Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003327.1 Hibiscus syriacus cultivar Beakdansim tig00007008_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: 65364
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:545 original size:6 final size:6
Alignment explanation
Indices: 534--608 Score: 96
Period size: 6 Copynumber: 12.5 Consensus size: 6
524 TCTCGTCTCG
** **
534 GGTCGT GGTCGT GGTCGT GGTAAT GGTAAT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
**
582 GGTAAT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
609 AATGGTATGG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.08, C:0.12, G:0.47, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:567 original size:24 final size:24
Alignment explanation
Indices: 539--614 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
529 TCTCGGGTCG
**
539 TGGTCGTGGTCGTGGTAATGGTAA
1 TGGTCGTGGTCGTGGTCGTGGTAA
563 TGGTCGTGGTCGTGGTCGTGGTAA
1 TGGTCGTGGTCGTGGTCGTGGTAA
587 TGGTCGTGGTCGTGGTCGTGGTAA
1 TGGTCGTGGTCGTGGTCGTGGTAA
611 TGGT
1 TGGT
615 ATGGTAATAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.11, C:0.11, G:0.45, T:0.34
Consensus pattern (24 bp):
TGGTCGTGGTCGTGGTCGTGGTAA
Found at i:568 original size:30 final size:30
Alignment explanation
Indices: 534--622 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
524 TCTCGTCTCG
534 GGTCGTGGTCGTGGTCGTGGTAATGGTAAT
1 GGTCGTGGTCGTGGTCGTGGTAATGGTAAT
**
564 GGTCGTGGTCGTGGTCGTGGTAATGGTCGT
1 GGTCGTGGTCGTGGTCGTGGTAATGGTAAT
**
594 GGTCGTGGTCGTGGTAATGGT-ATGGTAAT
1 GGTCGTGGTCGTGGTCGTGGTAATGGTAAT
623 ACGTGTCTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 6 0.11
30 47 0.89
ACGTcount: A:0.12, C:0.10, G:0.44, T:0.34
Consensus pattern (30 bp):
GGTCGTGGTCGTGGTCGTGGTAATGGTAAT
Found at i:614 original size:12 final size:12
Alignment explanation
Indices: 557--614 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
547 GTCGTGGTAA
557 TGGTAATGGTCG
1 TGGTAATGGTCG
**
569 TGGTCGTGGTCG
1 TGGTAATGGTCG
581 TGGTAATGGTCG
1 TGGTAATGGTCG
**
593 TGGTCGTGGTCG
1 TGGTAATGGTCG
605 TGGTAATGGT
1 TGGTAATGGT
615 ATGGTAATAC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.10, C:0.10, G:0.45, T:0.34
Consensus pattern (12 bp):
TGGTAATGGTCG
Found at i:750 original size:21 final size:21
Alignment explanation
Indices: 724--774 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
714 GAAATGGAAA
724 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
745 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
766 ATCGCAACG
1 ATCGCAACG
775 CGATTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:5348 original size:31 final size:31
Alignment explanation
Indices: 5301--5362 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5291 TTTCTACTTC
* * * *
5301 TTAATGTGGTCTTCTAACTCATAAAATAAAT
1 TTAACGTGGTCCTCTAACTCAGAAAACAAAT
*
5332 TTAACGTGGTCCTCTAATTCAGAAAACAAAT
1 TTAACGTGGTCCTCTAACTCAGAAAACAAAT
5363 CCAATATGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (31 bp):
TTAACGTGGTCCTCTAACTCAGAAAACAAAT
Found at i:5757 original size:12 final size:12
Alignment explanation
Indices: 5731--5772 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5721 TAATAAATTG
5731 AAATAAA-AGAA
1 AAATAAAGAGAA
*
5742 AAATAAAGATAA
1 AAATAAAGAGAA
5754 AAATAAAG-GAA
1 AAATAAAGAGAA
5765 AAACTAAA
1 AAA-TAAA
5773 TGATTGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 12 0.44
12 15 0.56
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (12 bp):
AAATAAAGAGAA
Found at i:7755 original size:60 final size:60
Alignment explanation
Indices: 7677--7795 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
7667 CAAGTGGTCA
* * * *
7677 TTTTATAACTTTTGATAGTC-GAATGACTCAACAGAATAACATGTCATAGTTGAGAGACCG
1 TTTTATAACTTTTAATAGTCGGAA-GACTCAACAAAATAACATCTCATAGTCGAGAGACCG
* * * *
7737 TTTTGTAACTTTTAATAGTCGGAAGACTTAACAAAATAATATCTTATAGTCGAGAGACC
1 TTTTATAACTTTTAATAGTCGGAAGACTCAACAAAATAACATCTCATAGTCGAGAGACC
7796 ATTCGTGTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
60 47 0.94
61 3 0.06
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (60 bp):
TTTTATAACTTTTAATAGTCGGAAGACTCAACAAAATAACATCTCATAGTCGAGAGACCG
Found at i:19977 original size:92 final size:92
Alignment explanation
Indices: 19818--20001 Score: 341
Period size: 92 Copynumber: 2.0 Consensus size: 92
19808 CTTTTGTTCT
* *
19818 TTTTACTCACGTTATCAGCATTTTTTATTAACAGGTCACTTAGGCGGCATGGTCAATCTTTACAG
1 TTTTACTCACGTTATCAGCATTTTTTATGAACAGGTCACTTAGACGGCATGGTCAATCTTTACAG
19883 AAAGTAAACAGAGGCATGATACTAGCC
66 AAAGTAAACAGAGGCATGATACTAGCC
*
19910 TTTTACTCACGTTATCAGCATTTTTTATGAACAGGTCACTTAGACGGCATGGTCAATCTTTAGAG
1 TTTTACTCACGTTATCAGCATTTTTTATGAACAGGTCACTTAGACGGCATGGTCAATCTTTACAG
19975 AAAGTAAACAGAGGCATGATACTAGCC
66 AAAGTAAACAGAGGCATGATACTAGCC
20002 CCTTTAGTAG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (92 bp):
TTTTACTCACGTTATCAGCATTTTTTATGAACAGGTCACTTAGACGGCATGGTCAATCTTTACAG
AAAGTAAACAGAGGCATGATACTAGCC
Found at i:28143 original size:60 final size:59
Alignment explanation
Indices: 28068--28189 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 59
28058 GTCTCCCGAT
* * * * * *
28068 TATAGGGTGATGCTTTGTTGAGTCTCCTGACTATTAAAAGTTATAAAATGATCACTCGAC
1 TATAGAGTGATGCTTTGTTAAGTCACATAACTATTAAAAGTTA-AAAATGATCACTCAAC
* * *
28128 TATAGAGTGTTGCTTTGTTAAGTCACATAACTATTAAAAGTTACAAATGGTCACTCAAC
1 TATAGAGTGATGCTTTGTTAAGTCACATAACTATTAAAAGTTAAAAATGATCACTCAAC
28187 TAT
1 TAT
28190 TCATATGTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 16 0.30
60 37 0.70
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (59 bp):
TATAGAGTGATGCTTTGTTAAGTCACATAACTATTAAAAGTTAAAAATGATCACTCAAC
Found at i:32109 original size:38 final size:36
Alignment explanation
Indices: 32067--32137 Score: 115
Period size: 38 Copynumber: 1.9 Consensus size: 36
32057 TTAGTTTTAT
*
32067 ATATTTTAATATTAATTTAATAAAATCATATATTTGAA
1 ATATTTTAATATTAATTCAA-AAAAT-ATATATTTGAA
32105 ATATTTTAATATTAATTCAAAAAATATATATTT
1 ATATTTTAATATTAATTCAAAAAATATATATTT
32138 ATATATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 8 0.25
37 5 0.16
38 19 0.59
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (36 bp):
ATATTTTAATATTAATTCAAAAAATATATATTTGAA
Found at i:33128 original size:2 final size:2
Alignment explanation
Indices: 33117--33152 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
33107 AGACAATTAC
33117 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33153 TTAAATAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35333 original size:29 final size:30
Alignment explanation
Indices: 35274--35435 Score: 95
Period size: 29 Copynumber: 5.5 Consensus size: 30
35264 TATCTTAACA
*
35274 TTAAAAAATATATTTT-ATTTTATATTAAT
1 TTAAAAAATATATTTTAAGTTTATATTAAT
** *
35303 TTATTAAATATATTTTAAGTTTAT-TTTAT
1 TTAAAAAATATATTTTAAGTTTATATTAAT
* * *
35332 TTAAAAAATAAATTTT-ACTCTTATTTTAA-
1 TTAAAAAATATATTTTAAGT-TTATATTAAT
* * * *
35361 CTAAAAAATATATCTT-ATTCTTATATTACCT
1 TTAAAAAATATATTTTAAGT-TTATATTA-AT
* *** *
35392 TT-AAAAATATATCTTATCCTTATATTAAC
1 TTAAAAAATATATTTTAAGTTTATATTAAT
*
35421 TT-AAAAATAGATTTT
1 TTAAAAAATATATTTT
35436 TATATTAACT
Statistics
Matches: 104, Mismatches: 23, Indels: 12
0.75 0.17 0.09
Matches are distributed among these distances:
28 2 0.02
29 71 0.68
30 30 0.29
31 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (30 bp):
TTAAAAAATATATTTTAAGTTTATATTAAT
Found at i:35400 original size:30 final size:30
Alignment explanation
Indices: 35364--35462 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 30
35354 ATTTTAACTA
35364 AAAAATATATCTTATTCTTATATTACCTTT
1 AAAAATATATCTTATTCTTATATTACCTTT
* *
35394 AAAAATATATCTTATCCTTATATTAAC-TT
1 AAAAATATATCTTATTCTTATATTACCTTT
* *
35423 AAAAATAGA---T-TT-TTATATTAACTTTT
1 AAAAATATATCTTATTCTTATATT-ACCTTT
35449 AAAAATATATCTTA
1 AAAAATATATCTTA
35463 AATTAAAGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
24 7 0.12
25 2 0.04
26 11 0.20
29 11 0.20
30 25 0.45
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.46
Consensus pattern (30 bp):
AAAAATATATCTTATTCTTATATTACCTTT
Found at i:35547 original size:28 final size:29
Alignment explanation
Indices: 35507--35576 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
35497 AAGATAAAAA
*
35507 TAAAATACT-TTTTGAA-CTAAAATAAGAT
1 TAAAATA-TATTTTGAAGCTAAAATAAGAC
* * *
35535 TAAAATATATTTTTAAGTTAGAATAAGAC
1 TAAAATATATTTTGAAGCTAAAATAAGAC
35564 TAAAATATATTTT
1 TAAAATATATTTT
35577 TAATGTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.03
28 13 0.36
29 22 0.61
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (29 bp):
TAAAATATATTTTGAAGCTAAAATAAGAC
Found at i:35559 original size:29 final size:30
Alignment explanation
Indices: 35527--35584 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
35517 TTTGAACTAA
*
35527 AATAAGATTAAAATATATTTTTAA-GTTAG
1 AATAAGACTAAAATATATTTTTAATGTTAG
35556 AATAAGACTAAAATATATTTTTAATGTTA
1 AATAAGACTAAAATATATTTTTAATGTTA
35585 AGAAGTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (30 bp):
AATAAGACTAAAATATATTTTTAATGTTAG
Found at i:38208 original size:18 final size:18
Alignment explanation
Indices: 38187--38226 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38177 AGACCCGGAG
*
38187 GATGAGGAGGACGATGAA
1 GATGACGAGGACGATGAA
* *
38205 GATGACGAGGATGATGAT
1 GATGACGAGGACGATGAA
38223 GATG
1 GATG
38227 GAGGTGAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.42, T:0.17
Consensus pattern (18 bp):
GATGACGAGGACGATGAA
Found at i:39370 original size:28 final size:28
Alignment explanation
Indices: 39338--39392 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
39328 GAACAGGTCT
* *
39338 TGACCCATTGACTTTGATTGATCCGACC
1 TGACCCATTGACTTTGATCGACCCGACC
**
39366 TGACCTGTTGACTTTGATCGACCCGAC
1 TGACCCATTGACTTTGATCGACCCGAC
39393 TCGTTGACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (28 bp):
TGACCCATTGACTTTGATCGACCCGACC
Found at i:39387 original size:23 final size:24
Alignment explanation
Indices: 39355--39403 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
39345 TTGACTTTGA
*
39355 TTGATCCGACCTGAC-CTGTTGACT
1 TTGATCCGACCCGACTC-GTTGACT
39379 TTGAT-CGACCCGACTCGTTGACT
1 TTGATCCGACCCGACTCGTTGACT
39402 TT
1 TT
39404 TTCCGTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.35
Consensus pattern (24 bp):
TTGATCCGACCCGACTCGTTGACT
Found at i:39412 original size:13 final size:13
Alignment explanation
Indices: 39394--39419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39384 CGACCCGACT
39394 CGTTGACTTTTTC
1 CGTTGACTTTTTC
39407 CGTTGACTTTTTC
1 CGTTGACTTTTTC
39420 GATGACGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.15, T:0.54
Consensus pattern (13 bp):
CGTTGACTTTTTC
Found at i:40046 original size:30 final size:30
Alignment explanation
Indices: 40004--40101 Score: 142
Period size: 30 Copynumber: 3.3 Consensus size: 30
39994 TTCTAATTAG
* *
40004 GCATGGGATTAATTCCACGTTATGACATCT
1 GCATGAGATTAATTCCACGTTCTGACATCT
* *
40034 ACATGAGATTAATTCCTCGTTCTGACATCT
1 GCATGAGATTAATTCCACGTTCTGACATCT
* *
40064 GCATGAGATTAATTCCCCGTTCTGACATTT
1 GCATGAGATTAATTCCACGTTCTGACATCT
40094 GCATGAGA
1 GCATGAGA
40102 ATATATCTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (30 bp):
GCATGAGATTAATTCCACGTTCTGACATCT
Found at i:40314 original size:26 final size:26
Alignment explanation
Indices: 40280--40369 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
40270 ATATCTAAAT
40280 TTTAATATTGTTCGATTAATATTTTG
1 TTTAATATTGTTCGATTAATATTTTG
* * * *
40306 TTTATTATT-TTACG-GTAAAATATCTG
1 TTTAATATTGTT-CGATTAATAT-TTTG
*
40332 AATTTTAATATTGTTCGATTATTATTTTG
1 ---TTTAATATTGTTCGATTAATATTTTG
*
40361 TTTATTATT
1 TTTAATATT
40370 TTATGTTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 7 0.15
26 21 0.45
29 13 0.28
30 6 0.13
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.58
Consensus pattern (26 bp):
TTTAATATTGTTCGATTAATATTTTG
Found at i:40330 original size:55 final size:55
Alignment explanation
Indices: 40264--40372 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
40254 ACATTCTGCT
40264 GGTAAAATATCTAAATTTTAATATTGTTCGATTAATATTTTGTTTATTATTTTAC
1 GGTAAAATATCTAAATTTTAATATTGTTCGATTAATATTTTGTTTATTATTTTAC
* *
40319 GGTAAAATATCTGAATTTTAATATTGTTCGATTATTATTTTGTTTATTATTTTA
1 GGTAAAATATCTAAATTTTAATATTGTTCGATTAATATTTTGTTTATTATTTTA
40373 TGTTTGAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (55 bp):
GGTAAAATATCTAAATTTTAATATTGTTCGATTAATATTTTGTTTATTATTTTAC
Found at i:41898 original size:23 final size:23
Alignment explanation
Indices: 41851--41915 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
41841 AACCAATTTT
* *
41851 GACCCGTTAACTATGA-TCGACTC
1 GACCCGTTAACTTTGACT-GAATC
41874 GACCCG-TAGACTTTGACTGAATC
1 GACCCGTTA-ACTTTGACTGAATC
41897 GACCCGTTAACTTTGACTG
1 GACCCGTTAACTTTGACTG
41916 TTGACCTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 2 0.05
23 32 0.86
24 3 0.08
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (23 bp):
GACCCGTTAACTTTGACTGAATC
Found at i:42548 original size:30 final size:30
Alignment explanation
Indices: 42509--42584 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
42499 TGCATTTCTA
**
42509 ATTTGGCATGAGATTAATTCCCTGTTCTGAC
1 ATTT-GCATGAGATTAATTCCCAATTCTGAC
*
42540 ATTTGCATGGGATTAATTCCCAATTCTGAC
1 ATTTGCATGAGATTAATTCCCAATTCTGAC
*
42570 ATCTGCATGAGATTA
1 ATTTGCATGAGATTA
42585 TATCTCCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 36 0.90
31 4 0.10
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (30 bp):
ATTTGCATGAGATTAATTCCCAATTCTGAC
Found at i:53350 original size:22 final size:22
Alignment explanation
Indices: 53325--53372 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
53315 TACTATAATT
53325 AATTTATAT-ATTTTCTTTAAAA
1 AATTTATATAATTTT-TTTAAAA
*
53347 AATTTATATAATTTTTTTACAA
1 AATTTATATAATTTTTTTAAAA
53369 AATT
1 AATT
53373 GAAAAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTATATAATTTTTTTAAAA
Found at i:58134 original size:2 final size:2
Alignment explanation
Indices: 58129--58193 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
58119 ATACATACAC
58129 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
* * *
58171 AC AT AC AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
58194 GTTGTTAAGG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:58295 original size:9 final size:9
Alignment explanation
Indices: 58281--58314 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
58271 ATATTATTAG
58281 TAAAAAATA
1 TAAAAAATA
58290 TAAAAAATA
1 TAAAAAATA
*
58299 TATAAAAATT
1 TA-AAAAATA
58309 TAAAAA
1 TAAAAA
58315 TTTTACTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
TAAAAAATA
Found at i:58426 original size:3 final size:3
Alignment explanation
Indices: 58418--58461 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
58408 GGAAGAGAGC
58418 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
58462 ATCTTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.