Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003015.1 Hibiscus syriacus cultivar Beakdansim tig00006253_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: 213378
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:141706 original size:152 final size:153
Alignment explanation
Indices: 141411--141710 Score: 403
Period size: 152 Copynumber: 2.0 Consensus size: 153
141401 ATTAGAAAAC
* * * *
141411 AGGTCAACATAATGTATCGACACTTGTGTAATTTGTGTCGATACTTATTGTCCAGGATGAATGCA
1 AGGTCAACATAAAGTATCGACACTTGTGTAATTTATGTCGATACTTATTGTCCAGAATGAATCCA
* * * *
141476 CAAATGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAA
66 CAAAAGAGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGACCCCAAAAACATCAAA
* *
141541 ACCGATAATTATAATGTATAAAT
131 ACCCATAAGTATAATGTATAAAT
*
141564 AGGTCAGCATAAAGTATCGACACTTGCTG-AATTTATGTCGATACTT-TTGGTCCAGAATGAATA
1 AGGTCAACATAAAGTATCGACACTTG-TGTAATTTATGTCGATACTTATT-GTCCAGAATGAAT-
* *
141627 CCA-AAAAG-GGTGCAAC-CATAAAGTGTTGATACATTTATAAAAAGTATCGACCCCGAAAACAT
63 CCACAAAAGAGGTGC-ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGACCCCAAAAACAT
*
141689 TAAAACCCATAAGTATAATGTA
127 CAAAACCCATAAGTATAATGTA
141711 ATAGGTAAAT
Statistics
Matches: 129, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
152 67 0.52
153 58 0.45
154 4 0.03
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (153 bp):
AGGTCAACATAAAGTATCGACACTTGTGTAATTTATGTCGATACTTATTGTCCAGAATGAATCCA
CAAAAGAGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGACCCCAAAAACATCAAA
ACCCATAAGTATAATGTATAAAT
Found at i:142073 original size:87 final size:87
Alignment explanation
Indices: 141971--142133 Score: 283
Period size: 87 Copynumber: 1.9 Consensus size: 87
141961 AAATAGGTCA
*
141971 ATATAAGCGCCACCTATTACATTATATAAG-AGCTACCTAATATGTTATTGTACTTGATAATATT
1 ATATAAGCGCCACCTATTACATTATATAAGCA-CTACATAATATGTTATTGTACTTGATAATATT
*
142035 TCCGGTTAAATGCCTATTTTATT
65 TCCGATTAAATGCCTATTTTATT
*
142058 ATATAAGCGCTACCTATTACATTATATAAGCACTACATAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCCACCTATTACATTATATAAGCACTACATAATATGTTATTGTACTTGATAATATTT
142123 CCGATTAAATG
66 CCGATTAAATG
142134 ATATAACATT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
87 71 0.99
88 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (87 bp):
ATATAAGCGCCACCTATTACATTATATAAGCACTACATAATATGTTATTGTACTTGATAATATTT
CCGATTAAATGCCTATTTTATT
Found at i:142105 original size:23 final size:23
Alignment explanation
Indices: 142055--142099 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
142045 TGCCTATTTT
* * *
142055 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCACTACATAATAC
142078 ATTATATAAGCACTACATAATA
1 ATTATATAAGCACTACATAATA
142100 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCACTACATAATAC
Found at i:148346 original size:21 final size:22
Alignment explanation
Indices: 148304--148349 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
148294 CCTAATTCCT
148304 TCTTCACTTCCCCGATCGCCTTC
1 TCTTCACTTCCCC-ATCGCCTTC
148327 TCTTC-CTTCCCC-TCGTCCTTC
1 TCTTCACTTCCCCATCG-CCTTC
148348 TC
1 TC
148350 CCCCGACCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.14
21 7 0.32
22 7 0.32
23 5 0.23
ACGTcount: A:0.04, C:0.50, G:0.07, T:0.39
Consensus pattern (22 bp):
TCTTCACTTCCCCATCGCCTTC
Found at i:148563 original size:23 final size:23
Alignment explanation
Indices: 148534--148584 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
148524 CTTTCACCGA
*
148534 CTTGCCATCATCTTTACTAGGAT
1 CTTGCCATCATCTTTACCAGGAT
148557 CTTGCCATCATCTTTACCAGGAT
1 CTTGCCATCATCTTTACCAGGAT
148580 CTTGC
1 CTTGC
148585 TTCTGTGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (23 bp):
CTTGCCATCATCTTTACCAGGAT
Found at i:152673 original size:24 final size:25
Alignment explanation
Indices: 152646--152695 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
152636 CAGAAAAAAG
152646 AAAGAAAATGCACAAG-AATTCAAT
1 AAAGAAAATGCACAAGAAATTCAAT
152670 AAAGAAAATGCACAAGAAATTCAAT
1 AAAGAAAATGCACAAGAAATTCAAT
152695 A
1 A
152696 GCATCAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (25 bp):
AAAGAAAATGCACAAGAAATTCAAT
Found at i:153855 original size:3 final size:3
Alignment explanation
Indices: 153849--153892 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
153839 ACTAAAAAAA
*
153849 TAT TATT TATT TAT TAT TAT TAT TAT TAT TAT TAAA TAT TAT TA
1 TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
153893 CAAATTTTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 28 0.76
4 9 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:153888 original size:22 final size:23
Alignment explanation
Indices: 153849--153892 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
153839 ACTAAAAAAA
* *
153849 TATTATTTATTTATTATTATTAT
1 TATTATTTATTAAATATTATTAT
153872 TATTA-TTATTAAATATTATTA
1 TATTATTTATTAAATATTATTA
153893 CAAATTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATTTATTAAATATTATTAT
Found at i:155136 original size:4 final size:4
Alignment explanation
Indices: 155096--155120 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
155086 ATTTCAGTCC
155096 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
155121 ATGGTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:156907 original size:11 final size:11
Alignment explanation
Indices: 156887--156923 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
156877 TATATTATTT
*
156887 TATTTTCTTGA
1 TATTTGCTTGA
156898 TATTTGCTTGA
1 TATTTGCTTGA
*
156909 TATTGGCTTGA
1 TATTTGCTTGA
156920 TATT
1 TATT
156924 GAATTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.19, C:0.08, G:0.16, T:0.57
Consensus pattern (11 bp):
TATTTGCTTGA
Found at i:159424 original size:2 final size:2
Alignment explanation
Indices: 159417--159443 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
159407 CCGTAAACAA
159417 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 A
159444 CAATAAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:160449 original size:4 final size:4
Alignment explanation
Indices: 160442--161367 Score: 1696
Period size: 4 Copynumber: 234.0 Consensus size: 4
160432 ATACATCAAC
160442 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
160490 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
160538 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
160586 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
160634 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
160682 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
160730 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
160778 ACAT ACGT ACAT ACAT ACAT ACAT ACGT ACAT ACAT ACAT --AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
160824 ACGTAT ACAT ACAT ACAT ACAT ACGT ACAT ACAT ACAT ATAT ACAT --AT
1 AC--AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
160872 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
160920 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
160966 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
161014 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
161062 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
161110 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
161158 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
161204 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
161252 ACAT ATAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
161300 ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
161346 ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT
161368 GACACATGAA
Statistics
Matches: 898, Mismatches: 10, Indels: 28
0.96 0.01 0.03
Matches are distributed among these distances:
2 12 0.01
4 882 0.98
6 4 0.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:161995 original size:33 final size:32
Alignment explanation
Indices: 161957--162063 Score: 92
Period size: 33 Copynumber: 3.3 Consensus size: 32
161947 CCTTTTCTCA
161957 TGAAACAACAAATCATCTTTGAGTAGTTTCCCT
1 TGAAACAA-AAATCATCTTTGAGTAGTTTCCCT
* * ** * *
161990 TGAAACGAATATTGTCTCTTGAGACAGTTTCTCT
1 TGAAACAAAAATCATCT-TTGAG-TAGTTTCCCT
* *
162024 TAAAAC-AAAATCATCTTTGAGTCGTTTCCCT
1 TGAAACAAAAATCATCTTTGAGTAGTTTCCCT
162055 AT-AAACAAA
1 -TGAAACAAA
162064 TTTTGTCTCT
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
31 11 0.19
32 14 0.25
33 19 0.33
34 13 0.23
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.34
Consensus pattern (32 bp):
TGAAACAAAAATCATCTTTGAGTAGTTTCCCT
Found at i:162061 original size:31 final size:31
Alignment explanation
Indices: 161966--162063 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 31
161956 ATGAAACAAC
* *
161966 AAATCATCTTTGAGTAGTTTCCCTTGAAACGA
1 AAATCATCTTTGAGTCGTTTCCCTTAAAAC-A
* ** * *
161998 ATATTGTCTCTTGAGACAGTTTCTCTTAAAACA
1 AAATCATCT-TTGAGTC-GTTTCCCTTAAAACA
162031 AAATCATCTTTGAGTCGTTTCCC-TATAAACA
1 AAATCATCTTTGAGTCGTTTCCCTTA-AAACA
162062 AA
1 AA
162064 TTTTGTCTCT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
30 2 0.04
31 13 0.25
32 12 0.24
33 12 0.24
34 12 0.24
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (31 bp):
AAATCATCTTTGAGTCGTTTCCCTTAAAACA
Found at i:162075 original size:67 final size:65
Alignment explanation
Indices: 161901--162116 Score: 188
Period size: 65 Copynumber: 3.2 Consensus size: 65
161891 AAAATTTTCT
* * ** *
161901 ATCTTTGAGATCGTTTCTCTTAAAACAAATCTTATTTTC-CTTGAGACCTTTTCTCATGAAACAA
1 ATCTTTGAG-TCGTTTCCCTTAAAACAAAT-TT-TGTTCTCTTGAGACAGTTTCTC-TTAAAC-A
161965 CAAATC
61 -AAATC
* * * *
161971 ATCTTTGAGTAGTTTCCCTTGAAACGAATATTG-TCTCTTGAGACAGTTTCTCTTAAAACAAAAT
1 ATCTTTGAGTCGTTTCCCTTAAAACAAATTTTGTTCTCTTGAGACAGTTTCTCTT-AAACAAAAT
162035 C
65 C
* * * * *
162036 ATCTTTGAGTCGTTTCCC-TATAAACAAATTTTGTCTCTCTTGAGATAGATTCTATTGAA-ATAA
1 ATCTTTGAGTCGTTTCCCTTA-AAACAAATTTTGT-TCTCTTGAGACAGTTTCTCTTAAACAAAA
162099 TC
64 TC
162101 ATCTTTGAGTCAGTTT
1 ATCTTTGAGTC-GTTT
162117 TTGTCATTTG
Statistics
Matches: 122, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
64 1 0.01
65 48 0.39
66 10 0.08
67 37 0.30
68 1 0.01
69 16 0.13
70 9 0.07
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (65 bp):
ATCTTTGAGTCGTTTCCCTTAAAACAAATTTTGTTCTCTTGAGACAGTTTCTCTTAAACAAAATC
Found at i:162502 original size:83 final size:82
Alignment explanation
Indices: 162359--162625 Score: 312
Period size: 83 Copynumber: 3.3 Consensus size: 82
162349 TAAAGATGGT
* * *
162359 CAGCCGTCCTTATCACGTAGGAACCGTGTCATCCCCTGATCAGACCTCCTCATCACGTAGGAGCC
1 CAGCCGTCCTCATCACATAGGAACCGTGTCATCCCCTGACCAGACCTCCT-ATCACGTAGGAGCC
*
162424 ATGTCACCCCTAGATAAC
65 GTGTCACCCCTAGATAAC
** * * *
162442 CAATCGTCCTCATCACATAGGAACTGAGTCATCCCCTGACCAGACCTCCTTATCATGTAGGAGCC
1 CAGCCGTCCTCATCACATAGGAACCGTGTCATCCCCTGACCAGACCTCC-TATCACGTAGGAGCC
*
162507 GTGTCACCCGTAGATAAC
65 GTGTCACCCCTAGATAAC
* ** * *
162525 CAGCCATCCTCATCATGTAGGAACCGTGCCATCCACC-GACCAGA----C-ATCGCGTAGGAGCC
1 CAGCCGTCCTCATCACATAGGAACCGTGTCATCC-CCTGACCAGACCTCCTATCACGTAGGAGCC
*
162584 GTGTCACCCTTAGATAAC
65 GTGTCACCCCTAGATAAC
*
162602 CAGCCGTCCTCATCGCATAGGAAC
1 CAGCCGTCCTCATCACATAGGAAC
162626 AATGTTATTA
Statistics
Matches: 157, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
77 49 0.31
79 1 0.01
83 104 0.66
84 3 0.02
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (82 bp):
CAGCCGTCCTCATCACATAGGAACCGTGTCATCCCCTGACCAGACCTCCTATCACGTAGGAGCCG
TGTCACCCCTAGATAAC
Found at i:162540 original size:43 final size:42
Alignment explanation
Indices: 162359--162552 Score: 152
Period size: 40 Copynumber: 4.6 Consensus size: 42
162349 TAAAGATGGT
*
162359 CAGCCGTCCTTATCACGTAGGAACCGTGTCATCCCCT-GAT---
1 CAGCC-TCCTCATCACGTAGGAACCGTGTCA-CCCCTAGATAAC
* *
162399 CAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTAGATAAC
1 CAG-CCTCCTCATCACGTAGGAACCGTGTCACCCCTAGATAAC
* * * * *
162442 CAATCGTCCTCATCACATAGGAACTGAGTCATCCCCT-G---AC
1 C-AGCCTCCTCATCACGTAGGAACCGTGTCA-CCCCTAGATAAC
* * * *
162482 CAGACCTCCTTATCATGTAGGAGCCGTGTCACCCGTAGATAAC
1 CAG-CCTCCTCATCACGTAGGAACCGTGTCACCCCTAGATAAC
*
162525 CAGCCATCCTCATCATGTAGGAACCGTG
1 CAGCC-TCCTCATCACGTAGGAACCGTG
162553 CCATCCACCG
Statistics
Matches: 120, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
39 10 0.08
40 52 0.43
41 2 0.02
42 2 0.02
43 48 0.40
44 6 0.05
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (42 bp):
CAGCCTCCTCATCACGTAGGAACCGTGTCACCCCTAGATAAC
Found at i:163429 original size:23 final size:23
Alignment explanation
Indices: 163398--163450 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
163388 ATCAGTCACA
* *
163398 ATGACAGAAGCAACAAATAAAA-AG
1 ATGA-AGAAACAA-AAAGAAAATAG
163422 ATGAAGAAACAAAAAGAAAATAG
1 ATGAAGAAACAAAAAGAAAATAG
163445 A-GAAGA
1 ATGAAGA
163451 TTCGGGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 12 0.46
23 10 0.38
24 4 0.15
ACGTcount: A:0.66, C:0.08, G:0.19, T:0.08
Consensus pattern (23 bp):
ATGAAGAAACAAAAAGAAAATAG
Found at i:167826 original size:33 final size:34
Alignment explanation
Indices: 167763--167845 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 34
167753 TATCATATAG
167763 TTTTCAAAAATGATTTTTAAAAATATTATATAAGT-
1 TTTTC-AAAATGATTTTTAAAAATATTATATAA-TA
* * * *
167798 TTTTCAAAATGTTTTTTTAAACTA-TATATTATA
1 TTTTCAAAATGATTTTTAAAAATATTATATAATA
167831 TTTTCAAAATGATTT
1 TTTTCAAAATGATTT
167846 CAAAACTGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 1 0.02
33 20 0.48
34 16 0.38
35 5 0.12
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (34 bp):
TTTTCAAAATGATTTTTAAAAATATTATATAATA
Found at i:167876 original size:35 final size:35
Alignment explanation
Indices: 167710--167886 Score: 129
Period size: 35 Copynumber: 5.1 Consensus size: 35
167700 AAAAAAAATT
** *
167710 AAACTATATATTATAT--TTTAAAAAACATGTTTTCA
1 AAACTATATATTATATAATTT-TCAAA-ATGATTTCA
* * **
167745 AAACTATATATCATATAGTTTTCAAAAATGATTTTT
1 AAACTATATATTATATAATTTTC-AAAATGATTTCA
* **
167781 AAA--A-ATATTATATAAGTTTTTCAAAATGTTTTTTT
1 AAACTATATATTATATAA--TTTTCAAAATG-ATTTCA
167816 AAACTATATA-T-TAT-ATTTTCAAAATGATTTCA
1 AAACTATATATTATATAATTTTCAAAATGATTTCA
* *
167848 AAACTGTATATTATATAATTTTCAAAATGCTTT-A
1 AAACTATATATTATATAATTTTCAAAATGATTTCA
167882 AAACT
1 AAACT
167887 TACGTATTGT
Statistics
Matches: 116, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
32 12 0.10
33 21 0.18
34 16 0.14
35 44 0.38
36 12 0.10
37 8 0.07
38 3 0.03
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.45
Consensus pattern (35 bp):
AAACTATATATTATATAATTTTCAAAATGATTTCA
Found at i:168560 original size:84 final size:83
Alignment explanation
Indices: 168440--169022 Score: 592
Period size: 84 Copynumber: 7.0 Consensus size: 83
168430 ATCTTATTGA
* * * * * * *
168440 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGTTGTGCCTTAGAGTTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
168505 CTCGAAGGTCTTTGGTTGG
65 CTCGAAGGTCTTTGGTTGG
* * * *
168524 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGTAGCTGAACATAGTCAAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTG-AGCTGAGCGTAGTCGAA
**
168589 CTCGAAGGTCTTTTGG-TCA
65 CTCGAAGGTC-TTTGGTTGG
* * * * * * *
168608 CAGATAACCCTTCTAGTCTTGAGTTATGATGTAAATGATGTGCCCTTGAAGTTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGA
*
168673 ACTCGAGGGTC--T--TTGG
64 ACTCGAAGGTCTTTGGTTGG
* * *
168689 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
*
168754 CTCGAAGGTCTTTGG-TGA
65 CTCGAAGGTCTTTGGTTGG
* * *
168772 CAGATAACCCTTCTAGCCTTAAGTTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAA
*
168837 CTCGAAGATCTTTTGGTTGG
65 CTCGAAGGTC-TTTGGTTGG
* * * ** * *
168857 CAGATAACCCTTATCGACTTAAGTTATGCTGTAAATGTTGTGCCCTGGAGCTGAATGAAATCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG-CCTTGAGCTGAGCGTAGTCGAA
*
168922 CTTGAAAGGGTC--T--TTGG
65 CTCG-AA-GGTCTTTGGTTGG
* * * * *
168939 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAATTGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAA
* *
169004 CTCAAAGGTCTTTTGTTGG
65 CTCGAAGGTCTTTGGTTGG
169023 GTATCCTTCT
Statistics
Matches: 406, Mismatches: 74, Indels: 38
0.78 0.14 0.07
Matches are distributed among these distances:
80 31 0.08
81 41 0.10
82 59 0.15
83 71 0.17
84 110 0.27
85 86 0.21
86 5 0.01
87 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (83 bp):
CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTGGTTGG
Found at i:168884 original size:249 final size:248
Alignment explanation
Indices: 168406--169021 Score: 799
Period size: 249 Copynumber: 2.5 Consensus size: 248
168396 CGTGTCATCG
* * * * * *
168406 AGCTGAATGGAATCGAACTCGATA--ATCTTATTGACAGATAGCCCTTCTTGCCTTGAGCTATGC
1 AGCTGAATGAAATCGAACTCGA-AGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
* * * *
168469 TGTAAATGTTGTGCCTTAGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
63 TGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCC
* * * *
168534 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGTAGCTGAACATAGTCAAACTCGAAGGTC
127 TTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAACATAGTCAAACTCGAAGATC
* * *
168599 TTTTGGTCACAGATAACCCTTCTAGTCTTGAGTTATGATGTAAATGATGTGCCCTTGA
192 TTTTGGTCACAGATAACCCTTATAGACTTAAGTTATGATGTAAATGATGTGCCC-TGA
* * *
168657 AGTTGAGTGTAATCGAACTCG-AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
1 AGCTGAATGAAATCGAACTCGAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
168721 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTC
66 AAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTC
* * * * *
168785 TAGCCTTAAGTTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTT
130 TAGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAACATAGTCAAACTCGAAGATCTTT
** * * * *
168850 TGGTTGGCAGATAACCCTTATCGACTTAAGTTATGCTGTAAATGTTGTGCCCTGG
195 TGG-TCACAGATAACCCTTATAGACTTAAGTTATGATGTAAATGATGTGCCCTGA
* *
168905 AGCTGAATGAAATCGAACTTGAAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTG
1 AGCTGAATGAAATCGAACTCG-AAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
* * *
168970 CAATTGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTG
65 CAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
169022 GGTATCCTTC
Statistics
Matches: 319, Mismatches: 39, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
248 93 0.29
249 117 0.37
250 85 0.27
251 24 0.08
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (248 bp):
AGCTGAATGAAATCGAACTCGAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
AAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCT
AGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAACATAGTCAAACTCGAAGATCTTTT
GGTCACAGATAACCCTTATAGACTTAAGTTATGATGTAAATGATGTGCCCTGA
Found at i:168908 original size:168 final size:166
Alignment explanation
Indices: 168437--169022 Score: 684
Period size: 168 Copynumber: 3.5 Consensus size: 166
168427 ATAATCTTAT
* * * * * * *
168437 TGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGTTGTGCCTTAGAGTTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGCCTTAAGCTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
168502 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
66 GAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
* * *
168567 CTTGTAGCTGAACATAGTCAAACTCGAAGGTCTTTTGG
130 CTTGGAGCTGAACGTAGTCGAACTCGAAGGTC-TTTGG
* * * * * * * *
168605 TCACAGATAACCCTTCTAGTCTTGAGTTATGA-TGTAAATGATGTGCCCTTGAAGTTGAGTGTAA
1 TGACAGATAACCCTTCTAGCCTTAAGCTAT-ACTGTAAATGATGTG-CCTTGGAGCTGAGCGTAG
* * *
168669 TCGAACTCGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
64 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
168731 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
129 CCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGG
*
168769 TGACAGATAACCCTTCTAGCCTTAAGTTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGCCTTAAGCTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * * *
168834 GAACTCGAAGATCTTTTGGTTGGCAGATAACCCTTATCGACTTAAGTTATGCTGTAAATGTTGTG
66 GAACTCGAAGGTC-TTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* * * * *
168899 CCCTGGAGCTGAATGAAATCGAACTTGAAAGGGTCTTT-G
129 CCTTGGAGCTGAACGTAGTCGAACTCG-AA-GGTCTTTGG
* * * * *
168938 -G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAATTGATGTGCCGTT-GAGCTGAGCGTAGT
1 TGACAGATAACCCTTCTAGCCTTAAGCTATACTGTAAATGATGTGCC-TTGGAGCTGAGCGTAGT
*
169000 CGAACTCAAAGGTCTTTTGTTGG
65 CGAACTCGAAGGTC-TTTGTTGG
169023 GTATCCTTCT
Statistics
Matches: 361, Mismatches: 46, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
163 28 0.08
164 45 0.12
165 73 0.20
166 6 0.02
167 69 0.19
168 102 0.28
169 31 0.09
170 7 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (166 bp):
TGACAGATAACCCTTCTAGCCTTAAGCTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGG
Found at i:169225 original size:106 final size:106
Alignment explanation
Indices: 169061--170088 Score: 1635
Period size: 106 Copynumber: 9.7 Consensus size: 106
169051 AATTGGATAT
* * *
169061 CCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCATTCGCTGTGAAGTTGAAATC
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* * * **
169126 GGCCCTGAGATTGGGAAACTGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* **
169167 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCATTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* *
169232 GGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTT
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
169273 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAATTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
169338 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* ** *
169379 CCTTCGTCGTGAAGTTGAATTTATGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
*
169444 GGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
*
169485 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
*
169550 GGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
*
169591 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
*
169656 GGCTCTGAATTTGAGAAGTTGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
169697 CCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCATTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* * *
169762 GGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
169803 CCTTCGTCGTGAAGTTGAACTTGCGTTATCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* *
169868 GGCTCTGAAATTGAGAAGTTGGTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* * *
169909 CCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCACTATCATTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* * *
169974 GGCTCTAGAAGTGGA-AAATTGTTTATTGACAACCAGCGGTC
66 GGCTCT-GAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* * * * *
170015 CCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATTTTCTTCGCTGCGAAGTTGAAATA
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
*
170080 GACTCTGAA
66 GGCTCTGAA
170089 TGAAATTGGA
Statistics
Matches: 862, Mismatches: 59, Indels: 3
0.93 0.06 0.00
Matches are distributed among these distances:
105 3 0.00
106 853 0.99
107 6 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
Found at i:175560 original size:35 final size:33
Alignment explanation
Indices: 175521--175675 Score: 136
Period size: 35 Copynumber: 4.5 Consensus size: 33
175511 AAAAAAAATT
*
175521 AAACTATATATTATATTTTAAAAAACATGTTTTCA
1 AAACTATATATTATATTTT-CAAAA-ATGTTTTCA
*
175556 AAACTATATATCATATAGTTTTCAAAAATGATTTTTA
1 AAACTATATAT--TATA-TTTTCAAAAATG-TTTTCA
* * **
175593 AAAATATTATATAAGT-TTTTC-AAAATGTTTTTTTT
1 AAACTA-TATATTA-TATTTTCAAAAATG--TTTTCA
*
175628 AAACTATATATTATATTTTC-AAAATGATTTCA
1 AAACTATATATTATATTTTCAAAAATGTTTTCA
175660 AAACTATATATTATAT
1 AAACTATATATTATAT
175676 AATTTTCAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
32 19 0.19
33 1 0.01
34 23 0.23
35 26 0.26
36 4 0.04
37 19 0.19
38 9 0.09
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (33 bp):
AAACTATATATTATATTTTCAAAAATGTTTTCA
Found at i:175697 original size:34 final size:35
Alignment explanation
Indices: 175521--175698 Score: 133
Period size: 35 Copynumber: 5.1 Consensus size: 35
175511 AAAAAAAATT
** *
175521 AAACTATATATTATAT--TTTAAAAAACATGTTTTCA
1 AAACTATATATTATATAATTT-TCAAA-ATGTTTTTA
* *
175556 AAACTATATATCATATAGTTTTCAAAAATGATTTTT-
1 AAACTATATATTATATAATTTTC-AAAATG-TTTTTA
*
175592 AAA--A-ATATTATATAAGTTTTTCAAAATGTTTTTTTT
1 AAACTATATATTATATAA--TTTTCAAAATG--TTTTTA
* *
175628 AAACTATATA-T-TAT-ATTTTCAAAATGATTTCA
1 AAACTATATATTATATAATTTTCAAAATGTTTTTA
*
175660 AAACTATATATTATATAATTTTCAAAATG-TGTTA
1 AAACTATATATTATATAATTTTCAAAATGTTTTTA
175694 AAACT
1 AAACT
175699 TACGTATTGT
Statistics
Matches: 117, Mismatches: 12, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
32 13 0.11
33 10 0.09
34 29 0.25
35 37 0.32
36 10 0.09
37 13 0.11
38 2 0.02
39 3 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (35 bp):
AAACTATATATTATATAATTTTCAAAATGTTTTTA
Found at i:182658 original size:19 final size:19
Alignment explanation
Indices: 182634--182670 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
182624 TAGAGGAAGC
*
182634 AAAGATTCCATGACTTTTT
1 AAAGATTCCATGAATTTTT
*
182653 AAAGATTTCATGAATTTT
1 AAAGATTCCATGAATTTT
182671 AAGGGAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (19 bp):
AAAGATTCCATGAATTTTT
Found at i:185860 original size:54 final size:54
Alignment explanation
Indices: 185794--186051 Score: 358
Period size: 54 Copynumber: 4.8 Consensus size: 54
185784 GATATGGAAT
* * * *
185794 TTCACAAACTCATTATGAATTCTGTGGGTTGCACACGTAGTGTCGATACAGTCA
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTCA
* * *
185848 TTCATAAACTCATTATGAATTCCATGGGTTGTATACATAGTGTCGATACGGTCA
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTCA
* ** *
185902 TTCATAAACCCATTATGAATTATGTGGGTTGCACACATAGTGCCGATACGGTCA
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTCA
* * **
185956 TTCATAAACTCATTATGAATTACGTGGGTTGCACA-A-AGTGTTGATATTGTCA
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTCA
*
186008 TTCATAAACTCATTATGAATTCCGTGGGTTGCACATATAGTGTC
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTC
186052 AAAAGTACAT
Statistics
Matches: 180, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
52 46 0.26
53 2 0.01
54 132 0.73
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (54 bp):
TTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTCA
Found at i:188708 original size:23 final size:24
Alignment explanation
Indices: 188682--188738 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
188672 TGAATTTCCT
188682 GAATGTACAAATAAA-GCCGCGTA
1 GAATGTACAAATAAAGGCCGCGTA
* * *
188705 GAAT-TGCACATAAAGTGTCGCGTA
1 GAATGTACAAATAAAG-GCCGCGTA
188729 GAATGTACAA
1 GAATGTACAA
188739 GAATGTACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
22 8 0.31
23 4 0.15
24 11 0.42
25 3 0.12
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (24 bp):
GAATGTACAAATAAAGGCCGCGTA
Found at i:193822 original size:46 final size:46
Alignment explanation
Indices: 193763--193873 Score: 141
Period size: 46 Copynumber: 2.4 Consensus size: 46
193753 TTATGTCTCT
* * * *
193763 TTTCACGCATTAATACATCCATTGATACAATTTAACTATGGCATCC
1 TTTCATGCCTTAATGCATCCATTCATACAATTTAACTATGGCATCC
* * * * *
193809 TTTCATGTCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCATTCATACAATTTAACTATGGCATCC
193855 TTTCATGCCTTAATGCATC
1 TTTCATGCCTTAATGCATC
193874 ATTTCATGCA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCATTCATACAATTTAACTATGGCATCC
Found at i:193859 original size:26 final size:24
Alignment explanation
Indices: 193793--193890 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 24
193783 ATTGATACAA
193793 TTTAACTATGGCATCCTTTCATG-T
1 TTTAA-TATGGCATCCTTTCATGCT
*
193817 CTT-A-AT-GCATCCTTTCATGCAT
1 TTTAATATGGCATCCTTTCATGC-T
193839 TTTAATTATGGCATCCTTTCATGC-
1 TTTAA-TATGGCATCCTTTCATGCT
* *
193863 CTT-A-AT-GCATCATTTCATGCAT
1 TTTAATATGGCATCCTTTCATGC-T
193885 TTTAAT
1 TTTAAT
193891 TATGAATTCG
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
20 26 0.44
21 4 0.07
22 5 0.08
23 4 0.07
24 4 0.07
25 2 0.03
26 14 0.24
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.45
Consensus pattern (24 bp):
TTTAATATGGCATCCTTTCATGCT
Found at i:193879 original size:46 final size:46
Alignment explanation
Indices: 193793--193894 Score: 177
Period size: 46 Copynumber: 2.2 Consensus size: 46
193783 ATTGATACAA
* * *
193793 TTTAACTATGGCATCCTTTCATGTCTTAATGCATCCTTTCATGCAT
1 TTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCAT
193839 TTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCAT
1 TTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCAT
193885 TTTAATTATG
1 TTTAATTATG
193895 AATTCGATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.45
Consensus pattern (46 bp):
TTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCAT
Found at i:193882 original size:20 final size:20
Alignment explanation
Indices: 193803--193882 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 20
193793 TTTAACTATG
*
193803 GCATCCTTTCATGTCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
193823 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
193848 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
193869 GCATCATTTCATGC
1 GCATCCTTTCATGC
193883 ATTTTAATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 26 0.52
21 2 0.04
22 2 0.04
23 2 0.04
24 2 0.04
25 2 0.04
26 14 0.28
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.42
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:194409 original size:20 final size:20
Alignment explanation
Indices: 194384--194435 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
194374 GTTTTGAAAT
194384 GGTATCGATACCTTCCCT-TC
1 GGTATCGATACC-TCCCTATC
*
194404 GGTATCGATA-CTCCCTCATT
1 GGTATCGATACCTCCCT-ATC
194424 GGTATCGATACC
1 GGTATCGATACC
194436 GATTGAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.18
19 1 0.04
20 21 0.75
21 1 0.04
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (20 bp):
GGTATCGATACCTCCCTATC
Found at i:201724 original size:103 final size:103
Alignment explanation
Indices: 201545--201757 Score: 363
Period size: 103 Copynumber: 2.1 Consensus size: 103
201535 GGCTCTACGC
* *
201545 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTAAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTAAT
* *
201610 CCTTGGAATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGAATATGTATATGATTCTTAAGGAATGATATGT
*
201648 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTAAT
*
201713 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGAATATGTATATGATTCTTAAGGAATGATATGT
*
201751 AGTCCTT
1 GGTCCTT
201758 ATGGACATTA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTAAT
CCCTAGAATATGTATATGATTCTTAAGGAATGATATGT
Found at i:201807 original size:23 final size:23
Alignment explanation
Indices: 201774--201841 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
201764 ATTATTATAT
201774 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
201797 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
201820 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
201842 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:205731 original size:20 final size:20
Alignment explanation
Indices: 205706--205798 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
205696 TTTTCCCAAT
205706 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
205726 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
205746 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
205767 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
205788 TCGCAATGCGA
1 TCGCAATGCGA
205799 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:205748 original size:41 final size:41
Alignment explanation
Indices: 205703--205798 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
205693 CGATTTTCCC
*
205703 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
205744 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
205785 AAATCGCAATGCGA
1 AATTCGCAATGCGA
205799 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:205811 original size:41 final size:41
Alignment explanation
Indices: 205725--205855 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
205715 GAATAAGTAA
* * * *
205725 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
205766 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
205807 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
205848 TTCGCAAC
1 ATCGCAAC
205856 ACGATACTGA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 69 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:205812 original size:20 final size:20
Alignment explanation
Indices: 205787--205881 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
205777 AATTGAGAAA
*
205787 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
205807 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
205828 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
205848 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
205868 TTCGCAACGCGATA
1 ATCGCAACGCGATA
205882 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:207737 original size:18 final size:18
Alignment explanation
Indices: 207716--207760 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
207706 TCCACTTCGG
*
207716 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
207734 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
207752 GAGCCATCA
1 GAGCCATCA
207761 TCTGATTGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:208285 original size:19 final size:20
Alignment explanation
Indices: 208231--208297 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
208221 TAGTTTACTT
* *
208231 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
208251 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
208271 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
208290 TCGCAACG
1 TCGCAACG
208298 ACAAAAGCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:208308 original size:14 final size:14
Alignment explanation
Indices: 208286--208343 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
208276 ATGCGAAATG
208286 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
208300 AAAAGCGCAACGCGAA
1 AAAATCGCAA--CGAC
208316 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
208332 AAAATCGCAACG
1 AAAATCGCAACG
208344 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:208328 original size:32 final size:33
Alignment explanation
Indices: 208272--208348 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 33
208262 AAATGGCTAT
*
208272 CGCAATGCGAAATGAAAATCGCAACGACAAAAG
1 CGCAACGCGAAATGAAAATCGCAACGACAAAAG
*
208305 CGCAACGCGAAATG-AAATCGCAACGACAAAAT
1 CGCAACGCGAAATGAAAATCGCAACGACAAAAG
208337 CGCAACGCGAAA
1 CGCAACGCGAAA
208349 CACAAATCGC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 29 0.69
33 13 0.31
ACGTcount: A:0.47, C:0.25, G:0.21, T:0.08
Consensus pattern (33 bp):
CGCAACGCGAAATGAAAATCGCAACGACAAAAG
Found at i:208377 original size:19 final size:19
Alignment explanation
Indices: 208355--208508 Score: 105
Period size: 19 Copynumber: 8.6 Consensus size: 19
208345 GAAACACAAA
*
208355 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
208374 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
*
208390 T--CGTTGC-AATTTCATT
1 TCGCGTTGCGATTTTCATT
*
208406 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
208422 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
208439 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
208458 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
208478 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
208498 TCGTGTTGCGA
1 TCGCGTTGCGA
208509 AAGTAAACTA
Statistics
Matches: 107, Mismatches: 15, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
13 1 0.01
14 17 0.16
15 3 0.03
16 6 0.06
17 2 0.02
18 12 0.11
19 37 0.35
20 29 0.27
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:208396 original size:14 final size:14
Alignment explanation
Indices: 208377--208434 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
208367 TTTCATTTCG
208377 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
208391 CGTTGCAATTTCATTT
1 CGTTGCGATTT--TGT
208407 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
208423 CGTTGCGATTTT
1 CGTTGCGATTTT
208435 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:208441 original size:33 final size:33
Alignment explanation
Indices: 208360--208450 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
208350 ACAAATCGCA
208360 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
208393 TTGC-AATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
208425 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
208451 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:208469 original size:20 final size:19
Alignment explanation
Indices: 208435--208489 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
208425 TTGCGATTTT
*
208435 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
208454 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
208474 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
208490 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:210502 original size:14 final size:15
Alignment explanation
Indices: 210483--210559 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
210473 CGAAATGGCT
210483 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
210497 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
210515 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
210534 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
210548 ATCGCAATGCGA
1 ATCGCAA-GCGA
210560 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:210515 original size:19 final size:19
Alignment explanation
Indices: 210493--210559 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
210483 ATCGCAACGA
210493 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
210512 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
210530 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
210544 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
210560 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:210992 original size:14 final size:14
Alignment explanation
Indices: 210973--211008 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
210963 ATTGTTTAAT
210973 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
210987 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
211001 TGATTTGT
1 TGATTTGT
211009 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:211150 original size:18 final size:18
Alignment explanation
Indices: 211127--211190 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
211117 CGCAACGAGA
211127 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
211145 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
211163 AAAATCGCAA--CG--A-G
1 -AAATCGCAATGCGAAATG
211177 AAATCGCAATGCGA
1 AAATCGCAATGCGA
211191 TTTTCATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.21
14 1 0.02
15 3 0.07
17 2 0.05
18 18 0.43
19 9 0.21
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:211180 original size:19 final size:19
Alignment explanation
Indices: 211125--211172 Score: 89
Period size: 18 Copynumber: 2.6 Consensus size: 19
211115 ATCGCAACGA
211125 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
211144 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
211162 GAAAATCGCAA
1 GAAAATCGCAA
211173 CGAGAAATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:211337 original size:631 final size:626
Alignment explanation
Indices: 210097--211423 Score: 2522
Period size: 631 Copynumber: 2.1 Consensus size: 626
210087 TGGTAAGTCA
*
210097 AATGCAAGTTTTGTTAACATATATACTCC-TTTGGTTTGAAAATGTTTGGTTAAGTACCAAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
210161 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
210226 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGTCACAAAGTTGTTGATTCTT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGTCACAAAGTTGTTGATTCTT
210291 GATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTAATTGATTGTAAAAGA
196 GATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTAATTGATTGTAAAAGA
210356 TGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGTTGA
261 TGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGTTGA
210421 TTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAACAGACTATCGCAACGCGAAATGGCTATC
326 TTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAACAGACTATCGCAACGCGAAATGGCTATC
210486 GCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATC
391 GCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATC
*
210551 GCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGCGATAG
456 GCAATGCGATTTTCATTTCGCGTTGCAATATTCTCGTTGCGATAACCATTTTCGCGTTGCGATAG
210616 TCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATAC
521 TCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATAC
210681 ATGCCTAACTGAAAATGTTAAAGTGCACACATAAAATACACAT
586 ATGCCTAACTGAAAATGTTAAAGTG--CACATAAAATACACAT
210724 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
210789 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTT-GTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
210853 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTAC-GGGTCACAAAGTTGTTGATTCT
210918 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
195 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTA-TTTTTGATTG-TTAATTGA-TTGTAA
210983 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
257 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
211048 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
322 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGC-AAACAGACTATCGCAACGCGAAATGG
211113 CTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAG-
386 CTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGA
211177 AAATCGCAATGCGATTTTCATTTCGCGTTGCAATATTCTCGTTGCGATAACCATTTTCGCGTTGC
451 AAATCGCAATGCGATTTTCATTTCGCGTTGCAATATTCTCGTTGCGATAACCATTTTCGCGTTGC
211242 GATAGTCAAATGAA-TAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACT
516 GATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACT
211306 AATACATGCCTAACTGAAAATGTTAAAAGTGCACATAAAATACACAT
581 AATACATGCCTAACTGAAAATGTT-AAAGTGCACATAAAATACACAT
211353 -ATGCAAGTTTTGTTAACATATATACTCCTTTT-GTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
211416 TCAATAAT
66 TCAATAAT
211424 AATTGTTAAA
Statistics
Matches: 691, Mismatches: 2, Indels: 14
0.98 0.00 0.02
Matches are distributed among these distances:
627 114 0.16
628 186 0.27
629 26 0.04
630 82 0.12
631 193 0.28
632 90 0.13
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (626 bp):
AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGTCACAAAGTTGTTGATTCTT
GATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTGATTGTTAATTGATTGTAAAAGA
TGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGTTGA
TTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAACAGACTATCGCAACGCGAAATGGCTATC
GCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATC
GCAATGCGATTTTCATTTCGCGTTGCAATATTCTCGTTGCGATAACCATTTTCGCGTTGCGATAG
TCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATAC
ATGCCTAACTGAAAATGTTAAAGTGCACATAAAATACACAT
Found at i:212329 original size:24 final size:24
Alignment explanation
Indices: 212273--212331 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
212263 AGTCAGTATT
* *
212273 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
212297 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
212321 CGAATTTTGAT
1 CGAAATTTGAT
212332 GATGTTTTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:212515 original size:12 final size:12
Alignment explanation
Indices: 212498--212534 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
212488 TTCATAATCT
212498 GAAGAAGAAAAA
1 GAAGAAGAAAAA
212510 GAAGAAGAAAAA
1 GAAGAAGAAAAA
212522 GAAGAAGAAAAA
1 GAAGAAGAAAAA
212534 G
1 G
212535 TCCCGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Done.