Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004363.1 Hibiscus syriacus cultivar Beakdansim tig00009557_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: 194349
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4420 original size:11 final size:11
Alignment explanation
Indices: 4404--4428 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4394 GTCGGTTCCT
4404 TCAAATATGAA
1 TCAAATATGAA
4415 TCAAATATGAA
1 TCAAATATGAA
4426 TCA
1 TCA
4429 GTCTCTTCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (11 bp):
TCAAATATGAA
Found at i:7668 original size:2 final size:2
Alignment explanation
Indices: 7661--7704 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
7651 TTATGAAAGA
7661 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
7703 AT
1 AT
7705 GACTACATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8252 original size:23 final size:23
Alignment explanation
Indices: 8222--8289 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
8212 CATCTTATAT
8222 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
8245 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* * *
8268 GGTACTTCGATGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
8290 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:11469 original size:25 final size:25
Alignment explanation
Indices: 11441--11490 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
11431 TTAATAATTG
* *
11441 AAAATTAGTTATGAAAAAATAAAAA
1 AAAATTAATTATAAAAAAATAAAAA
*
11466 AAAATTAATTTTAAAAAAATAAAAA
1 AAAATTAATTATAAAAAAATAAAAA
11491 CTTTTTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (25 bp):
AAAATTAATTATAAAAAAATAAAAA
Found at i:16349 original size:15 final size:14
Alignment explanation
Indices: 16291--16360 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
16281 CAAAATAATA
*
16291 TATATTTGATTTTT
1 TATATTTAATTTTT
16305 TAGTAATTTAA-TTTT
1 TA-T-ATTTAATTTTT
* **
16320 TATTTTTGGTATTTT
1 TATATTTAAT-TTTT
16335 TATATTTAATTTTT
1 TATATTTAATTTTT
*
16349 TATATTTTATTT
1 TATATTTAATTT
16361 AAACTATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
13 3 0.07
14 18 0.41
15 18 0.41
16 5 0.11
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (14 bp):
TATATTTAATTTTT
Found at i:16354 original size:22 final size:22
Alignment explanation
Indices: 16291--16356 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
16281 CAAAATAATA
* *
16291 TATATTTGATTTTTTAGTAATTT
1 TATATTTAATTTTTTA-TATTTT
* * **
16314 AAT-TTTTATTTTTGGTATTTT
1 TATATTTAATTTTTTATATTTT
16335 TATATTTAATTTTTTATATTTT
1 TATATTTAATTTTTTATATTTT
16357 ATTTAAACTA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
21 7 0.21
22 24 0.73
23 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (22 bp):
TATATTTAATTTTTTATATTTT
Found at i:16531 original size:21 final size:21
Alignment explanation
Indices: 16498--16543 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
16488 ATCGCTAATT
*
16498 AACACCGTAAAGTGCCACATC
1 AACAACGTAAAGTGCCACATC
* *
16519 AACAACGTGAAGTGTCACATC
1 AACAACGTAAAGTGCCACATC
16540 AACA
1 AACA
16544 TAATAACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.15
Consensus pattern (21 bp):
AACAACGTAAAGTGCCACATC
Found at i:18666 original size:21 final size:21
Alignment explanation
Indices: 18625--18667 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
18615 GAATGGAAAG
* *
18625 ATAGAGGAATAGGAGAGTGGA
1 ATAGAGAAATAGGAGAATGGA
18646 ATAGAGAAACTAGG-GAATGGA
1 ATAGAGAAA-TAGGAGAATGGA
18667 A
1 A
18668 ATCTTCACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.47, C:0.02, G:0.37, T:0.14
Consensus pattern (21 bp):
ATAGAGAAATAGGAGAATGGA
Found at i:22603 original size:15 final size:15
Alignment explanation
Indices: 22583--22613 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
22573 GGTTCCTTCA
22583 GATGCTACCAATGAG
1 GATGCTACCAATGAG
22598 GATGCTACCAATGAG
1 GATGCTACCAATGAG
22613 G
1 G
22614 CTCCTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (15 bp):
GATGCTACCAATGAG
Found at i:22620 original size:15 final size:15
Alignment explanation
Indices: 22587--22620 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22577 CCTTCAGATG
*
22587 CTACCAATGAGGATG
1 CTACCAATGAGGATC
*
22602 CTACCAATGAGGCTC
1 CTACCAATGAGGATC
22617 CTAC
1 CTAC
22621 AAAAAGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (15 bp):
CTACCAATGAGGATC
Found at i:23194 original size:38 final size:39
Alignment explanation
Indices: 23139--23215 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 39
23129 TTGGAAGACG
*
23139 TGAATAAAATTCCCATTCCGAGATCTGTACATGGCTTCA
1 TGAATAAAACTCCCATTCCGAGATCTGTACATGGCTTCA
23178 TGAAT-AAACTCCCATTCCGAGATCTGTACATGGCTTCA
1 TGAATAAAACTCCCATTCCGAGATCTGTACATGGCTTCA
23216 ATGTACCATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 32 0.86
39 5 0.14
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (39 bp):
TGAATAAAACTCCCATTCCGAGATCTGTACATGGCTTCA
Found at i:26487 original size:6 final size:6
Alignment explanation
Indices: 26476--26502 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
26466 GCTCGGCTCG
26476 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
26503 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:27083 original size:147 final size:147
Alignment explanation
Indices: 26633--27075 Score: 823
Period size: 147 Copynumber: 3.0 Consensus size: 147
26623 TATCAAGAGT
26633 TATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAGCTGAATAATGATA
1 TATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAGCTGAATAATGATA
* *
26698 CAATGAACCTGGACTATTTCTGAGTTAGGTTCATCTAGACGTTTCATCTGTTACAAATAAGAGAT
66 CAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAATAAGAGAT
26763 TTAATCCTGAAATTTTA
131 TTAATCCTGAAATTTTA
*
26780 TATTTGATTTAATTCCAGTGGTTACATGATATAATTTCGGGAGTTATAACAGCTGAATAATGATA
1 TATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAGCTGAATAATGATA
26845 CAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAATAAGAGAT
66 CAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAATAAGAGAT
26910 TTAATCCTGAAATTTTA
131 TTAATCCTGAAATTTTA
* *
26927 TATTTGATTTAATTCCAGGGGTTACACGATATAATTTCGGGAGTTATAACAACTGAATAATGATA
1 TATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAGCTGAATAATGATA
* *
26992 CAATGAACCTGGACTATTTCTAAGTCAGGTTCATCTAGACGTTTCAGCTGTTATAAATAAGAGAT
66 CAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAATAAGAGAT
27057 TTAATCCTGAAATTTTA
131 TTAATCCTGAAATTTTA
27074 TA
1 TA
27076 GACGATTTTA
Statistics
Matches: 288, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 288 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (147 bp):
TATTTGATTTAATTCCAGGGGTTACATGATATAATTTCGGGAGTTATAACAGCTGAATAATGATA
CAATGAACCTGGACTATTTCTGAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAATAAGAGAT
TTAATCCTGAAATTTTA
Found at i:32523 original size:5 final size:5
Alignment explanation
Indices: 32509--32577 Score: 75
Period size: 5 Copynumber: 13.8 Consensus size: 5
32499 GTCCGTCTGT
* * * * * * *
32509 CTCGT CTCGG CTCGG CACGG CACGG CTCGG CACGA CACGG CACGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
32559 CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCG
32578 TGGTCGTGGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.09, C:0.41, G:0.36, T:0.14
Consensus pattern (5 bp):
CTCGG
Found at i:32586 original size:6 final size:6
Alignment explanation
Indices: 32575--32623 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
32565 TCGGCTCGGC
* *
32575 TCGTGG TCGTGG TTGAGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
32623 T
1 T
32624 AATACGTGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.02, C:0.14, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:35280 original size:32 final size:32
Alignment explanation
Indices: 35160--35300 Score: 117
Period size: 32 Copynumber: 4.5 Consensus size: 32
35150 TATCTAAAGC
35160 TTGACCCAAACCC--AAATCAACCGATCTGATA
1 TTGACCC-AACCCGAAAATCAACCGATCTGATA
* * * * *
35191 TCGACCCGACTCG-AAATCAATCGATCTGAGA
1 TTGACCCAACCCGAAAATCAACCGATCTGATA
* * ** * *
35222 TTAACCCATCCCGACCACCAACCGATCTGATT
1 TTGACCCAACCCGAAAATCAACCGATCTGATA
* * *
35254 TTGACCCAACCCGAAAATCAATCGATCCGATC
1 TTGACCCAACCCGAAAATCAACCGATCTGATA
*
35286 TTGACCCGACCCGAA
1 TTGACCCAACCCGAA
35301 TTGAATTTCC
Statistics
Matches: 83, Mismatches: 25, Indels: 3
0.75 0.23 0.03
Matches are distributed among these distances:
30 3 0.04
31 30 0.36
32 50 0.60
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.19
Consensus pattern (32 bp):
TTGACCCAACCCGAAAATCAACCGATCTGATA
Found at i:38860 original size:5 final size:5
Alignment explanation
Indices: 38850--38877 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
38840 ATATTATCCC
38850 CACGT CACGT CACGT CACGT CACGT CAC
1 CACGT CACGT CACGT CACGT CACGT CAC
38878 ACATTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.43, G:0.18, T:0.18
Consensus pattern (5 bp):
CACGT
Found at i:39576 original size:31 final size:29
Alignment explanation
Indices: 39539--39614 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
39529 TGTATTTTAA
*
39539 TAAATGTAATATTTGTTCTTTGATAAAACAT
1 TAAATGTAATATTTG-T-TTTAATAAAACAT
* *
39570 TAAATGTGATATATTTGTTTTAATGAAATAT
1 TAAATGT-A-ATATTTGTTTTAATAAAACAT
*
39601 TAAACGTAATATTT
1 TAAATGTAATATTT
39615 ATATTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 6 0.15
30 1 0.03
31 23 0.59
32 2 0.05
33 7 0.18
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (29 bp):
TAAATGTAATATTTGTTTTAATAAAACAT
Found at i:39680 original size:29 final size:28
Alignment explanation
Indices: 39630--39689 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
39620 TTTTAAAATA
39630 TTTAAAACATTTAATATAATATCTATATT
1 TTTAAAACATTTAATATAATATCTA-ATT
* * * *
39659 TTTAAAATATTTAATGTCATATTTAATT
1 TTTAAAACATTTAATATAATATCTAATT
39687 TTT
1 TTT
39690 TATTTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTAAAACATTTAATATAATATCTAATT
Found at i:40051 original size:31 final size:31
Alignment explanation
Indices: 40013--40090 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
40003 CAGTTACGTC
40013 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACCATATTGCAAACGGACTAAATGTTG
40044 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACCATATTGCAAACGGACTAAATGTTG
**
40075 AGGGATTATATTGCAA
1 AGGGACCATATTGCAA
40091 GTTTTAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (31 bp):
AGGGACCATATTGCAAACGGACTAAATGTTG
Found at i:41998 original size:16 final size:16
Alignment explanation
Indices: 41977--42012 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
41967 TTAATATTTA
41977 GTCCGTTTGCAATATT
1 GTCCGTTTGCAATATT
41993 GTCCGTTTGCAATATT
1 GTCCGTTTGCAATATT
42009 GTCC
1 GTCC
42013 CTCAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (16 bp):
GTCCGTTTGCAATATT
Found at i:43341 original size:26 final size:26
Alignment explanation
Indices: 43292--43343 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
43282 GTCGCTTTTA
* *
43292 TTTTTCTTTAATTAAGATATAGTCAT
1 TTTTTATTTAATTAAGATACAGTCAT
*
43318 TTTTTATTTAATTAAGATGCAGTCAT
1 TTTTTATTTAATTAAGATACAGTCAT
43344 CCCGAGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.52
Consensus pattern (26 bp):
TTTTTATTTAATTAAGATACAGTCAT
Found at i:44152 original size:25 final size:27
Alignment explanation
Indices: 44114--44182 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 27
44104 ATTATATATA
* *
44114 TTAACTTAAAATATTTTTA-TATCAAC
1 TTAATTTAAAATATTTTTATTATAAAC
44140 TT-A-TT-AAATATATTTTATTATAAAC
1 TTAATTTAAAATAT-TTTTATTATAAAC
44165 TTAATTTAAAAATATTTT
1 TTAATTT-AAAATATTTT
44183 ATTTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
23 6 0.17
24 7 0.19
25 9 0.25
26 3 0.08
27 2 0.06
28 3 0.08
29 6 0.17
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAATTTAAAATATTTTTATTATAAAC
Found at i:44173 original size:27 final size:25
Alignment explanation
Indices: 44122--44185 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 25
44112 TATTAACTTA
*
44122 AAATAT-TTTTA-TATCAACTTATT
1 AAATATATTTTATTATAAACTTATT
44145 AAATATATTTTATTATAAACTTAATTT
1 AAATATATTTTATTATAAACTT-A-TT
*
44172 AAAAATATTTTATT
1 AAATATATTTTATT
44186 TTTATTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 6 0.17
24 5 0.14
25 8 0.23
26 1 0.03
27 15 0.43
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
AAATATATTTTATTATAAACTTATT
Found at i:49228 original size:19 final size:19
Alignment explanation
Indices: 49204--49241 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
49194 TTTTCCATAG
49204 CCTTTACTTCATCAAATAT
1 CCTTTACTTCATCAAATAT
49223 CCTTTACTTCATCAAATAT
1 CCTTTACTTCATCAAATAT
49242 TCTGCGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (19 bp):
CCTTTACTTCATCAAATAT
Found at i:52548 original size:24 final size:24
Alignment explanation
Indices: 52514--52596 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
52504 AATTCTGTTA
*
52514 TGATACCTGACATGGATTTTGATC
1 TGATACTTGACATGGATTTTGATC
* *
52538 TGATACTTGACCTGGATTCTGATC
1 TGATACTTGACATGGATTTTGATC
* *
52562 TGATACTTGACATGAATTTTGATT
1 TGATACTTGACATGGATTTTGATC
*
52586 TGATTCTTGAC
1 TGATACTTGAC
52597 TTGAATTATG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
TGATACTTGACATGGATTTTGATC
Found at i:52557 original size:48 final size:48
Alignment explanation
Indices: 52505--52596 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
52495 TTCGATTTGA
* *
52505 ATTCTGTTATGATACCTGACATGGATTTTGATCTGATACTTGACCTGG
1 ATTCTGATATGATACCTGACATGAATTTTGATCTGATACTTGACCTGG
* * * *
52553 ATTCTGATCTGATACTTGACATGAATTTTGATTTGATTCTTGAC
1 ATTCTGATATGATACCTGACATGAATTTTGATCTGATACTTGAC
52597 TTGAATTATG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (48 bp):
ATTCTGATATGATACCTGACATGAATTTTGATCTGATACTTGACCTGG
Found at i:52611 original size:24 final size:24
Alignment explanation
Indices: 52521--52618 Score: 81
Period size: 24 Copynumber: 4.1 Consensus size: 24
52511 TTATGATACC
* * * *
52521 TGACATGGATTTTGATCTGATACT
1 TGACATGAATTATGATTTGATTCT
* * * * *
52545 TGACCTGGATTCTGATCTGATACT
1 TGACATGAATTATGATTTGATTCT
*
52569 TGACATGAATTTTGATTTGATTCT
1 TGACATGAATTATGATTTGATTCT
* *
52593 TGACTTGAATTATGTTTTGATT-T
1 TGACATGAATTATGATTTGATTCT
52616 TGA
1 TGA
52619 TATATCCGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
23 4 0.06
24 60 0.94
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.46
Consensus pattern (24 bp):
TGACATGAATTATGATTTGATTCT
Found at i:56882 original size:24 final size:23
Alignment explanation
Indices: 56848--56930 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 23
56838 AATTTTGTTA
* *
56848 TGATACATGACATAGATTCTAATC
1 TGATACTTGACAT-GATTCTGATC
*
56872 TGATACTTGACCTGGATTCTGATC
1 TGATACTTGACAT-GATTCTGATC
*
56896 CGATACTTGACATGAATTCTGATC
1 TGATACTTGACATG-ATTCTGATC
56920 TGATACTTGAC
1 TGATACTTGAC
56931 CTAAATTATG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 1 0.02
24 50 0.98
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (23 bp):
TGATACTTGACATGATTCTGATC
Found at i:56947 original size:24 final size:24
Alignment explanation
Indices: 56848--56940 Score: 78
Period size: 24 Copynumber: 3.9 Consensus size: 24
56838 AATTTTGTTA
* * * *
56848 TGATACATGACATAGATTCTAATC
1 TGATACTTGACATAAATTATGATC
* ** *
56872 TGATACTTGACCTGGATTCTGATC
1 TGATACTTGACATAAATTATGATC
* * *
56896 CGATACTTGACATGAATTCTGATC
1 TGATACTTGACATAAATTATGATC
*
56920 TGATACTTGACCTAAATTATG
1 TGATACTTGACATAAATTATG
56941 TTTTGATTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (24 bp):
TGATACTTGACATAAATTATGATC
Found at i:58838 original size:111 final size:111
Alignment explanation
Indices: 58708--58931 Score: 396
Period size: 111 Copynumber: 2.0 Consensus size: 111
58698 AATCACAAAT
*
58708 GTCATGATATCATGACTTATTTTATTTATATTTGAGTCACTTAAACATTAATTGATATTTTATTA
1 GTCATGATATCATGACTTATTTTATTTATATTTAAGTCACTTAAACATTAATTGATATTTTATTA
* * *
58773 ATATT-TTTTTGTTGTTGAATTAAGCTCTTCGTTGATCACTCATTTC
66 ATATTATTTTT-TTATTAAATTAAGCTCGTCGTTGATCACTCATTTC
58819 GTCATGATATCATGACTTATTTTATTTATATTTAAGTCACTTAAACATTAATTGATATTTTATTA
1 GTCATGATATCATGACTTATTTTATTTATATTTAAGTCACTTAAACATTAATTGATATTTTATTA
58884 ATATTATTTTTTTATTAAATTAAGCTCGTCGTTGATCACTCATTTC
66 ATATTATTTTTTTATTAAATTAAGCTCGTCGTTGATCACTCATTTC
58930 GT
1 GT
58932 TGCTTATGTG
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
111 103 0.95
112 5 0.05
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (111 bp):
GTCATGATATCATGACTTATTTTATTTATATTTAAGTCACTTAAACATTAATTGATATTTTATTA
ATATTATTTTTTTATTAAATTAAGCTCGTCGTTGATCACTCATTTC
Found at i:65773 original size:22 final size:22
Alignment explanation
Indices: 65741--65797 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
65731 AATCGGTACC
* *
65741 CTGCTATAGTATTACTACAATA
1 CTGCTACAGTACTACTACAATA
* *
65763 CTGCTACAGTACTGCTATAATA
1 CTGCTACAGTACTACTACAATA
65785 CTGCTACAGTACT
1 CTGCTACAGTACT
65798 TCCGTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (22 bp):
CTGCTACAGTACTACTACAATA
Found at i:65775 original size:11 final size:11
Alignment explanation
Indices: 65741--65797 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
65731 AATCGGTACC
*
65741 CTGCTATAGTA
1 CTGCTACAGTA
* * *
65752 TTACTACAATA
1 CTGCTACAGTA
65763 CTGCTACAGTA
1 CTGCTACAGTA
* *
65774 CTGCTATAATA
1 CTGCTACAGTA
65785 CTGCTACAGTA
1 CTGCTACAGTA
65796 CT
1 CT
65798 TCCGTAAAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:65866 original size:6 final size:6
Alignment explanation
Indices: 65841--65878 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
65831 AAACGTTCAT
65841 CATTATA CATTTA TCATTTA CATTTA CATTTA CATTTA
1 CATT-TA CATTTA -CATTTA CATTTA CATTTA CATTTA
65879 TTACATGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 20 0.67
7 10 0.33
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
CATTTA
Found at i:65872 original size:12 final size:13
Alignment explanation
Indices: 65839--65879 Score: 66
Period size: 12 Copynumber: 3.2 Consensus size: 13
65829 TAAAACGTTC
65839 ATCATTATACATTT
1 ATCATT-TACATTT
65853 ATCATTTACATTT
1 ATCATTTACATTT
65866 A-CATTTACATTT
1 ATCATTTACATTT
65878 AT
1 AT
65880 TACATGCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.46
13 8 0.31
14 6 0.23
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (13 bp):
ATCATTTACATTT
Found at i:66674 original size:24 final size:24
Alignment explanation
Indices: 66647--66717 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
66637 CACCACAGCT
*
66647 CGTATAAATTGCACTGAAGTGCCA
1 CGTAGAAATTGCACTGAAGTGCCA
* * *
66671 CGTAGAATTTGCA-TCGAAGTACCG
1 CGTAGAAATTGCACT-GAAGTGCCA
* *
66695 CGTAGAAA-TGCACCGTAGTGCCA
1 CGTAGAAATTGCACTGAAGTGCCA
66718 TATAAGATTG
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
23 11 0.31
24 25 0.69
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (24 bp):
CGTAGAAATTGCACTGAAGTGCCA
Found at i:67115 original size:16 final size:16
Alignment explanation
Indices: 67094--67126 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
67084 TAATAAATAA
67094 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
67110 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
67126 A
1 A
67127 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:67216 original size:16 final size:16
Alignment explanation
Indices: 67195--67243 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
67185 TAATAAATAA
67195 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
*
67211 ACGAACATAAATAAAC
1 ACGAACATAAACAAAC
*
67227 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
67243 A
1 A
67244 TAAACGTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.61, C:0.22, G:0.08, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:67227 original size:26 final size:26
Alignment explanation
Indices: 67198--67247 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
67188 TAAATAAACG
*
67198 AACATAAACA-AACACGAACATAAATA
1 AACACAAACATAA-ACGAACATAAATA
*
67224 AACACGAACATAAACGAACATAAA
1 AACACAAACATAAACGAACATAAA
67248 CGTTGGAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.64, C:0.20, G:0.06, T:0.10
Consensus pattern (26 bp):
AACACAAACATAAACGAACATAAATA
Found at i:68295 original size:24 final size:24
Alignment explanation
Indices: 68268--68342 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
68258 TATTGGGTTA
* *
68268 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
* *
68292 AACATAACCGAACGAACATAGACG
1 AACATAAACGAACGAACATAAACG
** *
68316 AACATATTCGAACGAACATAACCG
1 AACATAAACGAACGAACATAAACG
68340 AAC
1 AAC
68343 GTTCACAAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.52, C:0.21, G:0.13, T:0.13
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:68305 original size:14 final size:14
Alignment explanation
Indices: 68288--68343 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
68278 AATGAACATA
68288 AACGAACATAACCG
1 AACGAACATAACCG
68302 AACGAACAT-A--G
1 AACGAACATAACCG
**
68313 -ACGAACATATTCG
1 AACGAACATAACCG
68326 AACGAACATAACCG
1 AACGAACATAACCG
68340 AACG
1 AACG
68344 TTCACAAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 2 0.06
14 24 0.69
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:69142 original size:19 final size:19
Alignment explanation
Indices: 69118--69163 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
69108 CTTAGCCTTG
*
69118 CTTTGATTCAATCCTAATT
1 CTTTGATTCAATCCTAATC
*
69137 CTTTGATTTAATCCTAATC
1 CTTTGATTCAATCCTAATC
69156 CTTTGATT
1 CTTTGATT
69164 ATTCCGGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.50
Consensus pattern (19 bp):
CTTTGATTCAATCCTAATC
Found at i:77020 original size:12 final size:12
Alignment explanation
Indices: 77003--77045 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
76993 GTTTTATCCT
77003 ATTTCTATTCTG
1 ATTTCTATTCTG
*
77015 ATTTCTACTCTG
1 ATTTCTATTCTG
* * *
77027 AATTCTGTTCTA
1 ATTTCTATTCTG
77039 ATTTCTA
1 ATTTCTA
77046 ATATCTCTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (12 bp):
ATTTCTATTCTG
Found at i:89333 original size:37 final size:37
Alignment explanation
Indices: 89261--89373 Score: 201
Period size: 37 Copynumber: 3.1 Consensus size: 37
89251 AGATTCTTCT
*
89261 CAATGCAAATCAAGCCTTCAC-AAAAGAGTAATGAAG
1 CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAG
89297 CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAG
1 CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAG
*
89334 CAATGCAAATTAAGCCTTCACAAAAAGAGTAGTGAAG
1 CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAG
89371 CAA
1 CAA
89374 GATCAGATCA
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
36 21 0.28
37 53 0.72
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.17
Consensus pattern (37 bp):
CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAG
Found at i:89565 original size:16 final size:16
Alignment explanation
Indices: 89544--89574 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
89534 GAGTGACGTT
89544 TATATATATTATTATA
1 TATATATATTATTATA
89560 TATATATATTATTAT
1 TATATATATTATTAT
89575 TATTATGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATATATTATTATA
Found at i:90160 original size:20 final size:20
Alignment explanation
Indices: 90124--90180 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
90114 GGCAAACCTA
90124 CAAGAGAACCAAACAACGAAAG
1 CAAGAGAA-C-AACAACGAAAG
*
90146 CAAGAGAACAACAACGGAAG
1 CAAGAGAACAACAACGAAAG
90166 CAAGAGAACAACAAC
1 CAAGAGAACAACAAC
90181 CAAGCAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 25 0.74
21 1 0.03
22 8 0.24
ACGTcount: A:0.58, C:0.23, G:0.19, T:0.00
Consensus pattern (20 bp):
CAAGAGAACAACAACGAAAG
Found at i:90203 original size:22 final size:21
Alignment explanation
Indices: 90168--90215 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
90158 AACGGAAGCA
*
90168 AGAGAACAACAACCAAGCAAC
1 AGAGAACAACAACCAACCAAC
*
90189 AGAGACACAATAACCAACCAAC
1 AGAGA-ACAACAACCAACCAAC
90211 AGAGA
1 AGAGA
90216 GAAATAGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.56, C:0.27, G:0.15, T:0.02
Consensus pattern (21 bp):
AGAGAACAACAACCAACCAAC
Found at i:102399 original size:37 final size:37
Alignment explanation
Indices: 102328--102440 Score: 201
Period size: 37 Copynumber: 3.1 Consensus size: 37
102318 AGATTTTTCT
102328 CAATGCAAATCAAGCCTTCAC-AAAAGAGTAGTGAAG
1 CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAG
*
102364 CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAA
1 CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAG
*
102401 CAATGCAAATTAAGCCTTCACAAAAAGAGTAGTGAAG
1 CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAG
102438 CAA
1 CAA
102441 GATCAGATCA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 21 0.29
37 52 0.71
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.17
Consensus pattern (37 bp):
CAATGCAAATCAAGCCTTCACAAAAAGAGTAGTGAAG
Found at i:103269 original size:20 final size:20
Alignment explanation
Indices: 103192--103269 Score: 86
Period size: 20 Copynumber: 3.8 Consensus size: 20
103182 GGGCAAACAT
103192 GCAAGAGAACCAAACAA-ATAAA
1 GCAAGAGAA-C-AACAACA-AAA
*
103214 GCAAGAGAACAAAAACAAAA
1 GCAAGAGAACAACAACAAAA
*
103234 GCAAGAGAACAACAACGAAA
1 GCAAGAGAACAACAACAAAA
* *
103254 GTAAGAGAACATCAAC
1 GCAAGAGAACAACAAC
103270 CAAGCAACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 39 0.78
21 2 0.04
22 9 0.18
ACGTcount: A:0.62, C:0.18, G:0.17, T:0.04
Consensus pattern (20 bp):
GCAAGAGAACAACAACAAAA
Found at i:113330 original size:33 final size:33
Alignment explanation
Indices: 113288--113354 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
113278 AACTGAGTTC
113288 TACCAACTGAGCTGAAC-GGACAATTTTAATTAA
1 TACCAACTGAGCTGAACAGG-CAATTTTAATTAA
* * *
113321 TACCAACTGAGTTGGACAGGTAATTTTAATTAA
1 TACCAACTGAGCTGAACAGGCAATTTTAATTAA
113354 T
1 T
113355 TAATTAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (33 bp):
TACCAACTGAGCTGAACAGGCAATTTTAATTAA
Found at i:114054 original size:24 final size:24
Alignment explanation
Indices: 114027--114103 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 24
114017 CGTTCATTTA
**
114027 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCGTGTTCGTTCGGTTATGTT
114051 CGTTCGGTTATGTTCGTTCGGTTATGTT
1 CGTTC-G---TGTTCGTTCGGTTATGTT
**
114079 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCGTGTTCGTTCGGTTATGTT
114103 C
1 C
114104 ATTTATGTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
24 24 0.53
25 1 0.02
28 20 0.44
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (24 bp):
CGTTCGTGTTCGTTCGGTTATGTT
Found at i:114056 original size:14 final size:14
Alignment explanation
Indices: 114037--114103 Score: 106
Period size: 14 Copynumber: 5.1 Consensus size: 14
114027 CGTTCGTGAA
114037 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
114051 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
114065 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
114079 CG-T---TTATGTT
1 CGTTCGGTTATGTT
114089 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
114103 C
1 C
114104 ATTTATGTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.18
11 1 0.02
13 1 0.02
14 38 0.78
ACGTcount: A:0.07, C:0.15, G:0.27, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:114069 original size:38 final size:38
Alignment explanation
Indices: 114027--114103 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
114017 CGTTCATTTA
114027 CGTTC-GTGAACGTTCGGTTATGTTCGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTTCGTTCGGTTATGTT
* * *
114065 CGTTCGGTTATGTTCGTTTATGTTCGTTCGGTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTTCGTTCGGTTATGTT
114103 C
1 C
114104 ATTTATGTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 33 0.94
39 2 0.06
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (38 bp):
CGTTCGGTAACGTTCGGTTATGTTCGTTCGGTTATGTT
Found at i:114123 original size:38 final size:37
Alignment explanation
Indices: 114044--114126 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
114034 GAACGTTCGG
* *
114044 TTATGTTCGTTCGGTTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGTTAGGTTA-GTTCAT
* *
114082 TTATGTTCGTTCGGTTATGTTCATTTATGTTCA-TTCAT
1 TTATGTTCGTTCGGTTATGTTC-GTTAGGTT-AGTTCAT
114120 TTATGTT
1 TTATGTT
114127 TAACCCAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 33 0.85
39 5 0.13
40 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.55
Consensus pattern (37 bp):
TTATGTTCGTTCGGTTATGTTCGTTAGGTTAGTTCAT
Found at i:114126 original size:24 final size:24
Alignment explanation
Indices: 114058--114113 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
114048 GTTCGTTCGG
*
114058 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCAT
114082 TTATGTTCGTTCGGTTATGTTCAT
1 TTATGTTCGTTCGGTTATGTTCAT
114106 TTATGTTC
1 TTATGTTC
114114 ATTCATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.55
Consensus pattern (24 bp):
TTATGTTCGTTCGGTTATGTTCAT
Found at i:115230 original size:16 final size:16
Alignment explanation
Indices: 115211--115277 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
115201 TTTATGTTTG
115211 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
115227 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
115243 TTTATGTTCGTGGTCG
1 TTTATGTTCGTGTTCA
115259 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
115273 TTTAT
1 TTTAT
115278 TAAATGAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 1 0.02
16 41 0.87
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:115246 original size:32 final size:32
Alignment explanation
Indices: 115205--115269 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
115195 CCAACGTTTA
* *
115205 TGTTTGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGGTCATTTATGTTCG
*
115237 TGTTCGTTTATGTTCGTGGTCGTTTATGTTCG
1 TGTTCGTTTATGTTCGTGGTCATTTATGTTCG
115269 T
1 T
115270 TTATTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.08, C:0.11, G:0.25, T:0.57
Consensus pattern (32 bp):
TGTTCGTTTATGTTCGTGGTCATTTATGTTCG
Found at i:115360 original size:16 final size:16
Alignment explanation
Indices: 115339--115371 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
115329 AAAAAAAATT
115339 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
115355 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
115371 T
1 T
115372 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:116476 original size:20 final size:21
Alignment explanation
Indices: 116448--116541 Score: 90
Period size: 20 Copynumber: 4.6 Consensus size: 21
116438 ACAGGTTCCA
116448 AAATT-GCAACGCGAA-AGTC
1 AAATTCGCAACGCGAATAGTC
*
116467 AAATTCGCAACGCGAATAGTT
1 AAATTCGCAACGCGAATAGTC
**
116488 AAA-TCGCAACGATAATATGT-
1 AAATTCGCAACGCGAATA-GTC
**
116508 AAA-TCGCAACGCGAATTCTCC
1 AAATTCGCAACGCGAATAGT-C
116529 AAATTCGCAACGC
1 AAATTCGCAACGC
116542 TAATTACCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
19 6 0.10
20 36 0.58
21 11 0.18
22 9 0.15
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (21 bp):
AAATTCGCAACGCGAATAGTC
Found at i:116655 original size:20 final size:20
Alignment explanation
Indices: 116632--116676 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
116622 AATTAGCGTT
* *
116632 GCGAAAATGAAATTCTCAAA
1 GCGAAAATCAAATTCGCAAA
* *
116652 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAAA
116672 GCGAA
1 GCGAA
116677 TAGTTAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (20 bp):
GCGAAAATCAAATTCGCAAA
Found at i:116905 original size:40 final size:40
Alignment explanation
Indices: 116857--116952 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
116847 AATTTGGAGA
* *
116857 ATTCGCGTTGCGATTTACATATTATCGTTGCGATTTACCT
1 ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
*
116897 ATTCGCGTTGAGAATTACATATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
116937 ATTCGCGTTGCGAATT
1 ATTCGCGTTGCGAATT
116953 TGGAAAATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.41
Consensus pattern (40 bp):
ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
Found at i:116939 original size:20 final size:20
Alignment explanation
Indices: 116861--116949 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
116851 TGGAGAATTC
116861 GCGTTGCGATTTACATATTA
1 GCGTTGCGATTTACATATTA
* * *
116881 TCGTTGCGATTTACCTATTC
1 GCGTTGCGATTTACATATTA
* *
116901 GCGTTGAGAATTACATATTA
1 GCGTTGCGATTTACATATTA
* *
116921 TCGTTGCGATTTA-ACTATTC
1 GCGTTGCGATTTACA-TATTA
116941 GCGTTGCGA
1 GCGTTGCGA
116950 ATTTGGAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
19 1 0.02
20 54 0.98
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
GCGTTGCGATTTACATATTA
Found at i:117072 original size:76 final size:76
Alignment explanation
Indices: 116969--117157 Score: 351
Period size: 76 Copynumber: 2.5 Consensus size: 76
116959 ATCACAACGT
*
116969 GAATTTCATTTTCGCAACGCTAATTACCTATGTAGGTAATTAACTATTCGCTTTGCGAATTTGAC
1 GAATTTCATTTTCGCAACGCTAATTACCTATATAGGTAATTAACTATTCGCTTTGCGAATTTGAC
117034 TTTCACGTTGC
66 TTTCACGTTGC
*
117045 GAATTTCATTTTCGCAACGCTATTTACCTATATAGGTAATTAACTATTCGCTTTGCGAATTTGAC
1 GAATTTCATTTTCGCAACGCTAATTACCTATATAGGTAATTAACTATTCGCTTTGCGAATTTGAC
*
117110 TTTCGCGTTGC
66 TTTCACGTTGC
117121 GAATTTCATTTTCGCAACGCTAATTACCTATATAGGT
1 GAATTTCATTTTCGCAACGCTAATTACCTATATAGGT
117158 TGGAGAATTC
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 109 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (76 bp):
GAATTTCATTTTCGCAACGCTAATTACCTATATAGGTAATTAACTATTCGCTTTGCGAATTTGAC
TTTCACGTTGC
Found at i:117133 original size:20 final size:20
Alignment explanation
Indices: 117091--117135 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
117081 TAATTAACTA
* *
117091 TTCGCTTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTCACT
*
117111 TTCGCGTTGCGAATTTCATT
1 TTCGCGTTGCGAATTTCACT
117131 TTCGC
1 TTCGC
117136 AACGCTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTCACT
Found at i:117222 original size:40 final size:40
Alignment explanation
Indices: 117164--117253 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
117154 AGGTTGGAGA
* * * *
117164 ATTCGCGTTGCGATTTACATATTATCGTTGTGATTTACCT
1 ATTCGCGTTGAGAGTTACATATTATCGTTGCGATTTAACT
117204 ATTCGCGTTGAGAGTTACATATTATCGTTGCGATTTAACT
1 ATTCGCGTTGAGAGTTACATATTATCGTTGCGATTTAACT
117244 ATTCGCGTTG
1 ATTCGCGTTG
117254 CGAATTTGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (40 bp):
ATTCGCGTTGAGAGTTACATATTATCGTTGCGATTTAACT
Found at i:117246 original size:20 final size:20
Alignment explanation
Indices: 117168--117256 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
117158 TGGAGAATTC
117168 GCGTTGCGATTTACATATTA
1 GCGTTGCGATTTACATATTA
* * * *
117188 TCGTTGTGATTTACCTATTC
1 GCGTTGCGATTTACATATTA
* *
117208 GCGTTGAGAGTTACATATTA
1 GCGTTGCGATTTACATATTA
* *
117228 TCGTTGCGATTTA-ACTATTC
1 GCGTTGCGATTTACA-TATTA
117248 GCGTTGCGA
1 GCGTTGCGA
117257 ATTTGACTTT
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
19 1 0.02
20 53 0.98
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (20 bp):
GCGTTGCGATTTACATATTA
Found at i:117268 original size:20 final size:21
Alignment explanation
Indices: 117229--117281 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
117219 TACATATTAT
*
117229 CGTTGCG-ATTTAACTATTCG
1 CGTTGCGAATTTGACTATTCG
117249 CGTTGCGAATTTGACT-TTCG
1 CGTTGCGAATTTGACTATTCG
*
117269 TGTTGCGAATTTG
1 CGTTGCGAATTTG
117282 GAAAATCGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.42
Consensus pattern (21 bp):
CGTTGCGAATTTGACTATTCG
Found at i:117365 original size:20 final size:20
Alignment explanation
Indices: 117342--117438 Score: 101
Period size: 20 Copynumber: 4.8 Consensus size: 20
117332 TAATTAACTA
117342 TTCGCGTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGACT
*
117362 TTCGCATTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGACT
*
117382 TTCGCGTTGCGATTTTGAAAC-
1 TTCGCGTTGCGAATTTG--ACT
* * *
117403 TT-GTGTTGCGAAATTGGA-G
1 TTCGCGTTGCG-AATTTGACT
117422 TTCGCGTTGCGAATTTG
1 TTCGCGTTGCGAATTTG
117439 TTGGTCATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.12
20 48 0.75
21 6 0.09
22 2 0.03
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTGACT
Found at i:117614 original size:30 final size:32
Alignment explanation
Indices: 117574--117643 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
117564 GGTTATTTAT
117574 AAATATATATATTTTTACATTAGGTGAGGCAA
1 AAATATATATATTTTTACATTAGGTGAGGCAA
117606 AAATATATATATTTTTACATTAGGTGAGGCAA
1 AAATATATATATTTTTACATTAGGTGAGGCAA
117638 AAATAT
1 AAATAT
117644 TTTACCAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (32 bp):
AAATATATATATTTTTACATTAGGTGAGGCAA
Found at i:119014 original size:3 final size:3
Alignment explanation
Indices: 119006--119049 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
118996 GTGTATGTAT
* * *
119006 TTA TTA TTA -TA ATA ATA ATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
119050 CAAATAATAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:119091 original size:20 final size:20
Alignment explanation
Indices: 119063--119100 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
119053 ATAATACAAT
*
119063 AAGTCTGGAGGCTCAATTAC
1 AAGTCTGGAGGCCCAATTAC
*
119083 AAGTTTGGAGGCCCAATT
1 AAGTCTGGAGGCCCAATT
119101 GATAACAAAA
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:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (20 bp):
AAGTCTGGAGGCCCAATTAC
Found at i:121317 original size:21 final size:21
Alignment explanation
Indices: 121291--121410 Score: 79
Period size: 21 Copynumber: 5.8 Consensus size: 21
121281 ATCAGTTCCC
*
121291 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATCA
*
121312 AGAATCGCAATGCGA-TAGTACA
1 AGAATCGCAACGCGATTA-T-CA
* ** *
121334 AG-TTCGCATTGCGATTTTCA
1 AGAATCGCAACGCGATTATCA
* * *
121354 AGAATCGCAACACGAATATGA
1 AGAATCGCAACGCGATTATCA
**
121375 A-AATCGCAACGCGAACAT-A
1 AGAATCGCAACGCGATTATCA
121394 TA-AATCGCAACGCGATT
1 -AGAATCGCAACGCGATT
121411 CTGACTATCG
Statistics
Matches: 78, Mismatches: 16, Indels: 11
0.74 0.15 0.10
Matches are distributed among these distances:
19 1 0.01
20 35 0.45
21 38 0.49
22 4 0.05
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATCA
Found at i:121405 original size:20 final size:20
Alignment explanation
Indices: 121356--121408 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
121346 GATTTTCAAG
* *
121356 AATCGCAACACGAATATGAA
1 AATCGCAACGCGAACATGAA
121376 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAACATGA-A
121396 AATCGCAACGCGA
1 AATCGCAACGCGA
121409 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATGAA
Found at i:121461 original size:20 final size:21
Alignment explanation
Indices: 121417--121509 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
121407 GATTCTGACT
* *
121417 ATCGCAACGAGTACCCGTAAA
1 ATCGCAACGCGTATCCGTAAA
121438 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
* * *
121458 ATCGTAACG-ATAATACGTAAA
1 ATCGCAACGCGT-ATCCGTAAA
121479 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
121499 ATCGCAACGCG
1 ATCGCAACGCG
121510 AATATAACTA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.02
20 28 0.46
21 31 0.51
22 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGTATCCGTAAA
Found at i:121467 original size:41 final size:41
Alignment explanation
Indices: 121417--121507 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
121407 GATTCTGACT
*
121417 ATCGCAACGAGT-ACCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGA-TAACACGTAAAATCGCAACGCGTATCCGTAA
* *
121458 ATCGTAACGATAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGATAACACGTAAAATCGCAACGCGTATCCGTAA
121499 ATCGCAACG
1 ATCGCAACG
121508 CGAATATAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 1 0.02
41 44 0.98
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGATAACACGTAAAATCGCAACGCGTATCCGTAA
Found at i:121594 original size:33 final size:33
Alignment explanation
Indices: 121537--121632 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
121527 ACTAATTTCG
121537 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* *
121571 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
121604 CGTTGCGATAGTCATTTCTGCGTTGCGAT
1 CGTTGCGATTTTCATTTC-GCATTGCGAT
121633 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 33 0.60
34 22 0.40
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:121983 original size:20 final size:21
Alignment explanation
Indices: 121958--122051 Score: 124
Period size: 20 Copynumber: 4.7 Consensus size: 21
121948 GACATTCATT
121958 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAATA
* *
121978 TGACTATCGCAACAC-GAAAA
1 TGACTATCGCAACGCGGAATA
* *
121998 TGACTATCGCAATGCGGGAT-
1 TGACTATCGCAACGCGGAATA
122018 TGACTATCGCAACGCGGAA-A
1 TGACTATCGCAACGCGGAATA
122038 TGACTATCGCAACG
1 TGACTATCGCAACG
122052 AGAGAATCGA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (21 bp):
TGACTATCGCAACGCGGAATA
Found at i:122080 original size:33 final size:33
Alignment explanation
Indices: 122034--122101 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
122024 TCGCAACGCG
**
122034 GAAATGACTATCGCAACGAGAGAATCGAAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGAAATGC
* *
122067 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGAAATGC
122100 GA
1 GA
122102 TAGTCATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGAAATGC
Found at i:122864 original size:26 final size:26
Alignment explanation
Indices: 122828--122881 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
122818 TCAAATCAGA
122828 CAATGATATGTAATTTATCATGCTGT
1 CAATGATATGTAATTTATCATGCTGT
122854 CAATGATATGTAATTTATCATGCTGT
1 CAATGATATGTAATTTATCATGCTGT
122880 CA
1 CA
122882 TATACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (26 bp):
CAATGATATGTAATTTATCATGCTGT
Found at i:123747 original size:42 final size:42
Alignment explanation
Indices: 123639--123749 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
123629 CTCTAGAATG
* * *
123639 TAGGGAGGGACCTCTTCAACGATGACAGTTGCCTCTTGAAAGG
1 TAGGGAGGG-CCTCTTGAACGATGACAGTGGCCTCTTGAAAGA
* ** * *
123682 T-GGGAGGGGACTCTTGAGGGATGATAGTGGCCTCTTGAATGA
1 TAGGGA-GGGCCTCTTGAACGATGACAGTGGCCTCTTGAAAGA
123724 TAAGGGA-GGCCTCTTGAACGATGACA
1 T-AGGGAGGGCCTCTTGAACGATGACA
123750 AGTGAGTCGG
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
42 45 0.85
43 4 0.08
44 4 0.08
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.23
Consensus pattern (42 bp):
TAGGGAGGGCCTCTTGAACGATGACAGTGGCCTCTTGAAAGA
Found at i:124254 original size:20 final size:20
Alignment explanation
Indices: 124231--124317 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
124221 GAAACTTAAA
*
124231 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
124251 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
124271 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
**
124291 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
124311 ATCGCAA
1 ATCGCAA
124318 CGAGAGAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:124409 original size:19 final size:19
Alignment explanation
Indices: 124381--124428 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
124371 GCGATGTTGT
* **
124381 CGTTGAGATTTTGGTTTCG
1 CGTTGCGATTTTCATTTCG
*
124400 CGTTGCGATTTTCATTTCT
1 CGTTGCGATTTTCATTTCG
124419 CGTTGCGATT
1 CGTTGCGATT
124429 CTCTCGTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:124675 original size:94 final size:94
Alignment explanation
Indices: 124529--124908 Score: 613
Period size: 94 Copynumber: 4.1 Consensus size: 94
124519 ATGGATTGTA
* * *
124529 TTAC-TTCAACCAAAATACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
124593 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
124622 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGGATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
124687 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
124716 TTACTTTCAACCAAAAGACAAAACAAAAACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
124781 TTAGCAGAATTGACAGCAACCAAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
124810 TTAC-TTCAACCAAAAGACAAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGAC-AAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
124874 TTTAGCA-ATATTGGTAGCAACCGAATAAAT
65 TTTAGCAGA-ATTGGCAGCAACCGAACAAAT
124904 TTACT
1 TTACT
124909 AAGCAATCTA
Statistics
Matches: 268, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
93 19 0.07
94 249 0.93
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:126627 original size:20 final size:20
Alignment explanation
Indices: 126604--126659 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
126594 TGAAATGAAA
126604 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
126624 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
*
126644 ATCACAACGAGAGAAT
1 ATCGCAACGAGAGAAT
126660 CGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:126681 original size:19 final size:19
Alignment explanation
Indices: 126595--126750 Score: 152
Period size: 19 Copynumber: 8.6 Consensus size: 19
126585 TCTTTTGGTT
*
126595 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
126614 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
126634 GGAAATGACTATCACAA--C
1 -GAAATGAAAATCGCAACGC
*
126652 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
126668 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
126687 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
126704 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
126720 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
126739 GAAATGAAAATC
1 GAAATGAAAATC
126751 ACAATATTTT
Statistics
Matches: 115, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
14 18 0.16
15 2 0.02
16 4 0.03
17 3 0.03
18 3 0.03
19 56 0.49
20 27 0.23
21 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:126708 original size:52 final size:52
Alignment explanation
Indices: 126603--126754 Score: 232
Period size: 52 Copynumber: 2.9 Consensus size: 52
126593 TTGAAATGAA
* ** **
126603 AATCGCAACGAGAGAATGACTATCGCAACGCGGAAATGACTATCACAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGC-GAAATGAAAATCACAACGAGAG
*
126657 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCACAACGAGAG
126709 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCACAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCACAA
126755 TATTTTTCTC
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
52 64 0.70
53 15 0.16
54 12 0.13
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCACAACGAGAG
Found at i:126813 original size:20 final size:20
Alignment explanation
Indices: 126765--126815 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
126755 TATTTTTCTC
** *
126765 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
126785 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
126805 GTTGCGATTTT
1 GTTGCGATTTT
126816 AAGTTTAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:126894 original size:11 final size:11
Alignment explanation
Indices: 126878--126908 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
126868 ACTTCAACCA
126878 AAAGACAAAAC
1 AAAGACAAAAC
126889 AAAGACAAAAC
1 AAAGACAAAAC
126900 AAAGACAAA
1 AAAGACAAA
126909 TACTAACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAGACAAAAC
Found at i:127411 original size:20 final size:20
Alignment explanation
Indices: 127386--127598 Score: 232
Period size: 20 Copynumber: 10.5 Consensus size: 20
127376 TTCAAAAATT
*
127386 GCGTTGCGATTTACGAATAC
1 GCGTTGCGATTTACGGATAC
* *
127406 GCGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAC
127426 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGATAC
* * *
127447 GCATTGCGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
* *
127467 TCGTTGCGATTTACAGATAC
1 GCGTTGCGATTTACGGATAC
* *
127487 GCGTTGCGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
*
127507 TCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
* *
127527 GCGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAC
127547 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGATAC
*
127568 GCGTTGCGATTTTACGGGTAC
1 GCGTTGCGA-TTTACGGATAC
*
127589 TCGTTGCGAT
1 GCGTTGCGAT
127599 AGTCAGAATC
Statistics
Matches: 160, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
20 108 0.68
21 52 0.32
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
GCGTTGCGATTTACGGATAC
Found at i:127541 original size:81 final size:82
Alignment explanation
Indices: 127387--127659 Score: 335
Period size: 81 Copynumber: 3.4 Consensus size: 82
127377 TCAAAAATTG
* *
127387 CGTTGCGATTTAC-GAATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCAT
1 CGTTGCGATTTACAG-ATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGT
127451 TGCGA-TTTACGTATTCT
65 TGCGATTTTACGTATTCT
127468 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
*
127532 GCGATTTTACGTATTGT
66 GCGATTTTACGTATTCT
* ** * * *
127549 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGGTACTCGTTGCGATAGT-CAGA-ATCGCG
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGAT-TTACGGATA-CGCG
* *
127612 TTGCGATTTATA--TGTTCG
64 TTGCGATTT-TACGTATTCT
* * *
127630 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
127660 CTTGAAAATC
Statistics
Matches: 170, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
80 38 0.22
81 94 0.55
82 35 0.21
83 3 0.02
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (82 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
GCGATTTTACGTATTCT
Found at i:127593 original size:41 final size:41
Alignment explanation
Indices: 127387--127598 Score: 338
Period size: 41 Copynumber: 5.2 Consensus size: 41
127377 TCAAAAATTG
* *
127387 CGTTGCGATTTACGAATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
127428 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
127468 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
127508 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
** *
127549 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGGTACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
127590 CGTTGCGAT
1 CGTTGCGAT
127599 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 76 0.48
41 83 0.52
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:127630 original size:20 final size:20
Alignment explanation
Indices: 127607--127659 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
127597 ATAGTCAGAA
*
127607 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
127627 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
127647 TCGCGTTGCGATT
1 TCGCGTTGCGATT
127660 CTTGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:127651 original size:40 final size:39
Alignment explanation
Indices: 127386--127659 Score: 216
Period size: 40 Copynumber: 6.8 Consensus size: 39
127376 TTCAAAAATT
* *
127386 GCGTTGCGATTTAC-GAATACGCGTTGCGATTTTACGTATT
1 GCGTTGCGATTTACAG-ATACGCGTTGCGATTTTATGT-TC
* * *
127426 GTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTC
1 G-CGTTGCGATTTACAGATACGCGTTGCGATTTTA--TGTTC
* *
127467 TCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTC
1 GCGTTGCGATTTACAGATACGCGTTGCGATTTTA--TGTTC
* * * *
127507 TCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT
1 GCGTTGCGATTTACAGATACGCGTTGCGATTTTATGT-TC
* * *
127547 GTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGGTAC
1 G-CGTTGCGATTTACAGATACGCGTTGCGATTTTA--TGTTC
* *
127589 TCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTC
1 GCGTTGCGAT-TTACAGATA-CGCGTTGCGATTT-TATGTTC
* * *
127629 GCGTTGCGATTTTCATATTCGCGTTGCGATT
1 GCGTTGCGATTTACAGATACGCGTTGCGATT
127660 CTTGAAAATC
Statistics
Matches: 196, Mismatches: 24, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
39 2 0.01
40 99 0.51
41 88 0.45
42 5 0.03
43 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.38
Consensus pattern (39 bp):
GCGTTGCGATTTACAGATACGCGTTGCGATTTTATGTTC
Found at i:127677 original size:21 final size:22
Alignment explanation
Indices: 127653--127704 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
127643 ATATTCGCGT
127653 TGCGATTCTTG-AAAATCGCAA
1 TGCGATTCTTGTAAAATCGCAA
* ** *
127674 TGCGAAT-TTGTACTATCGCAT
1 TGCGATTCTTGTAAAATCGCAA
127695 TGCGATTCTT
1 TGCGATTCTT
127705 CATAATAGCG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 3 0.12
21 19 0.79
22 2 0.08
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (22 bp):
TGCGATTCTTGTAAAATCGCAA
Found at i:127758 original size:20 final size:20
Alignment explanation
Indices: 127712--127762 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
127702 CTTCATAATA
127712 GCGTTGCGATTCTGGGAACT
1 GCGTTGCGATTCTGGGAACT
** *
127732 GATTTGCGATTCTGGAGATC-
1 GCGTTGCGATTCTGG-GAACT
127752 GCGTTGCGATT
1 GCGTTGCGATT
127763 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (20 bp):
GCGTTGCGATTCTGGGAACT
Found at i:128405 original size:30 final size:29
Alignment explanation
Indices: 128371--128452 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
128361 TTTTACTTTC
* * *
128371 ATTTTAATTTGTAAAAATATTTTTCTTTTT
1 ATTTTAATTTATAAAAATATTTTTC-ATTG
* *
128401 ATTTTAAATTATAAAAATATTTATCATTG
1 ATTTTAATTTATAAAAATATTTTTCATTG
*
128430 ATTGTAATTTAT-AAAATATTTTT
1 ATTTTAATTTATAAAAATATTTTT
128453 TCTCCTATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 10 0.23
29 12 0.27
30 22 0.50
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (29 bp):
ATTTTAATTTATAAAAATATTTTTCATTG
Found at i:128442 original size:29 final size:28
Alignment explanation
Indices: 128375--128511 Score: 98
Period size: 29 Copynumber: 4.7 Consensus size: 28
128365 ACTTTCATTT
* * * *
128375 TAATTTGTAAAAATATTTTTCTTTTTATTT
1 TAATTTATAAAAATATTTATC--TCTATTA
* *
128405 TAAATTATAAAAATATTTATCAT-TGATTG
1 TAATTTATAAAAATATTTATC-TCT-ATTA
*
128434 TAATTTAT-AAAATATTTTTTCTCCTATTA
1 TAATTTATAAAAATA-TTTATCT-CTATTA
* *
128463 TAATTTATAAAAAGATTTATCCTATATTA
1 TAATTTATAAAAATATTTAT-CTCTATTA
* *
128492 TAATTTACAAAAAGATTTAT
1 TAATTTATAAAAATATTTAT
128512 TCTCGGTTAT
Statistics
Matches: 89, Mismatches: 12, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
28 8 0.09
29 55 0.62
30 26 0.29
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (28 bp):
TAATTTATAAAAATATTTATCTCTATTA
Found at i:131566 original size:24 final size:24
Alignment explanation
Indices: 131480--131573 Score: 97
Period size: 23 Copynumber: 4.0 Consensus size: 24
131470 CAATCTTATA
* *
131480 TGGCACTACGGTGCAA-TTCTATG
1 TGGCACTTCGGTGCAATTTCTACG
131503 TGGCACTTCGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
131526 CGGTC-CTTCAGG-ACAATTTCTACG
1 TGG-CACTTC-GGTGCAATTTCTACG
*
131550 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
131574 AGCTGTGGTG
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
22 1 0.02
23 29 0.50
24 28 0.48
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:132238 original size:14 final size:14
Alignment explanation
Indices: 132219--132245 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
132209 TACTGTAGTA
132219 GGTACTGTTCATAC
1 GGTACTGTTCATAC
132233 GGTACTGTTCATA
1 GGTACTGTTCATA
132246 TTGTATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (14 bp):
GGTACTGTTCATAC
Found at i:135411 original size:18 final size:18
Alignment explanation
Indices: 135388--135429 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
135378 AATCAAGTAT
*
135388 GATATGGATCTGAATATG
1 GATATGGATATGAATATG
135406 GATATGGATATGAATATG
1 GATATGGATATGAATATG
*
135424 GTTATG
1 GATATG
135430 TATTTGGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (18 bp):
GATATGGATATGAATATG
Found at i:138150 original size:23 final size:23
Alignment explanation
Indices: 138124--138201 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
138114 TGGCACTATA
*
138124 GTGCAATTCTATGTGGCACTTCG
1 GTGCAATTCTACGTGGCACTTCG
* *
138147 GTGCATTTCTACGCGGTC-CTTCG
1 GTGCAATTCTACGTGG-CACTTCG
*
138170 G-GATAATTTCTACGTGGCACTTCG
1 GTG-CAA-TTCTACGTGGCACTTCG
138194 GTGCAATT
1 GTGCAATT
138202 TATACAAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
22 1 0.02
23 23 0.53
24 18 0.42
25 1 0.02
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.35
Consensus pattern (23 bp):
GTGCAATTCTACGTGGCACTTCG
Found at i:138192 original size:24 final size:24
Alignment explanation
Indices: 138130--138202 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
138120 TATAGTGCAA
* *
138130 TTCTATGTGGCACTTC-GGTGCAT
1 TTCTACGTGGCACTTCGGGTGAAT
*
138153 TTCTACGCGGTC-CTTCGGGAT-AAT
1 TTCTACGTGG-CACTTCGGG-TGAAT
138177 TTCTACGTGGCACTTC-GGTGCAAT
1 TTCTACGTGGCACTTCGGGTG-AAT
138201 TT
1 TT
138203 ATACAAGATG
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 1 0.03
23 15 0.38
24 23 0.57
25 1 0.03
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (24 bp):
TTCTACGTGGCACTTCGGGTGAAT
Found at i:138865 original size:14 final size:14
Alignment explanation
Indices: 138846--138873 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
138836 TACTGTAGCA
138846 GGTACTGTTCATAC
1 GGTACTGTTCATAC
138860 GGTACTGTTCATAC
1 GGTACTGTTCATAC
138874 CGTATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
GGTACTGTTCATAC
Found at i:141144 original size:21 final size:21
Alignment explanation
Indices: 141118--141166 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
141108 AGATGAGCTA
141118 TGACTTTGCAATAAG-GTTG-CT
1 TGACTTTGCAA-AAGTG-TGCCT
141139 TGACTTTGCAAAAGTGTGCCT
1 TGACTTTGCAAAAGTGTGCCT
141160 TGACTTT
1 TGACTTT
141167 TAATTATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (21 bp):
TGACTTTGCAAAAGTGTGCCT
Found at i:143960 original size:62 final size:63
Alignment explanation
Indices: 143813--143970 Score: 178
Period size: 63 Copynumber: 2.5 Consensus size: 63
143803 CCCTTGACAG
* * * *
143813 GTGCATCGATGCACTATCTATGCATCGATGCA-TAAATCACATTCGATGTTTGTATTTAAGGGG
1 GTGCATCGATGCACT-TCTGTGCATCGATACACTAAATCACATTCGATGTTTGTATTTAAAGGA
* * ** *
143876 GTGCATCGATGCACTACTTGTGCATCGATACACT-GATTGCATTCGATGTTT-TTTTTAAAGGA
1 GTGCATCGATGCACTTC-TGTGCATCGATACACTAAATCACATTCGATGTTTGTATTTAAAGGA
*
143938 GTGCATCGATGCACTTCATGTGCATTGATACAC
1 GTGCATCGATGCACTTC-TGTGCATCGATACAC
143971 CTTGAACAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
62 39 0.48
63 41 0.51
64 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTTCTGTGCATCGATACACTAAATCACATTCGATGTTTGTATTTAAAGGA
Found at i:147836 original size:64 final size:63
Alignment explanation
Indices: 147736--147856 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 63
147726 GCATAAATCC
* *
147736 CATTCGATGTTTGTATTTAAGGAGGTGCATCGATGCACTACTTGTGTATCGATACACTGATGG
1 CATTCGATGTTTGTATTTAAGGAGGTGCATCGATGCACTACATGTGCATCGATACACTGATGG
* *
147799 CATTCGATGTTTTTATTTTAAAGGA-GTGCATCGATGCACTTCATGTGCATCGATACAC
1 CATTCGATGTTTGTA-TTT-AAGGAGGTGCATCGATGCACTACATGTGCATCGATACAC
147857 CTTGAACCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
63 14 0.27
64 33 0.63
65 5 0.10
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (63 bp):
CATTCGATGTTTGTATTTAAGGAGGTGCATCGATGCACTACATGTGCATCGATACACTGATGG
Found at i:151310 original size:17 final size:17
Alignment explanation
Indices: 151285--151319 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
151275 GTAAATTTAT
* *
151285 TTTGGTTACATTAAATA
1 TTTGATTACAATAAATA
151302 TTTGATTACAATAAATA
1 TTTGATTACAATAAATA
151319 T
1 T
151320 GAGGGTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (17 bp):
TTTGATTACAATAAATA
Found at i:155010 original size:138 final size:139
Alignment explanation
Indices: 154751--155002 Score: 368
Period size: 138 Copynumber: 1.8 Consensus size: 139
154741 TTCATTTTCT
*
154751 GCAAAAAATCACAACAAAAGTTCACACATTCTCACTGCTATTAACAAGAGAAATACCAAACCAAT
1 GCAAAAAATCACAACAAAAGTTCACACATTCTCACTGCTATTAACAAGAGAAACACCAAACCAAT
* * **
154816 GATGTTCATGTTTTTTCTATCAAAAAACAAGTTTTCTTTCTCGATCATTAACTTCTGCAACATCC
66 GACGTTCATGTTTTTTCTATCAAAAAACAAGTTTTCTTTCTCGAACACCAACTTCTGCAACATCC
154881 ATTGTTTGG
131 ATTGTTTGG
* *
154890 GCAAAAAA-CACAACAAAAGTTCACACATTTTCACTGTTATTAACAAGAGAAAAACACCAAACCA
1 GCAAAAAATCACAACAAAAGTTCACACATTCTCACTGCTATTAACAAGAG--AAACACCAAACCA
* *
154954 ATGACGTTCATG-TTTTTCTATC-AAAACCCAGTTTTCTTTCT-GCAACACC
64 ATGACGTTCATGTTTTTTCTATCAAAAAACAAGTTTTCTTTCTCG-AACACC
155003 CATTTCTGGG
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
137 1 0.01
138 59 0.58
139 18 0.18
140 23 0.23
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (139 bp):
GCAAAAAATCACAACAAAAGTTCACACATTCTCACTGCTATTAACAAGAGAAACACCAAACCAAT
GACGTTCATGTTTTTTCTATCAAAAAACAAGTTTTCTTTCTCGAACACCAACTTCTGCAACATCC
ATTGTTTGG
Found at i:155483 original size:3 final size:3
Alignment explanation
Indices: 155475--155509 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
155465 AGGATCGAGG
155475 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
155510 GTTGTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:160197 original size:20 final size:20
Alignment explanation
Indices: 160154--160203 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
160144 GAACTGAGGT
* *
160154 AGTATCGATATTGACTTATC
1 AGTATCGATATTGACTCAGC
*
160174 AGTATCGATATTGACTCAGG
1 AGTATCGATATTGACTCAGC
*
160194 AGTATTGATA
1 AGTATCGATA
160204 CCTCCATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (20 bp):
AGTATCGATATTGACTCAGC
Found at i:163045 original size:16 final size:16
Alignment explanation
Indices: 163024--163060 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
163014 AGAGAAAGCC
163024 TTAATCTACCCTTAGT
1 TTAATCTACCCTTAGT
163040 TTAATCTACCCTTAGT
1 TTAATCTACCCTTAGT
163056 TTAAT
1 TTAAT
163061 TAGGGTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (16 bp):
TTAATCTACCCTTAGT
Found at i:164716 original size:30 final size:30
Alignment explanation
Indices: 164675--164735 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
164665 CGTCATTAGT
*
164675 GGTGCTCATCGCTACTCGTTGAACGTAGAA
1 GGTGCTAATCGCTACTCGTTGAACGTAGAA
164705 GGTGCTAATCGCTACTCGTTGAACGTAGAA
1 GGTGCTAATCGCTACTCGTTGAACGTAGAA
164735 G
1 G
164736 AATCATCCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (30 bp):
GGTGCTAATCGCTACTCGTTGAACGTAGAA
Found at i:170526 original size:2 final size:2
Alignment explanation
Indices: 170519--170544 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
170509 TGGATAATGT
170519 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
170545 AATCCACTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:171034 original size:23 final size:23
Alignment explanation
Indices: 171008--171065 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
170998 TAAACTACTT
* *
171008 AAAGTCAGAGAAAAACGTGTCAC
1 AAAGACAGAGAAAAACGTATCAC
* * *
171031 AAAGACAGAGATAAATGTATCAT
1 AAAGACAGAGAAAAACGTATCAC
171054 AAAGACAGAGAA
1 AAAGACAGAGAA
171066 CATGACACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.53, C:0.12, G:0.21, T:0.14
Consensus pattern (23 bp):
AAAGACAGAGAAAAACGTATCAC
Found at i:180021 original size:14 final size:14
Alignment explanation
Indices: 179993--180025 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
179983 ATGCATAATT
179993 ACTAATAAAACTAA
1 ACTAATAAAACTAA
180007 ACTAAGTAAAA-TAA
1 ACTAA-TAAAACTAA
180021 ACTAA
1 ACTAA
180026 AATAGTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.21
Consensus pattern (14 bp):
ACTAATAAAACTAA
Found at i:180319 original size:18 final size:17
Alignment explanation
Indices: 180286--180319 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
180276 GAATAATTAA
180286 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
180303 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
180320 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:188384 original size:18 final size:17
Alignment explanation
Indices: 188351--188384 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
188341 GAATAATTAA
188351 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
188368 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
188385 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:192148 original size:19 final size:20
Alignment explanation
Indices: 192112--192149 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
192102 TAACTTGATT
*
192112 GTTGACCAGACCTATTGACC
1 GTTGACCAGACCCATTGACC
*
192132 GTTGA-CAGACCCGTTGAC
1 GTTGACCAGACCCATTGAC
192150 TTTGACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (20 bp):
GTTGACCAGACCCATTGACC
Done.