *
6376351 ATGAATAAATAGTAAATCTAAGTAATAATATTTTCCCAAGTCAAGTG
1 ATGAACAAATAATAAATC-AAATAAGAATATTTTCCTAAGTCAAGTG
6376398 ATGAACAAATAATAAATCAAATTAAGAATATTTTCCTAAGTCAAGTG
1 ATGAACAAATAATAAATCAAA-TAAGAATATTTTCCTAAGTCAAGTG
* *
6376445 CAAGCAA-AAATAATGAATCAAGATAA-AATATTTT
1 -ATG-AACAAATAATAAATCAA-ATAAGAATATTTT
6376479 TCGAAGCAAA
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
46 2 0.02
47 78 0.74
48 22 0.21
49 3 0.03
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (46 bp):
ATGAACAAATAATAAATCAAATAAGAATATTTTCCTAAGTCAAGTG
Found at i:6385021 original size:19 final size:19
Alignment explanation
Indices: 6384981--6385022 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
6384971 ACTACTTAAT
* *
6384981 AAAAGAAATAAGTAAAAGA
1 AAAAGAAAAAAATAAAAGA
6385000 AAAAGAAAAAAATGAAAA-A
1 AAAAGAAAAAAAT-AAAAGA
6385019 AAAA
1 AAAA
6385023 TGAAGTGTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAAGAAAAAAATAAAAGA
Found at i:6397127 original size:36 final size:36
Alignment explanation
Indices: 6397040--6397134 Score: 154
Period size: 36 Copynumber: 2.6 Consensus size: 36
6397030 GCATTTCAAT
* * *
6397040 GATCAAGCACAATCTCTCAATATAATGCCTTTTATG
1 GATCAAGCACAACCTTTCAACATAATGCCTTTTATG
6397076 GATCAAGCACAACCTTTCAACATAATGCCTTTTATG
1 GATCAAGCACAACCTTTCAACATAATGCCTTTTATG
6397112 GATCAAGCACAACCTTTGCAACA
1 GATCAAGCACAACCTTT-CAACA
6397135 CTACCTTTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 50 0.91
37 5 0.09
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (36 bp):
GATCAAGCACAACCTTTCAACATAATGCCTTTTATG
Found at i:6397959 original size:21 final size:22
Alignment explanation
Indices: 6397915--6397965 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
6397905 TAAAGTATAC
* *
6397915 TCAAACAAGTTCAAAAACTCAT
1 TCAAACAACTTCAAAAACTAAT
6397937 TCAAACAACTTCAAAAA-TAAT
1 TCAAACAACTTCAAAAACTAAT
6397958 TCAAACAA
1 TCAAACAA
6397966 GTTGAAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.55, C:0.22, G:0.02, T:0.22
Consensus pattern (22 bp):
TCAAACAACTTCAAAAACTAAT
Found at i:6397980 original size:21 final size:21
Alignment explanation
Indices: 6397915--6397982 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
6397905 TAAAGTATAC
6397915 TCAAACAAGTTCAAAAACTCAT
1 TCAAACAAGTTCAAAAA-TCAT
* *
6397937 TCAAACAACTTCAAAAATAAT
1 TCAAACAAGTTCAAAAATCAT
* *
6397958 TCAAACAAGTTGAAAGATCAT
1 TCAAACAAGTTCAAAAATCAT
6397979 TCAA
1 TCAA
6397983 GTAATCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 24 0.60
22 16 0.40
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.24
Consensus pattern (21 bp):
TCAAACAAGTTCAAAAATCAT
Found at i:6398144 original size:21 final size:20
Alignment explanation
Indices: 6398076--6398144 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
6398066 TTCAAAAACA
* *
6398076 CATTCAAACAACTTCAAAAAT
1 CATTCAAACAAGTTC-AAGAT
6398097 -ATTCAAACAAGTTCAATGAT
1 CATTCAAACAAGTTCAA-GAT
*
6398117 CACTCAAACAAGTTCAGAGAT
1 CATTCAAACAAGTTCA-AGAT
6398138 CATTCAA
1 CATTCAA
6398145 GCAATTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.05
20 15 0.37
21 23 0.56
22 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (20 bp):
CATTCAAACAAGTTCAAGAT
Found at i:6398632 original size:15 final size:15
Alignment explanation
Indices: 6398608--6398639 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6398598 AAGGAAAATG
6398608 AATAAACAAATATTT
1 AATAAACAAATATTT
*
6398623 AATAAGCAAATATTT
1 AATAAACAAATATTT
6398638 AA
1 AA
6398640 CCTTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (15 bp):
AATAAACAAATATTT
Found at i:6401006 original size:29 final size:28
Alignment explanation
Indices: 6400952--6401067 Score: 133
Period size: 29 Copynumber: 4.0 Consensus size: 28
6400942 GTTTTCTTGT
*
6400952 TTTTCTTGTCTTAAATTAAGACAAACATG
1 TTTTCTTGTC-TAAATTAAGAAAAACATG
* * *
6400981 TTTTTTTGTCAAAATTAAAATAAAACATG
1 TTTTCTTGTCTAAATTAAGA-AAAACATG
* * *
6401010 TTTGCTTGCCTAAATTAAGACAAACATG
1 TTTTCTTGTCTAAATTAAGAAAAACATG
*
6401038 TTTTCTTGTTTAAATTAAGACAAAACATG
1 TTTTCTTGTCTAAATTAAGA-AAAACATG
6401067 T
1 T
6401068 AAAAGCTACC
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
28 32 0.45
29 39 0.55
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (28 bp):
TTTTCTTGTCTAAATTAAGAAAAACATG
Found at i:6402818 original size:2 final size:2
Alignment explanation
Indices: 6402813--6402839 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6402803 TTTTTTGTAT
6402813 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
6402840 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6412116 original size:44 final size:44
Alignment explanation
Indices: 6412057--6412166 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
6412047 TTCTTGAAGC
* * * *
6412057 AAGAAGAATTGATATTCAAG-GAGGCTAGAATCAATTCTTCATAT
1 AAGAAGAACTGATATTCAAGAAAGGCGAGAATCAATTC-TCAAAT
* * **
6412101 AAGAAGAACTAATATT-TAGAAAGGCGAGAATTGATTCTCAAAT
1 AAGAAGAACTGATATTCAAGAAAGGCGAGAATCAATTCTCAAAT
6412144 AAGAAGAACTGATATCTCAAGAA
1 AAGAAGAACTGATAT-TCAAGAA
6412167 TGAAGAATCG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
43 21 0.40
44 28 0.53
45 4 0.08
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.25
Consensus pattern (44 bp):
AAGAAGAACTGATATTCAAGAAAGGCGAGAATCAATTCTCAAAT
Found at i:6412151 original size:21 final size:20
Alignment explanation
Indices: 6412127--6412186 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
6412117 TAGAAAGGCG
6412127 AGAATTGATTCTCAAATAAGA
1 AGAATTGATTCTCAAA-AAGA
* *
6412148 AGAACTGATATCTCAAGAATGA
1 AGAATTGAT-TCTCAA-AAAGA
* *
6412170 AGAATCGATTCACAAAA
1 AGAATTGATTCTCAAAA
6412187 GCAGAAAGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.06
21 13 0.41
22 16 0.50
23 1 0.03
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.23
Consensus pattern (20 bp):
AGAATTGATTCTCAAAAAGA
Found at i:6419474 original size:36 final size:37
Alignment explanation
Indices: 6419403--6419476 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
6419393 CAGTCTCAAT
* * * *
6419403 CTTGCCTTTTCAACAAGGTTAGGCGTAACCTTTACAA
1 CTTGCCTTTTCAACAAGATCAGGCATAACCGTTACAA
*
6419440 CTTGCCTTTT-AATAAGATCAGGCATAACCGTTACAA
1 CTTGCCTTTTCAACAAGATCAGGCATAACCGTTACAA
6419476 C
1 C
6419477 ATGTCTATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 22 0.69
37 10 0.31
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (37 bp):
CTTGCCTTTTCAACAAGATCAGGCATAACCGTTACAA
Found at i:6429720 original size:42 final size:43
Alignment explanation
Indices: 6429634--6429724 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 43
6429624 TATTTTATTT
* * *
6429634 TATTTTATTTTTAAATATTAATAATTGATAATTTCAATATTAA
1 TATTTTATTTGTAAATATTAATAATTAATAATTTAAATATTAA
* *
6429677 TATTTTATTTGT-AAT-TTAATCATTAATATTTTAAAATATTAA
1 TATTTTATTTGTAAATATTAATAATTAATAATTT-AAATATTAA
6429719 TATTTT
1 TATTTT
6429725 TTAATTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 14 0.33
42 17 0.40
43 11 0.26
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (43 bp):
TATTTTATTTGTAAATATTAATAATTAATAATTTAAATATTAA
Found at i:6429727 original size:87 final size:86
Alignment explanation
Indices: 6429574--6429739 Score: 194
Period size: 87 Copynumber: 1.9 Consensus size: 86
6429564 TATTTCATTT
* * * * *
6429574 ATAATTTAATCATTAATATTTTATTTAATTTAAACATTATTATGATCAATTATTTTATTTTATTT
1 ATAATTTAATCATTAATATTTTATTTAATTTAAACATTAATATGATAAAATATTTAATATTATTT
*
6429639 TATTTTTAAATATTAATAATTG
66 TA-ATTTAAATATTAATAATTG
* **
6429661 ATAATTTCAAT-ATTAATATTTTATTTGTAATTTAATCATTAATATTTTAAAATA-TTAATATT-
1 ATAATTT-AATCATTAATATTTTA-TT-TAATTTAAACATTAATATGATAAAATATTTAATATTA
6429723 TTTTAATTTAAATATTA
63 TTTTAATTTAAATATTA
6429740 TTGTGATTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
86 11 0.16
87 24 0.36
88 11 0.16
89 21 0.31
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (86 bp):
ATAATTTAATCATTAATATTTTATTTAATTTAAACATTAATATGATAAAATATTTAATATTATTT
TAATTTAAATATTAATAATTG
Found at i:6429738 original size:22 final size:22
Alignment explanation
Indices: 6429643--6429739 Score: 64
Period size: 22 Copynumber: 4.5 Consensus size: 22
6429633 TTATTTTATT
* **
6429643 TTTAAATATTAATAATTGATAA
1 TTTAAATATTAATATTTTTTAA
*
6429665 TTTCAATATTAATATTTTATTTGTAA
1 TTTAAATATTAATA--TT-TTT-TAA
6429691 TTT-AATCATTAATA--TTTT-A
1 TTTAAAT-ATTAATATTTTTTAA
6429710 ---AAATATTAATATTTTTTAA
1 TTTAAATATTAATATTTTTTAA
6429729 TTTAAATATTA
1 TTTAAATATTA
6429740 TTGTGATTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 24
0.68 0.05 0.28
Matches are distributed among these distances:
16 7 0.12
17 3 0.05
18 4 0.07
19 2 0.03
20 1 0.02
21 3 0.05
22 21 0.36
24 1 0.02
25 4 0.07
26 13 0.22
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTAAATATTAATATTTTTTAA
Done.