Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002667.1 Hibiscus syriacus cultivar Beakdansim tig00005479_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 93504
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6656 original size:151 final size:151
Alignment explanation
Indices: 6382--6683 Score: 586
Period size: 151 Copynumber: 2.0 Consensus size: 151
6372 TATCATGGAG
*
6382 ATGGTTAATACTTTACCTAGGGACCATTAGGTTTATCTTTATTGTGAGGAACAAGTACATTATGA
1 ATGGTTAATACTTTACCTAGGGACCATTAGGTTCATCTTTATTGTGAGGAACAAGTACATTATGA
6447 AGGTAGAGTAGAACCTGAGGTTAGTCTGACTCAGAAGATGAGGATTATGTTGTTGAGTCATCCAC
66 AGGTAGAGTAGAACCTGAGGTTAGTCTGACTCAGAAGATGAGGATTATGTTGTTGAGTCATCCAC
6512 TGATGTATCTACATTTTCTGA
131 TGATGTATCTACATTTTCTGA
*
6533 ATGGTTAATACTTTACCTAGGGACCATTAGGTTCATCTTTATTGTGAGGAAGAAGTACATTATGA
1 ATGGTTAATACTTTACCTAGGGACCATTAGGTTCATCTTTATTGTGAGGAACAAGTACATTATGA
6598 AGGTAGAGTAGAACCTGAGGTTAGTCTGACTCAGAAGATGAGGATTATGTTGTTGAGTCATCCAC
66 AGGTAGAGTAGAACCTGAGGTTAGTCTGACTCAGAAGATGAGGATTATGTTGTTGAGTCATCCAC
6663 TGATGTATCTACATTTTCTGA
131 TGATGTATCTACATTTTCTGA
6684 CTCAGAAAAT
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 149 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (151 bp):
ATGGTTAATACTTTACCTAGGGACCATTAGGTTCATCTTTATTGTGAGGAACAAGTACATTATGA
AGGTAGAGTAGAACCTGAGGTTAGTCTGACTCAGAAGATGAGGATTATGTTGTTGAGTCATCCAC
TGATGTATCTACATTTTCTGA
Found at i:9073 original size:29 final size:29
Alignment explanation
Indices: 9023--9112 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 29
9013 ATTATACATT
* ** *
9023 TTATTTT-GTTGCTTGAAAGAATATCTTG
1 TTATTTTGGGTGCTTGATTGAATGTCTTG
9051 TTATTTTGGGTGCTTGATTGAATGTCTTG
1 TTATTTTGGGTGCTTGATTGAATGTCTTG
*
9080 TTATTTTGGGTGCTTGGTTGAATGTCTTG
1 TTATTTTGGGTGCTTGATTGAATGTCTTG
9109 TTAT
1 TTAT
9113 GTTAGTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 7 0.12
29 49 0.88
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.52
Consensus pattern (29 bp):
TTATTTTGGGTGCTTGATTGAATGTCTTG
Found at i:9199 original size:27 final size:26
Alignment explanation
Indices: 9138--9200 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
9128 TAGATTACAA
* *
9138 GAGATATAACCATCCCAACAACAAAT
1 GAGATAGAACCACCCCAACAACAAAT
* * *
9164 CAAACTAGAACCACCCCAACAACAAGT
1 GAGA-TAGAACCACCCCAACAACAAAT
9191 GGAGATAGAA
1 -GAGATAGAA
9201 TTTTCCCAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
26 2 0.07
27 24 0.86
28 2 0.07
ACGTcount: A:0.49, C:0.27, G:0.13, T:0.11
Consensus pattern (26 bp):
GAGATAGAACCACCCCAACAACAAAT
Found at i:12216 original size:152 final size:152
Alignment explanation
Indices: 11935--12245 Score: 604
Period size: 152 Copynumber: 2.0 Consensus size: 152
11925 ATGTAGATGA
*
11935 TTTGGTTAGTTTGTAAATGGTGTTTGTCCTATGTTATACTGGTTGGTATCATCTTCCAAATATAT
1 TTTGATTAGTTTGTAAATGGTGTTTGTCCTATGTTATACTGGTTGGTATCATCTTCCAAATATAT
12000 GAAAAATTTAGAAAAAATACGTTTGAGAAAATGAACATAGCGGAGTTGAACACATACTCGGTCCA
66 GAAAAATTTAGAAAAAATACGTTTGAGAAAATGAACATAGCGGAGTTGAACACATACTCGGTCCA
12065 ACACTCACCTGCCCTGTTGTCT
131 ACACTCACCTGCCCTGTTGTCT
12087 TTTGATTAGTTTGTAAATGGTGTTTGTCCTATGTTATACTGGTTGGTATCATCTTCCAAATATAT
1 TTTGATTAGTTTGTAAATGGTGTTTGTCCTATGTTATACTGGTTGGTATCATCTTCCAAATATAT
12152 GAAAAATTTAGAAAAAATACGTTTGAGAAAATGAACATAGCGGAGTTGAACACATACTCGGTCCA
66 GAAAAATTTAGAAAAAATACGTTTGAGAAAATGAACATAGCGGAGTTGAACACATACTCGGTCCA
*
12217 ACACTCACCTGTCCTGTTGTCT
131 ACACTCACCTGCCCTGTTGTCT
12239 TTTGATT
1 TTTGATT
12246 TTCTTTTAGA
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 157 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (152 bp):
TTTGATTAGTTTGTAAATGGTGTTTGTCCTATGTTATACTGGTTGGTATCATCTTCCAAATATAT
GAAAAATTTAGAAAAAATACGTTTGAGAAAATGAACATAGCGGAGTTGAACACATACTCGGTCCA
ACACTCACCTGCCCTGTTGTCT
Found at i:14945 original size:2 final size:2
Alignment explanation
Indices: 14938--15008 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
14928 TATTAGGTCA
14938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15009 GAATGTAAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18647 original size:23 final size:24
Alignment explanation
Indices: 18586--18648 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 24
18576 AAAAATATGC
*
18586 ATAATTAAATATAAATATAAAAGAT
1 ATAA-TAAATATATATATAAAAGAT
18611 A-AATAAAT-TATATATAGAAA-AT
1 ATAATAAATATATATATA-AAAGAT
18633 ATAATAAATAT-TATAT
1 ATAATAAATATATATAT
18649 CTTAGATAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 10 0.29
23 20 0.59
24 3 0.09
25 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (24 bp):
ATAATAAATATATATATAAAAGAT
Found at i:20510 original size:3 final size:3
Alignment explanation
Indices: 20502--20526 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20492 TTAAAATGGA
20502 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
20527 GGTTTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:21488 original size:25 final size:25
Alignment explanation
Indices: 21451--21506 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
21441 ATGACGTTTA
*
21451 GGTTAATAGGACAAATATATTTGTG
1 GGTTAATAGGACAAATATATTTGAG
*
21476 GGTTAATATGACAAATATATTTGAG
1 GGTTAATAGGACAAATATATTTGAG
21501 GGTTAA
1 GGTTAA
21507 AAGTAACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.36
Consensus pattern (25 bp):
GGTTAATAGGACAAATATATTTGAG
Found at i:21519 original size:27 final size:25
Alignment explanation
Indices: 21461--21513 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
21451 GGTTAATAGG
* * *
21461 ACAAATATATTTGTGGGTTAATATG
1 ACAAATATATTTGAGGGTTAAAATA
21486 ACAAATATATTTGAGGGTTAAAAGTA
1 ACAAATATATTTGAGGGTTAAAA-TA
21512 AC
1 AC
21514 CTAATAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.34
Consensus pattern (25 bp):
ACAAATATATTTGAGGGTTAAAATA
Found at i:24664 original size:25 final size:27
Alignment explanation
Indices: 24605--24668 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
24595 ATCTTTTTTT
* * *
24605 ATTATTCTTTAATTTTATTTTTTACTG
1 ATTATTTTTTATTTTTATTATTTACTG
24632 ATTA-TTTTTATTTTTATTATTT-CTG
1 ATTATTTTTTATTTTTATTATTTACTG
24657 -TTATTTTTTATT
1 ATTATTTTTTATT
24669 ATATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 3 0.09
25 11 0.33
26 15 0.45
27 4 0.12
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (27 bp):
ATTATTTTTTATTTTTATTATTTACTG
Found at i:28677 original size:106 final size:106
Alignment explanation
Indices: 28492--29274 Score: 1440
Period size: 106 Copynumber: 7.4 Consensus size: 106
28482 ACGAAGAAAA
*
28492 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
*
28557 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
28598 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
*
28663 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
28704 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
28769 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
28810 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
28875 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
28916 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
28981 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
29022 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
*
29087 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
29128 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
29193 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
29234 ATTGGACTCCAGACAACGTAAGTTCAACTTCACAACGAAGG
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
29275 ATGTTGGACT
Statistics
Matches: 661, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 661 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
Found at i:29274 original size:43 final size:43
Alignment explanation
Indices: 29213--29317 Score: 165
Period size: 43 Copynumber: 2.4 Consensus size: 43
29203 CAGAGCCAAT
**
29213 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
* *
29256 TTCAACTTCACAACGAAGGATGTTGGACTCGAGACAACACAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
*
29299 TTCAATTTCACAACGAAGG
1 TTCAACTTCACAACGAAGG
29318 GACGGCTGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
Found at i:29299 original size:149 final size:149
Alignment explanation
Indices: 29107--29390 Score: 433
Period size: 149 Copynumber: 1.9 Consensus size: 149
29097 CAGAGCCAAT
* * *
29107 TTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGAC
* * *
29172 CGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
66 CGCTGGTTGTCAACAACCAACTTCCCAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATT
29237 GGACTCCAGACAACGTAAG
131 GGACTCCAGACAACGTAAG
* * *
29256 TTCAACTTCACAACGAAGGATGTTGGACTCGAGACAACACAAGTTCAATTTCACAACGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGAC
* * ** * *
29321 GGCTGGTTGTCAACAACCAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATT
66 CGCTGGTTGTCAACAACCAACTTCCCAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATT
29386 GGACT
131 GGACT
29391 TAGAACAATG
Statistics
Matches: 120, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
149 120 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (149 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGAC
CGCTGGTTGTCAACAACCAACTTCCCAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGTAAG
Found at i:31122 original size:18 final size:17
Alignment explanation
Indices: 31082--31128 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
31072 TTAATATTAT
*
31082 TTAAT-TTATTTTTTTA
1 TTAATATTATTTTTGTA
*
31098 TTAATATTATTTTTGTG
1 TTAATATTATTTTTGTA
31115 TTATATATTCATTT
1 TTA-ATATT-ATTT
31129 AGATCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.19
17 12 0.46
18 5 0.19
19 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (17 bp):
TTAATATTATTTTTGTA
Found at i:31175 original size:25 final size:25
Alignment explanation
Indices: 31134--31199 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
31124 CATTTAGATC
* *
31134 TTTTTTA-TTATTCTTTTAATTTTA
1 TTTTTTACTGATTATTTTAATTTTA
*
31158 TTTTTTACTGATTATTTTTATTTTA
1 TTTTTTACTGATTATTTTAATTTTA
* *
31183 TTATTT-CTGTTTATTTT
1 TTTTTTACTGATTATTTT
31200 TTTATTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 17 0.47
25 19 0.53
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (25 bp):
TTTTTTACTGATTATTTTAATTTTA
Found at i:31201 original size:26 final size:25
Alignment explanation
Indices: 31141--31228 Score: 74
Period size: 25 Copynumber: 3.4 Consensus size: 25
31131 ATCTTTTTTA
* *
31141 TTATTCTTTTAATTTTATTTTTTACTG
1 TTATT-TTTTTATTTTATTATTT-CTG
31168 --ATTATTTTTATTTTATTATTTCTG
1 TTATT-TTTTTATTTTATTATTTCTG
* *
31192 TTTATTTTTTTATTATA-TATATTATG
1 -TTATTTTTTTATTTTATTAT-TTCTG
31218 TTATTTTTTTA
1 TTATTTTTTTA
31229 ATTCTTTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
24 3 0.06
25 32 0.62
26 14 0.27
27 3 0.06
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (25 bp):
TTATTTTTTTATTTTATTATTTCTG
Found at i:31892 original size:18 final size:20
Alignment explanation
Indices: 31868--31913 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31858 TATCATTTCT
31868 TAAAATTTTAA-A-ATTTTA
1 TAAAATTTTAATATATTTTA
* *
31886 TATAATTCTAATATATTTTA
1 TAAAATTTTAATATATTTTA
31906 TAAAATTT
1 TAAAATTT
31914 ATTAATAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 9 0.41
19 1 0.05
20 12 0.55
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAAATTTTAATATATTTTA
Found at i:35349 original size:221 final size:220
Alignment explanation
Indices: 34969--35427 Score: 674
Period size: 221 Copynumber: 2.1 Consensus size: 220
34959 AGTGTGATAT
34969 TCGGGTCGGGTTCAGGTTTAGGGTGAAAAAAACCGGACAGACCCGAAAACATATATAATTCAGGT
1 TCGGGTCGGGTTCAGGTTTAGGGTGAAAAAAACCGGACAGACCCGAAAACATATATAATTCAGGT
* * *
35034 CGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTTGGGTCGGGTTG
66 CGGCTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTTG
*
35099 GATTTCTAATTCATATATTCGGGTC-G-GGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGG
131 GATTTCTAATTCATATATT---GTCGGAGGTCGGATAAAACTTTATTTTGTTCGGGTCGGGTCGG
*
35162 GTTTTTTAAGTGTGATATTCGGGTCGAG
193 GGTTTTTAAGTGTGATATTCGGGTCGAG
* * * * *
35190 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACTGGACCGACCCGAAAATATATATAATTCGGGT
1 TCGGGTCGGGTTCAGGTTTAGGGTGAAAAAAACCGGACAGACCCGAAAACATATATAATTCAGGT
*
35255 CGGCTCGGATTAAGTCACTATTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTG
66 CGGCTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGG-T-
35320 GGTCGGATTTCTAATTCATATA-T-TCGGGTCAGGTCGGATAAAACTTTATTTTGTTCGGGTCGG
129 --T-GGATTTCTAATTCATATATTGTC-GG--AGGTCGGATAAAACTTTATTTTGTTCGGGTCGG
* *
35383 GTTGGGGTTTTTAAGTGTGATATTCGGGTTGAG
188 GTCGGGGTTTTTAAGTGTGATATTCGGGTCGAG
35416 TCGGGTCGGGTT
1 TCGGGTCGGGTT
35428 TTTTTAAGTG
Statistics
Matches: 215, Mismatches: 13, Indels: 15
0.88 0.05 0.06
Matches are distributed among these distances:
221 120 0.56
222 1 0.00
223 1 0.00
225 2 0.01
226 91 0.42
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (220 bp):
TCGGGTCGGGTTCAGGTTTAGGGTGAAAAAAACCGGACAGACCCGAAAACATATATAATTCAGGT
CGGCTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTTG
GATTTCTAATTCATATATTGTCGGAGGTCGGATAAAACTTTATTTTGTTCGGGTCGGGTCGGGGT
TTTTAAGTGTGATATTCGGGTCGAG
Found at i:35431 original size:37 final size:38
Alignment explanation
Indices: 35378--35449 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
35368 TTTTGTTCGG
*
35378 GTCGGGTTGGG-GTTTTTAAGTGTGATATTCGGGTTGA
1 GTCGGGTCGGGTGTTTTTAAGTGTGATATTCGGGTTGA
*
35415 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGT
1 GTCGGGTCGGGTGTTTTTAAGTGTGATATTCGGGT
35450 CGGGTTCGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 10 0.31
38 22 0.69
ACGTcount: A:0.12, C:0.07, G:0.39, T:0.42
Consensus pattern (38 bp):
GTCGGGTCGGGTGTTTTTAAGTGTGATATTCGGGTTGA
Found at i:35668 original size:248 final size:254
Alignment explanation
Indices: 35189--35763 Score: 867
Period size: 254 Copynumber: 2.2 Consensus size: 254
35179 TTCGGGTCGA
*
35189 GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACTGGACCGACCCGAAAATATATATAATTCGGG
1 GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGG
* *
35254 TCGGCTCGGATTAAGTCACTATTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTT
66 TCGGCTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCAGGTC-GGTT
35319 GGGTCGGATTTCTAATTCATATATTCGGGTCAGGTCGGATAAAACTTTATTTTGTTCGGGTCGGG
130 -GGTCGGATTTCTAATTCATATATTCGGGTCAGGTCGGATAAAACTTTATTTTGTTCGGGTCGGG
* * *
35384 TTGGGGTTTTTAAGTGTGATATTCGGGTTGAGTCGGGTCGGGTTTTTTTAAGTGTGATA-T
194 TCGGGGTTTTTAACTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATAGT
*
35444 -TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCTGAAAATATATATAATTCGGG
1 GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGG
*
35508 TCGGGC-CGGATTAAGTCACTTTTTTTATTAAATAAAAATAATTTTTTATTATTTCAGGTC-G-T
66 TC-GGCTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCAGGTCGGTT
* *
35570 -GTCGGATTTCTAATTCATATA-TCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGT
130 GGTCGGATTTCTAATTCATATATTCGGGTCAGGTCGGATAAAACTTTATTTTGTTCGGGTCGGGT
*
35633 CGGGTTTTTTAACTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGT
195 CGGGGTTTTTAACTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATA-----GT
* *
35698 CAGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAATCGGACCGACCCGAAAAAATATATATAAT
1 ---GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCG--AAAATATATATAAT
35763 T
61 T
35764 TTACCTTATA
Statistics
Matches: 293, Mismatches: 14, Indels: 21
0.89 0.04 0.06
Matches are distributed among these distances:
248 94 0.32
249 21 0.07
251 1 0.00
252 1 0.00
254 116 0.40
255 3 0.01
258 42 0.14
260 15 0.05
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (254 bp):
GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGG
TCGGCTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCAGGTCGGTTG
GTCGGATTTCTAATTCATATATTCGGGTCAGGTCGGATAAAACTTTATTTTGTTCGGGTCGGGTC
GGGGTTTTTAACTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATAGT
Found at i:35673 original size:37 final size:38
Alignment explanation
Indices: 35625--35709 Score: 129
Period size: 38 Copynumber: 2.3 Consensus size: 38
35615 ATTTTGTTCG
35625 GGTCGGGTCGGG-TTTTTTAACTGTGATATTCGGGTC-
1 GGTCGGGTCGGGTTTTTTTAACTGTGATATTCGGGTCA
* *
35661 GAGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCA
1 G-GTCGGGTCGGGTTTTTTTAACTGTGATATTCGGGTCA
35700 GGTCGGGTCG
1 GGTCGGGTCG
35710 AGTTCGGGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 1 0.02
37 11 0.25
38 31 0.70
39 1 0.02
ACGTcount: A:0.12, C:0.12, G:0.39, T:0.38
Consensus pattern (38 bp):
GGTCGGGTCGGGTTTTTTTAACTGTGATATTCGGGTCA
Found at i:38393 original size:2 final size:2
Alignment explanation
Indices: 38386--38420 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38376 AAATAATTTA
38386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38421 ATAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38439 original size:18 final size:17
Alignment explanation
Indices: 38418--38460 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
38408 ATATATATAT
38418 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
38436 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
38453 ATAA-AATA
1 ATAATAATA
38461 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:38916 original size:34 final size:34
Alignment explanation
Indices: 38873--38942 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
38863 TGAATCCTAG
38873 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
*
38907 TAAAATTCTATCATATTTTTAGGAGTTTGAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
38941 TA
1 TA
38943 GTAGGACGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (34 bp):
TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
Found at i:39798 original size:105 final size:105
Alignment explanation
Indices: 39491--40112 Score: 916
Period size: 105 Copynumber: 6.0 Consensus size: 105
39481 CATTGTTCCA
* * ** *
39491 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCT-AGAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * *
39555 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
39597 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
39657 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
39697 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
39762 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
39802 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
39867 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
39907 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
39972 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
40012 AGTCCAATATCCTTCGTTGGGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
* * *
40077 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
40113 CCTCGAGTGC
Statistics
Matches: 477, Mismatches: 31, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
99 1 0.00
100 83 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 304 0.64
106 75 0.16
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:40927 original size:65 final size:67
Alignment explanation
Indices: 40742--41147 Score: 226
Period size: 65 Copynumber: 5.9 Consensus size: 67
40732 GGAAACGATC
* * * *
40742 TCAAAGATATTTGTTGTTTCATGAGAAAC-GATCTCAAGGGA-ATAAAATTATGTTTTAAGGGAA
1 TCAAAGA-GTTTG-TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT-TGTTTTAAGGGAA
40805 ATAAAT
62 ATAAAT
** * * * *
40811 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
40876 AT
66 AT
* * * *
40878 TCAAAG-GTTT-TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT
1 TCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTTAAGGGAAA-T
*
40940 --GT
64 AAAT
* * * * * * * *
40942 CTCAAGAGAGACAAAACTT-AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAA
1 -TCAA-AGAG------TTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAG
* * *
41006 GAAAACATAT
58 GGAAATAAAT
* * * *
41016 TCAAATA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT-
1 TCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-TA
*
41078 -GT
65 AAT
* *
41080 CTCAAGATAGACGGAATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG
1 -TC-A-A-AGA--G-TTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGG
41144 GAAA
59 GAAA
41148 CTGTCTCAAG
Statistics
Matches: 264, Mismatches: 48, Indels: 47
0.74 0.13 0.13
Matches are distributed among these distances:
64 2 0.01
65 87 0.33
66 11 0.04
67 47 0.18
68 14 0.05
69 5 0.02
72 55 0.21
73 42 0.16
74 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (67 bp):
TCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:40938 original size:36 final size:35
Alignment explanation
Indices: 40887--41167 Score: 272
Period size: 36 Copynumber: 8.0 Consensus size: 35
40877 TTCAAAGGTT
* *
40887 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
40923 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
40958 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
40996 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
41025 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
41060 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGGAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
41097 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
41132 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
41168 CTCTTCTAGT
Statistics
Matches: 203, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 9 0.04
36 134 0.66
37 32 0.16
38 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:40998 original size:138 final size:137
Alignment explanation
Indices: 40835--41148 Score: 432
Period size: 138 Copynumber: 2.3 Consensus size: 137
40825 TTTCAAGAGT
* * * *
40835 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
40900 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
40964 TCCAAAAGA
129 TCCAAAAGA
* * * * *
40973 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * ** * *
41038 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGGAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
41103 CAAGAGA
131 CAAAAGA
*
41110 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
41149 TGTCTCAAGA
Statistics
Matches: 153, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
137 50 0.33
138 103 0.67
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:41217 original size:35 final size:35
Alignment explanation
Indices: 40887--41217 Score: 206
Period size: 36 Copynumber: 9.4 Consensus size: 35
40877 TTCAAAGGTT
* * *
40887 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA-A
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATC
*
40923 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAAGA-AAACTGTCTCAAGAGAGACAAATC
* * *
40959 TTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT-
1 TT-GTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATC
* * *
40996 TTGTTTCAAAGAAAACATAT-TC-----A-A-ATATT
1 TTGTTTC-AAGAAAAC-TGTCTCAAGAGAGACAAATC
*
41025 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATC
* * * *
41061 TTATTTCAAGGGAAACTGTCTCAAGATAGACGGAAT-
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATC
41097 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT-
1 TTGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATC
* *
41133 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATC
* * * *
41169 -T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATC
1 TTGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATC
*
41204 TTGTTTTAAGAAAA
1 TTGTTTCAAGAAAA
41218 ACAATCATGA
Statistics
Matches: 237, Mismatches: 34, Indels: 49
0.74 0.11 0.15
Matches are distributed among these distances:
28 7 0.03
29 14 0.06
30 1 0.00
31 1 0.00
34 4 0.02
35 38 0.16
36 130 0.55
37 39 0.16
38 3 0.01
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAAAACTGTCTCAAGAGAGACAAATC
Found at i:42124 original size:22 final size:22
Alignment explanation
Indices: 42098--42146 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
42088 TTGTGTTTGG
* *
42098 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
42120 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
42142 TCAAA
1 TCAAA
42147 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:42153 original size:22 final size:22
Alignment explanation
Indices: 42110--42153 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42100 AAAGGTTTGG
* * *
42110 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
42132 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
42154 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:42829 original size:15 final size:14
Alignment explanation
Indices: 42815--42884 Score: 54
Period size: 16 Copynumber: 4.8 Consensus size: 14
42805 TCTTTTTTTC
42815 TTTTGTTCTTGTTT
1 TTTTGTTCTTGTTT
42829 CTCTTT-TTCTTTGTTT
1 -T-TTTGTTC-TTGTTT
* *
42845 TTTT-TTTTTGCTT
1 TTTTGTTCTTGTTT
*
42858 TTTTGCTTCTTTTCTT
1 TTTTG-TTCTTGT-TT
42874 TTTTGTTCTTG
1 TTTTGTTCTTG
42885 ATTGGATCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
13 9 0.20
14 5 0.11
15 14 0.32
16 16 0.36
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (14 bp):
TTTTGTTCTTGTTT
Found at i:45949 original size:2 final size:2
Alignment explanation
Indices: 45944--45971 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45934 AAAAAGGAAA
45944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45972 CAAAGTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46132 original size:16 final size:17
Alignment explanation
Indices: 46099--46132 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
46089 GGGTCCTCTA
*
46099 GTTTAGTAATATATAAT
1 GTTTAATAATATATAAT
46116 GTTTAATAATA-ATAAT
1 GTTTAATAATATATAAT
46132 G
1 G
46133 ATAAGGACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (17 bp):
GTTTAATAATATATAAT
Found at i:46485 original size:18 final size:17
Alignment explanation
Indices: 46462--46504 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
46452 ATATATACAT
46462 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
46480 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
46497 ATAA-AATA
1 ATAATAATA
46505 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:46960 original size:34 final size:34
Alignment explanation
Indices: 46917--46986 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
46907 TGAATCCTAG
46917 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
*
46951 TAAAATTCTATCATATTTTTAGGAGTTTGAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
46985 TA
1 TA
46987 GTAGGACGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (34 bp):
TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
Found at i:47249 original size:14 final size:14
Alignment explanation
Indices: 47224--47261 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
47214 GAAAAATCAA
47224 AGAAAAAT-AAATC
1 AGAAAAATAAAATC
*
47237 AGAAAAATAAAATT
1 AGAAAAATAAAATC
47251 A-AAAAATAAAA
1 AGAAAAATAAAA
47262 ATAAAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (14 bp):
AGAAAAATAAAATC
Found at i:47253 original size:19 final size:19
Alignment explanation
Indices: 47226--47293 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
47216 AAAATCAAAG
**
47226 AAAAATAAATCAGAAAAAT
1 AAAAATAAAAAAGAAAAAT
* *
47245 AAAATTAAAAAATAAAAAT
1 AAAAATAAAAAAGAAAAAT
*
47264 AAAAATTGAACAAACGAAAAAT
1 AAAAA-T-AA-AAAAGAAAAAT
47286 AAAAATAA
1 AAAAATAA
47294 TAATGGGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 19 0.49
20 3 0.08
21 3 0.08
22 14 0.36
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (19 bp):
AAAAATAAAAAAGAAAAAT
Found at i:47261 original size:13 final size:13
Alignment explanation
Indices: 47226--47268 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
47216 AAAATCAAAG
*
47226 AAAAAT-AAATCA
1 AAAAATAAAATTA
47238 GAAAAATAAAATTA
1 -AAAAATAAAATTA
*
47252 AAAAATAAAAATA
1 AAAAATAAAATTA
47265 AAAA
1 AAAA
47269 TTGAACAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAATAAAATTA
Found at i:47286 original size:22 final size:20
Alignment explanation
Indices: 47237--47291 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
47227 AAAATAAATC
47237 AGAAAAAT-AAAATTAAAAA
1 AGAAAAATAAAAATTAAAAA
*
47256 ATAAAAATAAAAATTGAACAAA
1 AGAAAAATAAAAATT-AA-AAA
*
47278 CGAAAAATAAAAAT
1 AGAAAAATAAAAAT
47292 AATAATGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.23
20 6 0.20
21 2 0.07
22 15 0.50
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (20 bp):
AGAAAAATAAAAATTAAAAA
Found at i:57167 original size:2 final size:2
Alignment explanation
Indices: 57160--57217 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
57150 TCTCTTTTTG
57160 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57202 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
57218 ACATGTATCC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57473 original size:11 final size:11
Alignment explanation
Indices: 57459--57483 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57449 TATAAGTTAT
57459 TTTTTTATAAA
1 TTTTTTATAAA
57470 TTTTTTATAAA
1 TTTTTTATAAA
57481 TTT
1 TTT
57484 ATAAATTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTTATAAA
Found at i:58880 original size:16 final size:16
Alignment explanation
Indices: 58859--58889 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58849 GTTTCAAATT
58859 CAGATTCCAATTCCTA
1 CAGATTCCAATTCCTA
*
58875 CAGATTTCAATTCCT
1 CAGATTCCAATTCCT
58890 TCATAGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (16 bp):
CAGATTCCAATTCCTA
Found at i:58899 original size:18 final size:18
Alignment explanation
Indices: 58876--58912 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
58866 CAATTCCTAC
*
58876 AGATTTCAATTCCTTCAT
1 AGATTTCAATTCCCTCAT
58894 AGATTTCAATTCCCTCAT
1 AGATTTCAATTCCCTCAT
58912 A
1 A
58913 AACATTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (18 bp):
AGATTTCAATTCCCTCAT
Found at i:60797 original size:18 final size:18
Alignment explanation
Indices: 60774--60821 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
60764 ATCAGCAGCA
60774 GCAACGAAGCAAGAAGCT
1 GCAACGAAGCAAGAAGCT
60792 GCAACGAAGCAAGAAGCT
1 GCAACGAAGCAAGAAGCT
*
60810 GCAACAAAGCAA
1 GCAACGAAGCAA
60822 ATGCTAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.48, C:0.23, G:0.25, T:0.04
Consensus pattern (18 bp):
GCAACGAAGCAAGAAGCT
Found at i:78711 original size:23 final size:23
Alignment explanation
Indices: 78668--78717 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
78658 TTGAAGGTGT
* *
78668 TCGTTTAGTGTTCTTGAATATGG
1 TCGTTTAGTGTTCGTCAATATGG
* *
78691 TCGTTTAGTGTTCGTCTATATGT
1 TCGTTTAGTGTTCGTCAATATGG
78714 TCGT
1 TCGT
78718 GAACATGTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.50
Consensus pattern (23 bp):
TCGTTTAGTGTTCGTCAATATGG
Found at i:84316 original size:16 final size:17
Alignment explanation
Indices: 84295--84326 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
84285 ACTATTTCTA
84295 TCAG-AAAAAAATTATG
1 TCAGAAAAAAAATTATG
84311 TCAGAAAAAAAATTAT
1 TCAGAAAAAAAATTAT
84327 TTGATGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.25
Consensus pattern (17 bp):
TCAGAAAAAAAATTATG
Found at i:86356 original size:32 final size:33
Alignment explanation
Indices: 86315--86379 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
86305 CAAGAGAAAG
86315 AAAATTAGGATTGAAAAAC-TTTCTCTTGTGTT
1 AAAATTAGGATTGAAAAACTTTTCTCTTGTGTT
*
86347 AAAATTAGGATTGAAAAACTTTTCTTTTGTGTT
1 AAAATTAGGATTGAAAAACTTTTCTCTTGTGTT
86380 TGAATGCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (33 bp):
AAAATTAGGATTGAAAAACTTTTCTCTTGTGTT
Found at i:86687 original size:21 final size:20
Alignment explanation
Indices: 86639--86716 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
86629 ACTGTTATCC
* **
86639 AAGGGATCAATCCTTTTTCA
1 AAGGGATCGATCCTTTGGCA
*
86659 AGGGGATCGATCCTTTGGCCA
1 AAGGGATCGATCCTTTGG-CA
* *
86680 AAGGGATCGATCCTTTTGCT
1 AAGGGATCGATCCTTTGGCA
*
86700 AAGGGATCTATCCTTTG
1 AAGGGATCGATCCTTTG
86717 AGTCAGAGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (20 bp):
AAGGGATCGATCCTTTGGCA
Found at i:86696 original size:41 final size:41
Alignment explanation
Indices: 86639--86716 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
86629 ACTGTTATCC
*
86639 AAGGGATCAATCCTTTTTC-AAGGGGATCGATCCTTTGGCCA
1 AAGGGATCAATCCTTTTGCTAA-GGGATCGATCCTTTGGCCA
* *
86680 AAGGGATCGATCCTTTTGCTAAGGGATCTATCCTTTG
1 AAGGGATCAATCCTTTTGCTAAGGGATCGATCCTTTG
86717 AGTCAGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 31 0.94
42 2 0.06
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (41 bp):
AAGGGATCAATCCTTTTGCTAAGGGATCGATCCTTTGGCCA
Found at i:88194 original size:31 final size:31
Alignment explanation
Indices: 88156--88215 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
88146 TAAACTTTAT
* *
88156 GCATTAGGGGATAGTTTCAGTTATGCATCCA
1 GCATTAGGGGATAGTATCAATTATGCATCCA
88187 GCATTAGGGGATAGTATCAATTATGCATC
1 GCATTAGGGGATAGTATCAATTATGCATC
88216 TAGAACTGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (31 bp):
GCATTAGGGGATAGTATCAATTATGCATCCA
Found at i:89543 original size:28 final size:28
Alignment explanation
Indices: 89511--89570 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
89501 TAGTTTACCG
89511 TTTCTGAAAATCCTCCGATTTATATCCA
1 TTTCTGAAAATCCTCCGATTTATATCCA
*
89539 TTTCTGAAAATCCTCCGATTTATATCTA
1 TTTCTGAAAATCCTCCGATTTATATCCA
89567 TTTC
1 TTTC
89571 ATTACTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTCTGAAAATCCTCCGATTTATATCCA
Found at i:89827 original size:17 final size:17
Alignment explanation
Indices: 89805--89841 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
89795 GATAAAAAGT
*
89805 TTGCATCTAGATTCTGC
1 TTGCATCTAGATCCTGC
89822 TTGCATCTAGATCCTGC
1 TTGCATCTAGATCCTGC
89839 TTG
1 TTG
89842 TGATCCAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (17 bp):
TTGCATCTAGATCCTGC
Found at i:91189 original size:30 final size:31
Alignment explanation
Indices: 91131--91189 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
91121 TTAAACATTG
* *
91131 ATGTAAAATTTTAATATATTTTACATAAATT
1 ATGTAAAATTTTAATATATTTAAAATAAATT
91162 ATGTAAAA-TTTAATATGA-TTAAAATAAA
1 ATGTAAAATTTTAATAT-ATTTAAAATAAA
91190 AATAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (31 bp):
ATGTAAAATTTTAATATATTTAAAATAAATT
Found at i:91256 original size:15 final size:15
Alignment explanation
Indices: 91236--91268 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
91226 TTATCAACAT
91236 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
91251 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
91266 ATA
1 ATA
91269 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Done.