Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 101 of 135
Found at i:31356795 original size:17 final size:17
Alignment explanation
Indices: 31356758--31356795 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
31356748 CTATATGTTT
*
31356758 TTTTAATTTTTCATAAT
1 TTTTAATTTTTCATAAC
31356775 TTTTAATTTTT-ATATAC
1 TTTTAATTTTTCATA-AC
31356792 TTTT
1 TTTT
31356796 GAGTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATTTTTCATAAC
Found at i:31362978 original size:37 final size:38
Alignment explanation
Indices: 31362927--31363001 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 38
31362917 AGATATGGAT
31362927 AGGAAATGTACTTAGC-CTTTAAGTTACTTATGCTTGGG
1 AGGAAATGTACTTAGCAC-TTAAGTTACTTATGCTTGGG
* *
31362965 AGGAAA-GTACTTAGCACTTAAGTTATTTATGTTTGGG
1 AGGAAATGTACTTAGCACTTAAGTTACTTATGCTTGGG
31363002 GATGTCCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 27 0.79
38 7 0.21
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (38 bp):
AGGAAATGTACTTAGCACTTAAGTTACTTATGCTTGGG
Found at i:31365000 original size:25 final size:23
Alignment explanation
Indices: 31364958--31365018 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
31364948 ACACATAACT
*
31364958 GGTTTGCATATAGGTTCACATATAG
1 GGTTTGCATATAGATT--CATATAG
31364983 GGTTTGCATACTA-ATTCATATAG
1 GGTTTGCATA-TAGATTCATATAG
*
31365006 GGTCTGCATATAG
1 GGTTTGCATATAG
31365019 GCTCGCATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 2 0.06
23 16 0.50
25 12 0.38
26 2 0.06
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (23 bp):
GGTTTGCATATAGATTCATATAG
Found at i:31365219 original size:75 final size:75
Alignment explanation
Indices: 31365073--31365237 Score: 188
Period size: 75 Copynumber: 2.2 Consensus size: 75
31365063 ATACTTCATA
* * * * * ** *
31365073 TAGGGTTCGCACATATTGGCTATAGTTCGCCTAACATAGTTCGCATGTATAACCGTTTATGTAAC
1 TAGGGTTCGCATATATTGGCTACAATTCGCCTAACAGAGTTCCCATGTATAACAATTTATGTAAA
31365138 GGTTCGCACC
66 GGTTCGCACC
* * *
31365148 TAGGGTTTGCATATATTGGCTACAATTCGCCTATCAGAGTTCCCATGTATAATAATTTATG-AAA
1 TAGGGTTCGCATATATTGGCTACAATTCGCCTAACAGAGTTCCCATGTATAACAATTTATGTAAA
* *
31365212 GGATTCGCGCT
66 GG-TTCGCACC
*
31365223 TAGGATTCGCATATA
1 TAGGGTTCGCATATA
31365238 GGGTTTGCAC
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
74 4 0.05
75 70 0.95
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (75 bp):
TAGGGTTCGCATATATTGGCTACAATTCGCCTAACAGAGTTCCCATGTATAACAATTTATGTAAA
GGTTCGCACC
Found at i:31375012 original size:20 final size:19
Alignment explanation
Indices: 31374969--31375006 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31374959 CCCTGTATTA
31374969 AAAGATAAATAATTTTTAG
1 AAAGATAAATAATTTTTAG
31374988 AAAGATAAATAATTTTTAG
1 AAAGATAAATAATTTTTAG
31375007 TGAAGAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (19 bp):
AAAGATAAATAATTTTTAG
Found at i:31375513 original size:23 final size:23
Alignment explanation
Indices: 31375487--31375581 Score: 145
Period size: 23 Copynumber: 4.1 Consensus size: 23
31375477 CATTAGCGCA
*
31375487 CTCTCCGATTAGCACTGTGTGTG
1 CTCTCCGATTAGCACTTTGTGTG
31375510 CTCTCCGATTAGCACTTTGTGTG
1 CTCTCCGATTAGCACTTTGTGTG
* * *
31375533 CTCTCCGTTTAGCACTTCGTATG
1 CTCTCCGATTAGCACTTTGTGTG
*
31375556 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCCGATTAGCACTTTGTGTG
31375579 CTC
1 CTC
31375582 AGTACTTTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.13, C:0.27, G:0.21, T:0.39
Consensus pattern (23 bp):
CTCTCCGATTAGCACTTTGTGTG
Found at i:31381186 original size:23 final size:22
Alignment explanation
Indices: 31381152--31381227 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
31381142 ACGGTGGCCG
31381152 AAATTATT-TTTTTTACAAAATCA
1 AAATT-TTCTTTTTTA-AAAATCA
**
31381175 AAATTTTCTTTTTTTTAAA-CA
1 AAATTTTCTTTTTTAAAAATCA
*
31381196 AAATCATTACTTTTCTTAAAAATCA
1 AAAT--TTTCTTTT-TTAAAAATCA
31381221 AAATTTT
1 AAATTTT
31381228 TATTTCGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
21 6 0.14
22 5 0.12
23 20 0.48
24 5 0.12
25 6 0.14
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTTTCTTTTTTAAAAATCA
Found at i:31381268 original size:18 final size:19
Alignment explanation
Indices: 31381247--31381287 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31381237 ATAGTTAAAA
31381247 AAAAAG-AAAACTTTGTTT
1 AAAAAGTAAAACTTTGTTT
* *
31381265 AAAAAGTTAAACTTTTTTT
1 AAAAAGTAAAACTTTGTTT
31381284 AAAA
1 AAAA
31381288 TTACTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (19 bp):
AAAAAGTAAAACTTTGTTT
Found at i:31381459 original size:19 final size:18
Alignment explanation
Indices: 31381437--31381485 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
31381427 AAAAAAAATA
31381437 TTTTTAAAAATCTAATTA-T
1 TTTTTAAAAATC--ATTACT
*
31381456 TTTTAAAAAATCATTACT
1 TTTTTAAAAATCATTACT
31381474 TTTCTTAAAAAT
1 TTT-TTAAAAAT
31381486 TAAAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 4 0.15
19 18 0.69
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTTAAAAATCATTACT
Found at i:31381708 original size:17 final size:17
Alignment explanation
Indices: 31381666--31381776 Score: 123
Period size: 17 Copynumber: 6.3 Consensus size: 17
31381656 TTAAACCCAT
31381666 TTTAAGATTTATTTTAAA
1 TTTAA-ATTTATTTTAAA
* *
31381684 GATTAAATTTATTTTGAA
1 -TTTAAATTTATTTTAAA
*
31381702 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
31381719 TTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
* *
31381737 TTTAGATTTAATTTAAA
1 TTTAAATTTATTTTAAA
*
31381754 TTTAAATTCATATTTAAA
1 TTTAAATTTAT-TTTAAA
31381772 TTTAA
1 TTTAA
31381777 GACTTAATAA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
17 38 0.49
18 35 0.45
19 4 0.05
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:31381711 original size:6 final size:6
Alignment explanation
Indices: 31381686--31381776 Score: 64
Period size: 6 Copynumber: 15.7 Consensus size: 6
31381676 ATTTTAAAGA
* * * * **
31381686 TTAAAT TT-ATT TTGAAT TTAAAT TT-ATT TTAAGT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
31381731 TTAAAAT TTAGAT TT-AAT TTAAAT TTAAAT TCATAT TTAAAT TTAA
1 TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
31381777 GACTTAATAA
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
5 15 0.23
6 46 0.72
7 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:31381713 original size:35 final size:35
Alignment explanation
Indices: 31381666--31381776 Score: 127
Period size: 35 Copynumber: 3.1 Consensus size: 35
31381656 TTAAACCCAT
* *
31381666 TTTAAGATTTATTTTAAAGATTAAATTTATTTTGAA
1 TTTAA-ATTTATTTTAAAGTTTAAATTTATTTTAAA
*
31381702 TTTAAATTTATTTT-AAGTTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAGTTTAAATTTATTTT-AAA
* * *
31381737 TTTAGATTTAATTTAAA-TTTAAATTCATATTTAAA
1 TTTAAATTTATTTTAAAGTTTAAATTTAT-TTTAAA
31381772 TTTAA
1 TTTAA
31381777 GACTTAATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
34 15 0.23
35 39 0.61
36 10 0.16
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATTTTAAAGTTTAAATTTATTTTAAA
Found at i:31386614 original size:19 final size:19
Alignment explanation
Indices: 31386592--31386636 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31386582 TTATATTAGG
31386592 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
31386611 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
31386630 ATTTAAT
1 ATTTAAT
31386637 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:31387475 original size:22 final size:22
Alignment explanation
Indices: 31387436--31387496 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
31387426 TTCGACTTCC
** * *
31387436 CTATTTTCTACTTCTTTTAGTT
1 CTATTTTCTTTTTTTTTTAATT
31387458 CTATTTTCTTTTTTTTTTAATT
1 CTATTTTCTTTTTTTTTTAATT
* *
31387480 C-AGTTTCTTTTATTTTT
1 CTATTTTCTTTTTTTTTT
31387497 CCTTAGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTTTTTTTAATT
Found at i:31389059 original size:21 final size:21
Alignment explanation
Indices: 31389034--31389083 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
31389024 GAATTTCAGC
*
31389034 AGCAATCTATAGATTTCCAAA
1 AGCAAACTATAGATTTCCAAA
* * *
31389055 AGCAAACTGTGGATTTTCAAA
1 AGCAAACTATAGATTTCCAAA
*
31389076 AGAAAACT
1 AGCAAACT
31389084 GAGGCATCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (21 bp):
AGCAAACTATAGATTTCCAAA
Found at i:31389084 original size:21 final size:21
Alignment explanation
Indices: 31389045--31389084 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31389035 GCAATCTATA
*
31389045 GATTTCCAAAAGCAAACTGTG
1 GATTTCCAAAAGAAAACTGTG
*
31389066 GATTTTCAAAAGAAAACTG
1 GATTTCCAAAAGAAAACTG
31389085 AGGCATCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
GATTTCCAAAAGAAAACTGTG
Found at i:31393140 original size:8 final size:8
Alignment explanation
Indices: 31393123--31393171 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
31393113 AACCCAATTA
31393123 TTTTTA-T
1 TTTTTATT
31393130 TTTTTATT
1 TTTTTATT
31393138 TTTTTATT
1 TTTTTATT
*
31393146 TTTCTA-T
1 TTTTTATT
*
31393153 CTTTTATT
1 TTTTTATT
*
31393161 TATTTATT
1 TTTTTATT
31393169 TTT
1 TTT
31393172 GTCCAGGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
7 11 0.32
8 23 0.68
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTATT
Found at i:31393143 original size:15 final size:15
Alignment explanation
Indices: 31393123--31393171 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
31393113 AACCCAATTA
31393123 TTTTTATTTTTTATT
1 TTTTTATTTTTTATT
31393138 TTTTTATTTTTCTA-T
1 TTTTTATTTTT-TATT
*
31393153 CTTTTATTTATTTATT
1 TTTTTATTT-TTTATT
31393169 TTT
1 TTT
31393172 GTCCAGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 22 0.76
16 7 0.24
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTTTATT
Found at i:31393674 original size:10 final size:10
Alignment explanation
Indices: 31393659--31393684 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
31393649 TCTCTATCCG
31393659 AAAAAAAAGA
1 AAAAAAAAGA
31393669 AAAAAAAAGA
1 AAAAAAAAGA
31393679 AAAAAA
1 AAAAAA
31393685 TCCTTTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:31393976 original size:102 final size:102
Alignment explanation
Indices: 31393864--31394053 Score: 269
Period size: 102 Copynumber: 1.9 Consensus size: 102
31393854 ATGTGTTAGA
* * *
31393864 CTGAGTAACCGGGGTGGAGTGCTT-GGTTGTCATTTCACTTCGCTTCAAAAGGGCTAATGCATTC
1 CTGAGTAACCGGGATGGAGTGCTTAGG-TGTCATTTCACTTCGCGTCAAAAGGGCCAATGCATTC
31393928 -TAAA-AAAAAGAGAAGAAAAAAATTGAGAGCATGTTGGG
65 TTAAAGAAAAA-A-AAGAAAAAAATTGAGAGCATGTTGGG
* * *
31393966 CTGAGTAACCGGGATGGAGTGCTTAGGTGTCATTTCATTTCGCGTCAAAAGGTCCAATGTATTCT
1 CTGAGTAACCGGGATGGAGTGCTTAGGTGTCATTTCACTTCGCGTCAAAAGGGCCAATGCATTCT
*
31394031 TAAAGAAAAAAAAGGAAAAAATT
66 TAAAGAAAAAAAAGAAAAAAATT
31394054 CACAAAATAA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
102 66 0.85
103 7 0.09
104 5 0.06
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (102 bp):
CTGAGTAACCGGGATGGAGTGCTTAGGTGTCATTTCACTTCGCGTCAAAAGGGCCAATGCATTCT
TAAAGAAAAAAAAGAAAAAAATTGAGAGCATGTTGGG
Found at i:31394638 original size:19 final size:19
Alignment explanation
Indices: 31394616--31394660 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31394606 TTATATTAGG
31394616 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
31394635 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
31394654 ATTTAAT
1 ATTTAAT
31394661 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:31397321 original size:13 final size:12
Alignment explanation
Indices: 31397303--31397334 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
31397293 GTTATAACAA
31397303 AAAAAAACATAAC
1 AAAAAAACA-AAC
31397316 AAAAAAACAAAC
1 AAAAAAACAAAC
31397328 AAAAAAA
1 AAAAAAA
31397335 GAGAGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.84, C:0.12, G:0.00, T:0.03
Consensus pattern (12 bp):
AAAAAAACAAAC
Found at i:31397327 original size:17 final size:15
Alignment explanation
Indices: 31397296--31397334 Score: 57
Period size: 13 Copynumber: 2.8 Consensus size: 15
31397286 TCGACGTGTT
31397296 ATAACAAAAAAAAAC
1 ATAACAAAAAAAAAC
31397311 ATAAC--AAAAAAAC
1 ATAACAAAAAAAAAC
31397324 A-AACAAAAAAA
1 ATAACAAAAAAA
31397335 GAGAGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 9 0.41
14 5 0.23
15 5 0.23
ACGTcount: A:0.82, C:0.13, G:0.00, T:0.05
Consensus pattern (15 bp):
ATAACAAAAAAAAAC
Found at i:31398188 original size:19 final size:18
Alignment explanation
Indices: 31398160--31398200 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
31398150 GAACAAATAA
*
31398160 AAAAAGAAGAAAAAAAAGC
1 AAAAACAAGAAAAAAAA-C
*
31398179 AAAAACAAGAAGAAAAAC
1 AAAAACAAGAAAAAAAAC
31398197 AAAA
1 AAAA
31398201 TAGAAAGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAACAAGAAAAAAAAC
Found at i:31398205 original size:13 final size:12
Alignment explanation
Indices: 31398160--31398206 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
31398150 GAACAAATAA
31398160 AAAAAGAAGAAA-
1 AAAAAGAA-AAAC
31398172 AAAAAGCAAAAAC
1 AAAAAG-AAAAAC
*
31398185 AAGAAGAAAAAC
1 AAAAAGAAAAAC
31398197 AAAATAGAAA
1 AAAA-AGAAA
31398207 GGAGAGGTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAAC
Found at i:31399863 original size:76 final size:76
Alignment explanation
Indices: 31399734--31400420 Score: 1122
Period size: 76 Copynumber: 9.0 Consensus size: 76
31399724 TAAATCAAAC
* * *
31399734 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTCTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
31399799 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
31399810 ATCATTTCCTATCATCTTAAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
31399875 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * * * *
31399886 ATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTAGATAACAAGTCTCTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
31399951 GTAAGAGCAAG
66 GTAAGAGCAAG
*
31399962 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTAAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
31400027 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * * * *
31400038 ATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTCTATCTTTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
31400103 GTAAGAGCAAG
66 GTAAGAGCAAG
31400114 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
31400179 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * * *
31400190 ATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTTTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
31400255 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
31400266 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAAATGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
31400331 GTAAGAGCAAG
66 GTAAGAGCAAG
*
31400342 ATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA--TCTCTGAAATTG
31400407 AAGTAAGAGCAAG
64 AAGTAAGAGCAAG
31400420 A
1 A
31400421 CAGAGCATCA
Statistics
Matches: 563, Mismatches: 46, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
76 538 0.96
78 25 0.04
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:31400014 original size:152 final size:152
Alignment explanation
Indices: 31399738--31400511 Score: 1260
Period size: 152 Copynumber: 5.0 Consensus size: 152
31399728 TCAAACATCA
*
31399738 TTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTCTATCTCTGAAATTGAAGTAA
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTCTATCTCTGAAATTGAAGTAA
* *
31399803 GAGCAAGATCATTTCCTATCATCTTAAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGA
66 GAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGA
31399868 AATTGAAGTAAGAGCAAGATCT
131 AATTGAAGTAAGAGCAAGATCT
*
31399890 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTAGATAACAAGTCTCTATCTCTGAAATTGAAGTAA
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTCTATCTCTGAAATTGAAGTAA
*
31399955 GAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTAA
66 GAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGA
31400020 AATTGAAGTAAGAGCAAGATCT
131 AATTGAAGTAAGAGCAAGATCT
*
31400042 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTCTATCTTTGAAATTGAAGTAA
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTCTATCTCTGAAATTGAAGTAA
31400107 GAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGA
66 GAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGA
31400172 AATTGAAGTAAGAGCAAGATCT
131 AATTGAAGTAAGAGCAAGATCT
* *
31400194 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTTTGAAATTGAAGTAA
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTCTATCTCTGAAATTGAAGTAA
*
31400259 GAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGA
66 GAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGA
*
31400324 AAATGAAGTAAGAGCAAGATCT
131 AATTGAAGTAAGAGCAAGATCT
* * * *
31400346 TTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGT
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTCTA--TCTCTGAAATTGAAGT
*
31400411 AAGAGCAAGACAGAGCATCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAGGCTGGATATCA
64 ---------A-AGAG---CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
31400476 AGTCTTTATCTCTCTGAAATTGAAGTAAGAGCAAGA
116 AGTCTTTA--TCTCTGAAATTGAAGTAAGAGCAAGA
31400512 CAAAACCCTG
Statistics
Matches: 587, Mismatches: 18, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
152 489 0.83
154 15 0.03
163 1 0.00
164 4 0.01
167 53 0.09
169 25 0.04
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (152 bp):
TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTCTATCTCTGAAATTGAAGTAA
GAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGA
AATTGAAGTAAGAGCAAGATCT
Found at i:31400131 original size:228 final size:228
Alignment explanation
Indices: 31399734--31400511 Score: 1178
Period size: 228 Copynumber: 3.3 Consensus size: 228
31399724 TAAATCAAAC
* *
31399734 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTCTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
* * *
31399799 GTAAGAGCAAGATCATTTCCTATCATCTTAAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCT
66 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCT
* * * *
31399864 CTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTAGATAACA
131 CTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
*
31399929 AGTCTCTATCTCTGAAATTGAAGTAAGAGCAAG
196 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
* *
31399962 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTAAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
* * * *
31400027 GTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTCTATCT
66 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCT
* *
31400092 TTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
131 CTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
31400157 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
196 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
* * * *
31400190 ATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTTTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
31400255 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCT
66 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCT
*
31400320 CTGAAAATGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
131 CTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
31400385 AGTCTTTATCTCTCTGAAATTGAAGTAAGAGCAAGACAGAGCATCAAG
196 AGTCTTTA--TCTCTGAAATTGAAGT---------A-AGAG---CAAG
* *
31400433 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGGCTGGATATCAAGTCTTTATCTCTCTGAAATTG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTA--TCTCTGAAATTG
31400498 AAGTAAGAGCAAGA
64 AAGTAAGAGCAAGA
31400512 CAAAACCCTG
Statistics
Matches: 496, Mismatches: 37, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
228 400 0.81
230 16 0.03
239 1 0.00
240 4 0.01
243 50 0.10
245 25 0.05
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (228 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCT
CTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
Found at i:31400406 original size:40 final size:40
Alignment explanation
Indices: 31400355--31400503 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
31400345 TTTTCCTATC
31400355 CTCT-TGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
1 CTCTCTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
* *
31400394 CTCTCTGAAATTGAAGTAAGAGCAAGACAGAGCATCAAGATCATTTCCTAT
1 CTCTCTGAAATTGAAGTAA-AGC-TG---GA-TATCAAG-TC--TT--TAT
*
31400445 C-CTCTTGAAATTGAAGTAAGGCTGGATATCAAGTCTTTAT
1 CTCTC-TGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
31400485 CTCTCTGAAATTGAAGTAA
1 CTCTCTGAAATTGAAGTAA
31400504 GAGCAAGACA
Statistics
Matches: 91, Mismatches: 5, Indels: 27
0.74 0.04 0.22
Matches are distributed among these distances:
39 4 0.04
40 32 0.35
41 6 0.07
42 3 0.03
44 2 0.02
45 8 0.09
46 8 0.09
47 2 0.02
49 3 0.03
50 5 0.05
51 18 0.20
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (40 bp):
CTCTCTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
Found at i:31400458 original size:51 final size:45
Alignment explanation
Indices: 31400338--31400513 Score: 142
Period size: 40 Copynumber: 4.0 Consensus size: 45
31400328 GAAGTAAGAG
* *
31400338 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAA-AGCTGGATAT
1 CAAGATC-TTTCCTATCCTCTTGAAATTGAAGTAAGAGCAGGACAT
31400383 CAAG-TC-TT--TAT-CTCTCTGAAATTGAAGTAAGAGCAAGACAGAGCAT
1 CAAGATCTTTCCTATCCTCT-TGAAATTGAAGTAAGAGC-AG---GA-CAT
* *
31400429 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAG-GCTGGATAT
1 CAAGATC-TTTCCTATCCTCTTGAAATTGAAGTAAGAGCAGGACAT
*
31400474 CAAG-TC-TT--TAT-CTCTCTGAAATTGAAGTAAGAGCAAGACA
1 CAAGATCTTTCCTATCCTCT-TGAAATTGAAGTAAGAGCAGGACA
31400514 AAACCCTGAC
Statistics
Matches: 109, Mismatches: 7, Indels: 34
0.73 0.05 0.23
Matches are distributed among these distances:
39 8 0.07
40 35 0.32
41 8 0.07
42 5 0.05
44 4 0.04
45 12 0.11
46 8 0.07
47 2 0.02
49 3 0.03
50 2 0.02
51 18 0.17
52 4 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (45 bp):
CAAGATCTTTCCTATCCTCTTGAAATTGAAGTAAGAGCAGGACAT
Found at i:31400493 original size:91 final size:91
Alignment explanation
Indices: 31400338--31400513 Score: 334
Period size: 91 Copynumber: 1.9 Consensus size: 91
31400328 GAAGTAAGAG
*
31400338 CAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAA
31400403 ATTGAAGTAAGAGCAAGACAGAGCAT
66 ATTGAAGTAAGAGCAAGACAGAGCAT
*
31400429 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAGGCTGGATATCAAGTCTTTATCTCTCTGAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAA
31400494 ATTGAAGTAAGAGCAAGACA
66 ATTGAAGTAAGAGCAAGACA
31400514 AAACCCTGAC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (91 bp):
CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAA
ATTGAAGTAAGAGCAAGACAGAGCAT
Found at i:31401157 original size:18 final size:17
Alignment explanation
Indices: 31401129--31401179 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
31401119 TAAACTCATT
31401129 TTAAGATTTATTTTAAAGA
1 TTAA-ATTTATTTTAAA-A
* *
31401148 TTAAATTTATTTTGAAT
1 TTAAATTTATTTTAAAA
31401165 TTAAATTTATTTTAA
1 TTAAATTTATTTTAA
31401180 GTTTTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.48
18 11 0.38
19 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:31401173 original size:6 final size:6
Alignment explanation
Indices: 31401148--31401228 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
31401138 ATTTTAAAGA
* * * * *
31401148 TTAAAT TT-ATT TTGAAT TTAAAT TT-ATT TTAAGTT TTAAAAT TTAGAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TT-AAAT TTAAAT
* *
31401196 TT-AAT TTAAAT TTAAAT TCATAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
31401229 GACTTAATAA
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
5 12 0.20
6 38 0.64
7 7 0.12
8 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:31401190 original size:36 final size:35
Alignment explanation
Indices: 31401128--31401209 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 35
31401118 TTAAACTCAT
*
31401128 TTTAAGATTTATTTTAAAGATTAAATTTA-TTTTGAA
1 TTTAA-ATTTATTTTAAAGATTAAATTTAGATTT-AA
*
31401164 TTTAAATTTATTTT-AAGTTTTAAAATTTAGATTTAA
1 TTTAAATTTATTTTAAAG-ATT-AAATTTAGATTTAA
31401200 TTTAAATTTA
1 TTTAAATTTA
31401210 AATTCATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 3 0.07
35 11 0.27
36 24 0.59
37 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (35 bp):
TTTAAATTTATTTTAAAGATTAAATTTAGATTTAA
Found at i:31401198 original size:42 final size:43
Alignment explanation
Indices: 31401139--31401222 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
31401129 TTAAGATTTA
* * *
31401139 TTTTAAAGATTAAATTTATTTTGAATTTAAATTTAT-TTTAAG
1 TTTTAAAGATTAAATTTAATTTAAATTTAAATTCATATTTAAG
*
31401181 TTTTAAA-ATTTAGATTTAATTTAAATTTAAATTCATATTTAA
1 TTTTAAAGA-TTAAATTTAATTTAAATTTAAATTCATATTTAA
31401223 ATTTAAGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.03
42 30 0.83
43 5 0.14
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (43 bp):
TTTTAAAGATTAAATTTAATTTAAATTTAAATTCATATTTAAG
Found at i:31406065 original size:19 final size:19
Alignment explanation
Indices: 31406043--31406087 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31406033 TTATATTAGG
31406043 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
31406062 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
31406081 ATTTAAT
1 ATTTAAT
31406088 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:31406926 original size:22 final size:22
Alignment explanation
Indices: 31406887--31406947 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
31406877 TTCGACTTCC
** * *
31406887 CTATTTTCTACTTCTTTTAGTT
1 CTATTTTCTTTTTTTTTTAATT
31406909 CTATTTTCTTTTTTTTTTAATT
1 CTATTTTCTTTTTTTTTTAATT
* *
31406931 C-AGTTTCTTTTATTTTT
1 CTATTTTCTTTTTTTTTT
31406948 CCTTAGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTTTTTTTAATT
Found at i:31408514 original size:21 final size:21
Alignment explanation
Indices: 31408489--31408538 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
31408479 GAATTTCAGC
*
31408489 AGCAATCTATAGATTTCCAAA
1 AGCAAACTATAGATTTCCAAA
* * *
31408510 AGCAAACTGTGGATTTTCAAA
1 AGCAAACTATAGATTTCCAAA
*
31408531 AGAAAACT
1 AGCAAACT
31408539 GAGGCATCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (21 bp):
AGCAAACTATAGATTTCCAAA
Found at i:31408539 original size:21 final size:21
Alignment explanation
Indices: 31408500--31408539 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31408490 GCAATCTATA
*
31408500 GATTTCCAAAAGCAAACTGTG
1 GATTTCCAAAAGAAAACTGTG
*
31408521 GATTTTCAAAAGAAAACTG
1 GATTTCCAAAAGAAAACTG
31408540 AGGCATCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
GATTTCCAAAAGAAAACTGTG
Found at i:31414873 original size:20 final size:20
Alignment explanation
Indices: 31414829--31414901 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
31414819 GGTTTTTATA
31414829 ATTTTA-ATATTTTAAAAT-
1 ATTTTATATATTTTAAAATG
31414847 ATATTTATATATTTTAAAATG
1 AT-TTTATATATTTTAAAATG
* ** *
31414868 ATTTTAAATGATTTTTTATTG
1 ATTTTATAT-ATTTTAAAATG
31414889 ATTTTATA-ATTTT
1 ATTTTATATATTTT
31414902 TTACATTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.04
19 9 0.20
20 18 0.39
21 17 0.37
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTTTATATATTTTAAAATG
Found at i:31421266 original size:30 final size:29
Alignment explanation
Indices: 31421227--31421466 Score: 200
Period size: 30 Copynumber: 8.0 Consensus size: 29
31421217 ATTCGAGAGA
*
31421227 CCTCGAACTTTCTAAAAATCACATATTGAC
1 CCTCGAAC-TTCTAAAAATCACATTTTGAC
** * *
31421257 CCTTAAACTTCTCAAAAATTAC-GTTTGAC
1 CCTCGAACTTCT-AAAAATCACATTTTGAC
* *
31421286 CCTCGAACTTATCAAAAATTACATTTTGAC
1 CCTCGAACTTCT-AAAAATCACATTTTGAC
* * * *
31421316 TCTTGAACTTGTCAAAAATTACATTTTGAC
1 CCTCGAACTTCT-AAAAATCACATTTTGAC
31421346 CCTCGAAC-TCATCAAAAATTC-CATTTTGAC
1 CCTCGAACTTC-T-AAAAA-TCACATTTTGAC
* *
31421376 CCTCGAACTTCTCCAAAATCATATTTTGAC
1 CCTCGAACTTCT-AAAAATCACATTTTGAC
* *
31421406 CCTCAAACTTCTCAAAAATCATATTTTGAC
1 CCTCGAACTTCT-AAAAATCACATTTTGAC
* *
31421436 CC-CTGAAACTCCTCAAAATCACATTTTGAC
1 CCTC-G-AACTTCTAAAAATCACATTTTGAC
31421466 C
1 C
31421467 TCAAGCTCTC
Statistics
Matches: 178, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
29 32 0.18
30 137 0.77
31 9 0.05
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.33
Consensus pattern (29 bp):
CCTCGAACTTCTAAAAATCACATTTTGAC
Found at i:31421363 original size:60 final size:60
Alignment explanation
Indices: 31421227--31421466 Score: 256
Period size: 60 Copynumber: 4.0 Consensus size: 60
31421217 ATTCGAGAGA
* * * * *
31421227 CCTCGAACT-TTCTAAAAATCACATATTGACCCTTAAACTTCTCAAAAATTAC-GTTTGAC
1 CCTCGAACTCATC-AAAAATCACATTTTGACCCTTGAACTTCTCAAAAATCACATTTTGAC
* * * * *
31421286 CCTCGAACTTATCAAAAATTACATTTTGACTCTTGAACTTGTCAAAAATTACATTTTGAC
1 CCTCGAACTCATCAAAAATCACATTTTGACCCTTGAACTTCTCAAAAATCACATTTTGAC
* * *
31421346 CCTCGAACTCATCAAAAATTC-CATTTTGACCCTCGAACTTCTCCAAAATCATATTTTGAC
1 CCTCGAACTCATCAAAAA-TCACATTTTGACCCTTGAACTTCTCAAAAATCACATTTTGAC
* * * *
31421406 CCTCAAACTTC-TCAAAAATCATATTTTGACCCCTGAAACTCCTC-AAAATCACATTTTGAC
1 CCTCGAAC-TCATCAAAAATCACATTTTGACCCTTG-AACTTCTCAAAAATCACATTTTGAC
31421466 C
1 C
31421467 TCAAGCTCTC
Statistics
Matches: 154, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
59 45 0.29
60 99 0.64
61 10 0.06
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.33
Consensus pattern (60 bp):
CCTCGAACTCATCAAAAATCACATTTTGACCCTTGAACTTCTCAAAAATCACATTTTGAC
Found at i:31421405 original size:90 final size:88
Alignment explanation
Indices: 31421227--31421466 Score: 245
Period size: 90 Copynumber: 2.7 Consensus size: 88
31421217 ATTCGAGAGA
* ** * *
31421227 CCTCGAACTTTCTAAAAATCACATATTGACCCTTAAACTTCTCAAAAATTAC-GTTTGACCCTCG
1 CCTCGAACTTTC-AAAAATCACATTTTGACCCTCGAAC-TCTCAAAAATTCCATTTTGACCCTCG
*
31421291 AACTTATCAAAAATTACATTTTGAC
64 AACTTATCAAAAATCACATTTTGAC
* * *
31421316 TCTTGAACTTGTCAAAAATTACATTTTGACCCTCGAACTCATCAAAAATTCCATTTTGACCCTCG
1 CCTCGAACTT-TCAAAAATCACATTTTGACCCTCGAACTC-TCAAAAATTCCATTTTGACCCTCG
* * *
31421381 AACTTCTCCAAAATCATATTTTGAC
64 AACTTATCAAAAATCACATTTTGAC
* *
31421406 CCTCAAACTTCTCAAAAATCATATTTTGACCC-CTGAAACTCCTC-AAAA-TCACATTTTGACC
1 CCTCGAACTT-TCAAAAATCACATTTTGACCCTC-G-AACT-CTCAAAAATTC-CATTTTGACC
31421467 TCAAGCTCTC
Statistics
Matches: 126, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
88 2 0.02
89 42 0.33
90 75 0.60
91 6 0.05
92 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.33
Consensus pattern (88 bp):
CCTCGAACTTTCAAAAATCACATTTTGACCCTCGAACTCTCAAAAATTCCATTTTGACCCTCGAA
CTTATCAAAAATCACATTTTGAC
Found at i:31426190 original size:39 final size:39
Alignment explanation
Indices: 31426125--31426733 Score: 234
Period size: 39 Copynumber: 15.7 Consensus size: 39
31426115 AAGAAGCCAA
* * * * *
31426125 ATCTCTTT-CCCCGAGCCTAGGACAGATTGTAACCATTCG
1 ATCT-TTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* * *
31426164 ATCTTTTACCCCGAGCTTGGGGCAGA-T-CACCGTCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAAC--CATCCG
* * * * * *
31426203 ATATCTTACTCCGA-TTCTAGGGCAGATTGCAGCCATCCG
1 ATCTTTTACCCCGAGCT-TGGGGCAGATTGCAACCATCCG
* * * *
31426242 ATCTTTTATCCCGAGCTTGGGGCAAATTACGACCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* ** * * * *
31426281 ATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* ** * * * *
31426320 ATTTTTTACCTTGAGCCTAGAGCAGATTGCAGCCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* * * ** * * * *
31426359 ATCTTTTACCCCGAGCCTAGGACAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* * * *
31426398 ATCTCTTACCCCGAGCCT----CAGATTGCAGCCATCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* * * ** * * * *
31426433 ATCTTTTACCTCGAGCCTGAGGCAGATCACCATCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
** * *
31426472 ATCTCTTT-CCCCTTGCTTGGGGCAGATTACAGCCATCCG
1 ATCT-TTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* * * *** * *
31426511 ATCTTTTACCCCGAGCCTGAGGCAGATTACCGTCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* * ** *
31426550 ATCTCTTACCTC-ATGAC-AAGGGTAGATTGCAACCATCCG
1 ATCTTTTACCCCGA-G-CTTGGGGCAGATTGCAACCATCCG
** * *
31426589 ATCTTTTACCCCGAGCTTGGGATAGATTGCAGCCATTCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* * * ** * * * *
31426628 ATCTTTTACCTCGAGCCTGAGGCAGATCACTATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
* * * * *
31426667 ATCTCTTACCCCTTA-CTTGGGGTAAATTGCAGCCATCCG
1 ATCTTTTACCCC-GAGCTTGGGGCAGATTGCAACCATCCG
** *
31426706 ATCTTTTACCCTAAACTTGGGGCAGATT
1 ATCTTTTACCCCGAGCTTGGGGCAGATT
31426734 ACTGTCAGCC
Statistics
Matches: 406, Mismatches: 145, Indels: 38
0.69 0.25 0.06
Matches are distributed among these distances:
35 27 0.07
37 2 0.00
38 11 0.03
39 355 0.87
40 8 0.02
41 3 0.01
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (39 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATTGCAACCATCCG
Found at i:31426345 original size:117 final size:117
Alignment explanation
Indices: 31426125--31426735 Score: 463
Period size: 117 Copynumber: 5.3 Consensus size: 117
31426115 AAGAAGCCAA
* * * * *
31426125 ATCTCTTT-CCCCGAGCCTAGGACAGATTGTA-ACCATTCGATCTTTTACCCCGAGCTTGGGGCA
1 ATCT-TTTACCCCGAGCTTGGGACAGA-T-TACACCATCCGATCTTTTACCCCGAGCCTGAGGCA
* * ** *
31426188 GATCACCGTCAGCCAATATCTTA-CTCCGATTCTAGGGCAGATTGCAGCCATCCG
63 GATCACCATCAGCCAATCTCTTACCTCCGAGCCTAGAGCAGATTGCAGCCATCCG
* * * *
31426242 ATCTTTTATCCCGAGCTTGGGGCAAATTACGACCATCCGATCTTTTACCCCGAGCTTGAGGCAGA
1 ATCTTTTACCCCGAGCTTGGGACAGATTAC-ACCATCCGATCTTTTACCCCGAGCCTGAGGCAGA
* * *
31426307 TCACCATCAGCCAATTTTTTACCT-TGAGCCTAGAGCAGATTGCAGCCATCCG
65 TCACCATCAGCCAATCTCTTACCTCCGAGCCTAGAGCAGATTGCAGCCATCCG
* * * * * * *
31426359 ATCTTTTACCCCGAGCCTAGGACAGATCACCATCAGCCAATCTCTTACCCCGAGCCT----CAGA
1 ATCTTTTACCCCGAGCTTGGGACAGATTA-CACCATCCGATCTTTTACCCCGAGCCTGAGGCAGA
* *
31426420 TTGCAGCCAT---CCAATCTTTTACCT-CGAGCCT-GAGGCAGA-T-CA-CCATCAACCA
65 -T-CA-CCATCAGCCAATCTCTTACCTCCGAGCCTAGA-GCAGATTGCAGCCAT---CCG
** *
31426472 ATCTCTTT-CCCCTTGCTTGGGGCAGATTACAGCCATCCGATCTTTTACCCCGAGCCTGAGGCAG
1 ATCT-TTTACCCCGAGCTTGGGACAGATTACA-CCATCCGATCTTTTACCCCGAGCCTGAGGCAG
* * * * * * *
31426536 ATTACCGTCAGCCAATCTCTTACCT-C-ATGACAAGGGTAGATTGCAACCATCCG
64 ATCACCATCAGCCAATCTCTTACCTCCGA-GCCTAGAGCAGATTGCAGCCATCCG
* * * *
31426589 ATCTTTTACCCCGAGCTTGGGATAGATTGCAGCCATTCGATCTTTTACCTCGAGCCTGAGGCAGA
1 ATCTTTTACCCCGAGCTTGGGACAGATTACA-CCATCCGATCTTTTACCCCGAGCCTGAGGCAGA
* * * * * * *
31426654 TCACTATCAGCCAATCTCTTACC-CCTTA-CTTGGGGTAAATTGCAGCCATCCG
65 TCACCATCAGCCAATCTCTTACCTCC-GAGCCTAGAGCAGATTGCAGCCATCCG
** * *
31426706 ATCTTTTACCCTAAACTTGGGGCAGATTAC
1 ATCTTTTACCCCGAGCTTGGGACAGATTAC
31426736 TGTCAGCCAA
Statistics
Matches: 396, Mismatches: 68, Indels: 60
0.76 0.13 0.11
Matches are distributed among these distances:
110 4 0.01
111 2 0.01
112 5 0.01
113 70 0.18
114 7 0.02
115 5 0.01
116 13 0.03
117 278 0.70
118 5 0.01
119 3 0.01
120 4 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (117 bp):
ATCTTTTACCCCGAGCTTGGGACAGATTACACCATCCGATCTTTTACCCCGAGCCTGAGGCAGAT
CACCATCAGCCAATCTCTTACCTCCGAGCCTAGAGCAGATTGCAGCCATCCG
Found at i:31426434 original size:35 final size:36
Alignment explanation
Indices: 31426342--31426450 Score: 109
Period size: 35 Copynumber: 3.0 Consensus size: 36
31426332 GAGCCTAGAG
*
31426342 CAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGGA
1 CAGATTGCAGCCATCCAATCTTTTACCCCGAGCCT---A
*
31426381 CAGA-T-CA-CCATCAGCCAATCTCTTACCCCGAGCCT-
1 CAGATTGCAGCCAT---CCAATCTTTTACCCCGAGCCTA
*
31426416 CAGATTGCAGCCATCCAATCTTTTACCTCGAGCCT
1 CAGATTGCAGCCATCCAATCTTTTACCCCGAGCCT
31426451 GAGGCAGATC
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
35 23 0.38
36 5 0.08
37 4 0.07
38 5 0.08
39 23 0.38
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.24
Consensus pattern (36 bp):
CAGATTGCAGCCATCCAATCTTTTACCCCGAGCCTA
Found at i:31426457 original size:152 final size:152
Alignment explanation
Indices: 31426274--31426559 Score: 416
Period size: 152 Copynumber: 1.9 Consensus size: 152
31426264 CAAATTACGA
* * * *
31426274 CCATCCGATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAAT-T-TTTTACCTTGAGCC
1 CCATCCAATCTTTTACCCCGAGCCTGAGGCAGATCACCATCAACCAATCTCTTTCACCTT--GCC
*
31426337 TAGAGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCT-AGGACAGATCACCATCAGCCAATC
64 TAGAGCAGATTACAGCCATCCGATCTTTTACCCCGAGCCTGAGG-CAGATCACCATCAGCCAATC
31426401 TCTTACCCCGAGCCTCAGATTGCAG
128 TCTTACCCCGAGCCTCAGATTGCAG
* * * *
31426426 CCATCCAATCTTTTACCTCGAGCCTGAGGCAGATCACCATCAACCAATCTCTTTCCCCTTGCTTG
1 CCATCCAATCTTTTACCCCGAGCCTGAGGCAGATCACCATCAACCAATCTCTTTCACCTTGCCTA
* * *
31426491 GGGCAGATTACAGCCATCCGATCTTTTACCCCGAGCCTGAGGCAGATTACCGTCAGCCAATCTCT
66 GAGCAGATTACAGCCATCCGATCTTTTACCCCGAGCCTGAGGCAGATCACCATCAGCCAATCTCT
31426556 TACC
131 TACC
31426560 TCATGACAAG
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
152 108 0.91
153 4 0.03
154 7 0.06
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.25
Consensus pattern (152 bp):
CCATCCAATCTTTTACCCCGAGCCTGAGGCAGATCACCATCAACCAATCTCTTTCACCTTGCCTA
GAGCAGATTACAGCCATCCGATCTTTTACCCCGAGCCTGAGGCAGATCACCATCAGCCAATCTCT
TACCCCGAGCCTCAGATTGCAG
Found at i:31426616 original size:78 final size:76
Alignment explanation
Indices: 31426274--31426604 Score: 375
Period size: 78 Copynumber: 4.3 Consensus size: 76
31426264 CAAATTACGA
* * *
31426274 CCATCCGATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAATTTTTTACCT-TGAGCCT
1 CCATCCGATCTTTTACCCCGAGCCTGAGGCAGATCACCATCAGCCAATCTCTTACCTCT--G-CT
*
31426338 AGAGCAGATTGCAG
63 AGGGCAGATTGCAG
*
31426352 CCATCCGATCTTTTACCCCGAGCCT-AGGACAGATCACCATCAGCCAATCTCTTACC-C--CGAG
1 CCATCCGATCTTTTACCCCGAGCCTGAGG-CAGATCACCATCAGCCAATCTCTTACCTCTGCTAG
**
31426413 CCTCAGATTGCAG
65 -GGCAGATTGCAG
* * * * * *
31426426 CCATCCAATCTTTTACCTCGAGCCTGAGGCAGATCACCATCAACCAATCTCTTTCCCCTTGCTTG
1 CCATCCGATCTTTTACCCCGAGCCTGAGGCAGATCACCATCAGCCAATCTCTTACCTC-TGC-TA
*
31426491 GGGCAGATTACAG
64 GGGCAGATTGCAG
* * *
31426504 CCATCCGATCTTTTACCCCGAGCCTGAGGCAGATTACCGTCAGCCAATCTCTTACCTCATGACAA
1 CCATCCGATCTTTTACCCCGAGCCTGAGGCAGATCACCATCAGCCAATCTCTTACCTC-TG-CTA
* *
31426569 GGGTAGATTGCAA
64 GGGCAGATTGCAG
31426582 CCATCCGATCTTTTACCCCGAGC
1 CCATCCGATCTTTTACCCCGAGC
31426605 TTGGGATAGA
Statistics
Matches: 215, Mismatches: 28, Indels: 20
0.82 0.11 0.08
Matches are distributed among these distances:
73 3 0.01
74 58 0.27
75 4 0.02
77 3 0.01
78 145 0.67
79 2 0.01
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.25
Consensus pattern (76 bp):
CCATCCGATCTTTTACCCCGAGCCTGAGGCAGATCACCATCAGCCAATCTCTTACCTCTGCTAGG
GCAGATTGCAG
Found at i:31426676 original size:78 final size:78
Alignment explanation
Indices: 31426589--31426754 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 78
31426579 CAACCATCCG
* * * * *
31426589 ATCTTTTACCCC-GAGCTTGGGATAGATTGCAGCCATTCGATCTTTTA-CCTCGAGCCTGAGGCA
1 ATCTCTTACCCCTGA-CTTGGGATAAATTGCAGCCATCCGATCTTTTACCCT-AAACCTGAGGCA
31426652 GATCACTATCAGCCA
64 GATCACTATCAGCCA
* * * *
31426667 ATCTCTTACCCCTTACTTGGGGTAAATTGCAGCCATCCGATCTTTTACCCTAAACTTGGGGCAGA
1 ATCTCTTACCCCTGACTTGGGATAAATTGCAGCCATCCGATCTTTTACCCTAAACCTGAGGCAGA
* *
31426732 TTACTGTCAGCCA
66 TCACTATCAGCCA
31426745 ATCTCTTACC
1 ATCTCTTACC
31426755 TTGCGATAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
78 71 0.95
79 4 0.05
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (78 bp):
ATCTCTTACCCCTGACTTGGGATAAATTGCAGCCATCCGATCTTTTACCCTAAACCTGAGGCAGA
TCACTATCAGCCA
Found at i:31426754 original size:39 final size:38
Alignment explanation
Indices: 31426648--31426754 Score: 97
Period size: 39 Copynumber: 2.8 Consensus size: 38
31426638 TCGAGCCTGA
* * *
31426648 GGCAGATCACTATCAGCCAATCTCTTACCCCTTACTTGG
1 GGCAGATTACTGTCAGCCAATCTCTTA-CCCTAACTTGG
* * * * * * * *
31426687 GGTAAATTGCAGCCATCCGATCTTTTACCCTAAACTTGG
1 GGCAGATTACTGTCAGCCAATCTCTTACCCT-AACTTGG
31426726 GGCAGATTACTGTCAGCCAATCTCTTACC
1 GGCAGATTACTGTCAGCCAATCTCTTACC
31426755 TTGCGATAGA
Statistics
Matches: 48, Mismatches: 19, Indels: 2
0.70 0.28 0.03
Matches are distributed among these distances:
38 4 0.08
39 44 0.92
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (38 bp):
GGCAGATTACTGTCAGCCAATCTCTTACCCTAACTTGG
Found at i:31426774 original size:78 final size:77
Alignment explanation
Indices: 31426612--31426775 Score: 170
Period size: 78 Copynumber: 2.1 Consensus size: 77
31426602 AGCTTGGGAT
* * *
31426612 AGATTGCAGCCATTCGATCTTTTACCTCGAGCCTGAGGCAGATCACTATCAGCCAATCTCTTACC
1 AGATTGCAGCCATCCGATCTTTTACCTCAAACCTGAGGCAGATCACTATCAGCCAATCTCTTA-C
* * *
31426677 CCTTACTTGGGGT
65 CCTTACTAGAGGC
* * * * *
31426690 AAATTGCAGCCATCCGATCTTTTACC-CTAAACTTGGGGCAGATTACTGTCAGCCAATCTCTTA-
1 AGATTGCAGCCATCCGATCTTTTACCTC-AAACCTGAGGCAGATCACTATCAGCCAATCTCTTAC
*
31426753 CCTTGCGATAGAGGC
65 CCTTAC--TAGAGGC
31426768 AGATTGCA
1 AGATTGCA
31426776 ACTATCCAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
76 5 0.07
77 1 0.01
78 64 0.91
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (77 bp):
AGATTGCAGCCATCCGATCTTTTACCTCAAACCTGAGGCAGATCACTATCAGCCAATCTCTTACC
CTTACTAGAGGC
Found at i:31427454 original size:17 final size:16
Alignment explanation
Indices: 31427432--31427495 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 16
31427422 ATTGAATCCA
31427432 ATTTTAAGTTTAAATTT
1 ATTTTAA-TTTAAATTT
31427449 ATTTTAAATTTAAATTT
1 ATTTT-AATTTAAATTT
* *
31427466 ATTATATACTTAAATTT
1 ATTTTA-ATTTAAATTT
*
31427483 ATTTGAATTTAAA
1 ATTTTAATTTAAA
31427496 AAGAATGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.17
17 31 0.77
18 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTTTAATTTAAATTT
Found at i:31427549 original size:26 final size:26
Alignment explanation
Indices: 31427520--31427573 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
31427510 ACAAATTGTA
*
31427520 AAGCCCAATT-ACAAACCTAATGACCC
1 AAGCCCAATTAAAAAACC-AATGACCC
*
31427546 AAGCCCAATTAAAAAACCCATGACCC
1 AAGCCCAATTAAAAAACCAATGACCC
31427572 AA
1 AA
31427574 TTGCCTACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.46, C:0.33, G:0.07, T:0.13
Consensus pattern (26 bp):
AAGCCCAATTAAAAAACCAATGACCC
Found at i:31429119 original size:30 final size:30
Alignment explanation
Indices: 31429064--31429246 Score: 181
Period size: 30 Copynumber: 6.1 Consensus size: 30
31429054 GTTCAAGAGG
* *
31429064 CCCTCAAACTT-TCTAAAAATCACATTTTAA
1 CCCTTAAACTTCTC-AAAAATTACATTTTAA
* *
31429094 CTCTTAAACTTCTCAAAATTTACATTTTAA
1 CCCTTAAACTTCTCAAAAATTACATTTTAA
**
31429124 CCCTTAAACTAGAT-AAAAATTACATTTTAA
1 CCCTTAAACT-TCTCAAAAATTACATTTTAA
** * *
31429154 CCCTCGAACTTCTCAAAAATCACATTTTGA
1 CCCTTAAACTTCTCAAAAATTACATTTTAA
* *
31429184 CCCTCAAACTTCTTAAAAATTACATTTTAA
1 CCCTTAAACTTCTCAAAAATTACATTTTAA
* * * * *
31429214 CCCCTAAACTTCCCTAAAATCACATTTTGA
1 CCCTTAAACTTCTCAAAAATTACATTTTAA
31429244 CCC
1 CCC
31429247 CAAACTCTCT
Statistics
Matches: 125, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
29 1 0.01
30 121 0.97
31 3 0.02
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (30 bp):
CCCTTAAACTTCTCAAAAATTACATTTTAA
Found at i:31429276 original size:90 final size:90
Alignment explanation
Indices: 31429064--31429252 Score: 231
Period size: 90 Copynumber: 2.1 Consensus size: 90
31429054 GTTCAAGAGG
* * * * *
31429064 CCCTCAAACTT-TCTAAAAATCACATTTTAACTCTTAAACTTCTCAAAATTTACATTTTAACCCT
1 CCCTCAAACTTCTC-AAAAATCACATTTTGACCCTCAAACTTCTCAAAAATTACATTTTAACCCC
* *
31429128 TAAACTAGATAAAAATTACATTTTAA
65 TAAACTACATAAAAATCACATTTTAA
* *
31429154 CCCTCGAACTTCTCAAAAATCACATTTTGACCCTCAAACTTCTTAAAAATTACATTTTAACCCCT
1 CCCTCAAACTTCTCAAAAATCACATTTTGACCCTCAAACTTCTCAAAAATTACATTTTAACCCCT
* * *
31429219 AAACTTCCCT-AAAATCACATTTTGA
66 AAAC-TACATAAAAATCACATTTTAA
31429244 CCC-CAAACT
1 CCCTCAAACT
31429253 CTCTGAAACT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
89 5 0.06
90 75 0.89
91 4 0.05
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.33
Consensus pattern (90 bp):
CCCTCAAACTTCTCAAAAATCACATTTTGACCCTCAAACTTCTCAAAAATTACATTTTAACCCCT
AAACTACATAAAAATCACATTTTAA
Found at i:31429278 original size:60 final size:60
Alignment explanation
Indices: 31429064--31429252 Score: 213
Period size: 60 Copynumber: 3.2 Consensus size: 60
31429054 GTTCAAGAGG
* * * * * * *
31429064 CCCTCAAACTT-TCTAAAAATCACATTTTAACTCTTAAACTTCTCAAAATTTACATTTTAA
1 CCCTCAAACTTCT-TAAAAATTACATTTTAACCCCTAAACTTCCCAAAAATCACATTTTGA
* *** * *
31429124 CCCTTAAACTAGATAAAAATTACATTTTAA-CCCTCGAACTTCTCAAAAATCACATTTTGA
1 CCCTCAAACTTCTTAAAAATTACATTTTAACCCCT-AAACTTCCCAAAAATCACATTTTGA
*
31429184 CCCTCAAACTTCTTAAAAATTACATTTTAACCCCTAAACTTCCCTAAAATCACATTTTGA
1 CCCTCAAACTTCTTAAAAATTACATTTTAACCCCTAAACTTCCCAAAAATCACATTTTGA
31429244 CCC-CAAACT
1 CCCTCAAACT
31429253 CTCTGAAACT
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
59 8 0.07
60 97 0.89
61 4 0.04
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.33
Consensus pattern (60 bp):
CCCTCAAACTTCTTAAAAATTACATTTTAACCCCTAAACTTCCCAAAAATCACATTTTGA
Found at i:31437200 original size:30 final size:29
Alignment explanation
Indices: 31437164--31437323 Score: 89
Period size: 30 Copynumber: 5.3 Consensus size: 29
31437154 TTAATATAAC
31437164 ATTTGGTACTTGAACTTGACATTTTTCCTA
1 ATTTGGTACTTGAACTT-ACATTTTTCCTA
* * ** *
31437194 ATTTGGTACCTAAACTT-TTTTTTTGACTCA
1 ATTTGGTACTTGAACTTACATTTTT-CCT-A
31437224 ATTTGGTA-TCTGAACTTAACACTTTTTCCTA
1 ATTTGGTACT-TGAACTT-ACA-TTTTTCCTA
* * *
31437255 ATTTGGTACCTAAACTT---TTTTTGGACCCA
1 ATTTGGTACTTGAACTTACATTTTT---CCTA
*
31437284 ATTTGGTA-TCTGAACTTGACATTTTTTCTTA
1 ATTTGGTACT-TGAACTT-ACA-TTTTTCCTA
31437315 ATTTGGTAC
1 ATTTGGTAC
31437324 CTAAGCTTTT
Statistics
Matches: 96, Mismatches: 17, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
26 5 0.05
28 5 0.05
29 19 0.20
30 30 0.31
31 25 0.26
32 2 0.02
33 5 0.05
34 5 0.05
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (29 bp):
ATTTGGTACTTGAACTTACATTTTTCCTA
Found at i:31437260 original size:61 final size:60
Alignment explanation
Indices: 31437164--31437348 Score: 266
Period size: 60 Copynumber: 3.1 Consensus size: 60
31437154 TTAATATAAC
*
31437164 ATTTGGTA-CTTGAACTTGACATTTTTCCTAATTTGGTACCTAAACTTTTTTTTTGACTCA
1 ATTTGGTATC-TGAACTTGACATTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACTCA
* * *
31437224 ATTTGGTATCTGAACTTAACACTTTTTCCTAATTTGGTACCTAAAC-TTTTTTTGGACCCA
1 ATTTGGTATCTGAACTTGACA-TTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACTCA
* * *
31437284 ATTTGGTATCTGAACTTGACATTTTTTCTTAATTTGGTACCTAAGCTTTTTTTTAGATTCA
1 ATTTGGTATCTGAACTTGACA-TTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACTCA
31437345 ATTT
1 ATTT
31437349 AGTACCTAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
60 72 0.64
61 40 0.36
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (60 bp):
ATTTGGTATCTGAACTTGACATTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACTCA
Found at i:31439891 original size:107 final size:107
Alignment explanation
Indices: 31439700--31439916 Score: 317
Period size: 107 Copynumber: 2.0 Consensus size: 107
31439690 AGTAAATCTC
* * * * * **
31439700 TTTCTATAGAAACCAATAGCATCGTTATTCCCAGAAAATTGAGTTTATACTTAGAAAATAAATTT
1 TTTCAATAGAAACCAATAGAATAGTTATTCCAAGAAAATTGAATTTATACTTAGAAAATAAATAC
**
31439765 TGAATATTTCCGAGTAGAATAACAATATCTCAAAGTTGTGCG
66 TGAATATTTCCGAACAGAATAACAATATCTCAAAGTTGTGCG
*
31439807 TTTCAATAGAAACCAATAGAATAGTTATTCCAAGAAAATTGAATTTATACTTAGAAAATCAATAC
1 TTTCAATAGAAACCAATAGAATAGTTATTCCAAGAAAATTGAATTTATACTTAGAAAATAAATAC
* * *
31439872 TGCATATTTTCTAACAGAATAACAATATCTCAAAGTTGTGCG
66 TGAATATTTCCGAACAGAATAACAATATCTCAAAGTTGTGCG
31439914 TTT
1 TTT
31439917 TTAGTCCAAC
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
107 97 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (107 bp):
TTTCAATAGAAACCAATAGAATAGTTATTCCAAGAAAATTGAATTTATACTTAGAAAATAAATAC
TGAATATTTCCGAACAGAATAACAATATCTCAAAGTTGTGCG
Found at i:31440226 original size:24 final size:24
Alignment explanation
Indices: 31440197--31440244 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31440187 TTTTATTTCC
31440197 TAAAATAAATATTATTT-ATTAAAT
1 TAAAATAAATATT-TTTAATTAAAT
* *
31440221 TAAAATTATTATTTTTAATTAAAT
1 TAAAATAAATATTTTTAATTAAAT
31440245 AATTTTCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAAATAAATATTTTTAATTAAAT
Found at i:31448300 original size:17 final size:17
Alignment explanation
Indices: 31448280--31448313 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31448270 ATCACTCGTT
*
31448280 ATTTTAATAGCATTTTC
1 ATTTTAATAACATTTTC
31448297 ATTTTAATAACATTTTC
1 ATTTTAATAACATTTTC
31448314 CATATTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTTAATAACATTTTC
Found at i:31449434 original size:13 final size:14
Alignment explanation
Indices: 31449416--31449444 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31449406 TTATTTTTTT
31449416 TTATAATA-TATTA
1 TTATAATACTATTA
31449429 TTATAATACTATTA
1 TTATAATACTATTA
31449443 TT
1 TT
31449445 TACCATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATAATACTATTA
Found at i:31450934 original size:9 final size:9
Alignment explanation
Indices: 31450923--31450981 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
31450913 AATTTTAATT
*
31450923 AAAATCATT
1 AAAATCATA
31450932 AAAAT-ATA
1 AAAATCATA
31450940 AAAATCATA
1 AAAATCATA
**
31450949 AAAATTTTA
1 AAAATCATA
*
31450958 GAATATCATA
1 -AAAATCATA
*
31450968 AAAATTATA
1 AAAATCATA
31450977 AAAAT
1 AAAAT
31450982 ATTATAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 7 0.17
9 27 0.68
10 6 0.15
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATCATA
Found at i:31450945 original size:17 final size:17
Alignment explanation
Indices: 31450923--31451015 Score: 57
Period size: 19 Copynumber: 5.2 Consensus size: 17
31450913 AATTTTAATT
31450923 AAAATCATTAAAATATA
1 AAAATCATTAAAATATA
* *
31450940 AAAATCATAAAAATTTTA
1 AAAATCATTAAAA-TATA
* *
31450958 GAATATCATAAAAATTATA
1 -AAAATCATTAAAA-TATA
*
31450977 AAAAT-ATTATAAAAAATA
1 AAAATCA-T-TAAAATATA
31450995 ACAAAT-ATATAAAA-ATA
1 A-AAATCAT-TAAAATATA
31451012 AAAA
1 AAAA
31451016 AATATAAGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
16 3 0.05
17 17 0.27
18 19 0.30
19 25 0.39
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (17 bp):
AAAATCATTAAAATATA
Found at i:31450987 original size:11 final size:10
Alignment explanation
Indices: 31450959--31451062 Score: 73
Period size: 9 Copynumber: 11.0 Consensus size: 10
31450949 AAAATTTTAG
31450959 AATATCATAAA
1 AATAT-ATAAA
31450970 AAT-TATAAA
1 AATATATAAA
31450979 AATATTATAAA
1 AATA-TATAAA
*
31450990 AA-ATA-ACA
1 AATATATAAA
31450998 AATATATAAA
1 AATATATAAA
31451008 AATA-A-AAA
1 AATATATAAA
*
31451016 AATATA-AGA
1 AATATATAAA
31451025 AAT-TATAAA
1 AATATATAAA
* *
31451034 ATTAT-TATA
1 AATATATAAA
*
31451043 AATGACA-AAA
1 AAT-ATATAAA
31451053 AATATATAAA
1 AATATATAAA
31451063 TTATAAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
8 13 0.18
9 31 0.42
10 18 0.25
11 11 0.15
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (10 bp):
AATATATAAA
Found at i:31451005 original size:18 final size:17
Alignment explanation
Indices: 31450959--31451027 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 17
31450949 AAAATTTTAG
31450959 AATATCATAAAAATTATAAA
1 AATAT-ATAAAAA--ATAAA
31450979 AATATTATAAAAAATAACA
1 AATA-TATAAAAAATAA-A
31450998 AATATAT-AAAAATAAA
1 AATATATAAAAAATAAA
* *
31451014 AAAATATAAGAAAT
1 AATATATAAAAAAT
31451028 TATAAAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 7 0.16
17 13 0.30
18 7 0.16
19 5 0.11
20 11 0.25
21 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (17 bp):
AATATATAAAAAATAAA
Found at i:31451027 original size:9 final size:8
Alignment explanation
Indices: 31450932--31451071 Score: 64
Period size: 9 Copynumber: 15.5 Consensus size: 8
31450922 TAAAATCATT
31450932 AAAATATA
1 AAAATATA
31450940 AAAATCATA
1 AAAAT-ATA
*
31450949 AAAATTTTA
1 AAAA-TATA
*
31450958 GAATATCATA
1 -AAAAT-ATA
31450968 AAAATTATA
1 AAAA-TATA
31450977 AAAATATTA
1 AAAATA-TA
*
31450986 TAAAAAATAA
1 -AAAATAT-A
31450996 CAAATATATA
1 -AAA-ATATA
*
31451006 AAAATAAA
1 AAAATATA
31451014 AAAATATA
1 AAAATATA
31451022 AGAAATTATA
1 A-AAA-TATA
*
31451032 AAATTATTA
1 AAAATA-TA
* *
31451041 TAAATGACAA
1 AAAAT-A-TA
31451051 AAAATATA
1 AAAATATA
*
31451059 TAAATTATA
1 -AAAATATA
31451068 AAAA
1 AAAA
31451072 ATGAAAAAAT
Statistics
Matches: 100, Mismatches: 18, Indels: 28
0.68 0.12 0.19
Matches are distributed among these distances:
8 25 0.25
9 44 0.44
10 28 0.28
11 3 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (8 bp):
AAAATATA
Found at i:31451034 original size:18 final size:17
Alignment explanation
Indices: 31450932--31451071 Score: 86
Period size: 18 Copynumber: 7.8 Consensus size: 17
31450922 TAAAATCATT
31450932 AAAA-TATAAAAATCATA
1 AAAATTATAAAAAT-ATA
* *
31450949 AAAATTTTAGAATATCATA
1 AAAATTATA-AAAAT-ATA
31450968 AAAATTATAAAAATATTA
1 AAAATTATAAAAATA-TA
*
31450986 TAAAA-AATAACAAATATA
1 -AAAATTATAA-AAATATA
* *
31451004 TAAAAATAAAAAAATATA
1 -AAAATTATAAAAATATA
*
31451022 AGAAATTATAAAATTATTA
1 A-AAATTATAAAAATA-TA
* * *
31451041 TAAATGACAAAAAATATA
1 AAAATTA-TAAAAATATA
*
31451059 TAAATTATAAAAA
1 AAAATTATAAAAA
31451072 ATGAAAAAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
17 11 0.11
18 51 0.52
19 36 0.37
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATTATAAAAATATA
Found at i:31451040 original size:55 final size:55
Alignment explanation
Indices: 31450965--31451072 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
31450955 TTAGAATATC
* *
31450965 ATAAAAATTATAAAAATATTATAAAAAATAACAAATATATAAA-AATAAAAAAAT
1 ATAAAAATTATAAAAATATTATAAAAAACAAAAAATATATAAATAATAAAAAAAT
* ** *
31451019 ATAAGAAATTATAAAATTATTATAAATGACAAAAAATATATAAATTATAAAAAA
1 ATAA-AAATTATAAAAATATTATAAAAAACAAAAAATATATAAATAATAAAAAA
31451073 TGAAAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 4 0.09
55 34 0.74
56 8 0.17
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (55 bp):
ATAAAAATTATAAAAATATTATAAAAAACAAAAAATATATAAATAATAAAAAAAT
Found at i:31451043 original size:37 final size:36
Alignment explanation
Indices: 31450932--31451070 Score: 99
Period size: 37 Copynumber: 3.8 Consensus size: 36
31450922 TAAAATCATT
* * * *
31450932 AAAATATAAAAATCATAA-AAATTTTAGAATATCATA
1 AAAATAAAAAAAT-ATAATAAATTATAAAATATTATA
* * **
31450968 AAAATTATAAAAATATTATAAAAAATAACAA-ATATATA
1 AAAA-TAAAAAAATATAATAAATTATAA-AATAT-TATA
*
31451006 AAAATAAAAAAATATAAGAAATTATAAAATTATTAT-
1 AAAATAAAAAAATATAATAAATTATAAAA-TATTATA
31451042 -AAATGACAAAAAATAT-ATAAATTATAAAA
1 AAAAT-A-AAAAAATATAATAAATTATAAAA
31451071 AATGAAAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
35 4 0.05
36 22 0.27
37 46 0.55
38 11 0.13
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (36 bp):
AAAATAAAAAAATATAATAAATTATAAAATATTATA
Found at i:31451228 original size:12 final size:12
Alignment explanation
Indices: 31451211--31451235 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31451201 AATATAGACC
31451211 TTTGAGAAGTAT
1 TTTGAGAAGTAT
31451223 TTTGAGAAGTAT
1 TTTGAGAAGTAT
31451235 T
1 T
31451236 GTAATACACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TTTGAGAAGTAT
Found at i:31453176 original size:7 final size:7
Alignment explanation
Indices: 31453164--31453204 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
31453154 AATGGAACCC
31453164 AATTTTA
1 AATTTTA
31453171 AATTTTA
1 AATTTTA
31453178 AATTTTA
1 AATTTTA
*
31453185 AATTATTT
1 AATT-TTA
*
31453193 AAGTTTA
1 AATTTTA
31453200 AATTT
1 AATTT
31453205 ATTTTAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 24 0.83
8 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:31453192 original size:17 final size:17
Alignment explanation
Indices: 31453181--31453228 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
31453171 AATTTTAAAT
31453181 TTTAAA-TTA-TTTAAG
1 TTTAAATTTATTTTAAG
31453196 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAG
31453213 TTTAAATTTATTTTAA
1 TTTAAATTTATTTTAA
31453229 ACTAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.19
16 3 0.10
17 22 0.71
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:31453205 original size:6 final size:6
Alignment explanation
Indices: 31453167--31453246 Score: 53
Period size: 6 Copynumber: 13.8 Consensus size: 6
31453157 GGAACCCAAT
* * *
31453167 TTTAAA TTTTAAA TTTTAAA -TT--A TTTAAG TTTAAA TTT-AT TTTAAG
1 TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
31453213 TTTAAA TTT-AT TTTAAA CTAAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
31453247 TTAAAAATGT
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 10 0.18
6 31 0.54
7 13 0.23
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:31453236 original size:17 final size:17
Alignment explanation
Indices: 31453199--31453239 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
31453189 ATTTAAGTTT
** *
31453199 AAATTTATTTTAAGTTT
1 AAATTTATTTTAAACTA
31453216 AAATTTATTTTAAACTA
1 AAATTTATTTTAAACTA
31453233 AAATTTA
1 AAATTTA
31453240 AATTTAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAACTA
Found at i:31453347 original size:19 final size:20
Alignment explanation
Indices: 31453319--31453359 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31453309 AGTAGCCTGG
*
31453319 ACCAAGCCC-AATCACCCAA
1 ACCAAACCCAAATCACCCAA
*
31453338 ACCAAACCCAAATGACCCAA
1 ACCAAACCCAAATCACCCAA
31453358 AC
1 AC
31453360 ACTTAAAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.46, C:0.44, G:0.05, T:0.05
Consensus pattern (20 bp):
ACCAAACCCAAATCACCCAA
Found at i:31453972 original size:13 final size:12
Alignment explanation
Indices: 31453950--31453979 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
31453940 AAACACATTA
31453950 AATAATATTAAT
1 AATAATATTAAT
31453962 AATAATAATTAAT
1 AATAAT-ATTAAT
31453975 AATAA
1 AATAA
31453980 AAAAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:31455155 original size:30 final size:30
Alignment explanation
Indices: 31455077--31455361 Score: 96
Period size: 28 Copynumber: 9.9 Consensus size: 30
31455067 CCCAGAAGGT
*
31455077 CCCT-GAACTATC-CAAAAATCATATTTTGA
1 CCCTCGAACT-TCTCAAAAATCACATTTTGA
* * * *
31455106 CCC-CTACACTTTTCCAAAATCGCATTTTGA
1 CCCTCGA-ACTTCTCAAAAATCACATTTTGA
*
31455136 CCCTCGAACTTCTCAAAAATTACATTTTTG-
1 CCCTCGAACTTCTCAAAAATCACA-TTTTGA
* * * *
31455166 CTCTTGAACTTCT-AAAAATTACATTTT-T
1 CCCTCGAACTTCTCAAAAATCACATTTTGA
*
31455194 CCC-C-AGACTTC-CAAAAATTACATTTTG-
1 CCCTCGA-ACTTCTCAAAAATCACATTTTGA
* *
31455221 CCAC-C-AAGCTTC-CAAAAATTATATTTTTG-
1 CC-CTCGAA-CTTCTCAAAAATCACA-TTTTGA
*
31455250 CCCTC-AGACTTC-CAAAAATTACATTTT-A
1 CCCTCGA-ACTTCTCAAAAATCACATTTTGA
* * *
31455278 CCC-CTAAACTTTTCAAAAATTACCATTTT-A
1 CCCTC-GAACTTCTCAAAAATCA-CATTTTGA
* * *
31455308 -CCTCCAAACATC-C-AAAATTACCATTTT-A
1 CCCT-CGAACTTCTCAAAAATCA-CATTTTGA
* *
31455336 CCCTCAAATTTC-CAAAAATCACATTT
1 CCCTCGAACTTCTCAAAAATCACATTT
31455362 CTAACTTTAA
Statistics
Matches: 211, Mismatches: 22, Indels: 47
0.75 0.08 0.17
Matches are distributed among these distances:
26 1 0.00
27 23 0.11
28 62 0.29
29 60 0.28
30 57 0.27
31 8 0.04
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (30 bp):
CCCTCGAACTTCTCAAAAATCACATTTTGA
Found at i:31455192 original size:29 final size:28
Alignment explanation
Indices: 31455130--31455306 Score: 153
Period size: 29 Copynumber: 6.1 Consensus size: 28
31455120 CAAAATCGCA
31455130 TTTTGACCCTCGAACTTCTCAAAAATTACAT
1 TTTTG-CCCT-GAACTTC-CAAAAATTACAT
* *
31455161 TTTTGCTCTTGAACTTCTAAAAATTACAT
1 TTTTGC-CCTGAACTTCCAAAAATTACAT
* *
31455190 TTTTCCCCAG-ACTTCCAAAAATTACA-
1 TTTTGCCCTGAACTTCCAAAAATTACAT
* *
31455216 TTTTGCCAC-CAAGCTTCCAAAAATTATAT
1 TTTTGCC-CTGAA-CTTCCAAAAATTACAT
*
31455245 TTTTGCCCTCAGACTTCCAAAAATTACAT
1 TTTTGCCCTGA-ACTTCCAAAAATTACAT
** * *
31455274 TTTACCCCTAAACTTTTCAAAAATTACCAT
1 TTTTGCCCTGAAC-TTCCAAAAATTA-CAT
31455304 TTT
1 TTT
31455307 ACCTCCAAAC
Statistics
Matches: 123, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
26 6 0.05
27 17 0.14
28 19 0.15
29 59 0.48
30 15 0.12
31 7 0.06
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (28 bp):
TTTTGCCCTGAACTTCCAAAAATTACAT
Found at i:31455273 original size:57 final size:57
Alignment explanation
Indices: 31455130--31455276 Score: 176
Period size: 57 Copynumber: 2.6 Consensus size: 57
31455120 CAAAATCGCA
*** *
31455130 TTTTGACCCTC-GAACTTCTCAAAAATTACATTTTTGCTCTTGAACTTCTAAAAATTACAT
1 TTTTG-CCCTCAG-ACTTC-CAAAAATTACA-TTTTGCTCACCAACTTCCAAAAATTACAT
*
31455190 TTTT-CCC-CAGACTTCCAAAAATTACATTTTGC-CACCAAGCTTCCAAAAATTATAT
1 TTTTGCCCTCAGACTTCCAAAAATTACATTTTGCTCACCAA-CTTCCAAAAATTACAT
31455245 TTTTGCCCTCAGACTTCCAAAAATTACATTTT
1 TTTTGCCCTCAGACTTCCAAAAATTACATTTT
31455277 ACCCCTAAAC
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
54 3 0.04
55 24 0.31
56 14 0.18
57 29 0.37
58 4 0.05
60 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.37
Consensus pattern (57 bp):
TTTTGCCCTCAGACTTCCAAAAATTACATTTTGCTCACCAACTTCCAAAAATTACAT
Found at i:31455323 original size:29 final size:27
Alignment explanation
Indices: 31455172--31455361 Score: 184
Period size: 28 Copynumber: 6.7 Consensus size: 27
31455162 TTTGCTCTTG
* *
31455172 AACTTCTAAAAATTACATTTTTCCCCA
1 AACTTCCAAAAATTACATTTTACCCCA
* *
31455199 GACTTCCAAAAATTACATTTTGCCACCA
1 AACTTCCAAAAATTACATTTTACC-CCA
* * *
31455227 AGCTTCCAAAAATTATATTTTTGCCCTCA
1 AACTTCCAAAAATTACA-TTTTACCC-CA
*
31455256 GACTTCCAAAAATTACATTTTACCCCTA
1 AACTTCCAAAAATTACATTTTACCCC-A
*
31455284 AACTTTTCAAAAATTACCATTTTACCTCCA
1 AAC-TTCCAAAAATTA-CATTTTACC-CCA
*
31455314 AACATCC-AAAATTACCATTTTACCCTCA
1 AACTTCCAAAAATTA-CATTTTACCC-CA
* *
31455342 AATTTCCAAAAATCACATTT
1 AACTTCCAAAAATTACATTT
31455362 CTAACTTTAA
Statistics
Matches: 137, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
27 23 0.17
28 57 0.42
29 42 0.31
30 13 0.09
31 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34
Consensus pattern (27 bp):
AACTTCCAAAAATTACATTTTACCCCA
Found at i:31457623 original size:20 final size:19
Alignment explanation
Indices: 31457585--31457637 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
31457575 AAAAAATAAC
* *
31457585 AAAAT-TATGAAAGTATTT
1 AAAATATATAAAATTATTT
31457603 AAAAATATATAAAATTATTT
1 -AAAATATATAAAATTATTT
31457623 AAAATATTATAAAAT
1 AAAATA-TATAAAAT
31457638 ATATAAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAATATATAAAATTATTT
Found at i:31457638 original size:10 final size:9
Alignment explanation
Indices: 31457604--31457645 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
31457594 AAAGTATTTA
31457604 AAAATATAT
1 AAAATATAT
*
31457613 AAAATTATTT
1 AAAA-TATAT
31457623 AAAATATTAT
1 AAAATA-TAT
31457633 AAAATATAT
1 AAAATATAT
31457642 AAAA
1 AAAA
31457646 GTGCAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATATAT
Found at i:31458020 original size:9 final size:9
Alignment explanation
Indices: 31458006--31458259 Score: 72
Period size: 9 Copynumber: 26.3 Consensus size: 9
31457996 TTTTAATTTG
31458006 TTTTATAAT
1 TTTTATAAT
**
31458015 TTTTATGCT
1 TTTTATAAT
**
31458024 TTTTATGTT
1 TTTTATAAT
31458033 TTTCTATAAT
1 TTT-TATAAT
*
31458043 ATTTTGTTAA-
1 -TTTT-ATAAT
31458053 TTTTATTAAATT
1 TTTTA-T-AA-T
31458065 TTTTAATAAT
1 TTTT-ATAAT
31458075 TTTCTAT-AT
1 TTT-TATAAT
31458084 TTTTATATACT
1 TTTTATA-A-T
*
31458095 TTTTCT-AT
1 TTTTATAAT
31458103 TTTTCATAAT
1 TTTT-ATAAT
* *
31458113 ATATATATAT
1 TTTTATA-AT
* *
31458123 ATATCATAATAT
1 -TTTTAT-A-AT
*
31458135 TTTTTTAAT
1 TTTTATAAT
31458144 TTTTA-AAT
1 TTTTATAAT
*
31458152 ACATTTATAAT
1 --TTTTATAAT
*
31458163 TTATAT-AT
1 TTTTATAAT
*
31458171 TTTT-TCAT
1 TTTTATAAT
* *
31458179 TTATAATAAA
1 TT-TTATAAT
31458189 TTTTATAAT
1 TTTTATAAT
31458198 TTTCTAT-AT
1 TTT-TATAAT
31458207 TTTTATAAT
1 TTTTATAAT
31458216 TTCTATATATAT
1 TT-T-TATA-AT
*
31458228 TGTTTATGAT
1 T-TTTATAAT
*
31458238 TTTCTATATT
1 TTT-TATAAT
*
31458248 TTTTATGAT
1 TTTTATAAT
31458257 TTT
1 TTT
31458260 AATTTTAAAA
Statistics
Matches: 182, Mismatches: 33, Indels: 60
0.66 0.12 0.22
Matches are distributed among these distances:
7 1 0.01
8 23 0.13
9 70 0.38
10 43 0.24
11 30 0.16
12 13 0.07
13 2 0.01
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:31458056 original size:21 final size:21
Alignment explanation
Indices: 31458032--31458082 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
31458022 CTTTTTATGT
31458032 TTTTCTATAATATTTTGT-TAA
1 TTTTCTATAA-ATTTTGTATAA
* *
31458053 TTTTAT-TAAATTTTTTAATAA
1 TTTTCTATAAATTTTGT-ATAA
31458074 TTTTCTATA
1 TTTTCTATA
31458083 TTTTTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 6 0.25
20 3 0.12
21 13 0.54
22 2 0.08
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTCTATAAATTTTGTATAA
Found at i:31458208 original size:17 final size:16
Alignment explanation
Indices: 31458155--31458223 Score: 57
Period size: 16 Copynumber: 4.0 Consensus size: 16
31458145 TTTAAATACA
*
31458155 TTTATAATTTATATAT
1 TTTATAATTTCTATAT
* * *
31458171 TTTTTCATTTATAATAAAT
1 TTTATAATTTCT-AT--AT
31458190 TTTATAATTTTCTATATT
1 TTTATAA-TTTCTATA-T
31458208 TTTATAATTTCTATAT
1 TTTATAATTTCTATAT
31458224 ATATTGTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
16 11 0.26
17 11 0.26
18 8 0.19
19 9 0.21
20 4 0.09
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATAATTTCTATAT
Found at i:31458245 original size:23 final size:21
Alignment explanation
Indices: 31458202--31458258 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
31458192 TATAATTTTC
31458202 TATATTTTTATAATTTCTATA
1 TATATTTTTATAATTTCTATA
* *
31458223 TATATTGTTTATGATTT-TCTA
1 TATATT-TTTATAATTTCTATA
*
31458244 TAT-TTTTTATGATTT
1 TATATTTTTATAATTT
31458259 TAATTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.30
20 2 0.06
21 12 0.36
22 9 0.27
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.65
Consensus pattern (21 bp):
TATATTTTTATAATTTCTATA
Found at i:31458252 original size:19 final size:19
Alignment explanation
Indices: 31458189--31458259 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
31458179 TTATAATAAA
31458189 TTTTATAATTTTCTATA-T
1 TTTTATAATTTTCTATATT
*
31458207 TTTTATAATTTCTATATATAT
1 TTTTATAATTT-TCTATAT-T
*
31458228 TGTTTATGATTTTCTATATT
1 T-TTTATAATTTTCTATATT
*
31458248 TTTTATGATTTT
1 TTTTATAATTTT
31458260 AATTTTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 11 0.24
19 16 0.35
20 2 0.04
21 8 0.17
22 9 0.20
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTCTATATT
Found at i:31461730 original size:2 final size:2
Alignment explanation
Indices: 31461723--31461749 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31461713 CTTCTAGGGA
31461723 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
31461750 CAACTGACTT
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:31464740 original size:28 final size:28
Alignment explanation
Indices: 31464703--31464759 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
31464693 AGTTTGTTAA
* * *
31464703 TTTAATAAATAATAGTTATTTATAATAT
1 TTTAAGAAATAATACTGATTTATAATAT
31464731 TTTAAGAAATAATACTGATTTATAATAT
1 TTTAAGAAATAATACTGATTTATAATAT
31464759 T
1 T
31464760 ATAATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (28 bp):
TTTAAGAAATAATACTGATTTATAATAT
Found at i:31465493 original size:19 final size:17
Alignment explanation
Indices: 31465469--31465529 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 17
31465459 TTTTAAAAAA
*
31465469 TAATTTCTATATATATTTT
1 TAATTT-TA-ATATTTTTT
31465488 TAATTTTAATATTTTTTT
1 TAATTTTAATA-TTTTTT
31465506 TAATTTTTAATAATTTTTT
1 TAA-TTTTAAT-ATTTTTT
31465525 TAATT
1 TAATT
31465530 ATTTTATCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 22 0.58
20 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTAATATTTTTT
Found at i:31465507 original size:18 final size:18
Alignment explanation
Indices: 31465484--31465529 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 18
31465474 TCTATATATA
*
31465484 TTTTTAATTTTAATATTT
1 TTTTTAATTTTAATAATT
31465502 TTTTTAATTTTTAATAATT
1 TTTTTAA-TTTTAATAATT
31465521 TTTTTAATT
1 TTTTTAATT
31465530 ATTTTATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTAATTTTAATAATT
Found at i:31465512 original size:9 final size:9
Alignment explanation
Indices: 31465484--31465535 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
31465474 TCTATATATA
31465484 TTTTTAATT
1 TTTTTAATT
** *
31465493 TTAATATTT
1 TTTTTAATT
31465502 TTTTTAATT
1 TTTTTAATT
*
31465511 TTTAATAATT
1 TTT-TTAATT
31465521 TTTTTAATT
1 TTTTTAATT
*
31465530 ATTTTA
1 TTTTTA
31465536 TCTAAAAACG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
9 25 0.76
10 8 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTAATT
Found at i:31483056 original size:56 final size:56
Alignment explanation
Indices: 31482996--31483112 Score: 180
Period size: 56 Copynumber: 2.1 Consensus size: 56
31482986 CTTATGACTT
** *
31482996 CTAGTCAAAATAATCTCGGGTGTCCATAGTGTTATCCCAAGCGCCACTCATGGTTG
1 CTAGTCAAAATAATCTCAAGTGTCCATAGTGTTATCCCAAGCGCCACTCATGGTCG
* * *
31483052 CTAGTCAAAATAATCTCAAGTGTCCGTAGTGTTATCCCGAGTGCCACTCATGGTCG
1 CTAGTCAAAATAATCTCAAGTGTCCATAGTGTTATCCCAAGCGCCACTCATGGTCG
31483108 CTAGT
1 CTAGT
31483113 TAAGTTAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (56 bp):
CTAGTCAAAATAATCTCAAGTGTCCATAGTGTTATCCCAAGCGCCACTCATGGTCG
Found at i:31486384 original size:21 final size:21
Alignment explanation
Indices: 31486320--31486387 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
31486310 GAAGTTTTTA
*
31486320 GTATCGGTAGAAGC-ATGACTT
1 GTATCGGTAGAA-CTATCACTT
* * * *
31486341 GTTTCGATAGAAGTGA-CATTT
1 GTATCGGTAGAACT-ATCACTT
31486362 GTATCGGTAGAACTATCACTT
1 GTATCGGTAGAACTATCACTT
31486383 GTATC
1 GTATC
31486388 TTTAGAAATT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.34
Consensus pattern (21 bp):
GTATCGGTAGAACTATCACTT
Found at i:31486524 original size:16 final size:18
Alignment explanation
Indices: 31486500--31486538 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
31486490 TTATTGCCCT
31486500 TATTGAATTGA-GA-TTA
1 TATTGAATTGATGATTTA
*
31486516 TATTTAATTGATGATTTA
1 TATTGAATTGATGATTTA
31486534 TATTG
1 TATTG
31486539 TGTTTAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.53
17 2 0.11
18 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (18 bp):
TATTGAATTGATGATTTA
Found at i:31488922 original size:29 final size:29
Alignment explanation
Indices: 31488881--31489131 Score: 104
Period size: 29 Copynumber: 8.7 Consensus size: 29
31488871 AAATTGAGTC
*
31488881 AAAAATGG-GATTTTAGAAAGTTCGAGGGT
1 AAAAATGGTAATTTTAGAAA-TTCGAGGGT
* *
31488910 -AAAATGGTAATTTTGGTAAAATCG-GGGT
1 AAAAATGGTAATTTTAG-AAATTCGAGGGT
* *
31488938 TAAAAT-GTAATTTTTAGAAAATT-TAGAGGT
1 AAAAATGGTAA-TTTTAG-AAATTCGAG-GGT
*
31488968 -AAAATGGTAATTTTGGTAAAATT--AGGGCT
1 AAAAATGGTAATTTTAG--AAATTCGAGGG-T
* *
31488997 AAAAATGG-AATTTTAAAAAGTTTTG-GGGT
1 AAAAATGGTAATTTTAGAAA--TTCGAGGGT
* * *
31489026 CAAAAT-GTAATTTTGGTAAAATCGAGGGT
1 AAAAATGGTAATTTTAG-AAATTCGAGGGT
*
31489055 AAAAATGG-AATTTT-GTAAAACTT-GGGGGT
1 AAAAATGGTAATTTTAG--AAA-TTCGAGGGT
* * *
31489084 CAAAAT-GTAATTTTGTTGAAA-TCGATGGT
1 AAAAATGGTAA-TTT-TAGAAATTCGAGGGT
31489113 AAAAATGG-AATTTTAGAAA
1 AAAAATGGTAATTTTAGAAA
31489132 GTTTTAGAGT
Statistics
Matches: 172, Mismatches: 24, Indels: 54
0.69 0.10 0.22
Matches are distributed among these distances:
27 8 0.05
28 26 0.15
29 98 0.57
30 38 0.22
31 1 0.01
32 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAAATGGTAATTTTAGAAATTCGAGGGT
Found at i:31488953 original size:58 final size:59
Alignment explanation
Indices: 31488881--31489260 Score: 275
Period size: 58 Copynumber: 6.5 Consensus size: 59
31488871 AAATTGAGTC
* * *
31488881 AAAAATGGGA-TTTTAGAAAGTTCGAGGGT-AAAATGGTAATTTTGGTAAAA-TCGGGGT
1 AAAAATGGAATTTTTAGAAAGTTTGAGGGTCAAAAT-GTAATTTTGGTAAAATTAGGGGT
* * * *
31488938 TAAAATGTAATTTTTAGAAAATTT-AGAGGT-AAAATGGTAATTTTGGTAAAATTAGGGCT
1 AAAAATGGAATTTTTAGAAAGTTTGAG-GGTCAAAAT-GTAATTTTGGTAAAATTAGGGGT
* *
31488997 AAAAATGGAA-TTTTAAAAAGTTTTG-GGGTCAAAATGTAATTTTGGTAAAA-TCGAGGGT
1 AAAAATGGAATTTTTAGAAAG-TTTGAGGGTCAAAATGTAATTTTGGTAAAATTAG-GGGT
* * * * * *
31489055 AAAAATGGAATTTTGTA-AAA-CTTGGGGGTCAAAATGTAATTTTGTTGAAA-TCGATGGT
1 AAAAATGGAATTTT-TAGAAAGTTTGAGGGTCAAAATGTAATTTTGGTAAAATTAG-GGGT
* * * * **
31489113 AAAAATGGAA-TTTTAGAAAGTTTTAGAGTTAAAATATAATTTT-AAAAAAGTTTAGGGGT
1 AAAAATGGAATTTTTAGAAAGTTTGAGGGTCAAAATGTAATTTTGGTAAAA--TTAGGGGT
* ** * *
31489172 TAAAATATAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTGG-AAAAGTTTAGGGGT
1 AAAAATGGAATTTTTAGAAAGTTTGAGGGTCAAAATGTAATTTTGGTAAAA--TTAGGGGT
* ** * * *
31489232 TAAAATATAATTTTTGGATAGTTTAAGGG
1 AAAAATGGAATTTTTAGAAAGTTTGAGGG
31489261 CTTTCAGGGT
Statistics
Matches: 269, Mismatches: 37, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
56 2 0.01
57 23 0.09
58 131 0.49
59 38 0.14
60 75 0.28
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGAAAGTTTGAGGGTCAAAATGTAATTTTGGTAAAATTAGGGGT
Found at i:31489189 original size:60 final size:60
Alignment explanation
Indices: 31489123--31489255 Score: 212
Period size: 60 Copynumber: 2.2 Consensus size: 60
31489113 AAAAATGGAA
*
31489123 TTTTAGAAAGTTTTAGAGTTAAAATATAATTTTAAAAAAGTTTAGGGGTTAAAATATAAT
1 TTTTAGAAAGTTTTAGAGTCAAAATATAATTTTAAAAAAGTTTAGGGGTTAAAATATAAT
* **
31489183 TTTTAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATATAAT
1 TTTTAGAAAGTTTTAGAGTCAAAATATAATTTTAAAAAAGTTTAGGGGTTAAAATATAAT
* *
31489243 TTTTGGATAGTTT
1 TTTTAGAAAGTTT
31489256 AAGGGCTTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.40, C:0.01, G:0.18, T:0.41
Consensus pattern (60 bp):
TTTTAGAAAGTTTTAGAGTCAAAATATAATTTTAAAAAAGTTTAGGGGTTAAAATATAAT
Found at i:31489255 original size:30 final size:30
Alignment explanation
Indices: 31489123--31489256 Score: 157
Period size: 30 Copynumber: 4.5 Consensus size: 30
31489113 AAAAATGGAA
*
31489123 TTTTAGAAAGTTTTA-GAGTTAAAATATAAT
1 TTTTAGAAAG-TTTAGGGGTTAAAATATAAT
* *
31489153 TTTAAAAAAGTTTAGGGGTTAAAATATAAT
1 TTTTAGAAAGTTTAGGGGTTAAAATATAAT
*
31489183 TTTTAGAAAGTTTTA-GGGTCAAAATATAA-
1 TTTTAGAAAG-TTTAGGGGTTAAAATATAAT
*
31489212 TTTTGGAAAAGTTTAGGGGTTAAAATATAAT
1 TTTTAG-AAAGTTTAGGGGTTAAAATATAAT
* *
31489243 TTTTGGATAGTTTA
1 TTTTAGAAAGTTTA
31489257 AGGGCTTTCA
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
29 13 0.14
30 67 0.74
31 10 0.11
ACGTcount: A:0.40, C:0.01, G:0.18, T:0.41
Consensus pattern (30 bp):
TTTTAGAAAGTTTAGGGGTTAAAATATAAT
Found at i:31491563 original size:13 final size:13
Alignment explanation
Indices: 31491545--31491571 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31491535 CATTGACCGC
31491545 TGACCGTTGACTT
1 TGACCGTTGACTT
31491558 TGACCGTTGACTT
1 TGACCGTTGACTT
31491571 T
1 T
31491572 TTTCGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (13 bp):
TGACCGTTGACTT
Found at i:31492878 original size:137 final size:137
Alignment explanation
Indices: 31492656--31493078 Score: 774
Period size: 137 Copynumber: 3.1 Consensus size: 137
31492646 GATTTTGGGT
* *
31492656 TATTAATATACTTTGTTGGTAACTATTCGTTTTGGGTTGTAAACATAATTTATTTTGGGACTTTT
1 TATTAATATACTTTGTTGGTAACTATTCGTTTTGGGTTGTAAATACAATTTATTTTGGGACTTTT
31492721 GATATTTTATTTTTGGGAGTTTAATTAACATATTTTATTTTATTTTTAATTATAGATATAAAATT
66 GATATTTTATTTTTGGGAGTTTAATTAACATATTTTATTTTATTTTTAATTATAGATATAAAATT
31492786 ATATATA
131 ATATATA
31492793 TATTAATATACTTTGTTGGTAACTATTCGTTTTGGGTTGTAAATACAATTTATTTTGGGACTTTT
1 TATTAATATACTTTGTTGGTAACTATTCGTTTTGGGTTGTAAATACAATTTATTTTGGGACTTTT
*
31492858 GATATTTTATTTTTGGGAGTTTAATTAACCTATTTTATTTTATTTTTAATTATAGATATAAAATT
66 GATATTTTATTTTTGGGAGTTTAATTAACATATTTTATTTTATTTTTAATTATAGATATAAAATT
31492923 ATATATA
131 ATATATA
*
31492930 TATTAATATACTTTTTTGGTAACTATTCGTTTTGGGTTGTAAATACAATTTATTTTGGGACTTTT
1 TATTAATATACTTTGTTGGTAACTATTCGTTTTGGGTTGTAAATACAATTTATTTTGGGACTTTT
* *
31492995 GATATTTCATTTTTAGGAGTTTAATTAACATATTTTATTTTATTTTTAATTATAGATATAAAATT
66 GATATTTTATTTTTGGGAGTTTAATTAACATATTTTATTTTATTTTTAATTATAGATATAAAATT
31493060 ATATATA
131 ATATATA
31493067 TATATATATATA
1 TAT-TA-ATATA
31493079 TAGGTATATT
Statistics
Matches: 277, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
137 270 0.97
138 2 0.01
139 5 0.02
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (137 bp):
TATTAATATACTTTGTTGGTAACTATTCGTTTTGGGTTGTAAATACAATTTATTTTGGGACTTTT
GATATTTTATTTTTGGGAGTTTAATTAACATATTTTATTTTATTTTTAATTATAGATATAAAATT
ATATATA
Found at i:31500941 original size:27 final size:30
Alignment explanation
Indices: 31500872--31500941 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 30
31500862 TTCACGTTAT
*
31500872 AATATTATTATAATATTTAATTTCATAATA
1 AATATTATTATTATATTTAATTTCATAATA
*
31500902 ATTATTATT-TTATA-TTAA-TT-ATAAATA
1 AATATTATTATTATATTTAATTTCAT-AATA
31500929 AATA-TATTATTAT
1 AATATTATTATTAT
31500942 CCAAATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 6 0.17
27 13 0.37
28 4 0.11
29 4 0.11
30 8 0.23
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (30 bp):
AATATTATTATTATATTTAATTTCATAATA
Found at i:31509614 original size:24 final size:24
Alignment explanation
Indices: 31509587--31509639 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
31509577 AAAGTGGCGA
*
31509587 GTTCGCAGCATCATGGCAAACAAG
1 GTTCGCAACATCATGGCAAACAAG
**
31509611 GTTCGCAACATCATGGTGAACAAG
1 GTTCGCAACATCATGGCAAACAAG
31509635 GTTCG
1 GTTCG
31509640 TAGAAGACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (24 bp):
GTTCGCAACATCATGGCAAACAAG
Found at i:31510456 original size:29 final size:27
Alignment explanation
Indices: 31510424--31510481 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
31510414 ATAAAATCTA
**
31510424 AAAAATAAAAAGGCTAAATTTCTTAAAAT
1 AAAAATAAAAACACTAAA-TT-TTAAAAT
*
31510453 AAAAATATAAACACTAAATTTTAAAAT
1 AAAAATAAAAACACTAAATTTTAAAAT
31510480 AA
1 AA
31510482 CAAAGAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 9 0.35
28 2 0.08
29 15 0.58
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAATAAAAACACTAAATTTTAAAAT
Found at i:31515049 original size:22 final size:22
Alignment explanation
Indices: 31515021--31515065 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
31515011 ACCTCCAAAA
31515021 TAGCAGCATAATCTTTATCGAT
1 TAGCAGCATAATCTTTATCGAT
31515043 TAGCAGCATAATCTTTATCGAT
1 TAGCAGCATAATCTTTATCGAT
31515065 T
1 T
31515066 TTCTACCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (22 bp):
TAGCAGCATAATCTTTATCGAT
Found at i:31515908 original size:29 final size:28
Alignment explanation
Indices: 31515870--31515924 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
31515860 TTTTATTTTT
*
31515870 AAAAACTTATAA-ATATGTTTTAATTTACA
1 AAAAAATTATAATA-AT-TTTTAATTTACA
*
31515899 AAAAAATTATTATAATTTTTAATTTA
1 AAAAAATTATAATAATTTTTAATTTA
31515925 TCCTAACGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.43
29 12 0.52
30 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (28 bp):
AAAAAATTATAATAATTTTTAATTTACA
Found at i:31521780 original size:53 final size:54
Alignment explanation
Indices: 31521683--31521842 Score: 193
Period size: 56 Copynumber: 3.0 Consensus size: 54
31521673 TGAGAATTTG
* *
31521683 AAAAAAAA-ATTGGTGTTGGTCATTGCATGGTCGACA-CCCTTTTTTTATCTGAC
1 AAAAAAAATTTTGGTGTTGGTCATT-CATGATCGACATCCCTTTTTTTATCTGAC
*
31521736 -AAAAAAATTTTGGTGTTGGTCATGTCATGATTGACATCCCTTTTTCTTATCTGAC
1 AAAAAAAATTTTGGTGTTGGTCAT-TCATGATCGACATCCCTTTTT-TTATCTGAC
* * * *
31521791 AAAAAAAATTTTGGTTTTGGCCATACCATGATCGACAT-CTTTTTTTTATCTG
1 AAAAAAAATTTTGGTGTTGGTCAT-TCATGATCGACATCCCTTTTTTTATCTG
31521843 GTAAAAAATC
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
52 7 0.08
53 23 0.25
54 16 0.17
55 15 0.16
56 32 0.34
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (54 bp):
AAAAAAAATTTTGGTGTTGGTCATTCATGATCGACATCCCTTTTTTTATCTGAC
Found at i:31521997 original size:61 final size:59
Alignment explanation
Indices: 31521844--31522184 Score: 256
Period size: 59 Copynumber: 5.8 Consensus size: 59
31521834 TTTTATCTGG
* * * * ***
31521844 TAAAAAA-TCAAATTTTTTTGTGTTGGACAT-TACATGACTGACACCCCGTTTTAACT-GAA
1 TAAAAAATTCAAATTTTTTTGTGTTGGCCATGCA-ATGGCCGACACCCC-TTTTTGTTAG-A
* ** ** * *
31521903 TAAAAAAATCAAATTTTTGGGTGTTGATCATGCCATGGCCGACACCTCTTTTTGTTAGA
1 TAAAAAATTCAAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTGTTAGA
* * * * * *
31521962 TAAAAAATTCAAAATTTTTTTGGTGTTGGTCATGCCATGGTCGACACCCCCTTTTTTATTTGG
1 TAAAAAATTC-AAATTTTTTT-GTGTTGGCCATGCAATGGCCGACA-CCCC-TTTTTGTTAGA
* *
31522025 T-AAAAACTC-AATTTTTTTGTGTTGGCCAT---A-CGCCGACACCCCCTTTTTGTTAGA
1 TAAAAAATTCAAATTTTTTTGTGTTGGCCATGCAATGGCCGACA-CCCCTTTTTGTTAGA
* * *
31522079 TAAAAAATTCAATTTTTTTTTGTGTTGGCCATGCAATGGCCGACACCTCCTTTTT-TATCTGT
1 TAAAAAATTCAA-ATTTTTTTGTGTTGGCCATGCAATGGCCGACACC-CCTTTTTGT-T-AGA
*
31522141 TAAAAAATT--AATTTTTTTGTGTTGGCCATGCAATGACCGACACC
1 TAAAAAATTCAAATTTTTTTGTGTTGGCCATGCAATGGCCGACACC
31522185 AACTTTCCCT
Statistics
Matches: 230, Mismatches: 35, Indels: 34
0.77 0.12 0.11
Matches are distributed among these distances:
54 9 0.04
55 18 0.08
56 2 0.01
57 18 0.08
59 64 0.28
60 53 0.23
61 37 0.16
62 20 0.09
63 9 0.04
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (59 bp):
TAAAAAATTCAAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTGTTAGA
Found at i:31522067 original size:55 final size:57
Alignment explanation
Indices: 31522003--31522169 Score: 187
Period size: 57 Copynumber: 2.9 Consensus size: 57
31521993 ATGCCATGGT
* *
31522003 CGACACCCCCTTTTTTATTTGGTAAAAACTCAATTTTTTTGTGTTGGCCAT-A-CGC
1 CGACACCCCCTTTTTTATTTGATAAAAAATCAATTTTTTTGTGTTGGCCATAATCGC
* * *
31522058 CGACACCCCC-TTTTTGTTAGATAAAAAATTCAATTTTTTTTTGTGTTGGCCATGCAATGGC
1 CGACACCCCCTTTTTTATTTGATAAAAAA-TCAA--TTTTTTTGTGTTGGCCAT--AATCGC
* * * *
31522119 CGACACCTCCTTTTTTATCTGTTAAAAAATTAATTTTTTTGTGTTGGCCAT
1 CGACACCCCCTTTTTTATTTGATAAAAAATCAATTTTTTTGTGTTGGCCAT
31522170 GCAATGACCG
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
54 14 0.15
55 14 0.15
57 18 0.19
59 18 0.19
60 1 0.01
61 14 0.15
62 14 0.15
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (57 bp):
CGACACCCCCTTTTTTATTTGATAAAAAATCAATTTTTTTGTGTTGGCCATAATCGC
Found at i:31522112 original size:116 final size:116
Alignment explanation
Indices: 31521940--31522169 Score: 345
Period size: 116 Copynumber: 2.0 Consensus size: 116
31521930 TCATGCCATG
* * * *
31521940 GCCGACACCTCTTTTTGTTAGATAAAAAATTCAAAATTTTTTTGGTGTTGGTCATGCCATGGTCG
1 GCCGACACCCCTTTTTGTTAGATAAAAAATTCAAAATTTTTTTGGTGTTGGCCATGCAATGGCCG
* *
31522005 ACACCCCCTTTTTTATTTGGTAAAAACTCAATTTTTTTGTGTTGGCCATAC
66 ACACCCCCTTTTTTATCTGGTAAAAAATCAATTTTTTTGTGTTGGCCATAC
* *
31522056 GCCGACACCCCCTTTTTGTTAGATAAAAAATTC-AATTTTTTTTTGTGTTGGCCATGCAATGGCC
1 GCCGACA-CCCCTTTTTGTTAGATAAAAAATTCAAAATTTTTTTGGTGTTGGCCATGCAATGGCC
* * *
31522120 GACACCTCCTTTTTTATCTGTTAAAAAATTAATTTTTTTGTGTTGGCCAT
65 GACACCCCCTTTTTTATCTGGTAAAAAATCAATTTTTTTGTGTTGGCCAT
31522170 GCAATGACCG
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
116 78 0.76
117 24 0.24
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (116 bp):
GCCGACACCCCTTTTTGTTAGATAAAAAATTCAAAATTTTTTTGGTGTTGGCCATGCAATGGCCG
ACACCCCCTTTTTTATCTGGTAAAAAATCAATTTTTTTGTGTTGGCCATAC
Found at i:31522182 original size:59 final size:59
Alignment explanation
Indices: 31521832--31522184 Score: 244
Period size: 60 Copynumber: 5.9 Consensus size: 59
31521822 TCGACATCTT
* * * * * *
31521832 TTTTTTATCTGGTAAAAAATCAAATTTTTTTGTGTTGGACAT-TACATGACTGACA-CCCC
1 TTTTTTATCTGATAAAAAAT-TAATTTTTTTGTGTTGGCCATGCA-ATGGCCGACACCCCC
* * * ** ** * *
31521891 -GTTTTAACTGAATAAAAAAATCAAATTTTTGGGTGTTGATCATGCCATGGCCGACA-CCTC
1 TTTTTTATCTG-AT-AAAAAAT-TAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCC
* * * *
31521951 TTTTTGT-T-AGATAAAAAATTCAAAATTTTTTTGGTGTTGGTCATGCCATGGTCGACACCCCC
1 TTTTT-TATCTGATAAAAAATT---AATTTTTTT-GTGTTGGCCATGCAATGGCCGACACCCCC
* * * * *
31522013 TTTTTTATTTGGTAAAAACTCAATTTTTTTGTGTTGGCCAT---A-CGCCGACACCCCC
1 TTTTTTATCTGATAAAAAATTAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCC
* *
31522068 TTTTTGT-T-AGATAAAAAATTCAATTTTTTTTTGTGTTGGCCATGCAATGGCCGACACCTCC
1 TTTTT-TATCTGATAAAAAATT-AA--TTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCC
* *
31522129 TTTTTTATCTGTTAAAAAATTAATTTTTTTGTGTTGGCCATGCAATGACCGACACC
1 TTTTTTATCTGATAAAAAATTAATTTTTTTGTGTTGGCCATGCAATGGCCGACACC
31522185 AACTTTCCCT
Statistics
Matches: 235, Mismatches: 37, Indels: 44
0.74 0.12 0.14
Matches are distributed among these distances:
54 8 0.03
55 19 0.08
56 2 0.01
57 18 0.08
58 15 0.06
59 45 0.19
60 55 0.23
61 45 0.19
62 20 0.09
63 8 0.03
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (59 bp):
TTTTTTATCTGATAAAAAATTAATTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCC
Found at i:31523018 original size:18 final size:18
Alignment explanation
Indices: 31522989--31523033 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
31522979 TTTAAAAAAT
31522989 AATTAG-AATATACAAGA
1 AATTAGAAATATACAAGA
* *
31523006 AATTAGAAATATATAGGA
1 AATTAGAAATATACAAGA
31523024 AATTAGAAAT
1 AATTAGAAAT
31523034 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.27
Consensus pattern (18 bp):
AATTAGAAATATACAAGA
Found at i:31525244 original size:60 final size:58
Alignment explanation
Indices: 31525159--31525313 Score: 154
Period size: 60 Copynumber: 2.6 Consensus size: 58
31525149 GGAAAAAGTT
* *
31525159 GGTGTCGGCCATTGCATGACAAACACAAAAAAAATT-GATTTTTTACCAGATAAAAAAGGA
1 GGTGTCGGCCATTGCATGGCCAACAC-AAAAAAATTCGATTTTTTACCAGA-AAAAAA-GA
* * * *
31525219 GGTGTCGGCCA-TGCAATGGCCAACAC-CAAAAATTCGGATTTTTTATCTGACAAAAAGA
1 GGTGTCGGCCATTGC-ATGGCCAACACAAAAAAATTC-GATTTTTTACCAGAAAAAAAGA
* *
31525277 GAGTGTAGACCATTGCATGGCCAACACCAAAAAAATT
1 G-GTGTCGGCCATTGCATGGCCAACA-CAAAAAAATT
31525314 TAAATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
58 10 0.13
59 26 0.33
60 36 0.46
61 7 0.09
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (58 bp):
GGTGTCGGCCATTGCATGGCCAACACAAAAAAATTCGATTTTTTACCAGAAAAAAAGA
Found at i:31525370 original size:61 final size:61
Alignment explanation
Indices: 31525167--31525372 Score: 147
Period size: 60 Copynumber: 3.4 Consensus size: 61
31525157 TTGGTGTCGG
* * * * * * *
31525167 CCATTGCATGACAAACACAAAAAAAA-TT-GATTTTTTACCAGATAAAAA-AGGAGGTGTCGG
1 CCATTGCATGACCAACACAAAAAAAATTTAAATTTTTTATCTGACAAAAAGA-GA-GTGTAGA
* * ***
31525227 CCA-TGCAATGGCCAACAC--CAAAAATTCGGATTTTTTATCTGACAAAAAGAGAGTGTAGA
1 CCATTGC-ATGACCAACACAAAAAAAATTTAAATTTTTTATCTGACAAAAAGAGAGTGTAGA
* * * * * *
31525286 CCATTGCATGGCCAACACCAAAAAAATTTAAATTTTTTATTTGACAAAAAG-GGGTGTTGG
1 CCATTGCATGACCAACACAAAAAAAATTTAAATTTTTTATCTGACAAAAAGAGAGTGTAGA
* * *
31525346 TCATTGCGTGACCAATACAAAAAAAAT
1 CCATTGCATGACCAACACAAAAAAAAT
31525373 AATTTTTTAC
Statistics
Matches: 117, Mismatches: 22, Indels: 14
0.76 0.14 0.09
Matches are distributed among these distances:
58 5 0.04
59 23 0.20
60 62 0.53
61 27 0.23
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (61 bp):
CCATTGCATGACCAACACAAAAAAAATTTAAATTTTTTATCTGACAAAAAGAGAGTGTAGA
Found at i:31525487 original size:58 final size:59
Alignment explanation
Indices: 31525384--31525643 Score: 257
Period size: 59 Copynumber: 4.4 Consensus size: 59
31525374 ATTTTTTACT
* * *
31525384 AACACCAAAAAAATTTAAATTTTTTATCTGAAA-AAAAGGGGTGTCGACCATGGC-ATGGTC
1 AACACC-AAAAAATTT-AATTTTTTATATCAAATAAAAGGGGTGTCGACCAT-GCAATGGCC
* * * * *
31525444 AAGACCTAAAAATTTGATTTTTTAT-TCAAATAAAAGGGATGTCGTCCATGCAATGGCC
1 AACACCAAAAAATTTAATTTTTTATATCAAATAAAAGGGGTGTCGACCATGCAATGGCC
* *
31525502 AACACCCAAAAATTTGATTTTTTAT-TCAAATAAAAAGGGGTGTC-AGCCATGCAATGGCC
1 AACACCAAAAAATTTAATTTTTTATATCAAAT-AAAAGGGGTGTCGA-CCATGCAATGGCC
* * * *
31525561 AATACCAAAAAAATTAATTTTTT-TATCAGATAAAAAAGGGGTGTCGGCCATGGC-ATGGCC
1 AACACCAAAAAATTTAATTTTTTATATCA-A-ATAAAAGGGGTGTCGACCAT-GCAATGGCC
*
31525621 AACA-CAAAAAAATTAATTTTTTA
1 AACACCAAAAAATTTAATTTTTTA
31525644 CCAGATAAAA
Statistics
Matches: 172, Mismatches: 18, Indels: 20
0.82 0.09 0.10
Matches are distributed among these distances:
57 6 0.03
58 60 0.35
59 72 0.42
60 31 0.18
61 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (59 bp):
AACACCAAAAAATTTAATTTTTTATATCAAATAAAAGGGGTGTCGACCATGCAATGGCC
Found at i:31525554 original size:59 final size:59
Alignment explanation
Indices: 31525384--31525688 Score: 268
Period size: 58 Copynumber: 5.2 Consensus size: 59
31525374 ATTTTTTACT
* *
31525384 AACACCAAAAAAATTTAAATTTTTTA-TCTGAA-AAAAAGGGGTGTCGACCATGGCATGGTC
1 AACACCAAAAAAA-TT-AATTTTTTATTC-AAATAAAAAGGGGTGTCGACCATGGCATGGCC
* * * * * *
31525444 AAGACCTAAAAATTTGATTTTTTATTCAAAT-AAAAGGGATGTCGTCCAT-GCAATGGCC
1 AACACCAAAAAAATTAATTTTTTATTCAAATAAAAAGGGGTGTCGACCATGGC-ATGGCC
* * *
31525502 AACACCCAAAAATTTGATTTTTTATTCAAATAAAAAGGGGTGTC-AGCCAT-GCAATGGCC
1 AACACCAAAAAAATTAATTTTTTATTCAAATAAAAAGGGGTGTCGA-CCATGGC-ATGGCC
* * *
31525561 AATACCAAAAAAATTAATTTTTT-TATCAGATAAAAAAGGGGTGTCGGCCATGGCATGGCC
1 AACACCAAAAAAATTAATTTTTTAT-TCAAAT-AAAAAGGGGTGTCGACCATGGCATGGCC
* * *** * * *
31525621 AACA-CAAAAAAATTAATTTTTTA-CCAGATAAAAAAAAAGCGTCGACCATGACATGACC
1 AACACCAAAAAAATTAATTTTTTATTCAAAT-AAAAAGGGGTGTCGACCATGGCATGGCC
31525679 AACACCAAAA
1 AACACCAAAA
31525689 TTTTTTTGTC
Statistics
Matches: 207, Mismatches: 27, Indels: 23
0.81 0.11 0.09
Matches are distributed among these distances:
57 2 0.01
58 92 0.44
59 75 0.36
60 36 0.17
61 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (59 bp):
AACACCAAAAAAATTAATTTTTTATTCAAATAAAAAGGGGTGTCGACCATGGCATGGCC
Found at i:31525652 original size:117 final size:116
Alignment explanation
Indices: 31525384--31525654 Score: 291
Period size: 117 Copynumber: 2.3 Consensus size: 116
31525374 ATTTTTTACT
* * *
31525384 AACACCAAAAAAATTTAAATTTTTTATCTGAAAAAAAGGGGTGTCGACCATGGCATGGTCAAGAC
1 AACACCAAAAAAA-TT-AATTTTTTATCAGATAAAAAGGGGTGTCGACCATGGCATGGCCAAGAC
* * * * *
31525449 CTAAAAATTTGATTTTTTATTCAAATAAAAGGGATGTCGTCCATGCAATGGCC
64 CAAAAAAATTAATTTTTTATTCAAAAAAAAGGGATGTCGGCCATGCAATGGCC
* * * * *
31525502 AACACCCAAAAATTTGATTTTTTATTCAAATAAAAAGGGGTGTC-AGCCAT-GCAATGGCCAATA
1 AACACCAAAAAAATTAATTTTTTA-TCAGATAAAAAGGGGTGTCGA-CCATGGC-ATGGCCAAGA
*
31525565 CCAAAAAAATTAATTTTTT-TATCAGATAAAAAAGGGGTGTCGGCCATGGC-ATGGCC
63 CCAAAAAAATTAATTTTTTAT-TCA-A-AAAAAAGGGATGTCGGCCAT-GCAATGGCC
*
31525621 AACA-CAAAAAAATTAATTTTTTACCAGATAAAAA
1 AACACCAAAAAAATTAATTTTTTATCAGATAAAAA
31525655 AAAAGCGTCG
Statistics
Matches: 127, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
116 12 0.09
117 58 0.46
118 28 0.22
119 27 0.21
120 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (116 bp):
AACACCAAAAAAATTAATTTTTTATCAGATAAAAAGGGGTGTCGACCATGGCATGGCCAAGACCA
AAAAAATTAATTTTTTATTCAAAAAAAAGGGATGTCGGCCATGCAATGGCC
Found at i:31527843 original size:2 final size:2
Alignment explanation
Indices: 31527836--31527862 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31527826 CTGATGAATG
31527836 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
31527863 GTCACATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31543298 original size:5 final size:5
Alignment explanation
Indices: 31543288--31543314 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
31543278 ACCTTAACTC
31543288 TCTCA TCTCA TCTCA TCTCA TCTCA TC
1 TCTCA TCTCA TCTCA TCTCA TCTCA TC
31543315 ACTTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (5 bp):
TCTCA
Done.