Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 33
Found at i:2782191 original size:64 final size:63
Alignment explanation
Indices: 2782119--2782253 Score: 243
Period size: 64 Copynumber: 2.1 Consensus size: 63
2782109 AAAATCGCAA
*
2782119 TGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCACCGTT
1 TGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCACC-AT
*
2782183 TGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCACTGTTGCGATAGCACTGTTCACCAT
1 TGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCACCAT
2782246 TGCGATAG
1 TGCGATAG
2782254 TGATCAAAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
63 9 0.13
64 60 0.87
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.30
Consensus pattern (63 bp):
TGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCACCGTTGCGATAGCACTGTTCACCAT
Found at i:2782960 original size:21 final size:21
Alignment explanation
Indices: 2782934--2783015 Score: 146
Period size: 21 Copynumber: 3.9 Consensus size: 21
2782924 AATTCTCAAT
2782934 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
2782955 GTGAACAGTGCTATTGCAACG
1 GTGAACAGTGCTATCGCAACG
2782976 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
2782997 GTAAACAGTGCTATCGCAA
1 GTGAACAGTGCTATCGCAA
2783016 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:2783054 original size:21 final size:21
Alignment explanation
Indices: 2783038--2783099 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
2783028 CTATCGCATT
*
2783038 GCGAATTCGAAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
2783059 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
*
2783080 ACGAATTCGGAAAATCGCAA
1 GCGAATTCGGAAAATCGCAA
2783100 TGTGATAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.15
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:2784405 original size:94 final size:93
Alignment explanation
Indices: 2784182--2784530 Score: 381
Period size: 93 Copynumber: 3.9 Consensus size: 93
2784172 TTTTTAACCA
* * * *
2784182 TTAATCGAACCGAAACTTATTTGGAAATTATTAACCGAACCTAATTAACCGATTTTTTTCTTTTA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTCTTTAA
**
2784247 CATTAATCGAATTGAAATTATTTGACCG
66 CATTAATCGAATCAAAATTATTTGACCG
*
2784275 TTAATCTAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTCTTTAA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTCTTTAA
2784340 CATTAATCGAATCAAAATTATTTGACCG
66 CATTAATCGAATCAAAATTATTTGACCG
*
2784368 TTAATTCGAACCGAAATTTATTTGAAAATTATTAACCG----------A---ATTTGTTTCTTTA
1 TTAA-TCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTCTTTA
* * * *
2784420 ACTATTAATTGAACCGAAATTATTTGATCG
65 AC-ATTAATCGAATCAAAATTATTTGACCG
* * * *
2784450 TTAATCGAACCCAAATTTATTTGAAAATTAATAACCGAA-TAAAATAA---ATTATTTTTCTTTA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATT-TTTTTCTTTA
* *
2784511 ACCGTTAATCGAACCAAAAT
65 A-CATTAATCGAATCAAAAT
2784531 ATATGAAAAT
Statistics
Matches: 224, Mismatches: 19, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
81 45 0.20
82 27 0.12
84 1 0.00
90 4 0.02
91 24 0.11
92 1 0.00
93 90 0.40
94 32 0.14
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (93 bp):
TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTCTTTAA
CATTAATCGAATCAAAATTATTTGACCG
Found at i:2784468 original size:81 final size:81
Alignment explanation
Indices: 2784318--2784489 Score: 258
Period size: 81 Copynumber: 2.1 Consensus size: 81
2784308 ACCGAACCAA
* * *
2784318 ATTAACCG-ATTTTTTTCTTTAACATTAATCGAATCAAAATTATTTGACCGTTAATTCGAACCGA
1 ATTAACCGAATTTGTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATTCGAACCCA
2784382 AATTTATTTGAAAATT
66 AATTTATTTGAAAATT
* * *
2784398 ATTAACCGAATTTGTTTCTTTAACTATTAATTGAACCGAAATTATTTGATCGTTAA-TCGAACCC
1 ATTAACCGAATTTGTTTCTTTAAC-ATTAATCGAACCAAAATTATTTGACCGTTAATTCGAACCC
2784462 AAATTTATTTGAAAATT
65 AAATTTATTTGAAAATT
*
2784479 AATAACCGAAT
1 ATTAACCGAAT
2784490 AAAATAAATT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
80 8 0.10
81 48 0.58
82 27 0.33
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (81 bp):
ATTAACCGAATTTGTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATTCGAACCCA
AATTTATTTGAAAATT
Found at i:2784480 original size:27 final size:26
Alignment explanation
Indices: 2784423--2784481 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
2784413 TTCTTTAACT
* * **
2784423 ATTAATTGAACCGAAATTATTTGATC
1 ATTAATCGAACCCAAATTATTTGAAA
*
2784449 GTTAATCGAACCCAAATTTATTTGAAA
1 ATTAATCGAACCCAAA-TTATTTGAAA
2784476 ATTAAT
1 ATTAAT
2784482 AACCGAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (26 bp):
ATTAATCGAACCCAAATTATTTGAAA
Found at i:2784630 original size:135 final size:137
Alignment explanation
Indices: 2784481--2784726 Score: 370
Period size: 137 Copynumber: 1.8 Consensus size: 137
2784471 TGAAAATTAA
*
2784481 TAACCGAATAAAATAAATTATTTTTCTTTAACCGTTAATCGAACC-AAA-ATATATGAAAATTAT
1 TAACCGAATAAAATAAATTATTTTTCCTTAACCGTTAATCGAACCGAAATATATATGAAAATTAT
* * * * *
2784544 TAATCGAACCAAATCAACCTATTTTTTTCTTTAACCATTAATCGAAATTTATTTGAAATTTATTA
66 TAACCGAACCAAATCAACCAAATTTTTTATGTAACCATTAATCGAAATTTATTTGAAATTTATTA
2784609 ACCAAAT
131 ACCAAAT
* * *
2784616 TAACCTAATAAAATAAATTATTTTTCCTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTAT
1 TAACCGAATAAAATAAATTATTTTTCCTTAACCGTTAATCGAACCGAAATATATATGAAAATTAT
* * *
2784681 TAACCGAATCGAATTAACCAAATTTTTTATGTAACCATTAATCGAA
66 TAACCGAACCAAATCAACCAAATTTTTTATGTAACCATTAATCGAA
2784727 CTGAAATTTA
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
135 43 0.44
136 3 0.03
137 51 0.53
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (137 bp):
TAACCGAATAAAATAAATTATTTTTCCTTAACCGTTAATCGAACCGAAATATATATGAAAATTAT
TAACCGAACCAAATCAACCAAATTTTTTATGTAACCATTAATCGAAATTTATTTGAAATTTATTA
ACCAAAT
Found at i:2785171 original size:29 final size:30
Alignment explanation
Indices: 2785137--2785202 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
2785127 TTAACGGTGC
2785137 GGTGGTCTG-ATTGA-ATAATTAAAA-AGTTT
1 GGTGGTCTGAATTGAGATAA--AAAATAGTTT
2785166 GGTGGTC-GAATTGAGATAAAAAATAGTTT
1 GGTGGTCTGAATTGAGATAAAAAATAGTTT
2785195 GGTGGTCT
1 GGTGGTCT
2785203 CCCGTGTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
28 5 0.15
29 24 0.73
30 4 0.12
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.35
Consensus pattern (30 bp):
GGTGGTCTGAATTGAGATAAAAAATAGTTT
Found at i:2785662 original size:20 final size:20
Alignment explanation
Indices: 2785632--2785679 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2785622 TTTCTTGATC
2785632 GTCAT-CCCCTTCTTTCAAT
1 GTCATCCCCCTTCTTTCAAT
*
2785651 GTCATCCCCCTTCTTTCATT
1 GTCATCCCCCTTCTTTCAAT
2785671 GTCATCCCC
1 GTCATCCCC
2785680 AAGTAGGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.12, C:0.42, G:0.06, T:0.40
Consensus pattern (20 bp):
GTCATCCCCCTTCTTTCAAT
Found at i:2786565 original size:40 final size:40
Alignment explanation
Indices: 2786502--2786586 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
2786492 TTGTTTCAAT
* * *
2786502 CAATAATCAGTACATATAGCTCAATTGGGAATTAGACATC
1 CAATAATCAATACATATAGCTCAATTGAGAATTAGACAAC
* *
2786542 CAATAATCAATATATAT-GACTCAATTGAGAATTATACAAC
1 CAATAATCAATACATATAG-CTCAATTGAGAATTAGACAAC
2786582 CAATA
1 CAATA
2786587 TTAAAGTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.03
40 38 0.97
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (40 bp):
CAATAATCAATACATATAGCTCAATTGAGAATTAGACAAC
Found at i:2795824 original size:22 final size:22
Alignment explanation
Indices: 2795799--2795853 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2795789 TACTGTTCAC
*
2795799 GTACTGTTCATTACTATTTACA
1 GTACTGTTCATTACTATTAACA
* *
2795821 GTACTGTTCATTACTGTTAACG
1 GTACTGTTCATTACTATTAACA
*
2795843 GTATTGTTCAT
1 GTACTGTTCAT
2795854 ACCGTATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (22 bp):
GTACTGTTCATTACTATTAACA
Found at i:2799011 original size:43 final size:43
Alignment explanation
Indices: 2798945--2799040 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 43
2798935 TTAGCAAAGG
* * *
2798945 TTTGATTTTGGGAATGTCTTGAATCAAGAATTTTT-GGTAGAGT
1 TTTGATTTTGGGAATATCATGAATCAAG-ATTTTTGGGTAGAGA
*
2798988 TTTGATTTTGGGAATAAT-ATGAATCATGATTTTTGGGTAGAGA
1 TTTGATTTTGGGAAT-ATCATGAATCAAGATTTTTGGGTAGAGA
*
2799031 TATGATTTTG
1 TTTGATTTTG
2799041 AGATTTTGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 6 0.13
43 39 0.85
44 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.25, T:0.45
Consensus pattern (43 bp):
TTTGATTTTGGGAATATCATGAATCAAGATTTTTGGGTAGAGA
Found at i:2801720 original size:18 final size:18
Alignment explanation
Indices: 2801699--2801741 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2801689 GAAGACCTCG
*
2801699 AGAAAAAGGAC-GAGACAA
1 AGAAAAA-GACGGAGAAAA
*
2801717 AGAAAGAGACGGAGAAAA
1 AGAAAAAGACGGAGAAAA
2801735 AGAAAAA
1 AGAAAAA
2801742 CGTTGGAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.65, C:0.07, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAAAAGACGGAGAAAA
Found at i:2809646 original size:26 final size:26
Alignment explanation
Indices: 2809593--2809646 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
2809583 GAATCGTGAT
**
2809593 TTTTGGGTAGAGATCTAATTTTGAGA
1 TTTTGGGTAGAGATCTAATTAAGAGA
* * *
2809619 TTTTGGGTAGAGGTCTGATTAAGGGA
1 TTTTGGGTAGAGATCTAATTAAGAGA
2809645 TT
1 TT
2809647 AAGTTATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.41
Consensus pattern (26 bp):
TTTTGGGTAGAGATCTAATTAAGAGA
Found at i:2810712 original size:43 final size:43
Alignment explanation
Indices: 2810643--2810741 Score: 101
Period size: 43 Copynumber: 2.3 Consensus size: 43
2810633 TTTTTTGCAG
* * *
2810643 AGGTCTGATTTTGGTAATGTCTTGAATCAAGATTTTTGGGTAA
1 AGGTATGATTTTGGGAATGTCATGAATCAAGATTTTTGGGTAA
* ** * *
2810686 AGGTTTGATTTTGGGAATGGT-ATGAATCGTGGTTTTTGGGTAG
1 AGGTATGATTTTGGGAAT-GTCATGAATCAAGATTTTTGGGTAA
*
2810729 AGATATGATTTTG
1 AGGTATGATTTTG
2810742 AGTTTTTGGG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
43 44 0.96
44 2 0.04
ACGTcount: A:0.23, C:0.04, G:0.30, T:0.42
Consensus pattern (43 bp):
AGGTATGATTTTGGGAATGTCATGAATCAAGATTTTTGGGTAA
Found at i:2812327 original size:16 final size:17
Alignment explanation
Indices: 2812284--2812327 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2812274 AATTTCTATT
2812284 TTATTTTATTTTAGTCA
1 TTATTTTATTTTAGTCA
* * *
2812301 TTAATTAATTTT-GTTA
1 TTATTTTATTTTAGTCA
2812317 TTATTTTATTT
1 TTATTTTATTT
2812328 ATCAATATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (17 bp):
TTATTTTATTTTAGTCA
Found at i:2812491 original size:2 final size:2
Alignment explanation
Indices: 2812484--2812557 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
2812474 AGTCACATGA
2812484 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
2812526 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
2812558 GAAAGTTTCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2813777 original size:15 final size:16
Alignment explanation
Indices: 2813740--2813779 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2813730 TCTTTAATTA
2813740 TATTTTTAAAGTATTT
1 TATTTTTAAAGTATTT
* *
2813756 TAATTTTCAA-TATTT
1 TATTTTTAAAGTATTT
2813771 TATTTTTAA
1 TATTTTTAA
2813780 TTAAAATATC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTTTTAAAGTATTT
Found at i:2815584 original size:2 final size:2
Alignment explanation
Indices: 2815577--2815601 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2815567 TTGTTTTGTT
2815577 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 T
2815602 TAGTTTTTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2832266 original size:17 final size:17
Alignment explanation
Indices: 2832241--2832274 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2832231 ATTTTCGGTT
*
2832241 TTAATCTAAAATATTAC
1 TTAACCTAAAATATTAC
*
2832258 TTAACCTAAAATGTTAC
1 TTAACCTAAAATATTAC
2832275 CTAGTCCAAT
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:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (17 bp):
TTAACCTAAAATATTAC
Found at i:2835938 original size:2 final size:2
Alignment explanation
Indices: 2835931--2835971 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
2835921 TCTTTACAAA
2835931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
2835972 GGACTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2838592 original size:3 final size:3
Alignment explanation
Indices: 2838584--2838616 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2838574 GTGAGCCACC
2838584 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2838617 ATTTTTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2843616 original size:177 final size:179
Alignment explanation
Indices: 2843320--2843674 Score: 687
Period size: 177 Copynumber: 2.0 Consensus size: 179
2843310 AAGGTAATTA
2843320 GCTTAAAGGACAACTTCTCCCCACATGTTATATGATAACCCAAAACTGCCTAACAAGGCATTCAT
1 GCTTAAAGGACAACTTCTCCCCACATGTTATATGATAACCCAAAACTGCCTAACAAGGCATTCAT
2843385 CATTTCTTTTAGAGTCTGAGTTTTCCGCTCAACTACTCCATTTGGTTGAGGAGAATAAGGT-GTG
66 CATTTCTTTTAGAGTCTGAGTTTTCCGCTCAACTACTCCATTTGGTTGAGGAGAATAAGGTGGTG
2843449 TTACTTCGTGAATAATATCATGTTGTGGGTTCAACATCTTCA-CACCAC
131 TTACTTCGTGAATAATATCATGTTGTGGGTTCAACATCTTCACCACCAC
2843497 GCTTAAAGGACAACTTCTCCCCACATGTTATATGATAACCCAAAACTGCCTAACAAGGCATTCAT
1 GCTTAAAGGACAACTTCTCCCCACATGTTATATGATAACCCAAAACTGCCTAACAAGGCATTCAT
*
2843562 CATTTCTTTTAGAGTCTGAGTTTTCCGCTCAACTACTCTATTTGGTTGAGGAGAATAAGGTGGTG
66 CATTTCTTTTAGAGTCTGAGTTTTCCGCTCAACTACTCCATTTGGTTGAGGAGAATAAGGTGGTG
2843627 TTACTTCGTGAATAATATCATGTTGTGGGTTCAACATCTTCACCACCA
131 TTACTTCGTGAATAATATCATGTTGTGGGTTCAACATCTTCACCACCA
2843675 TGATCACTTC
Statistics
Matches: 175, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
177 125 0.71
178 45 0.26
179 5 0.03
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (179 bp):
GCTTAAAGGACAACTTCTCCCCACATGTTATATGATAACCCAAAACTGCCTAACAAGGCATTCAT
CATTTCTTTTAGAGTCTGAGTTTTCCGCTCAACTACTCCATTTGGTTGAGGAGAATAAGGTGGTG
TTACTTCGTGAATAATATCATGTTGTGGGTTCAACATCTTCACCACCAC
Found at i:2846259 original size:13 final size:12
Alignment explanation
Indices: 2846238--2846271 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
2846228 AGAAACAAGC
2846238 AAAAAATAATAG
1 AAAAAATAATAG
2846250 AAAAAGATAATAG
1 AAAAA-ATAATAG
*
2846263 AAAATATAA
1 AAAAAATAA
2846272 AGTTCCCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (12 bp):
AAAAAATAATAG
Found at i:2850455 original size:19 final size:17
Alignment explanation
Indices: 2850401--2850445 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
2850391 AATAATTGTT
2850401 ATAATATTTTTCTCTAA
1 ATAATATTTTTCTCTAA
2850418 ATAATATTTTTCTCTAA
1 ATAATATTTTTCTCTAA
2850435 ATAATATTTTT
1 ATAATATTTTT
2850446 TTAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAATATTTTTCTCTAA
Found at i:2851052 original size:12 final size:12
Alignment explanation
Indices: 2851044--2851150 Score: 106
Period size: 12 Copynumber: 8.9 Consensus size: 12
2851034 GAACGAGTTG
2851044 ATAAACGAGCTA
1 ATAAACGAGCTA
*
2851056 ATAAACGAGCTC
1 ATAAACGAGCTA
* * *
2851068 ATAAATGAACTC
1 ATAAACGAGCTA
2851080 ATAAACGAGCTA
1 ATAAACGAGCTA
*
2851092 ATAAACGAGCTC
1 ATAAACGAGCTA
* * *
2851104 ATAAATGAACTC
1 ATAAACGAGCTA
*
2851116 ATAAACGAGCTC
1 ATAAACGAGCTA
* * *
2851128 ATAAATGAACTC
1 ATAAACGAGCTA
2851140 ATAAACGAGCT
1 ATAAACGAGCT
2851151 TCTTCGTGAA
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.20
Consensus pattern (12 bp):
ATAAACGAGCTA
Found at i:2851089 original size:36 final size:36
Alignment explanation
Indices: 2851044--2851144 Score: 175
Period size: 36 Copynumber: 2.8 Consensus size: 36
2851034 GAACGAGTTG
2851044 ATAAACGAGCTAATAAACGAGCTCATAAATGAACTC
1 ATAAACGAGCTAATAAACGAGCTCATAAATGAACTC
2851080 ATAAACGAGCTAATAAACGAGCTCATAAATGAACTC
1 ATAAACGAGCTAATAAACGAGCTCATAAATGAACTC
* * *
2851116 ATAAACGAGCTCATAAATGAACTCATAAA
1 ATAAACGAGCTAATAAACGAGCTCATAAA
2851145 CGAGCTTCTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.20
Consensus pattern (36 bp):
ATAAACGAGCTAATAAACGAGCTCATAAATGAACTC
Found at i:2851161 original size:24 final size:24
Alignment explanation
Indices: 2851044--2851150 Score: 142
Period size: 24 Copynumber: 4.5 Consensus size: 24
2851034 GAACGAGTTG
* * *
2851044 ATAAACGAGCTAATAAACGAGCTC
1 ATAAACGAGCTCATAAATGAACTC
* * * * *
2851068 ATAAATGAACTCATAAACGAGCTA
1 ATAAACGAGCTCATAAATGAACTC
2851092 ATAAACGAGCTCATAAATGAACTC
1 ATAAACGAGCTCATAAATGAACTC
2851116 ATAAACGAGCTCATAAATGAACTC
1 ATAAACGAGCTCATAAATGAACTC
2851140 ATAAACGAGCT
1 ATAAACGAGCT
2851151 TCTTCGTGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.20
Consensus pattern (24 bp):
ATAAACGAGCTCATAAATGAACTC
Found at i:2852203 original size:11 final size:12
Alignment explanation
Indices: 2852183--2852253 Score: 65
Period size: 11 Copynumber: 5.9 Consensus size: 12
2852173 ACATTTGGTT
2852183 TTTTTATTATTA
1 TTTTTATTATTA
2852195 TTTTT-TTATTA
1 TTTTTATTATTA
*
2852206 TTATTATATATTA
1 TTTTTAT-TATTA
**
2852219 TTAGTATTATTA
1 TTTTTATTATTA
*
2852231 TATATTATTA-TA
1 T-TTTTATTATTA
*
2852243 TTATTATTATT
1 TTTTTATTATT
2852254 TATTACAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
11 18 0.35
12 16 0.31
13 18 0.35
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:2852206 original size:3 final size:3
Alignment explanation
Indices: 2852186--2852258 Score: 87
Period size: 3 Copynumber: 24.0 Consensus size: 3
2852176 TTTGGTTTTT
* *
2852186 TTA TTA TTA TT- TTT TTA TTA TTA TTA TATA TTA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
2852231 TATA TTA TTA -TA TTA TTA TTA TTTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA -TTA TTA
2852259 CAGATACAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.06
3 49 0.79
4 9 0.15
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2852217 original size:27 final size:29
Alignment explanation
Indices: 2852186--2852258 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
2852176 TTTGGTTTTT
*
2852186 TTATTATTATTTTTTTAT-TATTATTATA
1 TTATTATTATTTTATTATATATTATTATA
*
2852214 -TATTATTAGTATTATTATATATTATTATA
1 TTATTATTA-TTTTATTATATATTATTATA
2852243 TTATTATTA-TTTATTA
1 TTATTATTATTTTATTA
2852259 CAGATACAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 8 0.21
28 13 0.33
29 10 0.26
30 8 0.21
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (29 bp):
TTATTATTATTTTATTATATATTATTATA
Found at i:2856052 original size:15 final size:15
Alignment explanation
Indices: 2856025--2856063 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2856015 TAATTTACAT
2856025 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
2856039 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
2856054 TTTGCATTTG
1 TTTACATTTG
2856064 TATTTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:2856083 original size:20 final size:20
Alignment explanation
Indices: 2856054--2856092 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2856044 ATTTGGCATC
*
2856054 TTTGCATTTGTATTTTTATG
1 TTTGCATTTGTATTCTTATG
*
2856074 TTTGCTTTTGTATTCTTAT
1 TTTGCATTTGTATTCTTAT
2856093 TATTACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67
Consensus pattern (20 bp):
TTTGCATTTGTATTCTTATG
Found at i:2859225 original size:25 final size:26
Alignment explanation
Indices: 2859196--2859247 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
2859186 AAGTATACTC
*
2859196 ATCCAGCAAAGAAA-GAAAAAAGAAA
1 ATCCAGCAAAGAAAGGAAAAAAAAAA
2859221 ATCCAGCAAAGAAAGGAAAAAAAAAA
1 ATCCAGCAAAGAAAGGAAAAAAAAAA
2859247 A
1 A
2859248 AGAGGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.69, C:0.12, G:0.15, T:0.04
Consensus pattern (26 bp):
ATCCAGCAAAGAAAGGAAAAAAAAAA
Found at i:2859255 original size:16 final size:16
Alignment explanation
Indices: 2859234--2859264 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2859224 CAGCAAAGAA
2859234 AGGAAAAAAAAAAAAG
1 AGGAAAAAAAAAAAAG
2859250 AGGAAAAAAAAAAAA
1 AGGAAAAAAAAAAAA
2859265 AAAAAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AGGAAAAAAAAAAAAG
Found at i:2859255 original size:21 final size:21
Alignment explanation
Indices: 2859237--2859277 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2859227 CAAAGAAAGG
*
2859237 AAAAAAAAAAAAGAGGAAAAA
1 AAAAAAAAAAAAAAGGAAAAA
2859258 AAAAAAAAAAAAAAGGAAAA
1 AAAAAAAAAAAAAAGGAAAA
2859278 TTGAATCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAAGGAAAAA
Found at i:2859277 original size:16 final size:16
Alignment explanation
Indices: 2859232--2859266 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2859222 TCCAGCAAAG
2859232 AAAGGAAAAAAAAAAA
1 AAAGGAAAAAAAAAAA
*
2859248 AGAGGAAAAAAAAAAA
1 AAAGGAAAAAAAAAAA
2859264 AAA
1 AAA
2859267 AAAAAGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAGGAAAAAAAAAAA
Found at i:2863625 original size:47 final size:48
Alignment explanation
Indices: 2863565--2863659 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
2863555 ATGCTTACGA
* *
2863565 ACATCTGAGCAG-AAGC-CAGAAAAGGATGAAGGTATTGTCAAGTGTTT
1 ACATCTGAGCAGAAACCACAGAAAA-GATGAAGGTATTGTCAAATGTTT
* *
2863612 ACATCTTGA-CAGAAACCACAGGAAAGATGAATGTATTGTCAAATGTTT
1 ACATC-TGAGCAGAAACCACAGAAAAGATGAAGGTATTGTCAAATGTTT
2863660 TACGAACCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
47 8 0.20
48 27 0.66
49 6 0.15
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (48 bp):
ACATCTGAGCAGAAACCACAGAAAAGATGAAGGTATTGTCAAATGTTT
Found at i:2864464 original size:113 final size:113
Alignment explanation
Indices: 2864214--2864931 Score: 922
Period size: 113 Copynumber: 6.5 Consensus size: 113
2864204 TTAGCAAAGA
2864214 CTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTC---ATGAGAAGAACTCATCT
1 CTCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCT
2864276 GAAGAAGGAAGAAGAAATT-ATAA--AGAAGAATTTGTT-AACCTTTTG
65 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
2864321 CTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1 CTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
*
2864386 AAGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
2864434 CTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTA
1 CTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
*
2864499 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
2864547 CTCAAATCCATCATTTGATGAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1 CTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
*
2864612 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
* *** * ** *
2864660 CTCAAATTCATCACCCGGTGGATCAGCAGTGCC------AG-T--T-A-GAGAAGAACTCATCTG
1 CTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * * *
2864714 AAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
** * ** * *
2864762 -TTGAAT-CATCATTTGATGGATCAGCATCCCCAGGAAAGAGTTCATAATGAGAAGAACTCATAT
1 CTCAAATCCATCATTTGATGGATCAGCTTTTCCA-GAAAAAGTTCATAATGAGAAGAACTCATCT
* * *
2864825 GAAGAAGGAAG-AGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCA
65 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-G
** * * * * ****
2864873 CTTGAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGAACT
1 CTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT
2864932 TGTTCAACTT
Statistics
Matches: 550, Mismatches: 39, Indels: 39
0.88 0.06 0.06
Matches are distributed among these distances:
100 18 0.03
101 4 0.01
102 59 0.11
103 1 0.00
104 1 0.00
106 10 0.02
107 39 0.07
108 1 0.00
109 35 0.06
110 9 0.02
111 31 0.06
112 65 0.12
113 277 0.50
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
CTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
Found at i:2864856 original size:111 final size:113
Alignment explanation
Indices: 2864698--2864931 Score: 357
Period size: 112 Copynumber: 2.1 Consensus size: 113
2864688 GTGCCAGTTA
* **
2864698 GAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT-TG
1 GAGAAGAACTCATATGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCAC
*
2864762 TTGAA-TCATCATTTGATGGATCAGCATCCCCAGGAAAGAGTTCATAAT
66 TTGAATTCATCATTCGATGGATCAGCATCCCCAGG-AAGAGTTCATAAT
*
2864810 GAGAAGAACTCATATGAAGAAGGAAG-AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCAC
1 GAGAAGAACTCATATGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCAC
** **
2864874 TTGAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAAT
66 TTGAATTCATCATTCGATGGATCAGCATCCCCAGGAAGAGTTCATAAT
2864922 GAGAAGAACT
1 GAGAAGAACT
2864932 TGTTCAACTT
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
111 35 0.32
112 50 0.45
113 26 0.23
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (113 bp):
GAGAAGAACTCATATGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCAC
TTGAATTCATCATTCGATGGATCAGCATCCCCAGGAAGAGTTCATAAT
Found at i:2864897 original size:213 final size:215
Alignment explanation
Indices: 2864483--2864907 Score: 599
Period size: 213 Copynumber: 2.0 Consensus size: 215
2864473 AGTTCATAAT
* *
2864483 GAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGC
1 GAGAAGAACTCATCTAAAGAAGAAAGAAGAAATTCATAATGAGAAGAACTTGTTCAATCTTTTGC
* ** *
2864548 TCAAATCCATCATTTGATGAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
66 TCAAATCCATCATTTGATGAATCAGCATCCCCAGAAAAAGTTCATAATGAGAAGAACTCATATGA
* * *
2864613 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTCAAATTCATCACCCGG
131 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAATCTTTTACTCAAATTCATCACCCGA
2864678 TGGATCAGCAGTGCCAGTTA
196 TGGATCAGCAGTGCCAGTTA
* *
2864698 GAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTTG
1 GAGAAGAACTCATCTAAAGAAGAAAGAAGAAATTCATAATGAGAAGAACTTGTTCAATC-TTTTG
** * *
2864762 -TTGAAT-CATCATTTGATGGATCAGCATCCCCAGGAAAGAGTTCATAATGAGAAGAACTCATAT
65 CTCAAATCCATCATTTGATGAATCAGCATCCCCA-GAAAAAGTTCATAATGAGAAGAACTCATAT
* ** **
2864825 GAAGAAGGAAG-AGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCACTTGAATTCATCATT
129 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAATCTTTT-ACTCAAATTCATCACC
*
2864888 CGATGGATCAGCATTGCCAG
193 CGATGGATCAGCAGTGCCAG
2864908 GGCGAGTTCA
Statistics
Matches: 186, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
212 5 0.03
213 79 0.42
214 44 0.24
215 58 0.31
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (215 bp):
GAGAAGAACTCATCTAAAGAAGAAAGAAGAAATTCATAATGAGAAGAACTTGTTCAATCTTTTGC
TCAAATCCATCATTTGATGAATCAGCATCCCCAGAAAAAGTTCATAATGAGAAGAACTCATATGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAATCTTTTACTCAAATTCATCACCCGA
TGGATCAGCAGTGCCAGTTA
Found at i:2864958 original size:73 final size:71
Alignment explanation
Indices: 2864838--2865003 Score: 224
Period size: 73 Copynumber: 2.3 Consensus size: 71
2864828 GAAGGAAGAG
* * * *
2864838 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTCGATGGATCAGCATT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTCGAATTCATCACTCGATAGATCAACATT
*
2864903 GCCAGGGC
66 GCCA--GA
* ** *
2864911 GAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCACTCGATAGATCAACTTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTCGAATTCATCACTCGATAGATCAACATT
*
2864976 TCCAGA
66 GCCAGA
2864982 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
2865004 ATCTGAAAAG
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
71 22 0.27
73 60 0.73
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (71 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTCGAATTCATCACTCGATAGATCAACATT
GCCAGA
Found at i:2865067 original size:108 final size:111
Alignment explanation
Indices: 2864912--2865279 Score: 311
Period size: 108 Copynumber: 3.3 Consensus size: 111
2864902 TGCCAGGGCG
* * * *
2864912 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAAT-TCATCAC-TCGATAG-ATCAACT
1 AGTTCATAATGAGAAGAAGTTGTTCAACCTTTTGCT-GACTCT-ATCACATAGATAGCATCAACT
*
2864974 TTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAGGAAGAAGA
64 TTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGA
2865022 AG-TCATAATGAGAAG-AGTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAG
1 AGTTCATAATGAGAAGAAGTTGTTCAACCTTTTGC-TGACTCTATCAC--------ATAGAT-AG
*
2865085 CATCAACTTTTCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAA-AAGA
56 CATCAACTTTTC-CAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGA
* * * *
2865141 AGTTCATAAT--G-AG-AGTTATT-AACCTTTTGTTTAACTCTATCACAGAAGGAGATAGATCAT
1 AGTTCATAATGAGAAGAAGTTGTTCAACCTTTTG-CTGACTCTATCAC---A-TAGATAG--CAT
*
2865201 CAACCTTTCCAGAGAAGTTC---AT--GAAGAACTTATC-GAAGAGGAAGAAGA
59 CAACTTTTCCAGA-AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGA
* *
2865249 AGTTCATAATGAGAAGCATTTGTTCAACCTT
1 AGTTCATAATGAGAAGAAGTTGTTCAACCTT
2865280 GCCTTAATTC
Statistics
Matches: 215, Mismatches: 17, Indels: 49
0.77 0.06 0.17
Matches are distributed among these distances:
107 9 0.04
108 50 0.23
109 15 0.07
110 5 0.02
111 5 0.02
112 12 0.06
113 23 0.11
116 20 0.09
117 12 0.06
118 3 0.01
119 17 0.08
120 44 0.20
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (111 bp):
AGTTCATAATGAGAAGAAGTTGTTCAACCTTTTGCTGACTCTATCACATAGATAGCATCAACTTT
TCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGA
Found at i:2865239 original size:120 final size:117
Alignment explanation
Indices: 2864962--2865279 Score: 367
Period size: 120 Copynumber: 2.8 Consensus size: 117
2864952 TTCATCACTC
*
2864962 GATAGATCAACTTTTCC--AGAAAGTTCATAATGAGAAGAACTTATCTGAAAAGGAAGAAGAAGT
1 GATACATCAAC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAGGAAGAAGAAGT
* *
2865025 CATAATGAGAAGAGTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATA
65 CATAAT-AGAAGAGTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAGATA
* *
2865079 GATCAGCATCAACTTTTCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAA-AAGAAG
1 GAT-A-CATCAACTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAGGAAGAAGAAG
**
2865143 TTCATAAT-G-AGAGTTATT-AACCTTTTGTTTAACTCTATCACAGAAGGAGATA
64 -TCATAATAGAAGAGTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAGATA
*
2865195 GAT-CATCAACCTTTCCAGAG-AAGTTC---AT--GAAGAACTTATC-GAAGAGGAAGAAGAAGT
1 GATACATCAA-CTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAGGAAGAAGAAG-
* *
2865252 TCATAATGAGAAGCATTTGTTCAACCTT
64 TCATAAT-AGAAG-AGTTATTCAACCTT
2865280 GCCTTAATTC
Statistics
Matches: 179, Mismatches: 10, Indels: 28
0.82 0.05 0.13
Matches are distributed among these distances:
107 9 0.05
108 26 0.15
110 3 0.02
111 2 0.01
112 5 0.03
113 18 0.10
114 9 0.05
116 34 0.19
117 11 0.06
118 6 0.03
119 12 0.07
120 44 0.25
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (117 bp):
GATACATCAACTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAGGAAGAAGAAGTC
ATAATAGAAGAGTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAGATA
Found at i:2865616 original size:3 final size:3
Alignment explanation
Indices: 2865610--2865698 Score: 107
Period size: 3 Copynumber: 30.7 Consensus size: 3
2865600 TTGGTTTTTT
* *
2865610 TTA TTA -TA TT- TTT TTA TTA -TA CTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2865654 TTA TTA TATA TTA TTA TTA TTA TTTA TTA -TA TTA TTA TTA TTA TT
1 TTA TTA T-TA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
2865699 TTTACAGATA
Statistics
Matches: 77, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
2 10 0.13
3 61 0.79
4 6 0.08
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2865626 original size:10 final size:11
Alignment explanation
Indices: 2865607--2865702 Score: 79
Period size: 11 Copynumber: 8.5 Consensus size: 11
2865597 CATTTGGTTT
2865607 TTTTTATTATA
1 TTTTTATTATA
2865618 TTTTTTTATTATA
1 --TTTTTATTATA
* *
2865631 CTATTATTATTA
1 TTTTTATTA-TA
*
2865643 TTATTATTATA
1 TTTTTATTATA
*
2865654 TTATTA-TATA
1 TTTTTATTATA
*
2865664 TTATTATTAT-
1 TTTTTATTATA
*
2865674 TATTTATTATA
1 TTTTTATTATA
*
2865685 TTATTATTATTA
1 TTTTTATTA-TA
2865697 TTTTTA
1 TTTTTA
2865703 CAGATACAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
10 18 0.25
11 25 0.35
12 17 0.24
13 11 0.15
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTATTATA
Found at i:2865635 original size:21 final size:22
Alignment explanation
Indices: 2865610--2865697 Score: 117
Period size: 23 Copynumber: 4.0 Consensus size: 22
2865600 TTGGTTTTTT
*
2865610 TTATTATATT-TTTTTATTATA
1 TTATTATATTATTATTATTATA
*
2865631 CTATTATTATTATTATTATTATA
1 TTATTA-TATTATTATTATTATA
2865654 TTATTATA-TATTATTATTATTA
1 TTATTATATTATTATTATTA-TA
2865676 TTTATTATATTATTATTATTAT
1 -TTATTATATTATTATTATTAT
2865698 TTTTACAGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
21 16 0.27
22 8 0.14
23 24 0.41
24 11 0.19
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTATATTATTATTATTATA
Found at i:2869262 original size:16 final size:16
Alignment explanation
Indices: 2869241--2869271 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2869231 TAAAAAAAAT
2869241 TATATTAATTATTAAA
1 TATATTAATTATTAAA
*
2869257 TATATTTATTATTAA
1 TATATTAATTATTAA
2869272 CTTAATCTAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTAATTATTAAA
Found at i:2869484 original size:31 final size:31
Alignment explanation
Indices: 2869449--2869509 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2869439 TGACCACATC
2869449 TTAATTAAATAAAAACAAAAGTGATCATATA
1 TTAATTAAATAAAAACAAAAGTGATCATATA
** *
2869480 TTAATTAAATAAAAATGAAAGTGGTCATAT
1 TTAATTAAATAAAAACAAAAGTGATCATAT
2869510 TTTATGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAGTGATCATATA
Found at i:2870241 original size:142 final size:140
Alignment explanation
Indices: 2870067--2870354 Score: 526
Period size: 143 Copynumber: 2.0 Consensus size: 140
2870057 TTTTAAATAA
2870067 TAATAAATATTGGTTAACTACACAAATAATCA-TTATGTTTGTGTTTTGTCCACTTTTAGTCACT
1 TAATAAATATTGGTTAACTACACAAATAATCATTTATGTTTGTGTTTTGTCCACTTTTAGTCACT
2870131 AATTTCAAAAATCATAAGATATTGTCACTTTCATTTTTATTTAATT-AGATGTGGTCATCCCGAG
66 AATTTCAAAAATCATAAGATATTGTCACTTTCA-TTTTATTTAATTAAGATGTGGTCATCCCGAG
2870195 TTAATTACGGTT
130 TTAATTACGG-T
2870207 TAATAAATATTATGGTTAACTACACAAATAATCATTTATGTTTGTGTTTTGTCCACTTTTAGTCA
1 TAATAAATA-T-TGGTTAACTACACAAATAATCATTTATGTTTGTGTTTTGTCCACTTTTAGTCA
2870272 CTAATTTCAAAAATCATAAGATATTGTCACTTTCATTTTATTTAATTAAGATGTGGTCATCCCGA
64 CTAATTTCAAAAATCATAAGATATTGTCACTTTCATTTTATTTAATTAAGATGTGGTCATCCCGA
2870337 GTTAATTACGGT
129 GTTAATTACGGT
2870349 TAATAA
1 TAATAA
2870355 CAATTAAATA
Statistics
Matches: 144, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
140 9 0.06
141 1 0.01
142 41 0.28
143 93 0.65
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (140 bp):
TAATAAATATTGGTTAACTACACAAATAATCATTTATGTTTGTGTTTTGTCCACTTTTAGTCACT
AATTTCAAAAATCATAAGATATTGTCACTTTCATTTTATTTAATTAAGATGTGGTCATCCCGAGT
TAATTACGGT
Found at i:2874198 original size:21 final size:21
Alignment explanation
Indices: 2874172--2874216 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2874162 GATTTCTGGG
* *
2874172 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2874193 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2874214 CAA
1 CAA
2874217 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2875089 original size:31 final size:31
Alignment explanation
Indices: 2875010--2875117 Score: 182
Period size: 31 Copynumber: 3.5 Consensus size: 31
2875000 GGGTCGAGGG
2875010 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2875041 TTACCTA-GTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
2875071 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
2875102 TTACCTAGGTTCTTCG
1 TTACCTATGTTCTTCG
2875118 AATCTATGGA
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 30 0.42
31 42 0.58
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:2875126 original size:61 final size:61
Alignment explanation
Indices: 2875010--2875130 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
2875000 GGGTCGAGGG
* * *
2875010 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGTTCTTCGGAACATATGGACTGT
2875071 TTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTTCTTC-GAATC-TATGGACTG
1 TTACCTATGTCCTTCGGGACATATGGACTGATTACCTA-GTTCTTCGGAA-CATATGGACTG
2875131 GTCCTTCGGG
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
61 47 0.85
62 8 0.15
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (61 bp):
TTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGTTCTTCGGAACATATGGACTGT
Found at i:2878339 original size:21 final size:21
Alignment explanation
Indices: 2878313--2878357 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2878303 TGATTTCTGG
* *
2878313 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2878334 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2878355 CAA
1 CAA
2878358 ATGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2879185 original size:31 final size:31
Alignment explanation
Indices: 2879147--2879268 Score: 176
Period size: 31 Copynumber: 4.0 Consensus size: 31
2879137 AGGTCGAGGG
2879147 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2879178 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
** *
2879209 TTACCTATGCCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
2879240 TTACCTAGGTT-TTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
2879269 GTCCTTCGGG
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
30 15 0.18
31 68 0.82
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:2880602 original size:21 final size:21
Alignment explanation
Indices: 2880522--2880604 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
2880512 TCAATCCCCA
*
2880522 AAGGAGGG-ATCGATTCCCATTC
1 AAGG-GGGAATCGATTCCC-TTT
*
2880544 AA-GGGGAATCGTTTCCCTTT
1 AAGGGGGAATCGATTCCCTTT
*
2880564 AAGGGGGAATCGGTTTCCCTTT
1 AAGGGGGAATC-GATTCCCTTT
*
2880586 AAGGGGGTATCGATTCCCT
1 AAGGGGGAATCGATTCCCT
2880605 CTGCACTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
20 7 0.13
21 25 0.46
22 22 0.41
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (21 bp):
AAGGGGGAATCGATTCCCTTT
Found at i:2887963 original size:35 final size:35
Alignment explanation
Indices: 2887917--2887986 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2887907 TACCTTTCAC
2887917 GTTTGGTCGGAATTGTTTTGAATCAAGAGAAAATG
1 GTTTGGTCGGAATTGTTTTGAATCAAGAGAAAATG
2887952 GTTTGGTCGGAATTGTTTTGAATCAAGAGAAAATG
1 GTTTGGTCGGAATTGTTTTGAATCAAGAGAAAATG
2887987 TAGTCCCGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (35 bp):
GTTTGGTCGGAATTGTTTTGAATCAAGAGAAAATG
Found at i:2888840 original size:16 final size:16
Alignment explanation
Indices: 2888819--2888850 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2888809 ACTTTAATTG
2888819 AATAAAAATATTATTT
1 AATAAAAATATTATTT
*
2888835 AATAAATATATTATTT
1 AATAAAAATATTATTT
2888851 CGGGTCGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAAAAATATTATTT
Found at i:2893256 original size:158 final size:159
Alignment explanation
Indices: 2892952--2893283 Score: 447
Period size: 158 Copynumber: 2.1 Consensus size: 159
2892942 TCATTTCGAG
* * *
2892952 ACCGATTTTGTCATATTTTTACATATTAGATTGTTATGGATCGATAAATTTTTATAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACATATTAGATTGTTATAGATCAATAAATTTTTATAAAGTATCGA
* * *
2893017 CACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGTCGATACTTATAATAAAGT
66 CACTTTATTAGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
* *
2893082 ATAGAAACTTTCAACATATCGGTAACTCTTT
130 ATAGAAACTTTCAACAT-CCGGTAACGCTTT
* * * *
2893113 ACCGGTTTTGTCATATTTTTACCTGTTA-TTTGTTTATAGATCAATACA-TTTTATAAAGTATCG
1 ACCGGTTTTGTCATATTTTTACATATTAGATTG-TTATAGATCAATAAATTTTTATAAAGTATCG
*
2893176 ACACTTTATTAGTGCTATAA-TCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
65 ACACTTTATTAGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGT
* * *
2893240 ATCGACACTATT-AACATCCGGTAGCGCTTT
130 ATAGAAACT-TTCAACATCCGGTAACGCTTT
*
2893270 ACCTGTTTTGTCAT
1 ACCGGTTTTGTCAT
2893284 TTATAGACCG
Statistics
Matches: 152, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
157 23 0.15
158 54 0.36
159 2 0.01
160 36 0.24
161 37 0.24
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (159 bp):
ACCGGTTTTGTCATATTTTTACATATTAGATTGTTATAGATCAATAAATTTTTATAAAGTATCGA
CACTTTATTAGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAAGTA
TAGAAACTTTCAACATCCGGTAACGCTTT
Found at i:2893469 original size:112 final size:111
Alignment explanation
Indices: 2893233--2893527 Score: 445
Period size: 112 Copynumber: 2.7 Consensus size: 111
2893223 GATACTTATA
* *
2893233 ATAAAGTATCGACACTATT--A-ACATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
1 ATAAAGTATCGACACT-TTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGA
*
2893295 TTTTGCCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
65 TTTTGCCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* * * *
2893342 ATAAAGTATCAACACTTTCAATATATCTGGTAGTGCTTTACATGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
** *
2893407 TTTGTTATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGCCA-TTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
*
2893454 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG-G
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
2893518 TTTGCCATTT
66 TTTGCCATTT
2893528 ATAAATCGGT
Statistics
Matches: 165, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
108 2 0.01
109 15 0.09
110 4 0.02
111 48 0.29
112 96 0.58
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (111 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGCCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
Found at i:2893546 original size:20 final size:20
Alignment explanation
Indices: 2893497--2893547 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2893487 CGCTTTACCT
*
2893497 GTTTTGTCATTTATAGACCG
1 GTTTTGTCATTTATAAACCG
* *
2893517 G-TTTGCCATTTATAAATCG
1 GTTTTGTCATTTATAAACCG
2893536 GTTTTGTCATTT
1 GTTTTGTCATTT
2893548 TTACCTGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.49
Consensus pattern (20 bp):
GTTTTGTCATTTATAAACCG
Found at i:2895887 original size:13 final size:13
Alignment explanation
Indices: 2895869--2895915 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2895859 TGAGTATAAA
2895869 AAAAATAAATATT
1 AAAAATAAATATT
*
2895882 AAAAATAAA-AAT
1 AAAAATAAATATT
*
2895894 AAAAATTAAATAATG
1 AAAAA-TAAAT-ATT
2895909 AAAAATA
1 AAAAATA
2895916 CTAAAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.25
13 13 0.46
14 2 0.07
15 6 0.21
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (13 bp):
AAAAATAAATATT
Found at i:2895891 original size:19 final size:21
Alignment explanation
Indices: 2895869--2895915 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
2895859 TGAGTATAAA
*
2895869 AAAAATAAATATTAAA-AAT-
1 AAAAATAAAAATTAAATAATG
2895888 AAAAATAAAAATTAAATAATG
1 AAAAATAAAAATTAAATAATG
2895909 AAAAATA
1 AAAAATA
2895916 CTAAAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 15 0.60
20 3 0.12
21 7 0.28
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAAATAAAAATTAAATAATG
Found at i:2896057 original size:27 final size:31
Alignment explanation
Indices: 2895999--2896058 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 31
2895989 AAAATATGTT
2895999 TATAATATATACATATATTTACACTTTTATA
1 TATAATATATACATATATTTACACTTTTATA
2896030 TATAATA-ATA-ATA-A-TTACACTTTTATA
1 TATAATATATACATATATTTACACTTTTATA
2896057 TA
1 TA
2896059 ATTATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 15 0.52
28 1 0.03
29 3 0.10
30 3 0.10
31 7 0.24
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (31 bp):
TATAATATATACATATATTTACACTTTTATA
Found at i:2896083 original size:19 final size:18
Alignment explanation
Indices: 2896057--2896094 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2896047 CACTTTTATA
2896057 TAATTATTATATCAAAAT
1 TAATTATTATATCAAAAT
*
2896075 TAATATATTATATTAAAAT
1 TAAT-TATTATATCAAAAT
2896094 T
1 T
2896095 TTAAAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTATTATATCAAAAT
Found at i:2897357 original size:17 final size:17
Alignment explanation
Indices: 2897315--2897367 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2897305 AAGCAAAAAT
*
2897315 AATAAAAATAAAA-AGA
1 AATAAAAATAAAATACA
2897331 AATAAAAAATAAAATACA
1 AAT-AAAAATAAAATACA
* *
2897349 AATACAAATACAATACA
1 AATAAAAATAAAATACA
2897366 AA
1 AA
2897368 AATTATAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 3 0.09
17 24 0.75
18 5 0.16
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (17 bp):
AATAAAAATAAAATACA
Found at i:2897576 original size:20 final size:20
Alignment explanation
Indices: 2897548--2897586 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2897538 GTGCAAACCC
*
2897548 AAAAGTAAAAAAAAAAATAA
1 AAAAATAAAAAAAAAAATAA
*
2897568 AAAAATAAAAATAAAAATA
1 AAAAATAAAAAAAAAAATA
2897587 TATAAAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAAATAAAAAAAAAAATAA
Found at i:2897577 original size:14 final size:14
Alignment explanation
Indices: 2897554--2897629 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
2897544 ACCCAAAAGT
2897554 AAAAAA-AAAAATA
1 AAAAAATAAAAATA
2897567 AAAAAATAAAAATA
1 AAAAAATAAAAATA
*
2897581 AAAATATATAAAAT-
1 AAAAAATA-AAAATA
* * **
2897595 GAAATATGCAAAT-
1 AAAAAATAAAAATA
*
2897608 AAAAAATTAAAATA
1 AAAAAATAAAAATA
*
2897622 AAATAATA
1 AAAAAATA
2897630 TTATATTATA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
13 19 0.38
14 26 0.52
15 5 0.10
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:2899617 original size:32 final size:31
Alignment explanation
Indices: 2899568--2899658 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 31
2899558 TAGTAGACAC
* *
2899568 GATATCCTTCGTTGTGAAGTTGAAATCA-TG
1 GATACCCTTCGTCGTGAAGTTGAAATCATTG
* * * *
2899598 GATGGCCCCTTCGTCGTGAATTTGAGCATGATTG
1 GAT--ACCCTTCGTCGTGAAGTTGA-AATCATTG
*
2899632 GATATCCTTCGTCGTGAAGTTGAAATC
1 GATACCCTTCGTCGTGAAGTTGAAATC
2899659 CAATCTTTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
30 3 0.07
31 2 0.04
32 33 0.72
33 3 0.07
34 5 0.11
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (31 bp):
GATACCCTTCGTCGTGAAGTTGAAATCATTG
Found at i:2901337 original size:179 final size:181
Alignment explanation
Indices: 2901020--2901376 Score: 668
Period size: 179 Copynumber: 2.0 Consensus size: 181
2901010 TGAACGTCTT
2901020 AACAAAGAGTATAGTAAAGTTATATGCAAAAGATGCCCCATGTTGTCCGCACCTGTGTACACCTA
1 AACAAAGAGTATAGTAAAGTTATATGCAAAAGATGCCCCATGTTGTCCGCACCTGTGTACACCTA
2901085 AATACCAAGCCTCTTTTTTTCCCTCATGAGAGTAGAAGGCTATATTGGTTATTTGCAAGAGAAGG
66 AATACCAAGCCTCTTTTTTTCCCTCATGAGAGTAGAAGGCTATATTGGTTATTTGCAAGAGAAGG
2901150 GTAATG-TTTAGCGTA-CTTCATGAGGTAGGTCAAAATCCTTGTTTTATTA
131 GTAATGTTTTAGCGTATCTTCATGAGGTAGGTCAAAATCCTTGTTTTATTA
2901199 AACAAAGAGTATAGTAAAGTTATATGCAAAAGATGCCCCATGTTGTCCGCACCTGTGTACACCTA
1 AACAAAGAGTATAGTAAAGTTATATGCAAAAGATGCCCCATGTTGTCCGCACCTGTGTACACCTA
2901264 AATACCAAGCCTCTTTTTTTCCCTCATGAGAGTAGAAGGCTATATTGG-T-TTTGCAAGAGAAGG
66 AATACCAAGCCTCTTTTTTTCCCTCATGAGAGTAGAAGGCTATATTGGTTATTTGCAAGAGAAGG
2901327 GTACAATGTTTTAGCGTATCTTCATGAGGTAGGTCAAAATCCTTGTTTTA
131 GT--AATGTTTTAGCGTATCTTCATGAGGTAGGTCAAAATCCTTGTTTTA
2901377 CCGATTTTAA
Statistics
Matches: 174, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
177 16 0.09
178 1 0.01
179 117 0.67
180 9 0.05
181 31 0.18
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (181 bp):
AACAAAGAGTATAGTAAAGTTATATGCAAAAGATGCCCCATGTTGTCCGCACCTGTGTACACCTA
AATACCAAGCCTCTTTTTTTCCCTCATGAGAGTAGAAGGCTATATTGGTTATTTGCAAGAGAAGG
GTAATGTTTTAGCGTATCTTCATGAGGTAGGTCAAAATCCTTGTTTTATTA
Found at i:2905239 original size:2 final size:2
Alignment explanation
Indices: 2905232--2905274 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
2905222 ATACACATAC
2905232 AT AT AT AT AT AT AT A- AT AT AT AT A- 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
2905272 AT A
1 AT A
2905275 GCACCAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2907944 original size:28 final size:29
Alignment explanation
Indices: 2907904--2907961 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
2907894 ATTTTCACCT
2907904 AACTAAATTGATGTAAGCAATG-CATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2907932 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2907961 A
1 A
2907962 TTAATTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2908810 original size:53 final size:51
Alignment explanation
Indices: 2908717--2908865 Score: 158
Period size: 52 Copynumber: 2.9 Consensus size: 51
2908707 TGACACTCAG
* * *
2908717 AGCAACACCAAAAACAATG-AACTGAAGGTCAGAACGAGAACAATGCCGATC
1 AGCAACACCGAAAACAATGAAAGTGCAGGTCAGAACGAGAACAATG-CGATC
* *
2908768 AGCAAGCACCGAAAACAATGAAAGTGCAGGTCAGAACAAGAAC-ATGCGCTC
1 AGCAA-CACCGAAAACAATGAAAGTGCAGGTCAGAACGAGAACAATGCGATC
* * * * *
2908819 AGAGAAACACTGAAACCAATGAAAGTGCTGGGCAGAACGAGAACAAT
1 --AGCAACACCGAAAACAATGAAAGTGCAGGTCAGAACGAGAACAAT
2908866 TCCACTCAGA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
51 9 0.11
52 48 0.59
53 25 0.30
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (51 bp):
AGCAACACCGAAAACAATGAAAGTGCAGGTCAGAACGAGAACAATGCGATC
Found at i:2911655 original size:31 final size:31
Alignment explanation
Indices: 2911617--2911677 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
2911607 GCTCCACACT
2911617 AAGGATTTTCTAACAAATTCACTAGTTTGTG
1 AAGGATTTTCTAACAAATTCACTAGTTTGTG
2911648 AAGGATTTTCTAACAAATTCACTAGTTTGT
1 AAGGATTTTCTAACAAATTCACTAGTTTGT
2911678 TCTTACCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (31 bp):
AAGGATTTTCTAACAAATTCACTAGTTTGTG
Found at i:2912311 original size:2 final size:2
Alignment explanation
Indices: 2912306--2912340 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2912296 AAAAACATTC
*
2912306 AT AT AT AC 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 AT AT A
2912341 ACAATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2920599 original size:17 final size:17
Alignment explanation
Indices: 2920577--2920636 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
2920567 TTGGGATTAG
2920577 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
2920594 TTCTTCTTC-TTCA-GATAAG
1 TTCTTC-TCATT-ATG--AAC
2920613 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
2920630 TCCTTCT
1 TTCTTCT
2920637 GGAAATGCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
17 17 0.50
18 6 0.18
19 11 0.32
ACGTcount: A:0.20, C:0.25, G:0.07, T:0.48
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:2921347 original size:113 final size:113
Alignment explanation
Indices: 2920679--2921338 Score: 1034
Period size: 113 Copynumber: 5.8 Consensus size: 113
2920669 TAGAGTTATG
* * * *
2920679 CAAAAGGTTGAACAAGTTCTTTTCATTATGAAATTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * *
2920744 TTATGAACACT-TCTGGCAATGCTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
* * *
2920791 CAAAAGGTTGAACAAATTCTTCTTATCATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
2920856 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
**
2920904 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * ** *
2920969 TTATGAACTTTCTCTGGAAAATATGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
* ** *
2921017 GAAAAGGTTGAACAAGCTCTACTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
2921082 TTATGAACTTTCTCTAGAAAAGCTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
2921130 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
2921195 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
*
2921243 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
2921308 TTATGAACTTTCTCTGGAAAAGTTGATCCAT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCAT
2921339 TGAGTGATGG
Statistics
Matches: 507, Mismatches: 40, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
112 67 0.13
113 440 0.87
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
Found at i:2922504 original size:19 final size:17
Alignment explanation
Indices: 2922476--2922524 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
2922466 AAAATAAAAG
*
2922476 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
2922495 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
2922511 AATAAATTGAATTT
1 AATAAATTGAATTT
2922525 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:2922926 original size:34 final size:33
Alignment explanation
Indices: 2922879--2922961 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 33
2922869 TGACCCCCTC
2922879 TTTTTTTTC-TTTTTT-TTTCTCCTTCTCCTTCTT
1 TTTTTTTTCATTTTTTATTT-T-CTTCTCCTTCTT
* *
2922912 TTTTTTTTCATTTTTTCATTTTTTTCTTCTTCTT
1 TTTTTTTTCATTTTTT-ATTTTCTTCTCCTTCTT
2922946 TTTTTTTTCATTTTTT
1 TTTTTTTTCATTTTTT
2922962 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
33 9 0.20
34 32 0.71
35 1 0.02
36 3 0.07
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.80
Consensus pattern (33 bp):
TTTTTTTTCATTTTTTATTTTCTTCTCCTTCTT
Found at i:2930298 original size:15 final size:15
Alignment explanation
Indices: 2930275--2930306 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2930265 TGCAATGAAT
2930275 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2930290 AATGCATGTATGCAA
1 AATGAATGTATGCAA
2930305 AA
1 AA
2930307 GGTATTGATC
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2933605 original size:28 final size:27
Alignment explanation
Indices: 2933554--2933607 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
2933544 ATATTAATAA
*
2933554 AATAATATATATAAATACTATGAAAAT
1 AATAATATATATAAAAACTATGAAAAT
* *
2933581 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAACTATGAAAA
2933608 GAAAGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (27 bp):
AATAATATATATAAAAACTATGAAAAT
Found at i:2934115 original size:23 final size:25
Alignment explanation
Indices: 2934078--2934126 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
2934068 ATAATTATGA
*
2934078 AAAATATATTAATTTATATATAAAT
1 AAAATATATTAATTTATATAGAAAT
*
2934103 AAAATAT-TT-ATTTATTTAGAAAT
1 AAAATATATTAATTTATATAGAAAT
2934126 A
1 A
2934127 TCAGAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 2 0.09
25 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATATATTAATTTATATAGAAAT
Found at i:2934212 original size:20 final size:19
Alignment explanation
Indices: 2934173--2934214 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2934163 TTTCTTCAAT
2934173 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
2934192 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
2934212 ATT
1 ATT
2934215 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:2935707 original size:3 final size:3
Alignment explanation
Indices: 2935699--2935758 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
2935689 TAAAATTATT
* * *
2935699 TAA TAA TAA TAA TAA T-A TAA TAA TTA TAA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2935746 -AA T-A TAAA TAA TA
1 TAA TAA T-AA TAA TA
2935759 TTCGAATGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 6 0.13
3 39 0.83
4 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2935713 original size:26 final size:26
Alignment explanation
Indices: 2935683--2935748 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 26
2935673 TGTAATAGTA
2935683 AATAAATAAAATTAT-TTAATAATAAT
1 AATAAATAAAATTATATT-ATAATAAT
*
2935709 AATAATATAATAATTATAATTATAATTAT
1 AATAA-ATAA-AATTAT-ATTATAATAAT
2935738 AAT-AATAAAAT
1 AATAAATAAAAT
2935749 ATAAATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 8 0.23
27 8 0.23
28 7 0.20
29 10 0.29
30 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
AATAAATAAAATTATATTATAATAAT
Found at i:2938152 original size:31 final size:30
Alignment explanation
Indices: 2938056--2938158 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 30
2938046 TACCCCTATA
* *
2938056 TTTG-TTTCTTTGTTTTTGTTGTGATGGCT
1 TTTGTTTTCTTTGTTTTTGTTGTGGTGGGT
* * *
2938085 TTTGTTTCCTTTGCTTCTT-CTGTGG-GGGTT
1 TTTGTTTTCTTTG-TTTTTGTTGTGGTGGG-T
2938115 TTTGTTTTCTTTGTTTTTGTTGTGGTGGGT
1 TTTGTTTTCTTTGTTTTTGTTGTGGTGGGT
2938145 TTCTGTTTTCTTTG
1 TT-TGTTTTCTTTG
2938159 GTTTGCTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
29 10 0.17
30 32 0.53
31 18 0.30
ACGTcount: A:0.01, C:0.10, G:0.25, T:0.64
Consensus pattern (30 bp):
TTTGTTTTCTTTGTTTTTGTTGTGGTGGGT
Found at i:2938161 original size:16 final size:16
Alignment explanation
Indices: 2938111--2938162 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
2938101 CTTCTGTGGG
2938111 GGTTTTTGTTTTCTTT
1 GGTTTTTGTTTTCTTT
* ** *
2938127 -GTTTTTGTTGTGGTG
1 GGTTTTTGTTTTCTTT
*
2938142 GGTTTCTGTTTTCTTT
1 GGTTTTTGTTTTCTTT
2938158 GGTTT
1 GGTTT
2938163 GCTTTCATGG
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.00, C:0.06, G:0.27, T:0.67
Consensus pattern (16 bp):
GGTTTTTGTTTTCTTT
Found at i:2940200 original size:35 final size:35
Alignment explanation
Indices: 2940153--2940221 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
2940143 CTTTAGTTTA
2940153 GGGTTTAGAATGTAATTGAAGTATTTTGGAATTTG
1 GGGTTTAGAATGTAATTGAAGTATTTTGGAATTTG
* *
2940188 GGGTTTATAATGTAATTGAAGTGTTTTGGAATTT
1 GGGTTTAGAATGTAATTGAAGTATTTTGGAATTT
2940222 TGAATATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (35 bp):
GGGTTTAGAATGTAATTGAAGTATTTTGGAATTTG
Found at i:2945987 original size:90 final size:88
Alignment explanation
Indices: 2945829--2946002 Score: 312
Period size: 89 Copynumber: 2.0 Consensus size: 88
2945819 ACTAACACAC
2945829 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
*
2945894 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATT-GAAATTAATAAT
*
2945918 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
2945983 ATTTAATTAATTGAAATTAA
65 ATTTAATTAATTGAAATTAA
2946003 ATATTCATGA
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 41 0.50
90 41 0.50
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.45
Consensus pattern (88 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAATAAT
Found at i:2958591 original size:17 final size:17
Alignment explanation
Indices: 2958547--2958581 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2958537 TATAAATTTA
2958547 AATTATAATAAAAATAT
1 AATTATAATAAAAATAT
2958564 AATTATAATAAAAATAT
1 AATTATAATAAAAATAT
2958581 A
1 A
2958582 TTTTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTATAATAAAAATAT
Found at i:2959555 original size:27 final size:27
Alignment explanation
Indices: 2959521--2959575 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2959511 TGGGTAGAAG
2959521 CTTGGTAATTGGTTTTTGGGATTTGGA
1 CTTGGTAATTGGTTTTTGGGATTTGGA
2959548 CTTGGTAATTGGTTTTTGGGATTTGGA
1 CTTGGTAATTGGTTTTTGGGATTTGGA
2959575 C
1 C
2959576 CAATTTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.05, G:0.33, T:0.47
Consensus pattern (27 bp):
CTTGGTAATTGGTTTTTGGGATTTGGA
Found at i:2970657 original size:27 final size:25
Alignment explanation
Indices: 2970599--2970650 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2970589 ACAATCTGGC
2970599 TAACTAGGTTACAAGCTGAAATATA
1 TAACTAGGTTACAAGCTGAAATATA
2970624 TAACTAGGTTACAAGCTGAAATATA
1 TAACTAGGTTACAAGCTGAAATATA
2970649 TA
1 TA
2970651 TAGCTAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (25 bp):
TAACTAGGTTACAAGCTGAAATATA
Found at i:2971349 original size:24 final size:24
Alignment explanation
Indices: 2971322--2971394 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
2971312 CGTTCATTTA
2971322 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
2971346 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
2971370 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
2971394 C
1 C
2971395 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:2971351 original size:14 final size:14
Alignment explanation
Indices: 2971332--2971387 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
2971322 CGTTCGTGAA
2971332 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2971346 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2971360 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
2971370 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
2971384 CGTT
1 CGTT
2971388 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:2971404 original size:24 final size:23
Alignment explanation
Indices: 2971333--2971407 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
2971323 GTTCGTGAAC
* *
2971333 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
2971357 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
2971381 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
2971405 GTT
1 GTT
2971408 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:2972146 original size:10 final size:10
Alignment explanation
Indices: 2972131--2972189 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
2972121 GGGTCTCCAA
2972131 CGTTTATGTT
1 CGTTTATGTT
2972141 CGTTTATGTT
1 CGTTTATGTT
2972151 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
2972162 ATGTTCGTGTT
1 -CGTTTATGTT
2972173 CGTTTATGTT
1 CGTTTATGTT
2972183 CGTTTAT
1 CGTTTAT
2972190 TTATTAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 28 0.72
11 7 0.18
12 4 0.10
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:2972162 original size:16 final size:16
Alignment explanation
Indices: 2972137--2972193 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
2972127 CCAACGTTTA
*
2972137 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
2972153 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
2972169 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
2972185 T-TT-ATTTAT
1 TGTTCATTTAT
2972194 TAAATGAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 31 0.82
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:2972276 original size:16 final size:16
Alignment explanation
Indices: 2972255--2972287 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2972245 AAAAAAAAAT
2972255 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2972271 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2972287 T
1 T
2972288 CTATTTATTA
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:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2977734 original size:20 final size:20
Alignment explanation
Indices: 2977711--2977773 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2977701 AAATATTTTA
*
2977711 ATATTTCTAATAATATATAT-
1 ATATTTATAATAATATA-ATG
* *
2977731 ATATTTTTAATATTATAATG
1 ATATTTATAATAATATAATG
2977751 ATA-TTATAATAATATAA-G
1 ATATTTATAATAATATAATG
2977769 ATATT
1 ATATT
2977774 ATATTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.11
19 15 0.41
20 18 0.49
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (20 bp):
ATATTTATAATAATATAATG
Found at i:2977772 original size:29 final size:29
Alignment explanation
Indices: 2977740--2977795 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2977730 TATATTTTTA
2977740 ATATTATAATGATATTATAATAATATAAG
1 ATATTATAATGATATTATAATAATATAAG
* ** *
2977769 ATATTATATTTTTATTTTAATAATATA
1 ATATTATAATGATATTATAATAATATA
2977796 TAATACATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
ATATTATAATGATATTATAATAATATAAG
Found at i:2978038 original size:14 final size:14
Alignment explanation
Indices: 2978019--2978052 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2978009 ATTTTTTATT
2978019 AATAAAATTATAAA
1 AATAAAATTATAAA
*
2978033 AATAAAATTATAAT
1 AATAAAATTATAAA
2978047 AATAAA
1 AATAAA
2978053 TAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAAATTATAAA
Found at i:2978057 original size:17 final size:17
Alignment explanation
Indices: 2978028--2978060 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2978018 TAATAAAATT
2978028 ATAAAAATAAAATTATA
1 ATAAAAATAAAATTATA
2978045 ATAATAAAT-AAATTAT
1 ATAA-AAATAAAATTAT
2978061 TTCAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAAATAAAATTATA
Found at i:2979081 original size:11 final size:11
Alignment explanation
Indices: 2979048--2979106 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 11
2979038 AAAGTGTTTA
2979048 ATTTTTAATAT
1 ATTTTTAATAT
* *
2979059 -TTTAT-AGAT
1 ATTTTTAATAT
*
2979068 ATTTTTAATTT
1 ATTTTTAATAT
2979079 ATTTTTTAATAT
1 A-TTTTTAATAT
*
2979091 A-TTTAAATAT
1 ATTTTTAATAT
2979101 ATTTTT
1 ATTTTT
2979107 TACAATATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
9 3 0.08
10 17 0.47
11 6 0.17
12 10 0.28
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:2979085 original size:32 final size:33
Alignment explanation
Indices: 2979044--2979106 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
2979034 CATAAAAGTG
*
2979044 TTTAATTTTTAATAT-TTTATAGATATTTTTAA
1 TTTAATTTTTAATATATTTAAAGATATTTTTAA
* *
2979076 TTTATTTTTTAATATATTTAAATATATTTTT
1 TTTAATTTTTAATATATTTAAAGATATTTTT
2979107 TACAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (33 bp):
TTTAATTTTTAATATATTTAAAGATATTTTTAA
Found at i:2979103 original size:22 final size:22
Alignment explanation
Indices: 2979055--2979108 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2979045 TTAATTTTTA
* *
2979055 ATATTTTATAGATATTTTTAAT
1 ATATTTTTTAGATATTTTAAAT
*
2979077 TTATTTTTTA-ATATATTTAAAT
1 ATATTTTTTAGATAT-TTTAAAT
2979099 ATATTTTTTA
1 ATATTTTTTA
2979109 CAATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
ATATTTTTTAGATATTTTAAAT
Found at i:2979107 original size:24 final size:22
Alignment explanation
Indices: 2979075--2979133 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
2979065 GATATTTTTA
*
2979075 ATTTATTTTTTAATATATTTAAAT
1 ATTT-TTTTTTAATATATAT-AAT
**
2979099 ATATTTTTTACAATATATATAAT
1 AT-TTTTTTTTAATATATATAAT
2979122 ATTTTTATTTTA
1 ATTTTT-TTTTA
2979134 TTTTTAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 4 0.14
23 8 0.29
24 14 0.50
25 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTTTTTTAATATATATAAT
Found at i:2979107 original size:54 final size:51
Alignment explanation
Indices: 2979049--2979168 Score: 136
Period size: 51 Copynumber: 2.3 Consensus size: 51
2979039 AAGTGTTTAA
2979049 TTTTTAATATTTTATAGATATTTTTAATTTATTTTTTAATATATTTAAA-TATATT
1 TTTTTAATATTTTATA-ATATTTTTAATTTA-TTTTTAA-AT-TTTAAAGTA-ATT
* * *
2979104 TTTTACAATA-TATATAATATTTTTATTTTATTTTTAAATTTTAAAGTAATT
1 TTTT-TAATATTTTATAATATTTTTAATTTATTTTTAAATTTTAAAGTAATT
2979155 TATTTTAATATTTT
1 T-TTTTAATATTTT
2979169 TTAAAAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
51 14 0.25
52 9 0.16
53 7 0.12
54 13 0.23
55 9 0.16
56 4 0.07
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (51 bp):
TTTTTAATATTTTATAATATTTTTAATTTATTTTTAAATTTTAAAGTAATT
Found at i:2979114 original size:22 final size:21
Alignment explanation
Indices: 2979078--2979127 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2979068 ATTTTTAATT
*
2979078 TATTTTTTAATATATTTAAATA
1 TATTTTTTAATATATATAAA-A
*
2979100 TATTTTTTACA-ATATATATAA
1 TATTTTTTA-ATATATATAAAA
2979121 TATTTTT
1 TATTTTT
2979128 ATTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.32
22 16 0.64
23 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTTTAATATATATAAAA
Found at i:2980413 original size:19 final size:19
Alignment explanation
Indices: 2980382--2980450 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
2980372 TTTTTAATTT
2980382 TTTATT-ATATTTTATAAAA
1 TTTATTCAT-TTTTATAAAA
* *
2980401 TTTATTCATTTTTAGATAA
1 TTTATTCATTTTTATAAAA
* *
2980420 TTT-TACATTTTTTTAACAA
1 TTTATTCATTTTTATAA-AA
* *
2980439 ATTATTTATTTT
1 TTTATTCATTTT
2980451 AAATTCTCAA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
18 9 0.24
19 21 0.55
20 8 0.21
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTATTCATTTTTATAAAA
Found at i:2980695 original size:188 final size:187
Alignment explanation
Indices: 2980380--2980753 Score: 659
Period size: 188 Copynumber: 2.0 Consensus size: 187
2980370 TGTTTTTAAT
2980380 TTTTTATTATATTTTATAAAATTTATTCATTTTTAGATAATTTTACATTTTTTTAACAAATTATT
1 TTTTTATTATATTTTATAAAATTTATTCATTTTTAGATAATTTTACATTTTTTTAACAAATTATT
2980445 TATTTTAAATTCTCAAATACCTGTAATTTTTTAAAACTTTTTTCTACTCGAATTATTTGACCGAC
66 TATTTTAAATTCTCAAATACCTGTAATTTTTTAAAACTTTTTTCTACTCGAATTATTTGACCGAC
2980510 GAAGGCCC-TCTCTGCTCTC-TCTCTTTGTTTTTAACCACTGATGAAGGCTCCTCTTA
131 GAAGGCCCTTCTCTGCTCTCATCTCTTTG-TTTTAACCACTGATGAAGGCTCCTCTTA
2980566 TTTTTA-T-TATTTTATAAAATTTATTCATTTTTAAGATTAATTTTACATTTATTTTAACAAA-T
1 TTTTTATTATATTTTATAAAATTTATTCATTTTT-AGA-TAATTTTACATTT-TTTTAACAAATT
2980628 ATTTATATTTTAAATTCTCAAATACCTGTAATTTTTTAAAACTTTTTTCTACTCGAATTATTTGA
63 A-TT-TATTTTAAATTCTCAAATACCTGTAATTTTTTAAAACTTTTTTCTACTCGAATTATTTGA
2980693 CCGACGAAGGCCCTTCTCTGCTCTCATCTCTTTGTTTTAACCACTGATGAAGGCTCCTCTT
126 CCGACGAAGGCCCTTCTCTGCTCTCATCTCTTTGTTTTAACCACTGATGAAGGCTCCTCTT
2980754 TAATCACCCT
Statistics
Matches: 181, Mismatches: 0, Indels: 11
0.94 0.00 0.06
Matches are distributed among these distances:
184 25 0.14
185 4 0.02
186 21 0.12
187 12 0.07
188 73 0.40
189 38 0.21
190 8 0.04
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (187 bp):
TTTTTATTATATTTTATAAAATTTATTCATTTTTAGATAATTTTACATTTTTTTAACAAATTATT
TATTTTAAATTCTCAAATACCTGTAATTTTTTAAAACTTTTTTCTACTCGAATTATTTGACCGAC
GAAGGCCCTTCTCTGCTCTCATCTCTTTGTTTTAACCACTGATGAAGGCTCCTCTTA
Found at i:2995074 original size:21 final size:21
Alignment explanation
Indices: 2995050--2995089 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2995040 TCACGGGTGG
2995050 ATAA-ATATATATTTTTAATGT
1 ATAAGATATAT-TTTTTAATGT
*
2995071 ATAAGATCTATTTTTTAAT
1 ATAAGATATATTTTTTAAT
2995090 ATCTCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
ATAAGATATATTTTTTAATGT
Found at i:2996717 original size:65 final size:64
Alignment explanation
Indices: 2996576--2996738 Score: 170
Period size: 65 Copynumber: 2.5 Consensus size: 64
2996566 CGGTGCACTA
* * * * **
2996576 AGAGTGAATCGATGCATAAAATGCATTCTATGTTTTGAAAAAGCATGAGTGCATTGATGCATGGT
1 AGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAACCA-GAGTGCATCAATGCATGGT
* * *
2996641 ATA-TGCATCGATGAATCAAATGCATTCGATGTTTTCATTAAAACCCA-AGTGCATCAATGCATG
1 AGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCA--AAAA-CCAGAGTGCATCAATGCATG
2996704 G-
63 GT
* *
2996705 AGAGTGCATCGATGCATGAACTGCATTCGATGTT
1 AGAGTGCATCGATGCATAAAATGCATTCGATGTT
2996739 CAATTAATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
64 31 0.38
65 44 0.54
66 4 0.05
67 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (64 bp):
AGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAACCAGAGTGCATCAATGCATGGT
Found at i:2996774 original size:20 final size:20
Alignment explanation
Indices: 2996749--2996786 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2996739 CAATTAATTC
*
2996749 ATTGGTTCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2996769 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2996787 CCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2999438 original size:23 final size:23
Alignment explanation
Indices: 2999408--2999479 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
2999398 GCATGTCCTT
*
2999408 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAATGA
* * *
2999431 GTGCATCGGTGCACCTT-TATG-
1 GTGCATCGATGCACATTCAATGA
*
2999452 GTGTATCGATGCACATTCAATGA
1 GTGCATCGATGCACATTCAATGA
2999475 -TGCAT
1 GTGCAT
2999480 TAATGCACTG
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 14 0.37
22 9 0.24
23 15 0.39
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAATGA
Found at i:3005369 original size:19 final size:19
Alignment explanation
Indices: 3005345--3005418 Score: 139
Period size: 19 Copynumber: 3.9 Consensus size: 19
3005335 ATTAAAACCC
3005345 AAGTGCATCGATGCATGGA
1 AAGTGCATCGATGCATGGA
3005364 AAGTGCATCGATGCATGGA
1 AAGTGCATCGATGCATGGA
3005383 AAGTGCATCGATGCATGGA
1 AAGTGCATCGATGCATGGA
*
3005402 GAGTGCATCGATGCATG
1 AAGTGCATCGATGCATG
3005419 AACTGCATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (19 bp):
AAGTGCATCGATGCATGGA
Found at i:3005372 original size:65 final size:64
Alignment explanation
Indices: 3005236--3005379 Score: 182
Period size: 65 Copynumber: 2.2 Consensus size: 64
3005226 TTGGACCCTT
* * * ** * *
3005236 AGTGCATCGGTGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATTGATGCATGGTA
1 AGTGCATCGATGCATAAAACGCATTCGATGTTTTCAAAAAGCCCAAGTGCATCGATGCATGGAA
* *
3005300 TGTGCATCGATGCATCAAACGCATTCGATGTTTTCATTAAAA-CCCAAGTGCATCGATGCATGGA
1 AGTGCATCGATGCATAAAACGCATTCGATGTTTTCA--AAAAGCCCAAGTGCATCGATGCATGGA
3005364 A
64 A
3005365 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
3005380 GGAAAGTGCA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 31 0.46
65 33 0.49
66 4 0.06
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (64 bp):
AGTGCATCGATGCATAAAACGCATTCGATGTTTTCAAAAAGCCCAAGTGCATCGATGCATGGAA
Found at i:3005470 original size:20 final size:20
Alignment explanation
Indices: 3005445--3005482 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3005435 CAATTAATTC
3005445 ATTGGTACATCGATGCATGG
1 ATTGGTACATCGATGCATGG
* *
3005465 ATTGGTCCATCGGTGCAT
1 ATTGGTACATCGATGCAT
3005483 CCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (20 bp):
ATTGGTACATCGATGCATGG
Found at i:3020662 original size:25 final size:27
Alignment explanation
Indices: 3020633--3020685 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3020623 TAATATGATC
3020633 AATAAAAATTG-T-TATTTAAAAATAA
1 AATAAAAATTGATATATTTAAAAATAA
*
3020658 AATAAAAATTGATATATTTATAAATAA
1 AATAAAAATTGATATATTTAAAAATAA
3020685 A
1 A
3020686 TTTTTACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 11 0.44
26 1 0.04
27 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (27 bp):
AATAAAAATTGATATATTTAAAAATAA
Found at i:3021454 original size:16 final size:16
Alignment explanation
Indices: 3021433--3021464 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3021423 ACGAAATTAG
3021433 CGATGAACACTAATAA
1 CGATGAACACTAATAA
*
3021449 CGATGAGCACTAATAA
1 CGATGAACACTAATAA
3021465 ATTAAATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (16 bp):
CGATGAACACTAATAA
Found at i:3022100 original size:17 final size:17
Alignment explanation
Indices: 3022078--3022110 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3022068 CTGGTACACC
3022078 CTAATTCTTTTTCCCCT
1 CTAATTCTTTTTCCCCT
3022095 CTAATTCTTTTTCCCC
1 CTAATTCTTTTTCCCC
3022111 AAACCCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.36, G:0.00, T:0.52
Consensus pattern (17 bp):
CTAATTCTTTTTCCCCT
Done.