Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002361.1 Hibiscus syriacus cultivar Beakdansim tig00004820_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: 139981
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:7084 original size:31 final size:33
Alignment explanation
Indices: 7039--7102 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 33
7029 TAATTTTAAA
* *
7039 AAAATTAAAAGTTTAGGTACTAAA-ATA-AATT
1 AAAACTAAAAGTTTAAGTACTAAATATATAATT
* *
7070 AAAACTAATAGTTTAAGTATTAAATATATAATT
1 AAAACTAAAAGTTTAAGTACTAAATATATAATT
7103 TACCCAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 20 0.74
32 3 0.11
33 4 0.15
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (33 bp):
AAAACTAAAAGTTTAAGTACTAAATATATAATT
Found at i:7215 original size:26 final size:25
Alignment explanation
Indices: 7186--7244 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
7176 GGCATTTAAC
*
7186 TTTTTGATGCAATTAAATA-CTAAATA
1 TTTTT-ATACAATTAAATATCT-AATA
* *
7212 TTTTTATATAATTAGATATCTAATA
1 TTTTTATACAATTAAATATCTAATA
7237 TTTTTATA
1 TTTTTATA
7245 TAAATATAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (25 bp):
TTTTTATACAATTAAATATCTAATA
Found at i:7224 original size:25 final size:25
Alignment explanation
Indices: 7196--7247 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
7186 TTTTTGATGC
7196 AATTAAATA-CTAAATATTTTTATAT
1 AATTAAATATCT-AATATTTTTATAT
*
7221 AATTAGATATCTAATATTTTTATAT
1 AATTAAATATCTAATATTTTTATAT
7246 AA
1 AA
7248 ATATAGAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTAAATATCTAATATTTTTATAT
Found at i:23446 original size:27 final size:27
Alignment explanation
Indices: 23408--23473 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
23398 TTTTCCAAAC
23408 TGTCCATAAAACCACTCCAGGAATAAG
1 TGTCCATAAAACCACTCCAGGAATAAG
23435 TGTCCATAAAACCACTCCAGGAATAAG
1 TGTCCATAAAACCACTCCAGGAATAAG
23462 TGTCCATAAAAC
1 TGTCCATAAAAC
23474 TACATCTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.20
Consensus pattern (27 bp):
TGTCCATAAAACCACTCCAGGAATAAG
Found at i:31524 original size:52 final size:50
Alignment explanation
Indices: 31406--31532 Score: 128
Period size: 52 Copynumber: 2.5 Consensus size: 50
31396 TTGAGGTGAC
* ** * * * *
31406 GAGTTTTAATAAAAAAAATATTTTTATTCAAACTTTTTACTTCGATGTGAT
1 GAGTTTTAAT-AAAAAAATATTTTTATTAAAACTGGTCACTTCAACGAGAT
* * *
31457 AAATTTTAATTAAAAAATTATATTTTATTAAAACTGGTCACTTCAACGAGAT
1 GAGTTTTAA-TAAAAAAATAT-TTTTATTAAAACTGGTCACTTCAACGAGAT
*
31509 GAGTTTGAATAAAAAAATATTTTT
1 GAGTTTTAATAAAAAAATATTTTT
31533 TAATGAAACT
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
50 4 0.07
51 26 0.43
52 30 0.50
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (50 bp):
GAGTTTTAATAAAAAAATATTTTTATTAAAACTGGTCACTTCAACGAGAT
Found at i:34909 original size:12 final size:12
Alignment explanation
Indices: 34892--34917 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34882 AGCAGAGATA
34892 TGAACTCGGGCG
1 TGAACTCGGGCG
34904 TGAACTCGGGCG
1 TGAACTCGGGCG
34916 TG
1 TG
34918 GTGAATTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.42, T:0.19
Consensus pattern (12 bp):
TGAACTCGGGCG
Found at i:41630 original size:40 final size:37
Alignment explanation
Indices: 41559--41657 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 37
41549 ATACCTAAAG
*
41559 TTTAATTTTTGTTTCATTTT-A-ACACAATTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAATACACAATTAAAAAC
*
41594 TTTAGTTTTTGTTTCATTTTAATACACAGCCGTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAATACACA---ATTAAAAAC
* *
41634 TTTAGATTTAGTTTCATTTTAATA
1 TTTAGTTTTTGTTTCATTTTAATA
41658 TTCGTTCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
35 19 0.35
36 1 0.02
37 5 0.09
40 30 0.55
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.49
Consensus pattern (37 bp):
TTTAGTTTTTGTTTCATTTTAATACACAATTAAAAAC
Found at i:43988 original size:5 final size:5
Alignment explanation
Indices: 43989--44044 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
43979 TTATATTATA
* * * * *
43989 ATAAT ATAAT ATAAT ATAAT ATAAG ATATT ATATT ATATT TTAAT A-ATAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
44039 ATAAT A
1 ATAAT A
44045 ATTATTAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
4 1 0.02
5 41 0.95
6 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (5 bp):
ATAAT
Found at i:44041 original size:20 final size:21
Alignment explanation
Indices: 43962--44066 Score: 62
Period size: 20 Copynumber: 5.2 Consensus size: 21
43952 TTTTAAATAT
* *
43962 TATTTTAATAAAATCA-ATTA
1 TATTTTAATAATATAATATTA
*
43982 TATTATAATAATATAATATAATA
1 TATTTTAATAATATAATAT--TA
* * * *
44005 TAATATAA-GATATTATATTA
1 TATTTTAATAATATAATATTA
*
44025 TATTTTAATAATAT-ATAATA
1 TATTTTAATAATATAATATTA
44045 -ATTATTAATAA-A-AAT-TTA
1 TATT-TTAATAATATAATATTA
44063 TATT
1 TATT
44067 ATTTATTAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
18 2 0.03
19 9 0.13
20 33 0.49
21 6 0.09
22 8 0.12
23 9 0.13
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
TATTTTAATAATATAATATTA
Found at i:44076 original size:43 final size:44
Alignment explanation
Indices: 43978--44076 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 44
43968 AATAAAATCA
*
43978 ATTATATTA-TAATAATATAATATAATATAATATAAGATATTAT
1 ATTATATTATTAATAATATAATATAATATAATATAAAATATTAT
44021 ATTATATT-TTAATAATAT-ATAATAATTATTAATA-AAAAT-TTAT
1 ATTATATTATTAATAATATAAT-ATAA-TA-TAATATAAAATATTAT
44064 ATTAT-TTATTAAT
1 ATTATATTATTAAT
44077 TTCATAGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
42 4 0.08
43 35 0.70
44 6 0.12
45 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (44 bp):
ATTATATTATTAATAATATAATATAATATAATATAAAATATTAT
Found at i:48404 original size:2 final size:2
Alignment explanation
Indices: 48397--48426 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48387 ACAGAATGAT
48397 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
48427 CAGTGTTAGG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:50644 original size:20 final size:20
Alignment explanation
Indices: 50608--50645 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50598 ATCCTATTCC
**
50608 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
50628 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
50646 AACCAAACGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:50670 original size:175 final size:175
Alignment explanation
Indices: 50379--50712 Score: 641
Period size: 175 Copynumber: 1.9 Consensus size: 175
50369 GTAATCTTAC
* *
50379 ATTCCTGCTAAACCAACTAAACACAAAATGCAACATTCTCAGTAATCTTATTCCCTGGTAATCTT
1 ATTCCTGCTAAACCAACTAAACACAAAATGCAACATTCCCAGTAATCCTATTCCCTGGTAATCTT
50444 TTATTCCCACTGGTAATATTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
66 TTATTCCCACTGGTAATATTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
50509 AAATTATCTCATATAAGACGTTGTTACAAAATGCAATAAGATTAT
131 AAATTATCTCATATAAGACGTTGTTACAAAATGCAATAAGATTAT
50554 ATTCCTGCTAAACCAACTAAACACAAAATGCAACATTCCCAGTAATCCTATTCCCTGGTAATCTT
1 ATTCCTGCTAAACCAACTAAACACAAAATGCAACATTCCCAGTAATCCTATTCCCTGGTAATCTT
*
50619 TTATTCCCACTGGTAATCTTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
66 TTATTCCCACTGGTAATATTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
50684 AAATTATCTCATATAAGACGTTGTTACAA
131 AAATTATCTCATATAAGACGTTGTTACAA
50713 TTATTATTGT
Statistics
Matches: 156, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
175 156 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (175 bp):
ATTCCTGCTAAACCAACTAAACACAAAATGCAACATTCCCAGTAATCCTATTCCCTGGTAATCTT
TTATTCCCACTGGTAATATTACATTCCAACCAAACGCACTCTTAATGTAATAAGATTATAATATA
AAATTATCTCATATAAGACGTTGTTACAAAATGCAATAAGATTAT
Found at i:51571 original size:18 final size:18
Alignment explanation
Indices: 51548--51591 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
51538 ACATTCCTAG
* *
51548 TAATCTTATTCCCGCTGA
1 TAATCTTATTCCCACCGA
*
51566 TAATCTTATTTCCACCGA
1 TAATCTTATTCCCACCGA
51584 TAATCTTA
1 TAATCTTA
51592 CATTCCGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (18 bp):
TAATCTTATTCCCACCGA
Found at i:52291 original size:34 final size:34
Alignment explanation
Indices: 52239--52319 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
52229 AAAATTAGTT
* *
52239 TATTATTTTTAATGATAA-TTATGAAAATTATAAAAC
1 TATT-TTTTTAATAATAATTTA-AAAAATTA-AAAAC
* *
52275 TATTTTTTTAA-AATAATTTAAAAAATTACAAAT
1 TATTTTTTTAATAATAATTTAAAAAATTAAAAAC
52308 TATTTTTTTAAT
1 TATTTTTTTAAT
52320 TTTTTTACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 14 0.36
34 11 0.28
35 10 0.26
36 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (34 bp):
TATTTTTTTAATAATAATTTAAAAAATTAAAAAC
Found at i:52879 original size:24 final size:25
Alignment explanation
Indices: 52852--52898 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
52842 TTAAATCCCA
*
52852 ACGA-TTTTTTAAGCGGGGACGAGT
1 ACGAGTTTTTTAAACGGGGACGAGT
52876 ACGAGTTTTTTAAACGGGGACGA
1 ACGAGTTTTTTAAACGGGGACGA
52899 AGACTAGGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.28, C:0.13, G:0.32, T:0.28
Consensus pattern (25 bp):
ACGAGTTTTTTAAACGGGGACGAGT
Found at i:53952 original size:32 final size:32
Alignment explanation
Indices: 53903--53976 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
53893 AGTGAACAGT
* *
53903 TTTTCAAT-AAGTTTAATAGTTATTTTATAATA
1 TTTT-AATAAAGTATAATAATTATTTTATAATA
*
53935 TTTTAATAAAGTATAATAATTATTTTTTAATA
1 TTTTAATAAAGTATAATAATTATTTTATAATA
* *
53967 ATTTGATAAA
1 TTTTAATAAA
53977 ATTTAATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 3 0.08
32 33 0.92
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (32 bp):
TTTTAATAAAGTATAATAATTATTTTATAATA
Found at i:57939 original size:115 final size:114
Alignment explanation
Indices: 57760--57993 Score: 414
Period size: 115 Copynumber: 2.0 Consensus size: 114
57750 TGTTTGGATC
* *
57760 AATTACTCATTCAAATCTCTAAAATTATCAATTTTTTCTAACAAACTCTTATACGAGATAAGAGA
1 AATTTCTCATTCAAATCTCTAAAATTATCAATTTTTTCTAACAAACTCCTATACGAGATAAGAGA
57825 AAATACGATATGATATATTTCTTGGAGACCATAACCCCTTTATATAACT
66 AAATACGATATGATATATTTCTTGGAGACCATAACCCCTTTATATAACT
* *
57874 AATTTCTCATTCAAATCTCTGAAATTATCAATTTTTTTCTAACAAACTCCTCTACGAGATAAGAG
1 AATTTCTCATTCAAATCTCTAAAATTATCAA-TTTTTTCTAACAAACTCCTATACGAGATAAGAG
*
57939 AAAATACGATATGATATATTTCTTTGAGACCATAACCCCTTTATATAACT
65 AAAATACGATATGATATATTTCTTGGAGACCATAACCCCTTTATATAACT
57989 AATTT
1 AATTT
57994 AAGAATCAAT
Statistics
Matches: 114, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
114 29 0.25
115 85 0.75
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (114 bp):
AATTTCTCATTCAAATCTCTAAAATTATCAATTTTTTCTAACAAACTCCTATACGAGATAAGAGA
AAATACGATATGATATATTTCTTGGAGACCATAACCCCTTTATATAACT
Found at i:59303 original size:16 final size:15
Alignment explanation
Indices: 59279--59314 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
59269 ATTATATAAA
*
59279 ATATAATGAATTATTT
1 ATATTATGAATTA-TT
59295 ATATTATGAATTATT
1 ATATTATGAATTATT
59310 ATATT
1 ATATT
59315 TTGTATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATTATGAATTATT
Found at i:61860 original size:51 final size:50
Alignment explanation
Indices: 61723--61843 Score: 224
Period size: 50 Copynumber: 2.4 Consensus size: 50
61713 GACAAGTTTC
61723 AATAAAAAATATTTTTTATTCAAAATTTTCATCTCGATGTAGTAAAATTT
1 AATAAAAAATATTTTTTATTCAAAATTTTCATCTCGATGTAGTAAAATTT
61773 AATAAAAAATATTTTTTATTCAAAATTTTCATCTCGATGTAGTAAAATTT
1 AATAAAAAATATTTTTTATTCAAAATTTTCATCTCGATGTAGTAAAATTT
*
61823 AATAAAAAATTATATTTTATT
1 AATAAAAAA-TATTTTTTATT
61844 GAAACTCGTC
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
50 59 0.86
51 10 0.14
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (50 bp):
AATAAAAAATATTTTTTATTCAAAATTTTCATCTCGATGTAGTAAAATTT
Found at i:67669 original size:2 final size:2
Alignment explanation
Indices: 67662--67701 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
67652 GCATCTTATG
67662 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
67702 AAGAGGTCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69542 original size:40 final size:40
Alignment explanation
Indices: 69493--69596 Score: 190
Period size: 40 Copynumber: 2.6 Consensus size: 40
69483 GTACCTAAAG
*
69493 TTTAGTTTTTGTTTCATTTTAGTAAACCACTGTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTAAACCACTATTAAAAAC
*
69533 TTTAGTTTTTGTTTCATTTTAGTAAACCCCTATTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTAAACCACTATTAAAAAC
69573 TTTAGTTTTTGTTTCATTTTAGTA
1 TTTAGTTTTTGTTTCATTTTAGTA
69597 CACATTCAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.52
Consensus pattern (40 bp):
TTTAGTTTTTGTTTCATTTTAGTAAACCACTATTAAAAAC
Found at i:71533 original size:2 final size:2
Alignment explanation
Indices: 71526--71575 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
71516 AATTAATTGG
71526 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
71568 AT AT AT AT
1 AT AT AT AT
71576 TATCATTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84597 original size:5 final size:5
Alignment explanation
Indices: 84554--84589 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
84544 CAGCCCCCTG
84554 CACCC CACCC CACCC CACCC CACCC CACCC CACCC C
1 CACCC CACCC CACCC CACCC CACCC CACCC CACCC C
84590 CCACCCCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.81, G:0.00, T:0.00
Consensus pattern (5 bp):
CACCC
Found at i:85657 original size:8 final size:8
Alignment explanation
Indices: 85644--85673 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
85634 ATATACGTAC
85644 ATATATGT
1 ATATATGT
85652 ATATATGT
1 ATATATGT
85660 ATATATGT
1 ATATATGT
*
85668 ACATAT
1 ATATAT
85674 ATTTAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (8 bp):
ATATATGT
Found at i:89957 original size:41 final size:41
Alignment explanation
Indices: 89900--90059 Score: 284
Period size: 41 Copynumber: 3.9 Consensus size: 41
89890 GATTCGCAAC
*
89900 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATCGTT
*
89941 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATCGTT
*
89982 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATCGTT
*
90023 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAAT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAAT
90060 ATTGCATTTG
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 115 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (41 bp):
GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATCGTT
Found at i:89985 original size:20 final size:20
Alignment explanation
Indices: 89917--90027 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
89907 GCGAAGTTCG
*
89917 CGTTGCGATTCATTCCAAAT
1 CGTTGCGATTCATTCCAATT
** *
89937 CGTTGCGA-T-AGGCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
89956 CGCATTGCGATTCATTCCAATT
1 CG--TTGCGATTCATTCCAATT
** *
89978 CGTTGCGA-T-AGGCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
89997 CGCATTGCGATTCATTCCAATT
1 CG--TTGCGATTCATTCCAATT
90019 CGTTGCGAT
1 CGTTGCGAT
90028 AGGCGAAGTT
Statistics
Matches: 68, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
18 8 0.12
19 9 0.13
20 21 0.31
21 12 0.18
22 10 0.15
23 8 0.12
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAATT
Found at i:90936 original size:21 final size:21
Alignment explanation
Indices: 90910--91022 Score: 83
Period size: 21 Copynumber: 5.4 Consensus size: 21
90900 TATTTGGACT
*
90910 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* **
90931 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAACTTGGAATGA
*
90952 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* **
90973 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAACTTGGAATGA
90994 ATCGCAACGAA-TTGGAATGA
1 ATCGCAACGAACTTGGAATGA
91014 ATCGCAACG
1 ATCGCAACG
91023 CGAATCGCAA
Statistics
Matches: 69, Mismatches: 15, Indels: 17
0.68 0.15 0.17
Matches are distributed among these distances:
18 4 0.06
19 12 0.17
20 9 0.13
21 28 0.41
23 16 0.23
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATGA
Found at i:91021 original size:41 final size:42
Alignment explanation
Indices: 90908--91154 Score: 365
Period size: 42 Copynumber: 6.2 Consensus size: 42
90898 AATATTTGGA
90908 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
90950 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
90992 CTATCGCAACGAA-TTGGAATGAATCGCAACGCG-A------
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
91026 --ATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
91065 CTATCGCAACG-GTTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
91106 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
91148 CTATCGC
1 CTATCGC
91155 GTTGCGAATC
Statistics
Matches: 188, Mismatches: 6, Indels: 22
0.87 0.03 0.10
Matches are distributed among these distances:
31 1 0.01
32 29 0.15
33 1 0.01
40 1 0.01
41 68 0.36
42 88 0.47
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:91035 original size:32 final size:32
Alignment explanation
Indices: 90994--91058 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
90984 AACTTCGCCT
90994 ATCGCAACGAATTGGAATGAATCGCAACGCGA
1 ATCGCAACGAATTGGAATGAATCGCAACGCGA
*
91026 ATCGCAACGATTTGGAATGAATCGCAACGCGA
1 ATCGCAACGAATTGGAATGAATCGCAACGCGA
91058 A
1 A
91059 CTTCGACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.17
Consensus pattern (32 bp):
ATCGCAACGAATTGGAATGAATCGCAACGCGA
Found at i:91049 original size:20 final size:20
Alignment explanation
Indices: 91024--91095 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
91014 ATCGCAACGC
91024 GAATCGCAACGATTTGGAAT
1 GAATCGCAACGATTTGGAAT
* * *
91044 GAATCGCAACGCGAACTTCGACT
1 GAATCGCAA--CG-ATTTGGAAT
*
91067 --ATCGCAACGGTTTGGAAT
1 GAATCGCAACGATTTGGAAT
91085 GAATCGCAACG
1 GAATCGCAACG
91096 CGAACTTCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
18 5 0.12
19 2 0.05
20 18 0.45
21 7 0.17
22 2 0.05
23 6 0.15
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (20 bp):
GAATCGCAACGATTTGGAAT
Found at i:91072 original size:73 final size:76
Alignment explanation
Indices: 90952--91154 Score: 277
Period size: 73 Copynumber: 2.6 Consensus size: 76
90942 AACTTCGCCT
*
90952 ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATC
1 ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTGGAATGAATC
91017 GCAACGCG-A-
66 GCAACGCGAAC
**
91026 ATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGGTTTGGAATGAATC
1 ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTGGAATGAATC
91090 GCAACGCGAACTTCGCC
66 GCAACGCGAA------C
* *
91107 TATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGC
1 -ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGC
91155 GTTGCGAATC
Statistics
Matches: 114, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
73 60 0.53
74 10 0.09
82 9 0.08
83 35 0.31
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (76 bp):
ATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTGGAATGAATC
GCAACGCGAAC
Found at i:91213 original size:19 final size:19
Alignment explanation
Indices: 91189--91225 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
91179 CGATACCGGA
*
91189 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
*
91208 GATCGCATTGCGATTTAT
1 GATCGCATTGCGAATTAT
91226 TTGGTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:100844 original size:20 final size:21
Alignment explanation
Indices: 100819--100859 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
100809 TTTAATTTTC
100819 ATTTTTATTA-AAAAAATAAT
1 ATTTTTATTATAAAAAATAAT
100839 ATTTTTATTATTAAAAAATAA
1 ATTTTTATTA-TAAAAAATAA
100860 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTTTTATTATAAAAAATAAT
Found at i:104196 original size:17 final size:18
Alignment explanation
Indices: 104164--104202 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
104154 GACTTAAAAA
104164 TTTTATAAAATGATAT-T
1 TTTTATAAAATGATATAT
* *
104181 TTTTATAAACTTATATAT
1 TTTTATAAAATGATATAT
104199 TTTT
1 TTTT
104203 TTCTTGCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTATAAAATGATATAT
Found at i:111751 original size:39 final size:38
Alignment explanation
Indices: 111689--111769 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 38
111679 GGGGGGACTC
*
111689 ACTTTTTGGTGGATGAAATAGTCATTACCACATTACAT
1 ACTTCTTGGTGGATGAAATAGTCATTACCACATTACAT
*
111727 ACTTCTTGGTGGATGGAAATAGTCATTACCACATTCCAT
1 ACTTCTTGGTGGAT-GAAATAGTCATTACCACATTACAT
111766 ACTT
1 ACTT
111770 ATACCCCTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 13 0.32
39 27 0.68
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (38 bp):
ACTTCTTGGTGGATGAAATAGTCATTACCACATTACAT
Found at i:120032 original size:117 final size:118
Alignment explanation
Indices: 119822--120089 Score: 319
Period size: 117 Copynumber: 2.2 Consensus size: 118
119812 TACTAATATT
* * *
119822 GACCAAAACTGATAGTTTTAGGTACTAAACATTTTAAGTTTTTAACGGTAGGGTACTAAAATGAA
1 GACCAAAATTGATAG-TTTAGGTACTAAACATGTTAAGTTTTT-A--GTAGGCTACTAAAATGAA
**
119887 ATAAAAACTAAATGTTACGAATGATTTTGAAAA-A-AAAGAGTTTAGTTATTAAAATG
62 ATAAAAACTAAATGTTACGAATGATTTTGAAAAGATAAA-AGTTTAGTTATTAAAACA
*
119943 GACTAAAATTGATAGTTATAGGTACTAAA-AGTGTTAAGTTTTT-GTAGGCTACTAAAATGAAAT
1 GACCAAAATTGATAGTT-TAGGTACTAAACA-TGTTAAGTTTTTAGTAGGCTACTAAAATGAAAT
* * * * *
120006 AAAAATTAAATGTTATGTATGCTTTTGAAAAGATTAAAAGTTTAGTTGTTAAAACA
64 AAAAACTAAATGTTACGAATGATTTTGAAAAGA-TAAAAGTTTAGTTATTAAAACA
* *
120062 TACCAAAATTGATGGTTTAGGTACTAAA
1 GACCAAAATTGATAGTTTAGGTACTAAA
120090 TGCATAGTTT
Statistics
Matches: 128, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
117 46 0.36
118 12 0.09
119 29 0.23
120 6 0.05
121 35 0.27
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.34
Consensus pattern (118 bp):
GACCAAAATTGATAGTTTAGGTACTAAACATGTTAAGTTTTTAGTAGGCTACTAAAATGAAATAA
AAACTAAATGTTACGAATGATTTTGAAAAGATAAAAGTTTAGTTATTAAAACA
Found at i:120905 original size:27 final size:27
Alignment explanation
Indices: 120875--120938 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
120865 CATAAAATAT
120875 ATATTTTTAAATGAAAATAAAAATAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
* ** *
120902 ATATTTTTAAATTAATTTAATAATAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
*
120929 ATATATTTAA
1 ATATTTTTAA
120939 TAAGTTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATTTTTAAATGAAAATAAAAATAAA
Found at i:120951 original size:27 final size:26
Alignment explanation
Indices: 120896--120984 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 26
120886 TGAAAATAAA
*
120896 AATAAAATATTTT--TAAATTAATTTAAT
1 AATAAAATATTTTAATAAGTTAA--T-AT
120923 AATAAAATATATTTAATAAGTTAATAT
1 AATAAAATAT-TTTAATAAGTTAATAT
120950 AA-AAAATATTTT--TAAGTTAATAT
1 AATAAAATATTTTAATAAGTTAATAT
120973 ATATAAAATATT
1 A-ATAAAATATT
120985 ATGAATTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
23 12 0.21
24 1 0.02
25 11 0.20
26 7 0.12
27 14 0.25
28 4 0.07
30 7 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AATAAAATATTTTAATAAGTTAATAT
Found at i:120974 original size:25 final size:25
Alignment explanation
Indices: 120899--120984 Score: 86
Period size: 25 Copynumber: 3.3 Consensus size: 25
120889 AAATAAAAAT
* *
120899 AAAATATTTTTAAATTAATTTAATAA
1 AAAATATTTTTAAGTTAATAT-ATAA
120925 TAAAATATATTTAATAAGTT-A-ATATAA
1 -AAAATAT-TTT--TAAGTTAATATATAA
*
120952 AAAATATTTTTAAGTTAATATATAT
1 AAAATATTTTTAAGTTAATATATAA
120977 AAAATATT
1 AAAATATT
120985 ATGAATTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
23 6 0.12
24 1 0.02
25 16 0.31
26 7 0.14
27 11 0.22
28 4 0.08
29 1 0.02
30 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAATATTTTTAAGTTAATATATAA
Found at i:120994 original size:25 final size:25
Alignment explanation
Indices: 120940--121003 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
120930 TATATTTAAT
* *
120940 AAGTTAATATA-A-AAAATATTTTT
1 AAGTTAATATATATAAAATATTATG
120963 AAGTTAATATATATAAAATATTATG
1 AAGTTAATATATATAAAATATTATG
* *
120988 AATTTAAGTATTTATA
1 AAGTTAA-TATATATA
121004 CACTAAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.32
24 1 0.03
25 15 0.44
26 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (25 bp):
AAGTTAATATATATAAAATATTATG
Found at i:122080 original size:2 final size:2
Alignment explanation
Indices: 122073--122101 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
122063 ATACTTAAAT
122073 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 T
122102 TATCACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:122661 original size:21 final size:20
Alignment explanation
Indices: 122636--122682 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
122626 ATTTTATATT
*
122636 AGGGGAGCGAACTTAAATTTG
1 AGGGGA-CGAACTAAAATTTG
* *
122657 GGGGGATGAACTAAAATTTG
1 AGGGGACGAACTAAAATTTG
122677 AGGGGA
1 AGGGGA
122683 TGAAAACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.34, C:0.06, G:0.38, T:0.21
Consensus pattern (20 bp):
AGGGGACGAACTAAAATTTG
Found at i:122667 original size:20 final size:20
Alignment explanation
Indices: 122644--122686 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
122634 TTAGGGGAGC
* *
122644 GAACTTAAATTTGGGGGGAT
1 GAACTAAAATTTGAGGGGAT
122664 GAACTAAAATTTGAGGGGAT
1 GAACTAAAATTTGAGGGGAT
122684 GAA
1 GAA
122687 AACATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.33, T:0.26
Consensus pattern (20 bp):
GAACTAAAATTTGAGGGGAT
Found at i:123824 original size:32 final size:33
Alignment explanation
Indices: 123778--123844 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
123768 GGAGTGACCA
* *
123778 TTTTGTTACAAATCGATAATGTTAGTGA-TAAT
1 TTTTATTACAAATCGATAATATTAGTGACTAAT
123810 TTTTATTACAAATCGATAATATTAGTGACTAAT
1 TTTTATTACAAATCGATAATATTAGTGACTAAT
123843 TT
1 TT
123845 GTTACTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 26 0.81
33 6 0.19
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (33 bp):
TTTTATTACAAATCGATAATATTAGTGACTAAT
Found at i:124836 original size:19 final size:20
Alignment explanation
Indices: 124814--124852 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
124804 ACAAGTATAG
*
124814 ATTTAATTTAA-AAATTATT
1 ATTTAATATAAGAAATTATT
*
124833 ATTTGATATAAGAAATTATT
1 ATTTAATATAAGAAATTATT
124853 TCAAATACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTTAATATAAGAAATTATT
Found at i:130035 original size:23 final size:23
Alignment explanation
Indices: 130009--130053 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
129999 CACCACAGCT
*
130009 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
130032 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
130054 ATATAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:131873 original size:21 final size:21
Alignment explanation
Indices: 131849--131893 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
131839 TGTTGTTCGT
131849 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
131870 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
131891 TTG
1 TTG
131894 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Done.