Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005472.1 Hibiscus syriacus cultivar Beakdansim tig00012535_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: 106093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11181 original size:49 final size:49
Alignment explanation
Indices: 11087--11181 Score: 113
Period size: 49 Copynumber: 1.9 Consensus size: 49
11077 AAGTCCAACA
* * * *
11087 AATTTAACAAAATAAAGTAAGTATTAAATGAGAAATAATAAAAAATTAC
1 AATTTAACAAAATAAAGTAAATATCAAATGAGAAAAAAAAAAAAATTAC
*
11136 AATTTAACAAAATAAAGTAAATA-CAAAT-ATAATAAAAAAACAAAAT
1 AATTTAACAAAATAAAGTAAATATCAAATGAGAA-AAAAAAA-AAAAT
11182 ATATCGATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
47 3 0.08
48 9 0.23
49 27 0.69
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (49 bp):
AATTTAACAAAATAAAGTAAATATCAAATGAGAAAAAAAAAAAAATTAC
Found at i:13321 original size:17 final size:18
Alignment explanation
Indices: 13280--13318 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
13270 TTTATATTAA
13280 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
*
13297 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAG
13315 TAAA
1 TAAA
13319 TACAGAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:13602 original size:51 final size:51
Alignment explanation
Indices: 13471--13609 Score: 142
Period size: 50 Copynumber: 2.8 Consensus size: 51
13461 GCCCCCTGCA
* **
13471 CCGCGCTATACCCTACGTGTCAGATAAAT-AG-GTATAGCGCGGAGCAGGGG
1 CCGCGCTATACCCCACGTGTC-GCCAAATCAGCGTATAGCGCGGAGCAGGGG
** * *
13521 CCGCGCTATA-CCCACGTGTAACCCAGTCAGCGTATAGCGCGGTA-CAGGGG
1 CCGCGCTATACCCCACGTGTCGCCAAATCAGCGTATAGCGCGG-AGCAGGGG
* * *
13571 GCGCGCTATACCCCACGTGGCGCCAAATCAGCATATAGC
1 CCGCGCTATACCCCACGTGTCGCCAAATCAGCGTATAGC
13610 ATGGGTCAGG
Statistics
Matches: 71, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
48 2 0.03
49 10 0.14
50 36 0.51
51 23 0.32
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.17
Consensus pattern (51 bp):
CCGCGCTATACCCCACGTGTCGCCAAATCAGCGTATAGCGCGGAGCAGGGG
Found at i:13767 original size:25 final size:25
Alignment explanation
Indices: 13738--13800 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
13728 TGACGTTGCT
*
13738 TTTTAAAAAGTGAATTTTAAAAGTA
1 TTTTAAAAAGTGAATTTTAAAAATA
* *
13763 TTTTAGAAACG-AAATTTTAAAAATA
1 TTTTA-AAAAGTGAATTTTAAAAATA
*
13788 TTATTTAAAAGTG
1 TT-TTAAAAAGTG
13801 TAAATTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (25 bp):
TTTTAAAAAGTGAATTTTAAAAATA
Found at i:14000 original size:26 final size:26
Alignment explanation
Indices: 13910--14001 Score: 69
Period size: 27 Copynumber: 3.5 Consensus size: 26
13900 CTTGAATTAT
* *
13910 ATTTACACTTATATATGAATTATATCA
1 ATTTAAAC-TATAAATGAATTATATCA
* * **
13937 ATTTAAACTAT-AATAAATTTTAAAA
1 ATTTAAACTATAAATGAATTATATCA
** * *
13962 AAATATTATTATAAATGAATTATATCA
1 ATTTA-AACTATAAATGAATTATATCA
13989 ATTTAAACTATAA
1 ATTTAAACTATAA
14002 TAAAAATATA
Statistics
Matches: 45, Mismatches: 18, Indels: 5
0.66 0.26 0.07
Matches are distributed among these distances:
25 12 0.27
26 13 0.29
27 20 0.44
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (26 bp):
ATTTAAACTATAAATGAATTATATCA
Found at i:14585 original size:14 final size:15
Alignment explanation
Indices: 14549--14593 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
14539 TTCCAAAGTA
* *
14549 CTTAACATTTTTAAT
1 CTTAATATTTATAAT
14564 -TT-ATATTTA-AAT
1 CTTAATATTTATAAT
14576 CTTAATATTTATAAT
1 CTTAATATTTATAAT
14591 CTT
1 CTT
14594 TTACACGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 3 0.12
13 7 0.28
14 9 0.36
15 6 0.24
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
CTTAATATTTATAAT
Found at i:22428 original size:4 final size:4
Alignment explanation
Indices: 22419--22444 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
22409 CCTTGATGTT
22419 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
22445 GACCTTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:23262 original size:23 final size:23
Alignment explanation
Indices: 23231--23292 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
23221 TATTTGTATT
*
23231 TGTTTATTTATTGTTC-TAGAACA
1 TGTTCATTTATTGTTCAT-GAACA
*
23254 TGTTCATTTATATGTTCATTAACA
1 TGTTCATTTAT-TGTTCATGAACA
* *
23278 TGTTCGTTTAGTGTT
1 TGTTCATTTATTGTT
23293 AGTTTATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 14 0.42
24 18 0.55
25 1 0.03
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (23 bp):
TGTTCATTTATTGTTCATGAACA
Found at i:32283 original size:27 final size:26
Alignment explanation
Indices: 32235--32285 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
32225 GATACAGAAA
*
32235 AAAATAGGGTTATTGAGAATTTATTT
1 AAAATAGGGTTATTGAAAATTTATTT
* *
32261 AAAATAGGGTTTTTTAAATATTTAT
1 AAAATAGGGTTATTGAAA-ATTTAT
32286 CAAATTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (26 bp):
AAAATAGGGTTATTGAAAATTTATTT
Found at i:40637 original size:16 final size:16
Alignment explanation
Indices: 40591--40635 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
40581 TTCATGTAAA
40591 ATAAATATTTAAATTT
1 ATAAATATTTAAATTT
*
40607 AAAAATATTTAAATTT
1 ATAAATATTTAAATTT
40623 ATTAAATATTTAA
1 A-TAAATATTTAA
40636 TTAAGTAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATATTTAAATTT
Found at i:45437 original size:14 final size:14
Alignment explanation
Indices: 45418--45448 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
45408 ATTATTTTAG
*
45418 ATCAAATTTTATCT
1 ATCAAATTTTATAT
45432 ATCAAATTTTATAT
1 ATCAAATTTTATAT
45446 ATC
1 ATC
45449 CCTGGAGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (14 bp):
ATCAAATTTTATAT
Found at i:46000 original size:10 final size:10
Alignment explanation
Indices: 45985--46043 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
45975 CATTTAATAA
45985 ATAAACGAAC
1 ATAAACGAAC
45995 ATAAACGAAC
1 ATAAACGAAC
** *
46005 ACGAAC-ATAA
1 ATAAACGA-AC
46015 ATGAACACGAAC
1 AT-AA-ACGAAC
46027 ATAAACGAAC
1 ATAAACGAAC
46037 ATAAACG
1 ATAAACG
46044 TTGGAGACCT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:46010 original size:16 final size:16
Alignment explanation
Indices: 45989--46037 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
45979 TAATAAATAA
45989 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
46005 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
46021 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
46037 A
1 A
46038 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:46158 original size:31 final size:31
Alignment explanation
Indices: 46098--46213 Score: 205
Period size: 31 Copynumber: 3.7 Consensus size: 31
46088 AGTATTGCTG
* *
46098 AGCTCGACTCGAACTCAAAAAATTTCAAAGTC
1 AGCTCGACTCG-ACTCGAAAACTTTCAAAGTC
46130 AGCTCGACTCGACTCGAAAACTTTCAAAGTC
1 AGCTCGACTCGACTCGAAAACTTTCAAAGTC
46161 AGCTCGACTCGACTCGAAAACTTTCAAAGTC
1 AGCTCGACTCGACTCGAAAACTTTCAAAGTC
46192 AGCTCGACTCGACTCGAAAACT
1 AGCTCGACTCGACTCGAAAACT
46214 CGTGAGCTTA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
31 71 0.87
32 11 0.13
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (31 bp):
AGCTCGACTCGACTCGAAAACTTTCAAAGTC
Found at i:46370 original size:11 final size:11
Alignment explanation
Indices: 46329--46370 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
46319 TCGAGAATCG
*
46329 AGCTCGATTGA
1 AGCTCGACTGA
46340 AGCTCGATTCTG-
1 AGCTCGA--CTGA
46352 AGCTCGACTGA
1 AGCTCGACTGA
46363 AGCTCGAC
1 AGCTCGAC
46371 ATTGCCCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 3 0.11
11 15 0.56
12 7 0.26
13 2 0.07
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (11 bp):
AGCTCGACTGA
Found at i:46622 original size:23 final size:23
Alignment explanation
Indices: 46592--46638 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
46582 CATTAGCTTC
46592 GTGCTATGTAGAAGTTGAAAATT
1 GTGCTATGTAGAAGTTGAAAATT
46615 GTGCTATGTAGAAGTTGAAAATT
1 GTGCTATGTAGAAGTTGAAAATT
46638 G
1 G
46639 GGAGATGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (23 bp):
GTGCTATGTAGAAGTTGAAAATT
Found at i:51634 original size:3 final size:3
Alignment explanation
Indices: 51626--51652 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
51616 GGTCAAAAAA
51626 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
51653 ATCATACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:56109 original size:13 final size:13
Alignment explanation
Indices: 56091--56120 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
56081 GATACACTGC
56091 TACAGTGTACCGA
1 TACAGTGTACCGA
56104 TACAGTGTACCGA
1 TACAGTGTACCGA
56117 TACA
1 TACA
56121 TTCAATGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (13 bp):
TACAGTGTACCGA
Found at i:58077 original size:30 final size:30
Alignment explanation
Indices: 58041--58141 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 30
58031 TTCGAATCGA
58041 ATTAATCAATAACTGAACTTTAAAAAAATT
1 ATTAATCAATAACTGAACTTTAAAAAAATT
* * * ***
58071 ATTAATCATTAACTG-A--GTGAACCGA--
1 ATTAATCAATAACTGAACTTTAAAAAAATT
58096 ATTAATCAATAACTGAACTTTAAAAAAATT
1 ATTAATCAATAACTGAACTTTAAAAAAATT
*
58126 ATTAATCATTAACTGA
1 ATTAATCAATAACTGA
58142 GTGAACATAA
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
25 14 0.26
26 1 0.02
27 4 0.08
28 4 0.08
29 1 0.02
30 29 0.55
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.33
Consensus pattern (30 bp):
ATTAATCAATAACTGAACTTTAAAAAAATT
Found at i:58097 original size:55 final size:55
Alignment explanation
Indices: 58038--58147 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
58028 GATTTCGAAT
58038 CGAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGTGAAC
1 CGAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGTGAAC
58093 CGAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGTGAAC
1 CGAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGTGAAC
58148 ATAAAATTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (55 bp):
CGAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGTGAAC
Found at i:58586 original size:14 final size:14
Alignment explanation
Indices: 58564--58612 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
58554 TAAGTAATAT
*
58564 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
58578 GTTCATTTA---T-
1 GTTCATTTATGTTC
*
58588 GTTCATTTGTGTTC
1 GTTCATTTATGTTC
58602 GTTCATTTATG
1 GTTCATTTATG
58613 CGTGTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
10 8 0.29
11 1 0.04
13 1 0.04
14 18 0.64
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:58600 original size:24 final size:24
Alignment explanation
Indices: 58561--58612 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
58551 CGTTAAGTAA
*
58561 TATGTTCGTTTATGTTCGTTCATT
1 TATGTTCATTTATGTTCGTTCATT
*
58585 TATGTTCATTTGTGTTCGTTCATT
1 TATGTTCATTTATGTTCGTTCATT
58609 TATG
1 TATG
58613 CGTGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.58
Consensus pattern (24 bp):
TATGTTCATTTATGTTCGTTCATT
Found at i:58851 original size:24 final size:23
Alignment explanation
Indices: 58818--58889 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
58808 TTTATGCTCA
58818 TTTATTGTGTTCATTTACGTTCG
1 TTTATTGTGTTCATTTACGTTCG
* * * *
58841 TTTGTTTGTGTTCGTTAACGTTTG
1 TTT-ATTGTGTTCATTTACGTTCG
*
58865 TTTATTGTGTTCATTTATGTTCG
1 TTTATTGTGTTCATTTACGTTCG
58888 TT
1 TT
58890 AACATCCGTC
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.11, C:0.10, G:0.19, T:0.60
Consensus pattern (23 bp):
TTTATTGTGTTCATTTACGTTCG
Found at i:59446 original size:30 final size:31
Alignment explanation
Indices: 59410--59474 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
59400 AATTAAAATA
*
59410 AATTTAATATAAGAATAAAATATATTTAAT-
1 AATTTAAAATAAGAATAAAATATATTTAATG
* *
59440 AATTTAAAATAATAATATAATATATTTAATG
1 AATTTAAAATAAGAATAAAATATATTTAATG
59471 AATT
1 AATT
59475 AAGATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (31 bp):
AATTTAAAATAAGAATAAAATATATTTAATG
Found at i:59532 original size:30 final size:30
Alignment explanation
Indices: 59497--59578 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
59487 ATACTTGAAA
*
59497 AAAGTTAAAATAATAGT-AAAATATATTTTG
1 AAAGTTAAAATAA-AATAAAAATATATTTTG
* *
59527 AAAGTTTAAATAAAATAAAAATATATTTTT
1 AAAGTTAAAATAAAATAAAAATATATTTTG
* *
59557 AAA-TAAAAATTAAAATTAAAAT
1 AAAGTTAAAA-TAAAATAAAAAT
59579 TAAAATAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
29 6 0.14
30 38 0.86
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (30 bp):
AAAGTTAAAATAAAATAAAAATATATTTTG
Found at i:59572 original size:12 final size:12
Alignment explanation
Indices: 59557--59596 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
59547 ATATATTTTT
59557 AAATAAAAATTA
1 AAATAAAAATTA
*
59569 AAATTAAAATTA
1 AAATAAAAATTA
59581 AAATAAAAA-TA
1 AAATAAAAATTA
59592 AAATA
1 AAATA
59597 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAATAAAAATTA
Found at i:59604 original size:23 final size:24
Alignment explanation
Indices: 59534--59609 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 24
59524 TTGAAAGTTT
59534 AAAT-AAAATAAAAATATATTTTT-
1 AAATAAAAAT-AAAATATATTTTTA
***
59557 AAATAAAAATTAAAAT-TAAAATTA
1 AAATAAAAA-TAAAATATATTTTTA
59581 AAATAAAAATAAAATAT-TTTTTA
1 AAATAAAAATAAAATATATTTTTA
59604 AAATAA
1 AAATAA
59610 GTTAATAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 23 0.53
24 19 0.44
25 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AAATAAAAATAAAATATATTTTTA
Found at i:59623 original size:16 final size:17
Alignment explanation
Indices: 59602--59634 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59592 AAATATTTTT
59602 TAAAATA-AGTTAATAA
1 TAAAATATAGTTAATAA
*
59618 TAAAATATATTTAATAA
1 TAAAATATAGTTAATAA
59635 GTTAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAAATATAGTTAATAA
Found at i:59633 original size:25 final size:24
Alignment explanation
Indices: 59605--59678 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
59595 TATTTTTTAA
59605 AATAAGTTAATAATAAAATATATTT
1 AATAAGTTAATAATAAAA-ATATTT
59630 AATAAGTTAAT-ATAAAAATATTT
1 AATAAGTTAATAATAAAAATATTT
**
59653 TTTAAAGTTAATATATATAAAATATT
1 AAT-AAGTTAATA-ATA-AAAATATT
59679 ATGGATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.16
24 14 0.33
25 11 0.26
26 3 0.07
27 8 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AATAAGTTAATAATAAAAATATTT
Found at i:59660 original size:24 final size:26
Alignment explanation
Indices: 59605--59678 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 26
59595 TATTTTTTAA
59605 AATAAGTTAATA-ATAAAATATATTT
1 AATAAGTTAATATATAAAATATATTT
*
59630 AATAAGTTAATATA-AAAATATTTTT
1 AATAAGTTAATATATAAAATATATTT
*
59655 TA-AAGTTAATATATATAAA-ATATT
1 AATAAGTTAATATATA-AAATATATT
59679 ATGGATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
24 11 0.26
25 28 0.65
26 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AATAAGTTAATATATAAAATATATTT
Found at i:60513 original size:29 final size:30
Alignment explanation
Indices: 60481--60549 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
60471 AATGTGCGAT
** * *
60481 CCTTATTTGGTCATTT-TGAAATGTTATGC
1 CCTTATTTGACCATTTGTCAAATGTTAGGC
*
60510 CCTTATTCGACCATTTGTCAAATGTTAGGC
1 CCTTATTTGACCATTTGTCAAATGTTAGGC
60540 CCTTATTTGA
1 CCTTATTTGA
60550 ATAACCTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (30 bp):
CCTTATTTGACCATTTGTCAAATGTTAGGC
Found at i:61472 original size:32 final size:32
Alignment explanation
Indices: 61436--61496 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
61426 TAGGCAGTCC
*
61436 TTTATCCCATTGTTGGGATAATTTTTGTATCT
1 TTTATCCCATTGCTGGGATAATTTTTGTATCT
*
61468 TTTATCCCATTGCTGGGATTATTTTTGTA
1 TTTATCCCATTGCTGGGATAATTTTTGTA
61497 GAAGAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.52
Consensus pattern (32 bp):
TTTATCCCATTGCTGGGATAATTTTTGTATCT
Found at i:64234 original size:15 final size:15
Alignment explanation
Indices: 64214--64358 Score: 227
Period size: 15 Copynumber: 9.7 Consensus size: 15
64204 TATTTTGCTT
* * *
64214 AATCATTCAACACCG
1 AATCATTCAGCTCTG
64229 AATCATTCAGCTCTG
1 AATCATTCAGCTCTG
64244 AATCATTCAGCTCTG
1 AATCATTCAGCTCTG
* *
64259 AATCATTCAACACTG
1 AATCATTCAGCTCTG
*
64274 AATCATTCAGCACTG
1 AATCATTCAGCTCTG
64289 AATCATTCAGCTCTG
1 AATCATTCAGCTCTG
64304 AATCATTCAGCTCTG
1 AATCATTCAGCTCTG
*
64319 AATCATTCAGCTTTG
1 AATCATTCAGCTCTG
64334 AATCATTCAGCTCTG
1 AATCATTCAGCTCTG
64349 AATCATTCAG
1 AATCATTCAG
64359 AGGTGAGAAA
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 121 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (15 bp):
AATCATTCAGCTCTG
Found at i:65086 original size:23 final size:20
Alignment explanation
Indices: 65045--65085 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
65035 CGTCAACGAG
*
65045 TAATAATTCTGGCAATCTTC
1 TAATAATTATGGCAATCTTC
65065 TAATAATTATGGCAATCTTC
1 TAATAATTATGGCAATCTTC
65085 T
1 T
65086 TATATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
TAATAATTATGGCAATCTTC
Found at i:68694 original size:3 final size:3
Alignment explanation
Indices: 68680--68762 Score: 85
Period size: 3 Copynumber: 27.7 Consensus size: 3
68670 CTCGCTGCCA
* * * * *
68680 TCG TCA TCG TCG TCG TCG TCG TCA CCA TCG TCA TCG TCG TCG TCG TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
* * * *
68728 TCA CCA TCG TCA TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
68763 CTGAGCAGGT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.08, C:0.36, G:0.24, T:0.31
Consensus pattern (3 bp):
TCG
Found at i:68715 original size:27 final size:27
Alignment explanation
Indices: 68677--68756 Score: 160
Period size: 27 Copynumber: 3.0 Consensus size: 27
68667 CTCCTCGCTG
68677 CCATCGTCATCGTCGTCGTCGTCGTCA
1 CCATCGTCATCGTCGTCGTCGTCGTCA
68704 CCATCGTCATCGTCGTCGTCGTCGTCA
1 CCATCGTCATCGTCGTCGTCGTCGTCA
68731 CCATCGTCATCGTCGTCGTCGTCGTC
1 CCATCGTCATCGTCGTCGTCGTCGTC
68757 GTCGTCCTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.10, C:0.38, G:0.23, T:0.30
Consensus pattern (27 bp):
CCATCGTCATCGTCGTCGTCGTCGTCA
Found at i:68886 original size:33 final size:33
Alignment explanation
Indices: 68844--68917 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
68834 ACCGGCCTGC
68844 GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
1 GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
68877 GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
1 GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
68910 GAAAACTG
1 GAAAACTG
68918 TACAGGAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (33 bp):
GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
Found at i:70772 original size:111 final size:111
Alignment explanation
Indices: 70640--70861 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
70630 ATTACAAAAA
* *
70640 TTAATTCTTAATCTAATAATCATGCATTAAATAAATTAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
70705 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
70751 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
70816 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
70862 ATGATTTTCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
Found at i:71194 original size:50 final size:50
Alignment explanation
Indices: 71140--71265 Score: 130
Period size: 50 Copynumber: 2.5 Consensus size: 50
71130 AGATACCCAT
* ** *
71140 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGTGCCAGATCACC
1 GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGACGCCAAATCACC
* * ** * *
71190 GTATATCACGGGGCAGGGAGCGCGCTATACCCACGTGACGCCAAATCAGC
1 GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGACGCCAAATCACC
71240 GTATAACGC-GATTCAGGAGGG-GCGCT
1 GTATAACGCGGA-TCAGG-GGGCGCGCT
71266 TTACTGCTAC
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
49 1 0.02
50 57 0.95
51 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.16
Consensus pattern (50 bp):
GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGACGCCAAATCACC
Found at i:73404 original size:23 final size:23
Alignment explanation
Indices: 73352--73397 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
73342 ACAATCCAAA
73352 AGATTGATGAGTTTAATTAAATT
1 AGATTGATGAGTTTAATTAAATT
73375 AGATTGATGAGTTTAATTAAATT
1 AGATTGATGAGTTTAATTAAATT
73398 TAATTGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.43
Consensus pattern (23 bp):
AGATTGATGAGTTTAATTAAATT
Found at i:74862 original size:14 final size:14
Alignment explanation
Indices: 74843--74886 Score: 70
Period size: 14 Copynumber: 3.0 Consensus size: 14
74833 TAACAGACTT
74843 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
74857 GTCTGTTTTCTACACA
1 GTCTGTTTTCT--ACA
74873 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
74887 TGGTATCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:74875 original size:16 final size:16
Alignment explanation
Indices: 74843--74886 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
74833 TAACAGACTT
74843 GTCTGTTTTCT--ACA
1 GTCTGTTTTCTACACA
74857 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
74873 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
74887 TGGTATCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.39
16 17 0.61
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:75048 original size:7 final size:8
Alignment explanation
Indices: 75022--75058 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
75012 TCTCAATCTA
75022 ATTTTCAG
1 ATTTTCAG
75030 ATTTTCAG
1 ATTTTCAG
75038 ATTTT-AG
1 ATTTTCAG
*
75045 A-TTTCAA
1 ATTTTCAG
75052 ATTTTCA
1 ATTTTCA
75059 AAGCAACAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 3 0.12
7 5 0.19
8 18 0.69
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (8 bp):
ATTTTCAG
Found at i:78921 original size:16 final size:16
Alignment explanation
Indices: 78889--78948 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
78879 TAACAGACTT
78889 GTCTGTTTTCT--ACA
1 GTCTGTTTTCTACACA
78903 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
78919 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
*
78935 GTTTGTTTTCTACA
1 GTCTGTTTTCTACA
78949 TGAACTTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
14 11 0.26
16 32 0.74
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.48
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:82946 original size:24 final size:24
Alignment explanation
Indices: 82919--82967 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
82909 TGCATCCAAT
82919 TGTAAGGTCATTTATTGTAGTAAC
1 TGTAAGGTCATTTATTGTAGTAAC
82943 TGTAAGGTCATTTATTGTAGTAAC
1 TGTAAGGTCATTTATTGTAGTAAC
82967 T
1 T
82968 TTTCTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (24 bp):
TGTAAGGTCATTTATTGTAGTAAC
Found at i:90611 original size:31 final size:31
Alignment explanation
Indices: 90534--90603 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
90524 CTTTTAAAAC
* * *
90534 TTGCAATACAATCCCCTAACATTTAGTTCAT
1 TTGCAATACAGTCCCCCAACATTTAGTCCAT
*
90565 TTGCAATACAGTCCCCCAACATTTAGTCCGT
1 TTGCAATACAGTCCCCCAACATTTAGTCCAT
90596 TTGCAATA
1 TTGCAATA
90604 TGGTCCCCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (31 bp):
TTGCAATACAGTCCCCCAACATTTAGTCCAT
Found at i:93025 original size:20 final size:18
Alignment explanation
Indices: 93000--93036 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
92990 CTTATCCCTC
93000 TATATATAGAGACAACAT
1 TATATATAGAGACAACAT
93018 TATATATAGAGACAACAT
1 TATATATAGAGACAACAT
93036 T
1 T
93037 TTCTTTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (18 bp):
TATATATAGAGACAACAT
Found at i:93770 original size:6 final size:6
Alignment explanation
Indices: 93759--93786 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
93749 TCATCATCAA
93759 CAAGCT CAAGCT CAAGCT CAAGCT CAAG
1 CAAGCT CAAGCT CAAGCT CAAGCT CAAG
93787 GTATGTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.18, T:0.14
Consensus pattern (6 bp):
CAAGCT
Found at i:95590 original size:17 final size:17
Alignment explanation
Indices: 95568--95603 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
95558 AATTTTTAAT
*
95568 TACTCATCGATTAAGGG
1 TACTCATAGATTAAGGG
95585 TACTCATAGATTAAGGG
1 TACTCATAGATTAAGGG
95602 TA
1 TA
95604 GTTATTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (17 bp):
TACTCATAGATTAAGGG
Found at i:96168 original size:3 final size:3
Alignment explanation
Indices: 96160--96189 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
96150 CTTAAAAATA
96160 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
96190 AAAAGAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:97208 original size:2 final size:2
Alignment explanation
Indices: 97201--97230 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
97191 ATTTATTTTA
97201 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
97231 GCATATGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.