Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_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: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 18
Found at i:1229698 original size:17 final size:16
Alignment explanation
Indices: 1229669--1229710 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
1229659 ATCGCATATC
1229669 AATT-TTTTATCTTTTAA
1 AATTATTTTATC--TTAA
1229686 AATTATTTT-TCTTAA
1 AATTATTTTATCTTAA
1229701 AATTATTTTA
1 AATTATTTTA
1229711 AAAGATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTATTTTATCTTAA
Found at i:1230261 original size:17 final size:19
Alignment explanation
Indices: 1230224--1230286 Score: 78
Period size: 17 Copynumber: 3.5 Consensus size: 19
1230214 TTCATAGAAG
1230224 AATTAATAATAAGAGTAGT
1 AATTAATAATAAGAGTAGT
1230243 AATTAATAATAA-A-TAGT
1 AATTAATAATAAGAGTAGT
* * *
1230260 AAATAATAATAAGACTAAT
1 AATTAATAATAAGAGTAGT
1230279 -ATTAATAA
1 AATTAATAA
1230287 ATATCAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
17 15 0.38
18 9 0.23
19 15 0.38
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTAATAATAAGAGTAGT
Found at i:1230343 original size:15 final size:15
Alignment explanation
Indices: 1230296--1230348 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
1230286 AATATCAATG
* *
1230296 ATATTAATATTAGCA
1 ATATTAATAATAACA
* *
1230311 ATAATAATACT-A-A
1 ATATTAATAATAACA
1230324 ATATTAATAATAACA
1 ATATTAATAATAACA
1230339 ATATTAATAA
1 ATATTAATAA
1230349 CCCAGACAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 10 0.32
14 1 0.03
15 20 0.65
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (15 bp):
ATATTAATAATAACA
Found at i:1231466 original size:17 final size:18
Alignment explanation
Indices: 1231441--1231483 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1231431 CTTTAATGTG
* *
1231441 ATTTGAATTTTAAAATTA-
1 ATTT-AATTTAAAAATAAT
1231459 ATTTAATTTAAAAATAAT
1 ATTTAATTTAAAAATAAT
1231477 ATTTAAT
1 ATTTAAT
1231484 AATTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATTTAATTTAAAAATAAT
Found at i:1234317 original size:80 final size:80
Alignment explanation
Indices: 1234213--1234369 Score: 219
Period size: 80 Copynumber: 2.0 Consensus size: 80
1234203 TTTTAGATTG
* *
1234213 AAGCACATAAGTGCTCAATAATTTTAAAGCATAGAGGTGTCAGATTT-TAGATTGAAGCGA-AGA
1 AAGCACATAAGTCCTCAATAATTTTAAAGCAAAGAGGTGTCAG-TTTATAGATTGAAGC-ACAGA
*
1234276 GGTGTTCAATCATTTTA
64 GGTGCTCAATCATTTTA
* * * *
1234293 AAGCACATAGGTCCTTAATCATTTTAAAGCAAAGGGGTGTCAGTTTATAGATTGAAGCACAGAGG
1 AAGCACATAAGTCCTCAATAATTTTAAAGCAAAGAGGTGTCAGTTTATAGATTGAAGCACAGAGG
1234358 TGCTCAATCATT
66 TGCTCAATCATT
1234370 AATTCAAGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
79 4 0.06
80 64 0.94
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (80 bp):
AAGCACATAAGTCCTCAATAATTTTAAAGCAAAGAGGTGTCAGTTTATAGATTGAAGCACAGAGG
TGCTCAATCATTTTA
Found at i:1235359 original size:2 final size:2
Alignment explanation
Indices: 1235352--1235392 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1235342 TAGTCTCACA
1235352 AT AT AT AT AT 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 AT AT AT AT AT A
1235393 GCAGTGCCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1238851 original size:19 final size:20
Alignment explanation
Indices: 1238827--1238872 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1238817 CCAAAAACAA
*
1238827 GTATTTTCATT-AAAGTCAT
1 GTATTTTCATTAAAAATCAT
1238846 GTATTTTCATTAAAAATCAT
1 GTATTTTCATTAAAAATCAT
1238866 GTATTTT
1 GTATTTT
1238873 TAAAGGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
GTATTTTCATTAAAAATCAT
Found at i:1245056 original size:47 final size:46
Alignment explanation
Indices: 1244984--1245101 Score: 155
Period size: 47 Copynumber: 2.5 Consensus size: 46
1244974 AGTAAGGAGA
** *
1244984 AGGTGAAGTCAAGCTTGATCCGATGGATTTTACTCTTTTAAAGAAAG
1 AGGTGAAGTCGCGCTTGATCCGATGGATTTTACTCTTGTAAA-AAAG
* *
1245031 AGGTGAAGTCGCGCTTGATCTGATGGATTTTACTCTTGTAAATAAG
1 AGGTGAAGTCGCGCTTGATCCGATGGATTTTACTCTTGTAAAAAAG
* *
1245077 ATGGTGAATTCGCACTTGATCCGAT
1 A-GGTGAAGTCGCGCTTGATCCGAT
1245102 CAAATTTACT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 4 0.06
47 58 0.94
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (46 bp):
AGGTGAAGTCGCGCTTGATCCGATGGATTTTACTCTTGTAAAAAAG
Found at i:1245493 original size:54 final size:54
Alignment explanation
Indices: 1245411--1246161 Score: 957
Period size: 54 Copynumber: 13.9 Consensus size: 54
1245401 CCAATTTCCA
* * * * * * *
1245411 AAACTCAATATGAATTATGTGGATTGCACACATAGTACCGATACGATAATTCAC
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * * *
1245465 AAACTTATTATGAATTACGTAGGTTGCACACATAGTGTCAATACGGTAATTCAC
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * * * *
1245519 AAACTCATTATGAATTACGTGGTTTGCATACATAGTGTCGATACGATAATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
1245573 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * * * *
1245627 AAACTCGTTATGAATTATGTGGGTTGCACACACAATGTCAATACGGTAATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * *
1245681 AAACTCATTATGAATTATGTGGGTTGCACATATAGT-CCAATACGGTAATTTAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * * * *
1245734 AAACTCGTTATGAACTACGTGGGTTGCACTCATACTGCCAATATGGTAATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * *
1245788 AAACTCATTATGAACTACGTGGGTTGCACTCATAGTGCCAATACGGTAATTGAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * * ** *
1245842 AAACTTATTATCAATTATGTTCGTTGCACACATAGTGCCAATACAGTAATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* *
1245896 AAACTAATTATGAATTACGTGGGTTGCACACATAGTGCCACTACGGTAATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * * * *
1245950 AAACTCATTATGAATTATGTGGGTTGCACACATATTTCCAATATGATAATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * *
1246004 AAACTCATTAT-ATATTACGTGCGTTGCACACGTAGTGCCAATACAGTAATTCAT
1 AAACTCATTATGA-ATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * * *
1246058 AAACTCATTATGAATTACATGTGTTGCACACATATTGTCAATACGGTAATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
* * * * * *
1246112 AAACTCATTATAAATTACGTGAGTTGTACATATAGTACCAATACAGTAAT
1 AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAAT
1246162 ACAACATATA
Statistics
Matches: 604, Mismatches: 90, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
53 46 0.08
54 557 0.92
55 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (54 bp):
AAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGTAATTCAT
Found at i:1246314 original size:29 final size:30
Alignment explanation
Indices: 1246243--1246302 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1246233 CAATTTAAGG
1246243 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1246274 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1246303 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1246418 original size:29 final size:29
Alignment explanation
Indices: 1246385--1246446 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
1246375 GGTGTCAAAG
*
1246385 TGCATCCATGCACCCCTATAGTGCATCCA
1 TGCATCCATGCACCCCTATAGCGCATCCA
* * *
1246414 TGCATCCATGTATCCCTGTAGCGCATCCA
1 TGCATCCATGCACCCCTATAGCGCATCCA
1246443 TGCA
1 TGCA
1246447 CCTGTACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (29 bp):
TGCATCCATGCACCCCTATAGCGCATCCA
Found at i:1246617 original size:20 final size:20
Alignment explanation
Indices: 1246510--1246624 Score: 142
Period size: 20 Copynumber: 5.7 Consensus size: 20
1246500 AATGCAATTA
*
1246510 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTACT
*
1246530 GTGCATCGATGCAT-CAAGGCT
1 GTGCATCGATGCATCCTA--CT
1246551 GTGCATCGATGCATCCTACT
1 GTGCATCGATGCATCCTACT
**
1246571 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTACT
1246591 GTGCATCGATGCATCCTACT
1 GTGCATCGATGCATCCTACT
* * *
1246611 ATACATCCATGCAT
1 GTGCATCGATGCAT
1246625 GAAGGCTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 63 0.77
21 16 0.20
22 2 0.02
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTACT
Found at i:1247058 original size:32 final size:34
Alignment explanation
Indices: 1246991--1247060 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1246981 TTTTGTAAAG
* *
1246991 GGGAAAGGTTCTAGCTTATCTCGTATAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTATAAAAACTA
*
1247025 GGGAAAGGTTCTAGTTTAGCCCG-A-AAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTATAAAAACTA
1247057 GGGA
1 GGGA
1247061 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTTAGCCCGTATAAAAACTA
Found at i:1248634 original size:21 final size:19
Alignment explanation
Indices: 1248574--1248635 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 19
1248564 GCAAACGTTG
*
1248574 ATTTTGAAAATCAAAATGAA
1 ATTTTAAAAATCAAAAT-AA
**
1248594 ATTTTAAAAAAT-AATTTAA
1 ATTTT-AAAAATCAAAATAA
1248613 AGCTTTTAAAAATCAAAATAA
1 A--TTTTAAAAATCAAAATAA
1248634 AT
1 AT
1248636 GATTTAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
19 4 0.12
20 14 0.42
21 15 0.45
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
ATTTTAAAAATCAAAATAA
Found at i:1249884 original size:34 final size:30
Alignment explanation
Indices: 1249846--1249914 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
1249836 TTGATATAAC
1249846 AATTTAAGGAAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--AAAAAT-GTTTTTGGACTT-AATTG
*
1249880 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAAAAAAATGTTTTTGGACTTAATTG
1249909 AATTTA
1 AATTTA
1249915 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 12 0.36
31 5 0.15
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAAAAAAATGTTTTTGGACTTAATTG
Found at i:1249926 original size:29 final size:30
Alignment explanation
Indices: 1249856--1249914 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1249846 AATTTAAGGA
1249856 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
1249887 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
1249915 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:1250021 original size:21 final size:22
Alignment explanation
Indices: 1249995--1250052 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1249985 AGGGTGTCAA
*
1249995 AGTGCATCCATGTACC-CCTAC-
1 AGTGCATCCATGCACCTCC-ACT
*
1250016 AGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACCTCCACT
1250038 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1250053 TCAAACACCG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.22
Consensus pattern (22 bp):
AGTGCATCCATGCACCTCCACT
Found at i:1250246 original size:20 final size:22
Alignment explanation
Indices: 1250208--1250247 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1250198 TTTTAGTAGA
1250208 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1250230 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1250248 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1253215 original size:23 final size:23
Alignment explanation
Indices: 1253189--1253249 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1253179 TATTACCCTA
*
1253189 AAGGATCACGTAGAAATGTCCCG
1 AAGGACCACGTAGAAATGTCCCG
* *
1253212 AAGGAGCACGTAGAATTGTCCCG
1 AAGGACCACGTAGAAATGTCCCG
1253235 AAGGACCACGTAGAA
1 AAGGACCACGTAGAA
1253250 CCTCCAACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (23 bp):
AAGGACCACGTAGAAATGTCCCG
Found at i:1263296 original size:23 final size:22
Alignment explanation
Indices: 1263254--1263315 Score: 88
Period size: 23 Copynumber: 2.8 Consensus size: 22
1263244 ATAGGGCAGA
* *
1263254 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
*
1263276 GGGAACTGATTCCCCCATTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
1263299 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
1263316 AGGGGAATCG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:1263335 original size:20 final size:19
Alignment explanation
Indices: 1263297--1263339 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1263287 CCCCCATTGA
*
1263297 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATCCCCCCT
*
1263316 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
1263336 -GGGG
1 AGGGG
1263340 TTCTGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:1269133 original size:54 final size:54
Alignment explanation
Indices: 1269082--1269814 Score: 982
Period size: 54 Copynumber: 13.6 Consensus size: 54
1269072 CACAGTGTTC
* * * *
1269082 ATACGGTAATTCACAAACTCATTACGAATTACGTGGGTTGCACACATAGTGTCG
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * *
1269136 ATATGGTAATTCATAAACTCATTATGAATTATGTGGGTTGCACATATAGTGCCA
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * *
1269190 ATACGATAATTCATAAACTCATTAAT-AATTACATGGGTTGCACACATAATGCCA
1 ATACGGTAATTCATAAACTCATT-ATGAATTACGTGGGTTGCACACATAGTGCCA
* * * **
1269244 ATGCGGTAATTCATAAACTCATTATGAATTATGTGGGTTGCATACATAGTGTAA
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * * *
1269298 ATATGATAATTCATAAACTCATTATGAATTATGTGAGTTGCACACATAGTGCCA
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * * *
1269352 ATATGGTAATTCATAAATTAATTATGAATTACGTGGGTTGCACACATAGTGTCA
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * * *
1269406 ATACGGTAATTTATAAACTCATTATGAATTATGTGGGTTGAACATATAGTGCCA
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* *
1269460 AAACGGTAATTCATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCA
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * * * *
1269514 ATATGGTAATTCATAAACTAATAATGAATTACGTAGGTTACACACATAGTGCCA
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
** * * *
1269568 ATACGGTAATTCATAAACTCATTATGAATTATATGGGTTACACACATAGTGTCG
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * *
1269622 ATACGGTAATTTATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCC
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * *
1269676 ATATGGTAATTCATAAACTCATTATGAATTACATGTGTTGCACACATAGTGCCA
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * * * * *
1269730 ATACGATCATTCTTAAATTCATTATGAATTAAGTGGGTTACACACATAGTGCCA
1 ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
*
1269784 ATACGTTAATTCATAAACTCATTATGAATTA
1 ATACGGTAATTCATAAACTCATTATGAATTA
1269815 ATTTGTGCCA
Statistics
Matches: 594, Mismatches: 83, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 2 0.00
54 590 0.99
55 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (54 bp):
ATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
Found at i:1269232 original size:108 final size:108
Alignment explanation
Indices: 1269082--1270307 Score: 1423
Period size: 108 Copynumber: 11.6 Consensus size: 108
1269072 CACAGTGTTC
* * * * * *
1269082 ATACGGTAATTCACAAACTCATTACGAATTACGTGGGTTGCACACATAGTGTCGATATGGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAATT
* *
1269147 CATAAACTCATTATGAATTATGTGGGTTGCACATATAGTGCCA
66 CATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * *
1269190 ATACGATAATTCATAAACTCATTAAT-AATTACATGGGTTGCACACATAATGCCAATGCGGTAAT
1 ATACGGTAATTCATAAACTCATT-ATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAAT
* * **
1269254 TCATAAACTCATTATGAATTATGTGGGTTGCATACATAGTGTAA
65 TCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * ** * *
1269298 ATATGATAATTCATAAACTCATTATGAATTATGTGAGTTGCACACATAGTGCCAATATGGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAATT
* * *
1269363 CATAAATTAATTATGAATTACGTGGGTTGCACACATAGTGTCA
66 CATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* ** * * *
1269406 ATACGGTAATTTATAAACTCATTATGAATTATGTGGGTTGAACATATAGTGCCAAAACGGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAATT
*
1269471 CATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCA
66 CATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * * * * *
1269514 ATATGGTAATTCATAAACTAATAATGAATTACGTAGGTTACACACATAGTGCCAATACGGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAATT
** * * *
1269579 CATAAACTCATTATGAATTATATGGGTTACACACATAGTGTCG
66 CATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * *
1269622 ATACGGTAATTTATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCCATATGGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAATT
* *
1269687 CATAAACTCATTATGAATTACATGTGTTGCACACATAGTGCCA
66 CATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * * * * *
1269730 ATACGATCATTCTTAAATTCATTATGAATTA-AGTGGGTTACACACATAGTGCCAATACGTTAAT
1 ATACGGTAATTCATAAACTCATTATGAATTACA-TGGGTTGCACACATAGTGCCAATACGGTAAT
*
1269794 TCATAAACTCATTATGAATTA-----ATT-------T-GTGCCA
65 TCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* *
1269825 ATACGGTAATTCATAAACTCATTATGAATTA-AGTGGGTTGCAAACAAAGTGCCAATACGGTAAT
1 ATACGGTAATTCATAAACTCATTATGAATTACA-TGGGTTGCACACATAGTGCCAATACGGTAAT
* * * *
1269889 TCATAAACTTATTATGAATTACATGGGTTGCATACATAGTCCCA
65 TCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* ** * *
1269933 ATACTGTAATTCATAAACTCATTATGAATTATGTGGGTTGCATAAATAGTGCCAATACGGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAATT
* * * *
1269998 CTTAAATTCATTAAGAATTACGTGGGTTACACACATAGTGCCA
66 CATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* **
1270041 ATACAGTAATTCATAAACTCATTATGAATTA-AT---TT------ATA---CCAATAATGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAATT
* * * *
1270093 CATAAACTCATTATGAATTAAGTGGGTTGCAAACAAAGTGTCA
66 CATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* *
1270136 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCAGACATAGT-CCTAATACTGTAAT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCC-AATACGGTAAT
* * * **
1270200 TCATAAACTCACTATGAATTACATAGGTTGCACACATAGTGCTT
65 TCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
* * **
1270244 ATACGATAATTCATAAACTCATTATGAATTACGTATGTTGCACACATAGTGCCAATACGGTAAT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAAT
1270308 ACAACATATA
Statistics
Matches: 959, Mismatches: 128, Indels: 62
0.83 0.11 0.05
Matches are distributed among these distances:
95 159 0.17
96 3 0.00
98 3 0.00
99 2 0.00
100 2 0.00
103 2 0.00
104 2 0.00
105 3 0.00
107 7 0.01
108 773 0.81
109 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (108 bp):
ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCAATACGGTAATT
CATAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCA
Found at i:1269310 original size:162 final size:162
Alignment explanation
Indices: 1269082--1270307 Score: 1461
Period size: 162 Copynumber: 7.7 Consensus size: 162
1269072 CACAGTGTTC
* * * * *
1269082 ATACGGTAATTCACAAACTCATTACGAATTACGTGGGTTGCACACATAGTGTCGATATGGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGTCAATACGGTAATT
* *
1269147 CATAAACTCATTATGAATTATGTGGGTTGCACATATAGTGCCAATACGATAATTCATAAACTCAT
66 CATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGTAATTCATAAACTCAT
*
1269212 TAAT-AATTACATGGGTTGCACACATAATGCCA
131 T-ATGAATTACATGGGTTGCACACATAGTGCCA
* ** * * * *
1269244 ATGCGGTAATTCATAAACTCATTATGAATTATGTGGGTTGCATACATAGTGTAAATATGATAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGTCAATACGGTAATT
* * * *
1269309 CATAAACTCATTATGAATTATGTGAGTTGCACACATAGTGCCAATATGGTAATTCATAAATTAAT
66 CATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGTAATTCATAAACTCAT
* *
1269374 TATGAATTACGTGGGTTGCACACATAGTGTCA
131 TATGAATTACATGGGTTGCACACATAGTGCCA
* ** * * * *
1269406 ATACGGTAATTTATAAACTCATTATGAATTATGTGGGTTGAACATATAGTGCCAAAACGGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGTCAATACGGTAATT
* *
1269471 CATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATATGGTAATTCATAAACTAAT
66 CATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGTAATTCATAAACTCAT
* * * *
1269536 AATGAATTACGTAGGTTACACACATAGTGCCA
131 TATGAATTACATGGGTTGCACACATAGTGCCA
* * *
1269568 ATACGGTAATTCATAAACTCATTATGAATTATATGGGTTACACACATAGTGTCGATACGGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGTCAATACGGTAATT
* ** * *
1269633 TATAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCCATATGGTAATTCATAAACTCAT
66 CATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGTAATTCATAAACTCAT
*
1269698 TATGAATTACATGTGTTGCACACATAGTGCCA
131 TATGAATTACATGGGTTGCACACATAGTGCCA
* * * * * * *
1269730 ATACGATCATTCTTAAATTCATTATGAATTA-AGTGGGTTACACACATAGTGCCAATACGTTAAT
1 ATACGGTAATTCATAAACTCATTATGAATTACA-TGGGTTGCACACATAGTGTCAATACGGTAAT
*
1269794 TCATAAACTCATTATGAATTA-----ATT-------T-GTGCCAATACGGTAATTCATAAACTCA
65 TCATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGTAATTCATAAACTCA
* *
1269846 TTATGAATTA-AGTGGGTTGCAAACAAAGTGCCA
130 TTATGAATTACA-TGGGTTGCACACATAGTGCCA
* * ** *
1269879 ATACGGTAATTCATAAACTTATTATGAATTACATGGGTTGCATACATAGTCCCAATACTGTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGTCAATACGGTAATT
* * * *
1269944 CATAAACTCATTATGAATTATGTGGGTTGCATAAATAGTGCCAATACGGTAATTCTTAAATTCAT
66 CATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGTAATTCATAAACTCAT
* * *
1270009 TAAGAATTACGTGGGTTACACACATAGTGCCA
131 TATGAATTACATGGGTTGCACACATAGTGCCA
* **
1270041 ATACAGTAATTCATAAACTCATTATGAATTA-AT---TTATAC-CA-A---T-AAT---GTAATT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGTCAATACGGTAATT
* * * *
1270093 CATAAACTCATTATGAATTAAGTGGGTTGCAAACAAAGTGTCAATACGGTAATTCATAAACTCAT
66 CATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGTAATTCATAAACTCAT
*
1270158 TATGAATTACATGGGTTGCAGACATAGT-CCTA
131 TATGAATTACATGGGTTGCACACATAGTGCC-A
* * * * *
1270190 ATACTGTAATTCATAAACTCACTATGAATTACATAGGTTGCACACATAGTG-CTTATACGATAAT
1 ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGTC-AATACGGTAAT
* **
1270254 TCATAAACTCATTATGAATTACGTATGTTGCACACATAGTGCCAATACGGTAAT
65 TCATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGTAAT
1270308 ACAACATATA
Statistics
Matches: 919, Mismatches: 112, Indels: 66
0.84 0.10 0.06
Matches are distributed among these distances:
148 3 0.00
149 244 0.27
150 4 0.00
152 3 0.00
153 4 0.00
154 4 0.00
155 1 0.00
156 1 0.00
157 4 0.00
158 3 0.00
159 2 0.00
161 6 0.01
162 640 0.70
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (162 bp):
ATACGGTAATTCATAAACTCATTATGAATTACATGGGTTGCACACATAGTGTCAATACGGTAATT
CATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGTAATTCATAAACTCAT
TATGAATTACATGGGTTGCACACATAGTGCCA
Found at i:1269835 original size:41 final size:41
Alignment explanation
Indices: 1269778--1269856 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
1269768 TACACACATA
*
1269778 GTGCCAATACGTTAATTCATAAACTCATTATGAATTAATTT
1 GTGCCAATACGGTAATTCATAAACTCATTATGAATTAATTT
1269819 GTGCCAATACGGTAATTCATAAACTCATTATGAATTAA
1 GTGCCAATACGGTAATTCATAAACTCATTATGAATTAA
1269857 GTGGGTTGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (41 bp):
GTGCCAATACGGTAATTCATAAACTCATTATGAATTAATTT
Found at i:1269903 original size:54 final size:54
Alignment explanation
Indices: 1269819--1270072 Score: 359
Period size: 54 Copynumber: 4.7 Consensus size: 54
1269809 GAATTAATTT
*
1269819 GTGCCAATACGGTAATTCATAAACTCATTATGAATTAAGTGGGTTGCAAACAAA
1 GTGCCAATACGGTAATTCATAAACTCATTATGAATTAAGTGGGTTGCAAACATA
* *
1269873 GTGCCAATACGGTAATTCATAAACTTATTATGAATTACA-TGGGTTGCATACATA
1 GTGCCAATACGGTAATTCATAAACTCATTATGAATTA-AGTGGGTTGCAAACATA
* * *
1269927 GTCCCAATACTGTAATTCATAAACTCATTATGAATTATGTGGGTTGCATAA-ATA
1 GTGCCAATACGGTAATTCATAAACTCATTATGAATTAAGTGGGTTGCA-AACATA
* * * * * *
1269981 GTGCCAATACGGTAATTCTTAAATTCATTAAGAATTACGTGGGTTACACACATA
1 GTGCCAATACGGTAATTCATAAACTCATTATGAATTAAGTGGGTTGCAAACATA
*
1270035 GTGCCAATACAGTAATTCATAAACTCATTATGAATTAA
1 GTGCCAATACGGTAATTCATAAACTCATTATGAATTAA
1270073 TTTATACCAA
Statistics
Matches: 175, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 172 0.98
55 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (54 bp):
GTGCCAATACGGTAATTCATAAACTCATTATGAATTAAGTGGGTTGCAAACATA
Found at i:1270162 original size:54 final size:55
Alignment explanation
Indices: 1270087--1270307 Score: 290
Period size: 54 Copynumber: 4.1 Consensus size: 55
1270077 TACCAATAAT
* * * *
1270087 GTAATTCATAAACTCATTATGAATTA-AGTGGGTTGCAAACAAAGTGTC-AATACG
1 GTAATTCATAAACTCATTATGAATTACA-TAGGTTGCACACATAGTGCCTAATACG
* * *
1270141 GTAATTCATAAACTCATTATGAATTACATGGGTTGCAGACATAGT-CCTAATACT
1 GTAATTCATAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCTAATACG
* *
1270195 GTAATTCATAAACTCACTATGAATTACATAGGTTGCACACATAGTG-CTTATACG
1 GTAATTCATAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCTAATACG
* * *
1270249 ATAATTCATAAACTCATTATGAATTACGTATGTTGCACACATAGTGCC-AATACG
1 GTAATTCATAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCTAATACG
1270303 GTAAT
1 GTAAT
1270308 ACAACATATA
Statistics
Matches: 148, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
53 1 0.01
54 145 0.98
55 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (55 bp):
GTAATTCATAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCTAATACG
Found at i:1270236 original size:203 final size:203
Alignment explanation
Indices: 1269884--1270274 Score: 554
Period size: 203 Copynumber: 1.9 Consensus size: 203
1269874 TGCCAATACG
* * * *
1269884 GTAATTCATAAACTTATTATGAATTACATGGGTTGCATACATAGTCCCAATACTGTAATTCATAA
1 GTAATTCATAAACTCATTATGAATTACATGGGTTGCAAACAAAGTCCCAATACGGTAATTCATAA
** * * * *
1269949 ACTCATTATGAATTATGTGGGTTGCATAAATAGTGCCAATACGGTAATTCTTAAATTCATTAAGA
66 ACTCATTATGAATTACATGGGTTGCAGAAATAGTGCCAATACGGTAATTCATAAACTCACTAAGA
* *
1270014 ATTACGTGGGTTACACACATAGTGCCAATAC-AGTAATTCATAAACTCATTATGAATTAATTTAT
131 ATTACATAGGTTACACACATAGTGCCAATACGA-TAATTCATAAACTCATTATGAATTAATTTAT
1270078 ACCAATAAT
195 ACCAATAAT
**
1270087 GTAATTCATAAACTCATTATGAATTA-AGTGGGTTGCAAACAAAGTGTCAATACGGTAATTCATA
1 GTAATTCATAAACTCATTATGAATTACA-TGGGTTGCAAACAAAGTCCCAATACGGTAATTCATA
* * *
1270151 AACTCATTATGAATTACATGGGTTGCAGACATAGT-CCTAATACTGTAATTCATAAACTCACTAT
65 AACTCATTATGAATTACATGGGTTGCAGAAATAGTGCC-AATACGGTAATTCATAAACTCACTAA
* **
1270215 GAATTACATAGGTTGCACACATAGTGCTTATACGATAATTCATAAACTCATTATGAATTA
129 GAATTACATAGGTTACACACATAGTGCCAATACGATAATTCATAAACTCATTATGAATTA
1270275 CGTATGTTGC
Statistics
Matches: 165, Mismatches: 20, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
202 3 0.02
203 161 0.98
204 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (203 bp):
GTAATTCATAAACTCATTATGAATTACATGGGTTGCAAACAAAGTCCCAATACGGTAATTCATAA
ACTCATTATGAATTACATGGGTTGCAGAAATAGTGCCAATACGGTAATTCATAAACTCACTAAGA
ATTACATAGGTTACACACATAGTGCCAATACGATAATTCATAAACTCATTATGAATTAATTTATA
CCAATAAT
Found at i:1271576 original size:17 final size:17
Alignment explanation
Indices: 1271554--1271605 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1271544 CATTGAATAA
1271554 AGTTCATTAATTAAACT
1 AGTTCATTAATTAAACT
* *
1271571 AGTTCATTCATCAAACT
1 AGTTCATTAATTAAACT
1271588 AGTTCATTTAA-TAAACT
1 AGTTCA-TTAATTAAACT
1271605 A
1 A
1271606 ACTTTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 27 0.90
18 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (17 bp):
AGTTCATTAATTAAACT
Found at i:1272032 original size:24 final size:24
Alignment explanation
Indices: 1272005--1272058 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
1271995 TCAAAGCATT
*
1272005 CAAGGTTGATTTAATCATCCAAAC
1 CAAGGCTGATTTAATCATCCAAAC
*
1272029 CAAGGGCTGATTTAATCATTCAAAC
1 CAA-GGCTGATTTAATCATCCAAAC
1272054 CAAGG
1 CAAGG
1272059 GTTGTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (24 bp):
CAAGGCTGATTTAATCATCCAAAC
Found at i:1272039 original size:25 final size:25
Alignment explanation
Indices: 1272011--1272059 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1272001 CATTCAAGGT
1272011 TGATTTAATCATCCAAACCAAGGGC
1 TGATTTAATCATCCAAACCAAGGGC
*
1272036 TGATTTAATCATTCAAACCAAGGG
1 TGATTTAATCATCCAAACCAAGGG
1272060 TTGTTCATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (25 bp):
TGATTTAATCATCCAAACCAAGGGC
Found at i:1284824 original size:21 final size:20
Alignment explanation
Indices: 1284802--1284857 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
1284792 GGCAACCTAT
1284802 TTTTATTTTTTATTATTTAA
1 TTTTATTTTTTATTATTTAA
*
1284822 -TTT-TTGTTTA-TATTTAA
1 TTTTATTTTTTATTATTTAA
*
1284839 TTATATTTTTTATTTATTT
1 TTTTATTTTTTA-TTATTT
1284858 TTTCCATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 7 0.24
18 8 0.28
19 9 0.31
21 5 0.17
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTATTTTTTATTATTTAA
Found at i:1284852 original size:17 final size:16
Alignment explanation
Indices: 1284808--1284854 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1284798 CTATTTTTAT
1284808 TTTTTATTATTTAATT-
1 TTTTT-TTATTTAATTA
1284824 TTTGTTTATATTTAATTA
1 TTT-TTT-TATTTAATTA
1284842 TATTTTTTATTTA
1 T-TTTTTTATTTA
1284855 TTTTTTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 4 0.15
19 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTTTTATTTAATTA
Found at i:1288844 original size:2 final size:2
Alignment explanation
Indices: 1288833--1288869 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1288823 AAGGAAAAAA
*
1288833 AT AT AA AT AT AT AT AT A- 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
1288870 CAAAGTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1288854 original size:17 final size:17
Alignment explanation
Indices: 1288832--1288866 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1288822 AAAGGAAAAA
1288832 AATATAAATATATATAT
1 AATATAAATATATATAT
*
1288849 AATATATATATATATAT
1 AATATAAATATATATAT
1288866 A
1 A
1288867 TATCAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATAAATATATATAT
Found at i:1288917 original size:36 final size:35
Alignment explanation
Indices: 1288857--1288929 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 35
1288847 ATAATATATA
* * *
1288857 TATATATATATATCAAAGTATTAAAATATAATAAGC
1 TATATATATACACCAAAGTATTAAAATAGAA-AAGC
1288893 TATATATATACACCAAA-TACTTAAAATAGAAAAGC
1 TATATATATACACCAAAGTA-TTAAAATAGAAAAGC
1288928 TA
1 TA
1288930 CCCTCCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 8 0.24
36 25 0.76
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (35 bp):
TATATATATACACCAAAGTATTAAAATAGAAAAGC
Found at i:1289363 original size:18 final size:17
Alignment explanation
Indices: 1289342--1289384 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1289332 ATATATACAT
1289342 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
* *
1289360 ATAATAAAAATAAGTGA
1 ATAATAATAATAAATGA
1289377 ATAA-AATA
1 ATAATAATA
1289385 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1289808 original size:37 final size:36
Alignment explanation
Indices: 1289765--1289866 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1289755 ATAGTAGAAC
1289765 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1289802 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1289836 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1289867 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1294154 original size:12 final size:13
Alignment explanation
Indices: 1294139--1294169 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1294129 ATTTTTTTTT
1294139 AATAATTTTAAAA
1 AATAATTTTAAAA
1294152 ATATAATTTTAAAA
1 A-ATAATTTTAAAA
1294166 AATA
1 AATA
1294170 TATTAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATAATTTTAAAA
Found at i:1294157 original size:14 final size:15
Alignment explanation
Indices: 1294140--1294171 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1294130 TTTTTTTTTA
1294140 ATAATTTT-AAAAAT
1 ATAATTTTAAAAAAT
1294154 ATAATTTTAAAAAAT
1 ATAATTTTAAAAAAT
1294169 ATA
1 ATA
1294172 TTAATTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATTTTAAAAAAT
Found at i:1295135 original size:34 final size:37
Alignment explanation
Indices: 1295052--1295135 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 37
1295042 ATTATATACA
* *
1295052 TATTTTATT-TTTATTTACCTCTATTTATTTTTTATTT
1 TATTTTATTATTTATTTACATCTATTTACTTTTTA-TT
*
1295089 TATTTT-TATATTTCTTTACAT-T-TTTACTTTTTA-T
1 TATTTTAT-TATTTATTTACATCTATTTACTTTTTATT
1295123 TATTTTATTATTT
1 TATTTTATTATTT
1295136 TATTATTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
34 12 0.29
35 1 0.02
36 11 0.27
37 8 0.20
38 9 0.22
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (37 bp):
TATTTTATTATTTATTTACATCTATTTACTTTTTATT
Found at i:1295190 original size:8 final size:8
Alignment explanation
Indices: 1295076--1295181 Score: 71
Period size: 8 Copynumber: 12.9 Consensus size: 8
1295066 TTACCTCTAT
1295076 TTATTTT-
1 TTATTTTA
1295083 TTATTTTA
1 TTATTTTA
1295091 TT-TTTATA
1 TTATTT-TA
1295099 TT-TCTTTA
1 TTAT-TTTA
*
1295107 -CATTTTTA
1 TTA-TTTTA
*
1295115 CT-TTTTA
1 TTATTTTA
1295122 TTATTTTA
1 TTATTTTA
1295130 TTATTTTA
1 TTATTTTA
1295138 TTATTTTA
1 TTATTTTA
1295146 TTCA-TTTA
1 TT-ATTTTA
1295154 TATATTTACTATA
1 T-TA-TT--T-TA
1295167 TTATTTTA
1 TTATTTTA
1295175 TTATTTT
1 TTATTTT
1295182 TATAATTTTG
Statistics
Matches: 82, Mismatches: 3, Indels: 27
0.73 0.03 0.24
Matches are distributed among these distances:
7 16 0.20
8 51 0.62
9 6 0.07
10 1 0.01
11 2 0.02
12 3 0.04
13 3 0.04
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.72
Consensus pattern (8 bp):
TTATTTTA
Found at i:1295196 original size:37 final size:37
Alignment explanation
Indices: 1295128--1295199 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
1295118 TTTATTATTT
*
1295128 TATTATTTTATTATTTTATTCATTTATATATTTACTA
1 TATTATTTTATTATTTTATTAATTTATATATTTACTA
1295165 TATTATTTTATTATTTT-TATAATTT-TGATATTTAC
1 TATTATTTTATTATTTTAT-TAATTTAT-ATATTTAC
1295200 ATCTTTTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 2 0.06
37 30 0.94
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (37 bp):
TATTATTTTATTATTTTATTAATTTATATATTTACTA
Found at i:1295246 original size:22 final size:21
Alignment explanation
Indices: 1295194--1295248 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
1295184 TAATTTTGAT
*
1295194 ATTTACATCTTTTTACATTTAA
1 ATTTATAT-TTTTTACATTTAA
* *
1295216 TTTTCATATTTTTTAGATTTACA
1 ATTT-ATATTTTTTACATTTA-A
1295239 ATTTATATTT
1 ATTTATATTT
1295249 ATACTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTATATTTTTTACATTTAA
Found at i:1296189 original size:239 final size:240
Alignment explanation
Indices: 1295770--1296248 Score: 942
Period size: 239 Copynumber: 2.0 Consensus size: 240
1295760 TGAAAACCAA
1295770 TGTTTGATCCTATGGGAAATATTGATATTTTTTACTTCATTTGGAATTAGAAAGTCACTGCTGTA
1 TGTTTGATCCTATGGGAAATATTGATATTTTTTACTTCATTTGGAATTAGAAAGTCACTGCTGTA
1295835 CTTCATGTTAGGGGTATTTCTCCTCGAACCGAAGTATTGAAATATCGTTCTTTTACTTTAGAAAC
66 CTTCATGTTAGGGGTATTTCTCCTCGAACCGAAGTATTGAAATATCGTTCTTTTACTTTAGAAAC
1295900 CTTAAATTCTCGAAAAGAAATACCAGTAATTCTCTTCTTTAATTTGAAAGAGAGGGCACCATTCC
131 CTTAAATTCTCGAAAAGAAATACCAGTAATTCTCTTCTTTAATTTGAAAGAGAGGGCACCATTCC
1295965 ACTTCATATTAGAAGGAA-CTCTCCAGCCAAATGCAACGAACTGG
196 ACTTCATATTAGAAGGAACCTCTCCAGCCAAATGCAACGAACTGG
1296009 TGTTTGATCCTATGGGAAATATTGATATTTTTTACTTCATTTGGAATTAGAAAGTCACTGCTGTA
1 TGTTTGATCCTATGGGAAATATTGATATTTTTTACTTCATTTGGAATTAGAAAGTCACTGCTGTA
1296074 CTTCATGTTAGGGGTATTTCTCCTCGAACCGAAGTATTGAAATATCGTTCTTTTACTTTAGAAAC
66 CTTCATGTTAGGGGTATTTCTCCTCGAACCGAAGTATTGAAATATCGTTCTTTTACTTTAGAAAC
1296139 CTTAAATTCTCGAAAAGAAATACCAGTAATTCTCTTCTTTAATTTGAAAGAGAGGGCACCATTCC
131 CTTAAATTCTCGAAAAGAAATACCAGTAATTCTCTTCTTTAATTTGAAAGAGAGGGCACCATTCC
1296204 ACTTCATATTAGAAGGAACTCTCTCCAGCCAAATGCAACGAACTG
196 ACTTCATATTAGAAGGAAC-CTCTCCAGCCAAATGCAACGAACTG
1296249 TTGATTTTTC
Statistics
Matches: 238, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
239 213 0.89
241 25 0.11
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (240 bp):
TGTTTGATCCTATGGGAAATATTGATATTTTTTACTTCATTTGGAATTAGAAAGTCACTGCTGTA
CTTCATGTTAGGGGTATTTCTCCTCGAACCGAAGTATTGAAATATCGTTCTTTTACTTTAGAAAC
CTTAAATTCTCGAAAAGAAATACCAGTAATTCTCTTCTTTAATTTGAAAGAGAGGGCACCATTCC
ACTTCATATTAGAAGGAACCTCTCCAGCCAAATGCAACGAACTGG
Found at i:1298211 original size:60 final size:60
Alignment explanation
Indices: 1298095--1298228 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
1298085 TGGAACATAA
* * *
1298095 CATTTTGTAACTTTTAATAGTCATGGGACTCAACAAAGCAACTTCCTATAACCGGGGAAC
1 CATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAGCAACTTCATACAACCGGGGAAC
* * ** *
1298155 CATTTTGTAACTTTTAATA-TACAAGGGACTCAATAAAGTAA-TATCATACAGTCGGGGGAC
1 CATTTTGTAACTTTTAATAGT-CAAGGGACTCAACAAAGCAACT-TCATACAACCGGGGAAC
1298215 CATTTT-TATACTTT
1 CATTTTGTA-ACTTT
1298229 ACCATTCATT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 4 0.06
60 59 0.94
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAGCAACTTCATACAACCGGGGAAC
Found at i:1324283 original size:65 final size:64
Alignment explanation
Indices: 1324173--1324320 Score: 183
Period size: 65 Copynumber: 2.3 Consensus size: 64
1324163 TACACTTGGG
* * * *
1324173 GTGCATCAGTACACT-AATTACATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGGTA
1 GTGCATCGGTACA-TAAAATACATTCAATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGG-A
*
1324237 T
64 A
* *
1324238 GTGCATCGGTACATAAAATACATTCAATGTTTCAATAA-AATCAGGAGTGCATCGATGTATGGAA
1 GTGCATCGGTACATAAAATACATTCAATGTTTCAA-AAGAACCAGGAGTGCATCGATGCATGGAA
*
1324302 GTGTATCGGTACATAAAAT
1 GTGCATCGGTACATAAAAT
1324321 GCGTTCGAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 20 0.27
65 51 0.70
66 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATACATTCAATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGGAA
Found at i:1326952 original size:44 final size:44
Alignment explanation
Indices: 1326886--1326989 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 44
1326876 CGATGCACTG
* * **
1326886 CATAGTGTATCGATTCACATTCAAG-GCATGCATCGGTGTACCTT
1 CATAGTGTATCGATGCACATTCAAGTG-ATGCATCAGTACACCTT
* *
1326930 CATAGTGTATCGATGCATATTCAAGTGATGCATCAGTACACTTT
1 CATAGTGTATCGATGCACATTCAAGTGATGCATCAGTACACCTT
1326974 CATAGTGTATCGATGC
1 CATAGTGTATCGATGC
1326990 TAGTGCACAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 52 0.98
45 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAGTGATGCATCAGTACACCTT
Found at i:1332474 original size:65 final size:63
Alignment explanation
Indices: 1332400--1332534 Score: 182
Period size: 65 Copynumber: 2.1 Consensus size: 63
1332390 ACACTAATTA
* * * *
1332400 CATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTCTATGCATTAGTACATAAAAT
1 CATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGG-ATATGCACTA-TACACAAAAT
1332464 G
63 G
* *
1332465 CATTCGATGTTTCAATAAAATCAGGAGTGCATCGATGCATGGATGTGCACTATACACAAAATG
1 CATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGATATGCACTATACACAAAATG
1332528 CATTCGA
1 CATTCGA
1332535 ATTAGGGTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
63 17 0.27
64 7 0.11
65 37 0.59
66 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
CATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGATATGCACTATACACAAAATG
Found at i:1333855 original size:85 final size:84
Alignment explanation
Indices: 1333756--1333956 Score: 240
Period size: 85 Copynumber: 2.3 Consensus size: 84
1333746 GGTGGTACCG
* * **
1333756 ATACTACCCTGAGTATAGGTACCAAATTTGTATTCAATGTTTGGAAAATTAATCCTCAATATTGA
1 ATACTACCCCGAGTATA-GTACCAAATTTGCATTCAATGTTTGGAAAATTAATCCTCAATATCAA
1333821 TACCCTTACCTAGAGTATCA
65 TACCCTTACCTAGAGTATCA
* * ** * * * *
1333841 ATACTACCCCGAGTATTTGTACCAAATTCGCATTTGATGTTTGGAAAATTCATTCTCAGTGTCAA
1 ATACTACCCCGAGTA-TAGTACCAAATTTGCATTCAATGTTTGGAAAATTAATCCTCAATATCAA
*
1333906 TACCCTTACCTAGAGTATCG
65 TACCCTTACCTAGAGTATCA
*
1333926 ATATTACCCCGAAGTATCAGTACCAAATTTG
1 ATACTACCCCG-AGTAT-AGTACCAAATTTG
1333957 ACTACTAGGA
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
85 81 0.84
86 16 0.16
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (84 bp):
ATACTACCCCGAGTATAGTACCAAATTTGCATTCAATGTTTGGAAAATTAATCCTCAATATCAAT
ACCCTTACCTAGAGTATCA
Found at i:1339574 original size:123 final size:120
Alignment explanation
Indices: 1339358--1339581 Score: 358
Period size: 123 Copynumber: 1.8 Consensus size: 120
1339348 GCCTATACAG
* **
1339358 ACAACCTCACATGGGGTAACAAGCAAGAACAATCTGTACCTTGGATAAGATAACATGTTCAACAT
1 ACAACCTCACATGGGGTAACAAACAAGAACAAAATGTACCTTGGATAAGATAACATGTTCAACAT
1339423 CAAACCTTAACCAATTAACCTAAAACCTATTGACAACAGTACCCTCGCATGTGGC
66 CAAACCTTAACCAATTAACCTAAAACCTATTGACAACAGTACCCTCGCATGTGGC
* * *
1339478 ACAACCTCACATGGGGTAACAAACAAGAAGAACAAAATGTACCTTGGATCAGCTAACATGTTGAA
1 ACAACCTCACATGGGGTAACAAAC---AAGAACAAAATGTACCTTGGATAAGATAACATGTTCAA
*
1339543 CATCAAGCCTTAACCAATTAACCTAAAACCTATTGACAA
63 CATCAAACCTTAACCAATTAACCTAAAACCTATTGACAA
1339582 AAAGTACAGG
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
120 23 0.24
123 71 0.76
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.21
Consensus pattern (120 bp):
ACAACCTCACATGGGGTAACAAACAAGAACAAAATGTACCTTGGATAAGATAACATGTTCAACAT
CAAACCTTAACCAATTAACCTAAAACCTATTGACAACAGTACCCTCGCATGTGGC
Found at i:1339680 original size:10 final size:9
Alignment explanation
Indices: 1339664--1339689 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1339654 TTGAGGACAA
1339664 GAAAAAAAG
1 GAAAAAAAG
1339673 GAAAAAAAG
1 GAAAAAAAG
1339682 GAAAAAAA
1 GAAAAAAA
1339690 TAAGAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
GAAAAAAAG
Found at i:1340664 original size:2 final size:2
Alignment explanation
Indices: 1340657--1340688 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1340647 TTGAACTTAG
1340657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1340689 GAAAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1353478 original size:2 final size:2
Alignment explanation
Indices: 1353471--1353550 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1353461 TACGATAAAC
1353471 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
1353513 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
1353551 CAGAAAATCG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1368842 original size:20 final size:20
Alignment explanation
Indices: 1368817--1368870 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1368807 AGTGTTCACA
*
1368817 GGGGTATCGGTACCCTATAG
1 GGGGTATCGATACCCTATAG
1368837 GGGGTATCGATACCCTATAG
1 GGGGTATCGATACCCTATAG
1368857 GGGGTATCGATACC
1 GGGGTATCGATACC
1368871 ATACTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (20 bp):
GGGGTATCGATACCCTATAG
Found at i:1371588 original size:21 final size:22
Alignment explanation
Indices: 1371493--1371596 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 22
1371483 GTACCATCAG
* *
1371493 GGGGTATCGATACCCATTCAAGG
1 GGGGTATCGATACCTATTCAA-A
* *
1371516 GAGGGTATCGATATCTATT-GAA
1 G-GGGTATCGATACCTATTCAAA
*
1371538 GAGGTATCGATACCTATTCAAA
1 GGGGTATCGATACCTATTCAAA
*
1371560 GGGGGTATCGATACC-ATTCTCAA
1 -GGGGTATCGATACCTATTC-AAA
*
1371583 -GGGTATCTATACCT
1 GGGGTATCGATACCT
1371597 TATGCACAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
21 27 0.41
22 7 0.11
23 17 0.26
24 15 0.23
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (22 bp):
GGGGTATCGATACCTATTCAAA
Found at i:1371588 original size:44 final size:44
Alignment explanation
Indices: 1371473--1371596 Score: 121
Period size: 44 Copynumber: 2.8 Consensus size: 44
1371463 AAAATCCGAA
* * * *
1371473 GAGGGTATCGGTACC-A-TCAGGGGGTATCGATACCCATTCAAGG
1 GAGGGTATCGATACCTATTCA-AGGGTATCGATACCTATTCAAAG
* *
1371516 GAGGGTATCGATATCTATTGAAGAGGTATCGATACCTATTCAAAG
1 GAGGGTATCGATACCTATTCAAG-GGTATCGATACCTATTCAAAG
*
1371561 G-GGGTATCGATACC-ATTCTCAAGGGTATCTATACCT
1 GAGGGTATCGATACCTA-T-TCAAGGGTATCGATACCT
1371597 TATGCACAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
43 14 0.21
44 27 0.40
45 26 0.39
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (44 bp):
GAGGGTATCGATACCTATTCAAGGGTATCGATACCTATTCAAAG
Found at i:1375431 original size:22 final size:21
Alignment explanation
Indices: 1375389--1375428 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1375379 GAGTTTATTT
*
1375389 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1375410 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1375429 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1377407 original size:19 final size:19
Alignment explanation
Indices: 1377343--1377417 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 19
1377333 ATATGCCTTA
* * *
1377343 GGGTATCGGTACCATCTGAG
1 GGGTATCGATACC-TATGGG
1377363 GGGTATCGATACC-ATTGCATGG
1 GGGTATCGATACCTA-TG---GG
1377385 GGGTATCGATACCTATGGG
1 GGGTATCGATACCTATGGG
*
1377404 GGGTATAGATACCT
1 GGGTATCGATACCT
1377418 TTTGAGCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 17 0.37
20 12 0.26
22 16 0.35
23 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (19 bp):
GGGTATCGATACCTATGGG
Found at i:1379299 original size:85 final size:84
Alignment explanation
Indices: 1379197--1379384 Score: 218
Period size: 85 Copynumber: 2.2 Consensus size: 84
1379187 TAGATAATCG
*
1379197 GCGGCATTTGTAT-AAAAAACACCGCTATATAAC-AGACCTTTTACGGCGTTTGTAATAAACACT
1 GCGGCATTTGTATCAAAAAACACCGCTAAATAACTAGACCTTTTACGGCGTTTGTAA-AAACACT
*
1379260 GCTATAGATATAGAGCTTTT
65 GCTATAGATATAGACCTTTT
* ** * * * * * * **
1379280 GCGGCTTTTGTATCCAAAAAATGCTGCTAAATATCTCGACCTTTTATGGTGTTTTTAAAAACGTT
1 GCGGCATTTGTAT-CAAAAAACACCGCTAAATAACTAGACCTTTTACGGCGTTTGTAAAAACACT
*
1379345 GCTATAGATATAGTCCTTTT
65 GCTATAGATATAGACCTTTT
1379365 GCGGCATTTGTATCAAAAAA
1 GCGGCATTTGTATCAAAAAA
1379385 ATGTCGTTAT
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
83 12 0.14
84 7 0.08
85 50 0.57
86 18 0.21
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (84 bp):
GCGGCATTTGTATCAAAAAACACCGCTAAATAACTAGACCTTTTACGGCGTTTGTAAAAACACTG
CTATAGATATAGACCTTTT
Found at i:1379385 original size:85 final size:86
Alignment explanation
Indices: 1379231--1379420 Score: 231
Period size: 85 Copynumber: 2.2 Consensus size: 86
1379221 CTATATAACA
* * *
1379231 GACCTTTTACGGCGTTTGTAATAAACACTGCTATAGATATAGAGCTTTTGCGGCTTTTGTATCCA
1 GACCTTTTACGGCGTTTGTAATAAACACTGCTATAGATATAGACCTTTTGCGGCATTTGTATCAA
1379296 AAAAATG-CTGCTAAATATCTC
66 AAAAATGTC-GCTAAATATCTC
* * * ** *
1379317 GACCTTTTATGGTGTTTTTAA-AAACGTTGCTATAGATATAGTCCTTTTGCGGCATTTGTATCAA
1 GACCTTTTACGGCGTTTGTAATAAACACTGCTATAGATATAGACCTTTTGCGGCATTTGTATCAA
* *
1379381 AAAAATGTCGTTATATATCTC
66 AAAAATGTCGCTAAATATCTC
* * *
1379402 AACCTTTTGCCGCGTTTGT
1 GACCTTTTACGGCGTTTGT
1379421 CCCACAAACG
Statistics
Matches: 86, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
85 67 0.78
86 19 0.22
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (86 bp):
GACCTTTTACGGCGTTTGTAATAAACACTGCTATAGATATAGACCTTTTGCGGCATTTGTATCAA
AAAAATGTCGCTAAATATCTC
Found at i:1386527 original size:12 final size:12
Alignment explanation
Indices: 1386510--1386550 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1386500 GTAGTATTAA
1386510 TTCATATTGCAT
1 TTCATATTGCAT
*
1386522 TTCATATTGTAT
1 TTCATATTGCAT
*
1386534 TTCATGTTGCAT
1 TTCATATTGCAT
1386546 TTCAT
1 TTCAT
1386551 TATTCATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.54
Consensus pattern (12 bp):
TTCATATTGCAT
Found at i:1386563 original size:24 final size:24
Alignment explanation
Indices: 1386516--1386565 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1386506 TTAATTCATA
* *
1386516 TTGCATTTCATATTGTATTTCATG
1 TTGCATTTCATATTGCATTGCATG
1386540 TTGCATTTCATTATT-CATTGCATG
1 TTGCATTTCA-TATTGCATTGCATG
1386564 TT
1 TT
1386566 AAATAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.54
Consensus pattern (24 bp):
TTGCATTTCATATTGCATTGCATG
Found at i:1391178 original size:20 final size:20
Alignment explanation
Indices: 1391153--1391190 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1391143 GTTTTATCTT
1391153 TATTTTAATTATTACTATTG
1 TATTTTAATTATTACTATTG
*
1391173 TATTTTACTTATTACTAT
1 TATTTTAATTATTACTAT
1391191 GACGATACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (20 bp):
TATTTTAATTATTACTATTG
Found at i:1391993 original size:28 final size:28
Alignment explanation
Indices: 1391961--1392018 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
1391951 TTCATTGTTA
*
1391961 ATATTCATTTACGTTTATATTCATATTC
1 ATATTCATTTACGCTTATATTCATATTC
1391989 ATATTCATTTACGCTTATATTCATATTC
1 ATATTCATTTACGCTTATATTCATATTC
1392017 AT
1 AT
1392019 TCATAAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.03, T:0.52
Consensus pattern (28 bp):
ATATTCATTTACGCTTATATTCATATTC
Found at i:1396682 original size:18 final size:18
Alignment explanation
Indices: 1396659--1396696 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1396649 AGTCAATTGA
1396659 AACCCGATCCTTATCTCT
1 AACCCGATCCTTATCTCT
*
1396677 AACCCGCTCCTTATCTCT
1 AACCCGATCCTTATCTCT
1396695 AA
1 AA
1396697 GGTAGACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.39, G:0.05, T:0.32
Consensus pattern (18 bp):
AACCCGATCCTTATCTCT
Found at i:1401611 original size:26 final size:25
Alignment explanation
Indices: 1401558--1401613 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
1401548 CAATACAATT
1401558 AAATAAAAAAAATCAATAATTTTTGA
1 AAATAAAAAAAA-CAATAATTTTTGA
1401584 AAATAACAAAAAA-AA-AATTATTTCGA
1 AAATAA-AAAAAACAATAATT-TTT-GA
1401610 AAAT
1 AAAT
1401614 TCATAGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 4 0.15
25 5 0.19
26 12 0.44
27 6 0.22
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (25 bp):
AAATAAAAAAAACAATAATTTTTGA
Found at i:1402080 original size:21 final size:22
Alignment explanation
Indices: 1402018--1402080 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
1402008 GCATGGCCTT
*
1402018 GTGCATCAATGCACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
*
1402041 GTGCATCGATGCATC-TTCATGA
1 GTGCATCGATGCA-CATTCAGGA
*
1402063 -TGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
1402081 AAGGGATGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.43
22 3 0.09
23 15 0.43
24 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:1405946 original size:22 final size:21
Alignment explanation
Indices: 1405906--1405946 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1405896 GAGATTCTTT
* *
1405906 TCATTTTTTATTTTCAAAATA
1 TCATTTTTTATTATAAAAATA
1405927 TCATTTTTATATTATAAAAA
1 TCATTTTT-TATTATAAAAA
1405947 CAATTTCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (21 bp):
TCATTTTTTATTATAAAAATA
Found at i:1408069 original size:64 final size:63
Alignment explanation
Indices: 1407937--1408077 Score: 155
Period size: 63 Copynumber: 2.2 Consensus size: 63
1407927 AAAAGTATAT
* * *
1407937 GTGCATCGATGCATGGCTTGTGCATCGATGCATAAAACAATTCGATGTTTTAATATACATGGA
1 GTGCATCGATGCATGGCTTGTGCATCGATACACAAAACAATTCGATGTTTTAATATACAAGGA
* * *
1408000 GTGCATCGATGCATGG-TGTGTGTATCGGTACACAAAAGCCATTCGATGTTCAATTAA-A-ACAA
1 GTGCATCGATGCATGGCT-TGTGCATCGATACACAAAA-CAATTCGATGTT---TTAATATACAA
1408062 GG-
61 GGA
1408064 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1408078 TGATTTATTC
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 31 0.46
64 25 0.37
65 5 0.07
66 1 0.01
67 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCATGGCTTGTGCATCGATACACAAAACAATTCGATGTTTTAATATACAAGGA
Found at i:1410585 original size:18 final size:18
Alignment explanation
Indices: 1410562--1410606 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1410552 GTATACCTAC
1410562 AATAAATAAAGA-AATGAA
1 AATAAA-AAAGATAATGAA
*
1410580 AATAAAACAGATAATGAA
1 AATAAAAAAGATAATGAA
1410598 AATATAAAA
1 AATA-AAAA
1410607 TAACTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (18 bp):
AATAAAAAAGATAATGAA
Found at i:1415014 original size:20 final size:21
Alignment explanation
Indices: 1414976--1415014 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1414966 CATCAAGGTC
*
1414976 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCATGAAATCT
1414997 TTTGTCGAAGCCAT-AAAT
1 TTTGTCGAAGCCATGAAAT
1415015 TCCTACAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (21 bp):
TTTGTCGAAGCCATGAAATCT
Found at i:1418238 original size:46 final size:48
Alignment explanation
Indices: 1418171--1418266 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
1418161 TTTAAAATAT
1418171 AAAACGATGTTTCAAAATTG-AAAAATG-AAAACAAACTCATATCCAA
1 AAAACGATGTTTCAAAATTGAAAAAATGAAAAACAAACTCATATCCAA
1418217 AAAACGATGTTTCAAAATTGAAAAAATGAAAAACAAACTCATATCCAA
1 AAAACGATGTTTCAAAATTGAAAAAATGAAAAACAAACTCATATCCAA
1418265 AA
1 AA
1418267 CCAACAACGA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 20 0.42
47 7 0.15
48 21 0.44
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (48 bp):
AAAACGATGTTTCAAAATTGAAAAAATGAAAAACAAACTCATATCCAA
Found at i:1418267 original size:46 final size:45
Alignment explanation
Indices: 1418171--1418266 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 45
1418161 TTTAAAATAT
1418171 AAAACGATGTTTCAAAATTGAAAAATGAAAACAAACTCATATCCAA
1 AAAACGATGTTTCAAAATTGAAAAATGAAAACAAACTCATATCC-A
1418217 AAAACGATGTTTCAAAATTGAAAAAATGAAAAACAAACTCATATCCA
1 AAAACGATGTTTCAAAATTG-AAAAATG-AAAACAAACTCATATCCA
1418264 AAA
1 AAA
1418267 CCAACAACGA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
46 20 0.42
47 11 0.23
48 17 0.35
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (45 bp):
AAAACGATGTTTCAAAATTGAAAAATGAAAACAAACTCATATCCA
Found at i:1421414 original size:21 final size:21
Alignment explanation
Indices: 1421388--1421453 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
1421378 CATTTTGGTG
*
1421388 ATGAGGGAATCGATCCCCCCC
1 ATGAGGGAACCGATCCCCCCC
* *
1421409 ATGAGGGAACCGATTCCCCCT
1 ATGAGGGAACCGATCCCCCCC
* *
1421430 TTGAATGGGAACCGATTCCCCCC
1 ATG-A-GGGAACCGATCCCCCCC
1421453 A
1 A
1421454 CAGGGGAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 20 0.54
22 1 0.03
23 16 0.43
ACGTcount: A:0.24, C:0.35, G:0.23, T:0.18
Consensus pattern (21 bp):
ATGAGGGAACCGATCCCCCCC
Found at i:1421652 original size:20 final size:20
Alignment explanation
Indices: 1421605--1421652 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1421595 CTTCAAATAT
* * *
1421605 CATCTAAA-CTTGCAATCAT
1 CATCTAAATCGTGCAAACAA
1421624 CAT-TAAATCGTGCAAACAA
1 CATCTAAATCGTGCAAACAA
1421643 CATCTAAATC
1 CATCTAAATC
1421653 CCCTCAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 14 0.58
20 6 0.25
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (20 bp):
CATCTAAATCGTGCAAACAA
Found at i:1422358 original size:197 final size:197
Alignment explanation
Indices: 1422014--1422408 Score: 749
Period size: 197 Copynumber: 2.0 Consensus size: 197
1422004 TAATTGATTG
1422014 CATACATTTGTTTTAAAATTGCAGGTTATTCAATCTATTCGATTTCCTTCACCATGTCTAATCCT
1 CATACATTTGTTTTAAAATTGCAGGTTATTCAATCTATTCGATTTCCTTCACCATGTCTAATCCT
1422079 AAACGTGCTAGGTCTTCATCTAGTCGTTCTAGTCGTCAACCAAATCCACCTCCAAATCATCCTCC
66 AAACGTGCTAGGTCTTCATCTAGTCGTTCTAGTCGTCAACCAAATCCACCTCCAAATCATCCTCC
1422144 TATTCCTCAAAATCCTATTCCAAATC-TGATCCTAACTTGACTATCTAAAATTC-TTTTTCAATC
131 TATTCCTCAAAATCCTATTCCAAATCTTGATCCTAACTTGACTATCTAAAATTCTTTTTTCAATC
1422207 AA
196 AA
1422209 CATACATTTGTTTTTAAAATTGCAGGTTATTCAATCTATTCCGATTTCCTTCACCATGTCTAATC
1 CATACATTTG-TTTTAAAATTGCAGGTTATTCAATCTATT-CGATTTCCTTCACCATGTCTAATC
*
1422274 CTAAACGTGCTAGGTCTTCATCTAGTCGTTCTAGTCGTCAACCAAATCCACCTCCAAATCCTCCT
64 CTAAACGTGCTAGGTCTTCATCTAGTCGTTCTAGTCGTCAACCAAATCCACCTCCAAATCATCCT
1422339 CCTATTCCTCAAAATCCTATTCCAAATCTTGATCCTAACTTGACTATCTAAAATTCTTTTTTCAA
129 CCTATTCCTCAAAATCCTATTCCAAATCTTGATCCTAACTTGACTATCTAAAATTCTTTTTTCAA
1422404 TCAA
194 TCAA
1422408 C
1 C
1422409 CGGGTCCTAA
Statistics
Matches: 195, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
195 10 0.05
196 29 0.15
197 116 0.59
198 27 0.14
199 13 0.07
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (197 bp):
CATACATTTGTTTTAAAATTGCAGGTTATTCAATCTATTCGATTTCCTTCACCATGTCTAATCCT
AAACGTGCTAGGTCTTCATCTAGTCGTTCTAGTCGTCAACCAAATCCACCTCCAAATCATCCTCC
TATTCCTCAAAATCCTATTCCAAATCTTGATCCTAACTTGACTATCTAAAATTCTTTTTTCAATC
AA
Found at i:1423600 original size:15 final size:16
Alignment explanation
Indices: 1423582--1423621 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1423572 TTTTAACATT
1423582 TTGAATTT-TGGAATG
1 TTGAATTTGTGGAATG
*
1423597 TTGAATTTGTGGATTG
1 TTGAATTTGTGGAATG
1423613 -TGAATTTGT
1 TTGAATTTGT
1423622 TTGGATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (16 bp):
TTGAATTTGTGGAATG
Found at i:1428900 original size:6 final size:6
Alignment explanation
Indices: 1428881--1428952 Score: 58
Period size: 6 Copynumber: 11.5 Consensus size: 6
1428871 CTTGAAGAAG
* *
1428881 AAAAG- AAAATA AAAAGA AAAATA AAAAGA AAAAGA AAATAGA AAATA-A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA-AGA AAA-AGA
*
1428929 AAAGGAA ATAGAAGA AAAAGA AAA
1 AAAAG-A A-A-AAGA AAAAGA AAA
1428953 GGAGGGTTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
5 4 0.07
6 35 0.64
7 11 0.20
8 3 0.05
9 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (6 bp):
AAAAGA
Found at i:1428903 original size:12 final size:11
Alignment explanation
Indices: 1428881--1428938 Score: 71
Period size: 12 Copynumber: 5.0 Consensus size: 11
1428871 CTTGAAGAAG
1428881 AAAAGAAAATA
1 AAAAGAAAATA
1428892 AAAAGAAAAATA
1 AAAAG-AAAATA
*
1428904 AAAAGAAAAAGA
1 AAAAG-AAAATA
1428916 AAATAGAAAATA
1 AAA-AGAAAATA
*
1428928 AAAAGGAAATA
1 AAAAGAAAATA
1428939 GAAGAAAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 12 0.29
12 28 0.67
13 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (11 bp):
AAAAGAAAATA
Found at i:1428912 original size:18 final size:17
Alignment explanation
Indices: 1428886--1428952 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 17
1428876 AGAAGAAAAG
*
1428886 AAAATAAAAAGAAAAATA
1 AAAAGAAAAAG-AAAATA
1428904 AAAAGAAAAAGAAAATA
1 AAAAGAAAAAGAAAATA
* *
1428921 GAAAATAAAAAGGAAAT-
1 -AAAAGAAAAAGAAAATA
*
1428938 AGAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
1428953 GGAGGGTTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
16 12 0.29
17 6 0.14
18 24 0.57
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAAGAAAATA
Found at i:1434614 original size:20 final size:20
Alignment explanation
Indices: 1434589--1434631 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1434579 ATTAGTTATT
1434589 AAATAAACTTTTAAAAAATA
1 AAATAAACTTTTAAAAAATA
1434609 AAATAAACTTTTAAAAAATA
1 AAATAAACTTTTAAAAAATA
1434629 AAA
1 AAA
1434632 CTTATGGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAAACTTTTAAAAAATA
Found at i:1435012 original size:14 final size:15
Alignment explanation
Indices: 1434993--1435024 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1434983 CTTAATGCAA
1434993 AAAATAAAAA-AAAT
1 AAAATAAAAACAAAT
1435007 AAAATAAAAACAAAT
1 AAAATAAAAACAAAT
1435022 AAA
1 AAA
1435025 GAAAAGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAATAAAAACAAAT
Found at i:1449136 original size:27 final size:28
Alignment explanation
Indices: 1449083--1449138 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1449073 AGGGTTTGGA
**
1449083 GTTACTTTAGGTTATTTTACAGTTTAGG
1 GTTACTTTAGGTTATTTTACACATTAGG
* *
1449111 GTTA-TTTTGGTTATTTTATACATTAGG
1 GTTACTTTAGGTTATTTTACACATTAGG
1449138 G
1 G
1449139 GTAATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.52
Consensus pattern (28 bp):
GTTACTTTAGGTTATTTTACACATTAGG
Found at i:1452248 original size:32 final size:32
Alignment explanation
Indices: 1452212--1452306 Score: 122
Period size: 32 Copynumber: 3.0 Consensus size: 32
1452202 AAGGGAGCAC
*
1452212 CTTGGGGCCTGAGAGCCTACCCAAGAAAGATT
1 CTTGGGGCCTGAGAGCCTATCCAAGAAAGATT
* * *
1452244 CTTGGAGCCTCAGAGCCTATCAAAGAAAGATT
1 CTTGGGGCCTGAGAGCCTATCCAAGAAAGATT
*
1452276 C-TCGGGCCTTG-GAGCCTATCCAAGAAAGATT
1 CTTGGGGCC-TGAGAGCCTATCCAAGAAAGATT
1452307 TTCGGTACCA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 24 0.44
32 30 0.56
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.21
Consensus pattern (32 bp):
CTTGGGGCCTGAGAGCCTATCCAAGAAAGATT
Found at i:1452294 original size:31 final size:31
Alignment explanation
Indices: 1452216--1452311 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
1452206 GAGCACCTTG
* *
1452216 GGGCC-TGAGAGCCTACCCAAGAAAGATTCTT
1 GGGCCTTG-GAGCCTATCCAAGAAAGATTCTC
** *
1452247 GGAGCCTCAGAGCCTATCAAAGAAAGATTCTC
1 GG-GCCTTGGAGCCTATCCAAGAAAGATTCTC
*
1452279 GGGCCTTGGAGCCTATCCAAGAAAGATTTTC
1 GGGCCTTGGAGCCTATCCAAGAAAGATTCTC
1452310 GG
1 GG
1452312 TACCACAGTG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
31 29 0.54
32 25 0.46
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (31 bp):
GGGCCTTGGAGCCTATCCAAGAAAGATTCTC
Found at i:1452795 original size:90 final size:89
Alignment explanation
Indices: 1452639--1452813 Score: 269
Period size: 90 Copynumber: 2.0 Consensus size: 89
1452629 CCTAACACAC
* * * *
1452639 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTACAGCCAAGTTACCCTAATAATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
*
1452704 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
* * *
1452729 CCTTTTACATCCAAGTTACCCTAATAATATTAGGGATTTTATTATTTTAACTTAATTAAATATAT
1 CCTTTTACAGCCAAGTTACCCTAATAATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
1452794 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
1452814 ATATTCGAGA
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 7 0.09
90 70 0.91
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTACAGCCAAGTTACCCTAATAATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAATAAT
Found at i:1459104 original size:16 final size:16
Alignment explanation
Indices: 1459083--1459119 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1459073 ACTAGAACAT
1459083 GCATCTCATACTTATC
1 GCATCTCATACTTATC
1459099 GCATCTCATACTTATC
1 GCATCTCATACTTATC
1459115 GCATC
1 GCATC
1459120 AACCAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.35
Consensus pattern (16 bp):
GCATCTCATACTTATC
Found at i:1459642 original size:90 final size:90
Alignment explanation
Indices: 1459489--1459666 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
1459479 CCTAACACAC
*
1459489 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
1459554 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
1459579 CCTTTTATATCCAAGTTACTCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1459644 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
1459667 TTCGAGATTA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:1461756 original size:27 final size:28
Alignment explanation
Indices: 1461713--1461771 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
1461703 AAGGTTTAGA
*
1461713 GGTACTTTAGGTAATTTTACACTTTATG
1 GGTACTTTAGGTAATTTTACACTTTAAG
*
1461741 GGTA-TTTTGGTAATTTTACACTTTAAG
1 GGTACTTTAGGTAATTTTACACTTTAAG
1461768 GGTA
1 GGTA
1461772 ATTCTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.46
Consensus pattern (28 bp):
GGTACTTTAGGTAATTTTACACTTTAAG
Found at i:1461781 original size:27 final size:27
Alignment explanation
Indices: 1461724--1461783 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
1461714 GTACTTTAGG
* * *
1461724 TAATTTTACACTTTATGGGTATTTTGG
1 TAATTTTACACTTTAAGGGTATTCTGA
1461751 TAATTTTACACTTTAAGGGTAATTCT-A
1 TAATTTTACACTTTAAGGGT-ATTCTGA
1461778 TAATTT
1 TAATTT
1461784 CGATATAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.50
Consensus pattern (27 bp):
TAATTTTACACTTTAAGGGTATTCTGA
Found at i:1462329 original size:25 final size:27
Alignment explanation
Indices: 1462300--1462362 Score: 67
Period size: 32 Copynumber: 2.2 Consensus size: 27
1462290 CAACTAATGG
1462300 ACCAATC-AT-TTCTATTCAAGCACGT
1 ACCAATCAATGTTCTATTCAAGCACGT
1462325 ACCAATTATCAATGGGTTCTATTCAAGCACGT
1 ACC-A--ATCAAT--GTTCTATTCAAGCACGT
1462357 ACCAAT
1 ACCAAT
1462363 TATCGATCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
25 3 0.10
26 1 0.03
28 3 0.10
29 4 0.13
31 1 0.03
32 19 0.61
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.30
Consensus pattern (27 bp):
ACCAATCAATGTTCTATTCAAGCACGT
Found at i:1462658 original size:30 final size:30
Alignment explanation
Indices: 1462613--1462684 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
1462603 GACTTTTCCT
*
1462613 TCAAAGTCAATGGTCAACAGGTTGACTCAA
1 TCAAAGTCAACGGTCAACAGGTTGACTCAA
* ** **
1462643 TCAATGTCAACGGTCAATGGGTTGACTCGG
1 TCAAAGTCAACGGTCAACAGGTTGACTCAA
*
1462673 TCAAAGTTAACG
1 TCAAAGTCAACG
1462685 AGTTGACCCG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (30 bp):
TCAAAGTCAACGGTCAACAGGTTGACTCAA
Found at i:1464960 original size:3 final size:3
Alignment explanation
Indices: 1464954--1464987 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1464944 TATTAAGTAT
*
1464954 ATA ATA ATA ATA GTA ATA ATA ATA AT- ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1464988 TATATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1465894 original size:28 final size:27
Alignment explanation
Indices: 1465863--1465915 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1465853 TAATCCAGGG
*
1465863 TTTAAAGGTACTTTAGGTCATTTTACAC
1 TTTAAAGGCA-TTTAGGTCATTTTACAC
* *
1465891 TTTAAGGGCATTTTGGTCATTTTAC
1 TTTAAAGGCATTTAGGTCATTTTAC
1465916 CCTCTATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (27 bp):
TTTAAAGGCATTTAGGTCATTTTACAC
Found at i:1466820 original size:37 final size:36
Alignment explanation
Indices: 1466752--1466838 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 36
1466742 TTAACTTTTT
*
1466752 CGTCAAAGTCAACGTCAACGGTCAACAGGTTGACTA
1 CGTCAAAGTCAACGTCAACGATCAACAGGTTGACTA
**
1466788 CGTCAAAGTC-ACTAGTCAACGATCAATGGGTTGACT-
1 CGTCAAAGTCAAC--GTCAACGATCAACAGGTTGACTA
*
1466824 CGGTCCAAGTCAACG
1 C-GTCAAAGTCAACG
1466839 AGTTGACCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
35 2 0.05
36 12 0.28
37 27 0.63
38 2 0.05
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (36 bp):
CGTCAAAGTCAACGTCAACGATCAACAGGTTGACTA
Found at i:1468847 original size:66 final size:66
Alignment explanation
Indices: 1468731--1468858 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
1468721 ATTTCGTAAG
* ** *
1468731 GAATTACCAGTCGGTGTTGAACCTATAAAAGGAATTACCAACATCAACTGAACCTGCCAGAGATA
1 GAATTACCAGTAGGTGCAGAACCTATAAAAGGAATTACCAACAGCAACTGAACCTGCCAGAGATA
1468796 A
66 A
* * * * *
1468797 GAATTACTAGTAGGTGCAGAACTTATAAAAGGAATTACCCATAGCGACTGAACCTGCCAGAG
1 GAATTACCAGTAGGTGCAGAACCTATAAAAGGAATTACCAACAGCAACTGAACCTGCCAGAG
1468859 TCTTCATACC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (66 bp):
GAATTACCAGTAGGTGCAGAACCTATAAAAGGAATTACCAACAGCAACTGAACCTGCCAGAGATA
A
Found at i:1471760 original size:28 final size:27
Alignment explanation
Indices: 1471728--1471787 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
1471718 TATTCCATGG
* *
1471728 TTTAGAGGCACTTTAT-GTCATTTTACAC
1 TTTAGAGGCA-TTT-TGGCCATTTAACAC
*
1471756 TTTAGGGGCATTTTGGCCATTTAACAC
1 TTTAGAGGCATTTTGGCCATTTAACAC
1471783 TTTAG
1 TTTAG
1471788 GGGTAATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 18 0.64
28 9 0.32
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (27 bp):
TTTAGAGGCATTTTGGCCATTTAACAC
Found at i:1475983 original size:28 final size:27
Alignment explanation
Indices: 1475952--1476019 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
1475942 TATTCCAGGG
* * * *
1475952 TTTAGAGGTACTTTAGGTTATTTTGCAC
1 TTTAG-GGTAATTTAGATCATTTTACAC
*
1475980 TTTAGGGTAATTTTGATCATTTTACAC
1 TTTAGGGTAATTTAGATCATTTTACAC
1476007 TTTAGGGGTAATT
1 TTTA-GGGTAATT
1476020 ATATAATTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (27 bp):
TTTAGGGTAATTTAGATCATTTTACAC
Found at i:1475994 original size:18 final size:17
Alignment explanation
Indices: 1475961--1475994 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1475951 GTTTAGAGGT
*
1475961 ACTTTAGGTTATTTTGC
1 ACTTTAGGTAATTTTGC
1475978 ACTTTAGGGTAATTTTG
1 ACTTTA-GGTAATTTTG
1475995 ATCATTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (17 bp):
ACTTTAGGTAATTTTGC
Found at i:1480055 original size:28 final size:27
Alignment explanation
Indices: 1480024--1480088 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
1480014 TATTCCAGGG
* *
1480024 TTTAGAGGTACTTTAGGTTATTTTACAC
1 TTTAGGGGTA-TTTAGGTCATTTTACAC
* *
1480052 TTTAGGGGCATTTTGGTCATTTTACAC
1 TTTAGGGGTATTTAGGTCATTTTACAC
1480079 TTTAGGGGTA
1 TTTAGGGGTA
1480089 ATTATATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 24 0.75
28 8 0.25
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.45
Consensus pattern (27 bp):
TTTAGGGGTATTTAGGTCATTTTACAC
Found at i:1485573 original size:45 final size:45
Alignment explanation
Indices: 1485512--1485782 Score: 515
Period size: 45 Copynumber: 6.0 Consensus size: 45
1485502 ATAAATTTTC
*
1485512 TTACCAATATATTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
*
1485557 TTACAAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1485602 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1485647 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1485692 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
*
1485737 TTACCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1485782 T
1 T
1485783 GTATGTTTAT
Statistics
Matches: 222, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 222 1.00
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
Found at i:1485812 original size:7 final size:7
Alignment explanation
Indices: 1485800--1485836 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1485790 TATCATTCAT
1485800 TAAACCA
1 TAAACCA
1485807 TAAACCA
1 TAAACCA
* *
1485814 TAGACTA
1 TAAACCA
1485821 TAAACCA
1 TAAACCA
1485828 TAAACCA
1 TAAACCA
1485835 TA
1 TA
1485837 GCCCAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.54, C:0.24, G:0.03, T:0.19
Consensus pattern (7 bp):
TAAACCA
Found at i:1486384 original size:24 final size:24
Alignment explanation
Indices: 1486348--1486396 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1486338 AGTCTTCCTG
1486348 ATGATGTACAAAACATCTATGTAC
1 ATGATGTACAAAACATCTATGTAC
* *
1486372 ATGATGTATAAAACGTCTATGTAC
1 ATGATGTACAAAACATCTATGTAC
1486396 A
1 A
1486397 ATTTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (24 bp):
ATGATGTACAAAACATCTATGTAC
Found at i:1486955 original size:30 final size:31
Alignment explanation
Indices: 1486899--1486958 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1486889 AACCATTCAC
* * *
1486899 AACTTTTCCAAAATTGTCAAATTGGTCCCCT
1 AACTTTTCAAAAATTGACAAAATGGTCCCCT
1486930 AACTTTTCAAAAATT-ACAAAATGGTCCCC
1 AACTTTTCAAAAATTGACAAAATGGTCCCC
1486959 AAATTTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (31 bp):
AACTTTTCAAAAATTGACAAAATGGTCCCCT
Found at i:1486970 original size:31 final size:31
Alignment explanation
Indices: 1486899--1486966 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
1486889 AACCATTCAC
* * * *
1486899 AACTTTTCCAAAATTGTCAAATTGGTCCCCT
1 AACTTTTCAAAAATTGACAAAATGGTCCCCA
1486930 AACTTTTCAAAAATT-ACAAAATGGTCCCCA
1 AACTTTTCAAAAATTGACAAAATGGTCCCCA
*
1486960 AATTTTT
1 AACTTTT
1486967 TCAAGGCTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.35
Consensus pattern (31 bp):
AACTTTTCAAAAATTGACAAAATGGTCCCCA
Found at i:1489893 original size:9 final size:8
Alignment explanation
Indices: 1489879--1490024 Score: 105
Period size: 9 Copynumber: 16.8 Consensus size: 8
1489869 CTCTCATCTT
1489879 TTTTTTTCC
1 TTTTTTT-C
1489888 TTTTTTTC
1 TTTTTTTC
1489896 TATTTTTTCC
1 T-TTTTTT-C
* *
1489906 TCTTTCTC
1 TTTTTTTC
* *
1489914 TTCCTCTTC
1 TT-TTTTTC
1489923 TTTTTTTTC
1 -TTTTTTTC
1489932 TTTTTTTTC
1 -TTTTTTTC
1489941 TTTTTTTC
1 TTTTTTTC
1489949 TTTTTTT-
1 TTTTTTTC
*
1489956 TTTCTTCTCTA
1 TTT-TT-T-TC
1489967 TTTTTTTC
1 TTTTTTTC
* *
1489975 TTGTTTTG
1 TTTTTTTC
1489983 TTTTTTTC
1 TTTTTTTC
1489991 TATTTTTTC
1 T-TTTTTTC
1490000 TATTTTTTTC
1 --TTTTTTTC
1490010 TTTTTCTTC
1 TTTTT-TTC
1490019 TTTTTT
1 TTTTTT
1490025 AAGCTTTTTT
Statistics
Matches: 112, Mismatches: 13, Indels: 25
0.75 0.09 0.17
Matches are distributed among these distances:
7 3 0.03
8 41 0.37
9 50 0.45
10 14 0.12
11 4 0.04
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.79
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1489946 original size:16 final size:16
Alignment explanation
Indices: 1489925--1490024 Score: 96
Period size: 17 Copynumber: 5.9 Consensus size: 16
1489915 TCCTCTTCTT
1489925 TTTTTTCTTTTTTTTC
1 TTTTTTCTTTTTTTTC
1489941 TTTTTTTCTTTTTTTT-
1 -TTTTTTCTTTTTTTTC
*
1489957 TTCTTCTCTATTTTTTTC
1 TT-TTTTCT-TTTTTTTC
* *
1489975 TTGTTTTGTTTTTTTCTA
1 TT-TTTTCTTTTTTT-TC
1489993 TTTTTTCTATTTTTTTC
1 TTTTTTCT-TTTTTTTC
1490010 -TTTTTCTTCTTTTTT
1 TTTTTTCTT-TTTTTT
1490025 AAGCTTTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.04
16 18 0.26
17 34 0.49
18 15 0.21
ACGTcount: A:0.03, C:0.12, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTC
Found at i:1489972 original size:45 final size:43
Alignment explanation
Indices: 1489875--1490000 Score: 123
Period size: 43 Copynumber: 2.9 Consensus size: 43
1489865 TCATCTCTCA
* * *
1489875 TCTTTTTTTTTCCTTTTTTTCTATTTTTTC-CTCTTTCTCTTCC
1 TCTTTTTTTTTTCTTTTTTTCT-TTTTTTCTTTTTTTCTCTTCC
*
1489918 TCTTCTTTTTTTTCTTTTTTTTCTTTTTTTCTTTTTTT-T-TTCT
1 TCTT-TTTTTTTTC-TTTTTTTCTTTTTTTCTTTTTTTCTCTTCC
* * *
1489961 TCTCTATTTTTTTCTTGTTTTGTTTTTTTCTATTTTTTCT
1 TCT-TTTTTTTTTCTTTTTTTCTTTTTTTCT-TTTTTTCT
1490001 ATTTTTTTCT
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
42 15 0.21
43 24 0.34
44 18 0.26
45 13 0.19
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (43 bp):
TCTTTTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTCTTCC
Found at i:1490023 original size:51 final size:48
Alignment explanation
Indices: 1489878--1490024 Score: 145
Period size: 52 Copynumber: 2.9 Consensus size: 48
1489868 TCTCTCATCT
*
1489878 TTTTTTTTCCTTTTTTTCTATTTTTTCCTCTTTCTCTTCCTCTTCTTTTTTTTC
1 TTTTTTTT-CTTTTTTTCTATTTTTT--TCTTTTTCTT-CT-TT-TTTTTTTTC
* * *
1489932 TTTTTTTTCTTTTTTTCT-TTTTTTT-TTCTTCTCTATTTTTTTCTTGTTT
1 TTTTTTTTCTTTTTTTCTATTTTTTTCTTTTTCT-TCTTTTTTT-TT-TTC
1489981 TGTTTTTTTCTATTTTTTCTATTTTTTTCTTTTTCTTCTTTTTT
1 T-TTTTTTTCT-TTTTTTCTATTTTTTTCTTTTTCTTCTTTTTT
1490025 AAGCTTTTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
47 4 0.05
48 4 0.05
49 9 0.11
50 11 0.14
51 8 0.10
52 20 0.25
53 16 0.20
54 8 0.10
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (48 bp):
TTTTTTTTCTTTTTTTCTATTTTTTTCTTTTTCTTCTTTTTTTTTTTC
Found at i:1490034 original size:1 final size:1
Alignment explanation
Indices: 1489923--1490024 Score: 51
Period size: 1 Copynumber: 102.0 Consensus size: 1
1489913 CTTCCTCTTC
* * * * * * * * * *
1489923 TTTTTTTTCTTTTTTTTCTTTTTTTCTTTTTTTTTTCTTCTCTATTTTTTTCTTGTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
1489988 TTCTATTTTTTCTATTTTTTTCTTTTTCTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1490025 AAGCTTTTTT
Statistics
Matches: 67, Mismatches: 34, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.03, C:0.12, G:0.02, T:0.83
Consensus pattern (1 bp):
T
Found at i:1492717 original size:45 final size:45
Alignment explanation
Indices: 1492651--1492831 Score: 301
Period size: 45 Copynumber: 4.0 Consensus size: 45
1492641 ATAAATTTTC
*
1492651 TTACCAATATA-TTGACAATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTT-ACCATTTATCCCATAAGCTCGTAAGCTTATT
*
1492696 TTACAAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1492741 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
* * *
1492786 TTACCAATATACTTAGCATTTATCCCATAAGATCATAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1492831 T
1 T
1492832 GTATGTTTAT
Statistics
Matches: 129, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
45 127 0.98
46 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
Found at i:1492741 original size:25 final size:25
Alignment explanation
Indices: 1492713--1492786 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
1492703 TATACTTACC
1492713 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
* *
1492738 ATTT-TACCAATATA-CT--T-A-C-C
1 ATTTAT-CCCATA-AGCTCGTAAGCTT
1492758 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
1492783 ATTT
1 ATTT
1492787 TACCAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 2 0.06
22 2 0.06
23 2 0.06
24 2 0.06
25 15 0.42
26 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (25 bp):
ATTTATCCCATAAGCTCGTAAGCTT
Found at i:1493398 original size:24 final size:24
Alignment explanation
Indices: 1493366--1493411 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1493356 CTTCCTAATA
*
1493366 ATGTATAAAACATCTATGTACATG
1 ATGTATAAAACATCTACGTACATG
1493390 ATGTATAAAACATCTACGTACA
1 ATGTATAAAACATCTACGTACA
1493412 ATGTCATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (24 bp):
ATGTATAAAACATCTACGTACATG
Found at i:1495014 original size:29 final size:29
Alignment explanation
Indices: 1494981--1495053 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
1494971 TAAATCACAT
* * **
1494981 ATTTGTCCCTTAACTTTTTAAAATTTATA
1 ATTTGTCACTAAACTTTACAAAATTTATA
*
1495010 CTTTGGTCACTAAACTTTACAAAATTTATA
1 ATTT-GTCACTAAACTTTACAAAATTTATA
1495040 ATTTGGTCACTAAA
1 ATTT-GTCACTAAA
1495054 TAAATATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 3 0.08
30 34 0.92
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (29 bp):
ATTTGTCACTAAACTTTACAAAATTTATA
Found at i:1496887 original size:66 final size:66
Alignment explanation
Indices: 1496769--1496896 Score: 193
Period size: 66 Copynumber: 1.9 Consensus size: 66
1496759 GGTCCGTAAC
* *
1496769 GAATTACCAGTCGGTGTTGAACCAATAAAAGGAATTACCAACAACTAATGAACCTGCCAGAGATA
1 GAATTACCAGTCGGTGTAGAACCAATAAAAGGAATTACCAACAACGAATGAACCTGCCAGAGATA
1496834 G
66 G
** ** *
1496835 GAATTACCAGTCGGTGTAGAACTTATAAAAGGAATTACCCGCAACGACTGAACCTGCCAGAG
1 GAATTACCAGTCGGTGTAGAACCAATAAAAGGAATTACCAACAACGAATGAACCTGCCAGAG
1496897 TCTTCATACT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (66 bp):
GAATTACCAGTCGGTGTAGAACCAATAAAAGGAATTACCAACAACGAATGAACCTGCCAGAGATA
G
Found at i:1498894 original size:37 final size:36
Alignment explanation
Indices: 1498848--1498925 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 36
1498838 TGACTTTTTC
* *
1498848 GTCAAAGTCACCAGTCAAA-GGGGTGACTCGGTCAAA
1 GTCAAAGTCAACAGT-AAATGGGGTGACTCAGTCAAA
* * *
1498884 GTCAACAGTCAACAGTAAATGGGTTGAGTCAGTTAAA
1 GTCAA-AGTCAACAGTAAATGGGGTGACTCAGTCAAA
1498921 GTCAA
1 GTCAA
1498926 TGAGTTGACC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 8 0.23
37 27 0.77
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (36 bp):
GTCAAAGTCAACAGTAAATGGGGTGACTCAGTCAAA
Found at i:1500895 original size:13 final size:13
Alignment explanation
Indices: 1500877--1500924 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1500867 GTCGGGTCAA
1500877 GCAGGTCAGGCTG
1 GCAGGTCAGGCTG
*
1500890 GCAGGTC-GGGTAG
1 GCAGGTCAGGCT-G
* *
1500903 GCAGGTCGGGCAG
1 GCAGGTCAGGCTG
1500916 GCAGGTCAG
1 GCAGGTCAG
1500925 ACCCGGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 3 0.10
13 24 0.83
14 2 0.07
ACGTcount: A:0.17, C:0.21, G:0.50, T:0.12
Consensus pattern (13 bp):
GCAGGTCAGGCTG
Found at i:1500909 original size:26 final size:27
Alignment explanation
Indices: 1500867--1500922 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1500857 AGTTGACGTA
*
1500867 GTCGGGTCAAGCAGGTCAGGCTGGCAG
1 GTCGGGTCAAGCAGGTCAGGCAGGCAG
* *
1500894 GTCGGGT-AGGCAGGTCGGGCAGGCAG
1 GTCGGGTCAAGCAGGTCAGGCAGGCAG
1500920 GTC
1 GTC
1500923 AGACCCGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.16, C:0.21, G:0.48, T:0.14
Consensus pattern (27 bp):
GTCGGGTCAAGCAGGTCAGGCAGGCAG
Found at i:1505581 original size:22 final size:22
Alignment explanation
Indices: 1505553--1505797 Score: 445
Period size: 22 Copynumber: 11.1 Consensus size: 22
1505543 TATTTAAATC
1505553 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
*
1505575 TATTTTAAAACATGGATTGATT
1 TATTTTAAAATATGGATTGATT
1505597 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
1505619 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
*
1505641 TATTTTAAAATATAGATTGATT
1 TATTTTAAAATATGGATTGATT
1505663 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
1505685 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
***
1505707 TATTTTAAAATATGGAAAAATT
1 TATTTTAAAATATGGATTGATT
1505729 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
1505751 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
1505773 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
1505795 TAT
1 TAT
1505798 GTTGGGATTT
Statistics
Matches: 213, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 213 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (22 bp):
TATTTTAAAATATGGATTGATT
Done.