Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005396.1 Hibiscus syriacus cultivar Beakdansim tig00012367_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: 70218
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:7144 original size:193 final size:192
Alignment explanation
Indices: 6883--7283 Score: 520
Period size: 193 Copynumber: 2.1 Consensus size: 192
6873 TGACATTTAT
* * **
6883 ATAACATCACTATATAATTAATATTCAATGACAACTAATTATGTACTAAATTATGTAAAATTTCG
1 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTACGTACTAAATTAAATAAAATTTCG
* ** * * *
6948 TTATTGAT-GATTTATATCGTCATGAATAATACATTAAAATTAACATATATGTGACGAAAGAGAT
66 TTATTGATAG-CTTATATCGTCACAAATAATACATTAAAATCAACATATATATGACGAAAAAGAT
* *
7012 ATTGTCAAATTTTTAGTGACATAATATAAAT-GTTACCTAATAATATTATGAATGATGTTTA-GC
130 ACTGTCAAATTTTTAGTGACATAATAT--ATCGTTACCTAATAATATTATGAATGATGATTATGC
* * * ** ** *
7075 ATAACGTCACTTTATAATTTATATTCTATGACAGTTGGTTACGTCACTAAATTAAATAAGATTTC
1 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTACGT-ACTAAATTAAATAAAATTTC
* * *
7140 GTTATTGATAGCTTATATTGTCACAAATAATGCATTAAAATCAACTTATATATGACGAAAAAGAT
65 GTTATTGATAGCTTATATCGTCACAAATAATACATTAAAATCAACATATATATGACGAAAAAGAT
*
7205 ACTGTCACATTTTTAGTGACATAATATATCGTTACCTAATAATATTATGAATGATGATTATGC
130 ACTGTCAAATTTTTAGTGACATAATATATCGTTACCTAATAATATTATGAATGATGATTATGC
*
7268 ATAACGTCACCATATA
1 ATAACGTCACTATATA
7284 GAATGTCACC
Statistics
Matches: 179, Mismatches: 26, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
191 2 0.01
192 64 0.36
193 112 0.63
194 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (192 bp):
ATAACGTCACTATATAATTAATATTCAATGACAACTAATTACGTACTAAATTAAATAAAATTTCG
TTATTGATAGCTTATATCGTCACAAATAATACATTAAAATCAACATATATATGACGAAAAAGATA
CTGTCAAATTTTTAGTGACATAATATATCGTTACCTAATAATATTATGAATGATGATTATGC
Found at i:8196 original size:18 final size:19
Alignment explanation
Indices: 8161--8205 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
8151 ATATGATTCA
*
8161 AAAATAAAAATTAGACTTT
1 AAAATAAAAATTAAACTTT
8180 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
*
8198 ATAATAAA
1 AAAATAAA
8206 TATCAGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:9824 original size:17 final size:17
Alignment explanation
Indices: 9790--9824 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9780 AATTTTTTTA
9790 ATTTTTTTTAAAATAAT
1 ATTTTTTTTAAAATAAT
9807 ATTTTATTTTAAAA-AAT
1 ATTTT-TTTTAAAATAAT
9824 A
1 A
9825 AAAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTTTTTAAAATAAT
Found at i:14772 original size:14 final size:14
Alignment explanation
Indices: 14753--14785 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
14743 GATAAACTGG
14753 AAATAGAGAA-AGTA
1 AAATAGAGAAGAG-A
14767 AAATAGAGAAGAGA
1 AAATAGAGAAGAGA
14781 AAATA
1 AAATA
14786 AGTAAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (14 bp):
AAATAGAGAAGAGA
Found at i:15235 original size:2 final size:2
Alignment explanation
Indices: 15224--15263 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
15214 ATGATAATAC
15224 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15264 ATTAACGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17248 original size:105 final size:105
Alignment explanation
Indices: 16872--17707 Score: 1163
Period size: 105 Copynumber: 8.0 Consensus size: 105
16862 GTATTGTTCC
* * * ** * * * *
16872 GAGTCCAATATCCTCCGCTGTGAAGTTGAATTTGGTTTTGGAACTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTG-TTGTTGACAA
** * * * * *
16937 TTAGCCGCCCCTTCG-CTGTGAAGTT-AAGCTTGTGCTGTCTC
65 CCAGCGGTCCCTTCGTC-GTGAAGTTGAA-CTTGCGTTGTCTG
* * * * **
16978 GAGTCTAATATCCTTCACTGTGAAGTTGAAATTGACTCTG-AA-T--GAAACT-TTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
*
17038 CAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
17078 GAGTCCAATATCC-T---TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
17139 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
17179 GAGTCCGATATTCTTTGTTGTGAAGTTGAAATCGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
* *
17244 CAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGCCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
17284 GAGTCCGATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
* *
17349 CAGCGGTCCATTCGTCGTGAATTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
17389 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATCGGCTCCGAAATTTGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
*
17454 CGGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
17494 GAGTCCAATATCCTTCTCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGCTGTTGTTGACAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
17559 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
17599 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCCGAAATTGGGAAGTTGTTATTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
17664 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
17704 GAGT
1 GAGT
17708 GATATCCTCC
Statistics
Matches: 663, Mismatches: 56, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
96 21 0.03
97 2 0.00
98 1 0.00
99 1 0.00
100 53 0.08
101 64 0.10
102 6 0.01
104 1 0.00
105 481 0.73
106 33 0.05
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:30971 original size:23 final size:23
Alignment explanation
Indices: 30936--30992 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
30926 CAAAACACTA
*
30936 CTAGTATAAAACCGCCCATAACAT
1 CTAGTA-AAAACCACCCATAACAT
* **
30960 CTAGTAAAAACCACCCTTAATTT
1 CTAGTAAAAACCACCCATAACAT
30983 CTAGTAAAAA
1 CTAGTAAAAA
30993 AATCATTTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.25
Consensus pattern (23 bp):
CTAGTAAAAACCACCCATAACAT
Found at i:31381 original size:43 final size:44
Alignment explanation
Indices: 31286--31395 Score: 138
Period size: 44 Copynumber: 2.6 Consensus size: 44
31276 TCGTGGTGTT
* *
31286 TATAACAAAAATGCCACTAAAGTACATGACTATGGCGGCGTTTA
1 TATAAAAAAAATGCCACTAAAGTACAAGACTATGGCGGCGTTTA
*
31330 TATAAAAAAAATGCCA-TAAAGGTACAAGACTATTGCGGCG-TT-
1 TATAAAAAAAATGCCACTAAA-GTACAAGACTATGGCGGCGTTTA
* *
31372 T-GAACAAAAATGCCACTAAAGTAC
1 TATAAAAAAAATGCCACTAAAGTAC
31396 GAGTATATAG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
41 16 0.27
42 5 0.08
43 6 0.10
44 32 0.54
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (44 bp):
TATAAAAAAAATGCCACTAAAGTACAAGACTATGGCGGCGTTTA
Found at i:31414 original size:41 final size:41
Alignment explanation
Indices: 31364--31519 Score: 172
Period size: 41 Copynumber: 3.9 Consensus size: 41
31354 CAAGACTATT
* * *
31364 GCGGCGTTTGAACAAAAATGCCACTAAAGTACGAGTATATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTATATA
* * * * *
31405 GCGGTGTTTGTATTAAAACGCCACTAAA-AACTAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTATATA
** * *
31445 GCGATGTTTGTAT-AAAACGCCACTAAACTACGAGTTTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTATATA
* *
31485 GTGGCGTTTGTATAAAAACGCCACTAAAGAACGAG
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
31520 CTTATCGAGG
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 14 0.15
40 40 0.42
41 42 0.44
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTATATA
Found at i:31455 original size:40 final size:41
Alignment explanation
Indices: 31378--31512 Score: 166
Period size: 40 Copynumber: 3.3 Consensus size: 41
31368 CGTTTGAACA
* *
31378 AAAATGCCACTAAAGTACGAGTATATAGCGGTGTTTGTATT
1 AAAACGCCACTAAACTACGAGTATATAGCGGTGTTTGTATT
* * * *
31419 AAAACGCCACTAAA-AACTAGTCTATAGCGATGTTTGTA-T
1 AAAACGCCACTAAACTACGAGTATATAGCGGTGTTTGTATT
* * * *
31458 AAAACGCCACTAAACTACGAGTTTATAGTGGCGTTTGTATA
1 AAAACGCCACTAAACTACGAGTATATAGCGGTGTTTGTATT
31499 AAAACGCCACTAAA
1 AAAACGCCACTAAA
31513 GAACGAGCTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
39 15 0.19
40 38 0.47
41 27 0.34
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (41 bp):
AAAACGCCACTAAACTACGAGTATATAGCGGTGTTTGTATT
Found at i:34639 original size:15 final size:16
Alignment explanation
Indices: 34605--34642 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
34595 TATTTAAGTG
*
34605 ATAAAAGCGATTAATAA
1 ATAAAAGCAATT-ATAA
34622 ATAAAAGCAATT-TAA
1 ATAAAAGCAATTATAA
34637 ATAAAA
1 ATAAAA
34643 AATAAGAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (16 bp):
ATAAAAGCAATTATAA
Found at i:43684 original size:19 final size:19
Alignment explanation
Indices: 43656--43700 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
43646 TTGTTATGAG
*
43656 TTTTAGCCATAAAACTATA
1 TTTTAACCATAAAACTATA
43675 TTTTAACCATAAAACTATA
1 TTTTAACCATAAAACTATA
43694 TTTTAAC
1 TTTTAAC
43701 AAACTCAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (19 bp):
TTTTAACCATAAAACTATA
Found at i:48391 original size:15 final size:16
Alignment explanation
Indices: 48371--48400 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48361 TATTAGAATA
48371 ATTTATTT-AATATTT
1 ATTTATTTCAATATTT
48386 ATTTATTTCAATATT
1 ATTTATTTCAATATT
48401 ATTATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTATTTCAATATTT
Found at i:48430 original size:25 final size:25
Alignment explanation
Indices: 48388--48435 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
48378 TAATATTTAT
*
48388 TTATTTCAATATTATTATTAAAATA
1 TTATTTCAATATTATTATAAAAATA
*
48413 TTATTTCTATAATT-TTATAAAAA
1 TTATTTCAAT-ATTATTATAAAAA
48436 AAATATCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATTTCAATATTATTATAAAAATA
Found at i:48543 original size:22 final size:23
Alignment explanation
Indices: 48518--48568 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
48508 ATATTATATT
48518 ATATTTTTAAAATTATTAAT-AA
1 ATATTTTTAAAATTATTAATAAA
* * *
48540 ATATATTTTAATATTTTTATTAAA
1 ATAT-TTTTAAAATTATTAATAAA
48564 ATATT
1 ATATT
48569 ATCATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.17
23 14 0.58
24 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTTTTAAAATTATTAATAAA
Found at i:50081 original size:187 final size:187
Alignment explanation
Indices: 49766--50138 Score: 737
Period size: 187 Copynumber: 2.0 Consensus size: 187
49756 TGGTTTTTGC
*
49766 TCGAGGAAGAAAGGAGAGTTAGGAAGAGGGTCGGTTTGAGTTTTGGCCGAGGAGGTTACTCGGGT
1 TCGAGGAAGAAAGGAGAGTTAGGAAGAGGGTCGGTCTGAGTTTTGGCCGAGGAGGTTACTCGGGT
49831 TTGTGATGGCCAACGGCGTTGAGGAGTTCCTTGCGAGCGGCACCGGCGTTGGAGCTTGGCTTTAA
66 TTGTGATGGCCAACGGCGTTGAGGAGTTCCTTGCGAGCGGCACCGGCGTTGGAGCTTGGCTTTAA
49896 GCCTTCTCGGCCGCCTGAAAGGAGGAGAGGAAGACTGAGAGAGGAAGATGAACCGGT
131 GCCTTCTCGGCCGCCTGAAAGGAGGAGAGGAAGACTGAGAGAGGAAGATGAACCGGT
49953 TCGAGGAAGAAAGGAGAGTTAGGAAGAGGGTCGGTCTGAGTTTTGGCCGAGGAGGTTACTCGGGT
1 TCGAGGAAGAAAGGAGAGTTAGGAAGAGGGTCGGTCTGAGTTTTGGCCGAGGAGGTTACTCGGGT
50018 TTGTGATGGCCAACGGCGTTGAGGAGTTCCTTGCGAGCGGCACCGGCGTTGGAGCTTGGCTTTAA
66 TTGTGATGGCCAACGGCGTTGAGGAGTTCCTTGCGAGCGGCACCGGCGTTGGAGCTTGGCTTTAA
50083 GCCTTCTCGGCCGCCTGAAAGGAGGAGAGGAAGACTGAGAGAGGAAGATGAACCGG
131 GCCTTCTCGGCCGCCTGAAAGGAGGAGAGGAAGACTGAGAGAGGAAGATGAACCGG
50139 GGGGTAGTTT
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 185 1.00
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (187 bp):
TCGAGGAAGAAAGGAGAGTTAGGAAGAGGGTCGGTCTGAGTTTTGGCCGAGGAGGTTACTCGGGT
TTGTGATGGCCAACGGCGTTGAGGAGTTCCTTGCGAGCGGCACCGGCGTTGGAGCTTGGCTTTAA
GCCTTCTCGGCCGCCTGAAAGGAGGAGAGGAAGACTGAGAGAGGAAGATGAACCGGT
Found at i:50643 original size:4 final size:4
Alignment explanation
Indices: 50634--50666 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
50624 CGCTAACTTG
50634 TTAT TTAT TTAT TTAT TTAT TTAT TTA- TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
50667 TATATTCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:51021 original size:2 final size:2
Alignment explanation
Indices: 50973--51006 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
50963 AGCCCCATGA
50973 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
51007 GCATATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52810 original size:3 final size:3
Alignment explanation
Indices: 52802--52833 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
52792 CATTCATTAA
52802 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52834 GATAAGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54456 original size:19 final size:19
Alignment explanation
Indices: 54432--54471 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
54422 ATTATTGACC
54432 TGACCCGAACCGTTAACTT
1 TGACCCGAACCGTTAACTT
**
54451 TGACCCGGCCCGTTAACTT
1 TGACCCGAACCGTTAACTT
54470 TG
1 TG
54472 GTCAGAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.28
Consensus pattern (19 bp):
TGACCCGAACCGTTAACTT
Found at i:56417 original size:31 final size:31
Alignment explanation
Indices: 56382--56460 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 31
56372 GATCCTTAGA
* *
56382 TAGGCTCTGCGGCCCCGAGATCTTTCTTGGG
1 TAGGCTCTGAGGCCCCGAGAACTTTCTTGGG
*
56413 TAGGCCTCCGAGGCCCCGAGAACTTTCTTGGG
1 TAGG-CTCTGAGGCCCCGAGAACTTTCTTGGG
*
56445 TAGGCTCTTAGGCCCC
1 TAGGCTCTGAGGCCCC
56461 CCAAGGTGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 14 0.33
32 28 0.67
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (31 bp):
TAGGCTCTGAGGCCCCGAGAACTTTCTTGGG
Found at i:63567 original size:20 final size:20
Alignment explanation
Indices: 63519--63580 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
63509 AACTTAAATC
*
63519 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
63539 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
63557 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
63576 AAAAT
1 AAAAT
63581 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:63660 original size:63 final size:64
Alignment explanation
Indices: 63575--63732 Score: 248
Period size: 63 Copynumber: 2.5 Consensus size: 64
63565 TTATATGATA
63575 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
63639 TAAAATTAATATCTATAATAT-ATATTAAAATATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
* * *
63702 TAAAATTAAAATCAAATAATATAAAATTAAA
1 TAAAATTAATATC-TATAATATAATATTAAA
63733 TATAAAACCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
62 28 0.32
63 38 0.44
64 14 0.16
65 7 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (64 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:63669 original size:37 final size:37
Alignment explanation
Indices: 63592--63678 Score: 108
Period size: 37 Copynumber: 2.3 Consensus size: 37
63582 AAATATCTAT
*
63592 AATA-TAATATTAAAAAATTAATATTTAATTTATTTAA
1 AATATTAATATT-AAAAATTAATATTTAATATATTTAA
63629 AA-ATTAATATT-AAAATTAATATCTATAATATATATTAA
1 AATATTAATATTAAAAATTAATAT-T-TAATATAT-TTAA
63667 AATATTAATATT
1 AATATTAATATT
63679 TAATTTATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
35 11 0.25
36 2 0.05
37 16 0.36
38 6 0.14
39 9 0.20
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (37 bp):
AATATTAATATTAAAAATTAATATTTAATATATTTAA
Found at i:63682 original size:25 final size:25
Alignment explanation
Indices: 63635--63703 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
63625 TTAAAAATTA
63635 ATATT-AAAATTAATATCTATAATAT
1 ATATTAAAAATTAATAT-TATAATAT
*
63660 ATATTAAAATATTAATATT-TAATTT
1 ATATTAAAA-ATTAATATTATAATAT
63685 AT-TTAAAAAATTAATATTA
1 ATATT-AAAAATTAATATTA
63704 AAATTAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 11 0.28
25 16 0.41
26 4 0.10
27 8 0.21
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATTAAAAATTAATATTATAATAT
Found at i:63697 original size:24 final size:26
Alignment explanation
Indices: 63640--63703 Score: 87
Period size: 24 Copynumber: 2.5 Consensus size: 26
63630 AATTAATATT
63640 AAAATTAATATCTATAATATATATTAA
1 AAAATTAATAT-TATAATATATATTAA
* *
63667 AATATTAATATT-TAATTTAT-TTAA
1 AAAATTAATATTATAATATATATTAA
63691 AAAATTAATATTA
1 AAAATTAATATTA
63704 AAATTAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 15 0.45
25 7 0.21
26 1 0.03
27 10 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AAAATTAATATTATAATATATATTAA
Found at i:63736 original size:12 final size:11
Alignment explanation
Indices: 63691--63739 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
63681 ATTTATTTAA
63691 AAAATTAATATT
1 AAAATTAATA-T
*
63703 AAAATTAAAAT
1 AAAATTAATAT
*
63714 CAAA-TAATAT
1 AAAATTAATAT
63724 AAAATTAAATAT
1 AAAATT-AATAT
63736 AAAA
1 AAAA
63740 CCTCTTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 8 0.26
11 5 0.16
12 18 0.58
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:64819 original size:23 final size:22
Alignment explanation
Indices: 64793--64835 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
64783 TATAAAAAAT
64793 TATTTTTCATTAAATATTTTTGG
1 TATTTTTCATTAAAT-TTTTTGG
* *
64816 TATTTTTTATTTAATTTTTT
1 TATTTTTCATTAAATTTTTT
64836 AAATAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (22 bp):
TATTTTTCATTAAATTTTTTGG
Found at i:65986 original size:103 final size:103
Alignment explanation
Indices: 65868--66105 Score: 297
Period size: 104 Copynumber: 2.3 Consensus size: 103
65858 AATTTCAAAT
* * *
65868 TTGTTTTACTTGAAACAATAAATTTTATCTCACTCGAGATTGTTATTTC-GAA-TCAAA-TTTCA
1 TTGTTTCACTCGAAACAA-AAATTTTATCTCACTCGAGATTGTT-TTTCAGAAGACAAACTTT-A
*
65930 TCTCGCTTGAGAT-GGTTTCCTTTGAAATACAAGTTTTGAAA
63 TCTCGCTTGAG-TCAGTTTCCTTTGAAATACAAGTTTTGAAA
* * * *
65971 TTGTTTCACTCGAAACAAAGAATTTTGTCTCACTTGATATTGTTTTTCATAAGACAAACTTTATC
1 TTGTTTCACTCGAAACAAA-AATTTTATCTCACTCGAGATTGTTTTTCAGAAGACAAACTTTATC
*
66036 TCGCTTGAGTCAGTTTCCTTTGAAATGCAAGTTTTGAAA
65 TCGCTTGAGTCAGTTTCCTTTGAAATACAAGTTTTGAAA
* *
66075 TTGTTTCACCCGAAA-TAAAATTTTATCTCAC
1 TTGTTTCACTCGAAACAAAAATTTTATCTCAC
66106 ATAAGATAAC
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
102 17 0.14
103 42 0.36
104 56 0.47
105 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (103 bp):
TTGTTTCACTCGAAACAAAAATTTTATCTCACTCGAGATTGTTTTTCAGAAGACAAACTTTATCT
CGCTTGAGTCAGTTTCCTTTGAAATACAAGTTTTGAAA
Found at i:66683 original size:116 final size:118
Alignment explanation
Indices: 66500--66721 Score: 304
Period size: 117 Copynumber: 1.9 Consensus size: 118
66490 AACAAAAAAA
* * * *
66500 GAGAAGAAGTTCATTATGAGAAGAACTTGTTCAACCTTTTCCCAAATCCATCACAAAAAAAGGTG
1 GAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACATTTTCCCAAATACATCACAAAAAAAGGTG
** *
66565 GATCGAAATTTTCAATGG-AGAGTTCATAATGAGAAGAACTAGTTCAAAAAGG
66 GATCGAAATTCCCAATGGAAAAGTTCATAATGAGAAGAACTAGTTCAAAAAGG
* * **
66617 GAGAAGAAGTTCGTAATAAGAAGAACTTGTT-AACATTTTCCCAAATACATCACAGAAGGAGGTG
1 GAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACATTTTCCCAAATACATCACAAAAAAAGGTG
* * *
66681 GATTGACATTCCCAATGGAAAAGTTCATAATGAGAATAACT
66 GATCGAAATTCCCAATGGAAAAGTTCATAATGAGAAGAACT
66722 TGTAGCTTAG
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
116 42 0.47
117 48 0.53
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (118 bp):
GAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACATTTTCCCAAATACATCACAAAAAAAGGTG
GATCGAAATTCCCAATGGAAAAGTTCATAATGAGAAGAACTAGTTCAAAAAGG
Done.