Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012141.1 Kokia drynarioides strain JFW-HI SEQ_127140, 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: 461594
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 104 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:468 original size:15 final size:15
Alignment explanation
Indices: 437--505 Score: 70
Period size: 15 Copynumber: 4.6 Consensus size: 15
427 CCTAGTAAAC
*
437 TGTAGTTTGGG-CTTT
1 TGTA-TTTGGGCCATT
452 TGTATTTGGGCCATT
1 TGTATTTGGGCCATT
**
467 TGTAACTGGGCCATT
1 TGTATTTGGGCCATT
482 TGT-TATTGGGCCATT
1 TGTAT-TTGGGCCATT
*
497 TGTAATTGG
1 TGTATTTGG
506 ACTTTGTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.13
15 39 0.87
ACGTcount: A:0.14, C:0.12, G:0.29, T:0.45
Consensus pattern (15 bp):
TGTATTTGGGCCATT
Found at i:560 original size:17 final size:17
Alignment explanation
Indices: 538--580 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
528 TTGGACTTTC
538 TAAATTTAATCTTATAA
1 TAAATTTAATCTTATAA
555 TAAATTTAATCTTATAA
1 TAAATTTAATCTTATAA
572 TAAATTTAA
1 TAAATTTAA
581 ATTTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTTAATCTTATAA
Found at i:590 original size:17 final size:16
Alignment explanation
Indices: 538--610 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 16
528 TTGGACTTTC
538 TAAATTT-AATCTTATAA
1 TAAATTTAAAT-TTA-AA
555 TAAATTT-AATCTTATAA
1 TAAATTTAAAT-TTA-AA
572 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
*
589 TAAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
605 TAAATT
1 TAAATT
611 CAATTTCCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
16 8 0.15
17 40 0.77
18 4 0.08
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:622 original size:16 final size:17
Alignment explanation
Indices: 570--623 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
560 TTAATCTTAT
*
570 AATAAATTTAAATTTCA
1 AATAAACTTAAATTTCA
587 AATAAACTTAAATTT-A
1 AATAAACTTAAATTTCA
* *
603 AATAAA-TTCAATTTCC
1 AATAAACTTAAATTTCA
619 AATAA
1 AATAA
624 GCCCAGACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.21
16 12 0.36
17 14 0.42
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAAACTTAAATTTCA
Found at i:2624 original size:2 final size:2
Alignment explanation
Indices: 2617--2655 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2607 GAAAAGGAAG
*
2617 GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA G- GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2656 ATAAATGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2967 original size:16 final size:14
Alignment explanation
Indices: 2948--2981 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
2938 AATTGTAAAA
2948 AAAATTATTTTATGTT
1 AAAATTA-TTTAT-TT
2964 AAAATTATTTATTT
1 AAAATTATTTATTT
2978 AAAA
1 AAAA
2982 GGTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 5 0.28
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
AAAATTATTTATTT
Found at i:3685 original size:6 final size:6
Alignment explanation
Indices: 3674--3717 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
3664 TGATGGAAGA
3674 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GG
1 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GG
3718 CGATTCTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GGAGTG
Found at i:7460 original size:278 final size:279
Alignment explanation
Indices: 6962--7466 Score: 958
Period size: 278 Copynumber: 1.8 Consensus size: 279
6952 ATAATAATCA
6962 TTCAATTTAAAACTGGTAATCCTTTGATTTAAAATTAATTTAGTAATAGTTGAAAAAGTCTTTTA
1 TTCAATTTAAAACTGGTAATCCTTTGATTTAAAATTAATTTAGTAATAGTTGAAAAAGTCTTTTA
*
7027 ACTTTTTAAAAAAAAAAAATTAAGCAAATAGAAGCATAAATTGCGAGACCCAACCCCTCGAAGGT
66 ACTTTTTAAAAAAAAAAAATTAAGCAAATAGAAGCATAAATTGCGAGACCCAACCCCTCAAAGGT
*
7092 GACATAGCGAAGACCCAAGTCAAGGCGAAGAAGGAAACAAGTTTTCGTTGGTGGTTTCATAAAGC
131 GACATAGCGAAGACCCAAGTCAAGGCGAAGAAAGAAACAAGTTTTCGTTGGTGGTTTCATAAAGC
7157 CACTTTAATCGGAAGTGGAGTTGATTGGTGATTGGTTATCTTTCCACTGTTTTATGCTTCCAGAG
196 CACTTTAATCGGAAGTGGAGTTGATTGGTGATTGGTTATCTTTCCACTGTTTTATGCTTCCAGAG
7222 ATGTCAGCTCAGCTTGCTT
261 ATGTCAGCTCAGCTTGCTT
* *
7241 TTCAATTTAAAACTGGTAATCCTTTGTTTTGAAATTAATTTAGTAATAGTTGAAAAAGTCTTTTA
1 TTCAATTTAAAACTGGTAATCCTTTGATTTAAAATTAATTTAGTAATAGTTGAAAAAGTCTTTTA
*
7306 ACTTTTT-TAAAAAAAAAATTAAGCAAATAGAAGCATAAATTGCGAGACCCAACCCCTCAAAGGT
66 ACTTTTTAAAAAAAAAAAATTAAGCAAATAGAAGCATAAATTGCGAGACCCAACCCCTCAAAGGT
7370 GACATAGCGAAGACCCAAGTCAAGGCGAAGAAAGAAACAAGTTTTCGTTGGTGGTTTCATAAAGC
131 GACATAGCGAAGACCCAAGTCAAGGCGAAGAAAGAAACAAGTTTTCGTTGGTGGTTTCATAAAGC
7435 CACTTTAATCGGAAGTGGAGTTGATTGGTGAT
196 CACTTTAATCGGAAGTGGAGTTGATTGGTGAT
7467 AAAAGTAAAA
Statistics
Matches: 221, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
278 151 0.68
279 70 0.32
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (279 bp):
TTCAATTTAAAACTGGTAATCCTTTGATTTAAAATTAATTTAGTAATAGTTGAAAAAGTCTTTTA
ACTTTTTAAAAAAAAAAAATTAAGCAAATAGAAGCATAAATTGCGAGACCCAACCCCTCAAAGGT
GACATAGCGAAGACCCAAGTCAAGGCGAAGAAAGAAACAAGTTTTCGTTGGTGGTTTCATAAAGC
CACTTTAATCGGAAGTGGAGTTGATTGGTGATTGGTTATCTTTCCACTGTTTTATGCTTCCAGAG
ATGTCAGCTCAGCTTGCTT
Found at i:8066 original size:21 final size:21
Alignment explanation
Indices: 8040--8082 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8030 CAAAGCAGTG
*
8040 ACAAAAAATGAAAAAATAACA
1 ACAAAAAATGAAAAAACAACA
* *
8061 ACAAAACATGGAAAAACAACA
1 ACAAAAAATGAAAAAACAACA
8082 A
1 A
8083 GATTTTTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.72, C:0.14, G:0.07, T:0.07
Consensus pattern (21 bp):
ACAAAAAATGAAAAAACAACA
Found at i:8237 original size:15 final size:16
Alignment explanation
Indices: 8219--8257 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
8209 ATTAACTTTA
8219 AAAATATTAAAA-AAT
1 AAAATATTAAAATAAT
8234 AAAATA--AAAATAAT
1 AAAATATTAAAATAAT
8248 AAAA-ATTAAA
1 AAAATATTAAA
8258 TTAAAGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 5 0.24
14 7 0.33
15 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATTAAAATAAT
Found at i:8242 original size:20 final size:21
Alignment explanation
Indices: 8217--8262 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
8207 TAATTAACTT
*
8217 TAAAAATATTAAAAAATAAAA
1 TAAAAATAATAAAAAATAAAA
* *
8238 TAAAAATAATAAAAATTAAAT
1 TAAAAATAATAAAAAATAAAA
8259 TAAA
1 TAAA
8263 GCAAAGTGGG
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAATAATAAAAAATAAAA
Found at i:38700 original size:30 final size:30
Alignment explanation
Indices: 38664--38725 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
38654 TAGTTATGCC
**
38664 TTCCTAAATTGTTTTATTAAACAAAGAGCA
1 TTCCTAAATCATTTTATTAAACAAAGAGCA
* * *
38694 TTCCTAAATCATTTTGTTAAATAATGAGCA
1 TTCCTAAATCATTTTATTAAACAAAGAGCA
38724 TT
1 TT
38726 GTTTATAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (30 bp):
TTCCTAAATCATTTTATTAAACAAAGAGCA
Found at i:41953 original size:252 final size:251
Alignment explanation
Indices: 41488--41995 Score: 944
Period size: 252 Copynumber: 2.0 Consensus size: 251
41478 ACAGCATCAA
* *
41488 TTCAGGGTGGTTGAATAATCCCCGGTTACACTATCATGGATCATGGTTATTCAGCACTGAGATCT
1 TTCAGGGTGGTTGAATAACCCCCCGTTACACTATCATGGATCATGGTTATTCAGCACTGAGATCT
*
41553 TTTCTAGGGGCCGAGGATGCAGGGTTTTGTTTTGTCTTTGAATGAGATAGGGGATAATGTTACAA
66 TTTCTAGGGGCCAAGGATGCAGGGTTTTGTTTTGTCTTTGAATGAGATAGGGGATAATGTTACAA
41618 TTCTAGACTGAATTCCTGCCTTGAATTTTATAAACACTAAAATATTTCTTTCATCAGCAATGGTG
131 TTCTAGACTGAATTCCTGCCTTGAATTTTATAAACACTAAAATATTTCTTTCATCAGCAATGGTG
41683 GCTGCAGAATCAATTTGACATTTTGAGGGGCAGTTCATTGTTTTAGTAATATGTGT
196 GCTGCAGAATCAATTTGACATTTTGAGGGGCAGTTCATTGTTTTAGTAATATGTGT
*
41739 TTCAGGGTGGTTGAATACCCCCCCGTTACACTATCATGGATCATGGTTATTCAGCACTGAGATCT
1 TTCAGGGTGGTTGAATAACCCCCCGTTACACTATCATGGATCATGGTTATTCAGCACTGAGATCT
41804 TTTCTAGGGGCCAAGGATGCAGGGTTTTGTTTTGTCTTTGAATGATGATAGGGGATAATGTTACA
66 TTTCTAGGGGCCAAGGATGCAGGGTTTTGTTTTGTCTTTGAATGA-GATAGGGGATAATGTTACA
*
41869 ATTCTAGACTGAATTCCTGCCTTGAATTTTATAAATACTAAAATATTTCTTTCATCAGCAATGGT
130 ATTCTAGACTGAATTCCTGCCTTGAATTTTATAAACACTAAAATATTTCTTTCATCAGCAATGGT
*
41934 GGCTGCAGAGTCAATTTGACATTTTGAGGGGCAGTTCATTGTTTTAGTAATATGTGT
195 GGCTGCAGAATCAATTTGACATTTTGAGGGGCAGTTCATTGTTTTAGTAATATGTGT
*
41991 GTCAG
1 TTCAG
41996 AAATGACAGG
Statistics
Matches: 249, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
251 106 0.43
252 143 0.57
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (251 bp):
TTCAGGGTGGTTGAATAACCCCCCGTTACACTATCATGGATCATGGTTATTCAGCACTGAGATCT
TTTCTAGGGGCCAAGGATGCAGGGTTTTGTTTTGTCTTTGAATGAGATAGGGGATAATGTTACAA
TTCTAGACTGAATTCCTGCCTTGAATTTTATAAACACTAAAATATTTCTTTCATCAGCAATGGTG
GCTGCAGAATCAATTTGACATTTTGAGGGGCAGTTCATTGTTTTAGTAATATGTGT
Found at i:47192 original size:172 final size:172
Alignment explanation
Indices: 46906--47249 Score: 688
Period size: 172 Copynumber: 2.0 Consensus size: 172
46896 TTTGTTAGTC
46906 GGGTAGAGGTATGATATTTCATAAATGCTTTTGGCTTAGTTTTGAAATTTTAGGGAGCTACGTGT
1 GGGTAGAGGTATGATATTTCATAAATGCTTTTGGCTTAGTTTTGAAATTTTAGGGAGCTACGTGT
46971 TAGTTTCTAAATTCGAGTTATGACTTTCACAAAATTTTTTCTACATGAATGAATTCCGCATAAAT
66 TAGTTTCTAAATTCGAGTTATGACTTTCACAAAATTTTTTCTACATGAATGAATTCCGCATAAAT
47036 GCTCAGGCAAACTAATTATGATTATTGAGAAATCATCACTGG
131 GCTCAGGCAAACTAATTATGATTATTGAGAAATCATCACTGG
47078 GGGTAGAGGTATGATATTTCATAAATGCTTTTGGCTTAGTTTTGAAATTTTAGGGAGCTACGTGT
1 GGGTAGAGGTATGATATTTCATAAATGCTTTTGGCTTAGTTTTGAAATTTTAGGGAGCTACGTGT
47143 TAGTTTCTAAATTCGAGTTATGACTTTCACAAAATTTTTTCTACATGAATGAATTCCGCATAAAT
66 TAGTTTCTAAATTCGAGTTATGACTTTCACAAAATTTTTTCTACATGAATGAATTCCGCATAAAT
47208 GCTCAGGCAAACTAATTATGATTATTGAGAAATCATCACTGG
131 GCTCAGGCAAACTAATTATGATTATTGAGAAATCATCACTGG
47250 ATAAATACTA
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (172 bp):
GGGTAGAGGTATGATATTTCATAAATGCTTTTGGCTTAGTTTTGAAATTTTAGGGAGCTACGTGT
TAGTTTCTAAATTCGAGTTATGACTTTCACAAAATTTTTTCTACATGAATGAATTCCGCATAAAT
GCTCAGGCAAACTAATTATGATTATTGAGAAATCATCACTGG
Found at i:49893 original size:12 final size:12
Alignment explanation
Indices: 49876--49901 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49866 TGATATTGAA
49876 AATTATTATAGT
1 AATTATTATAGT
49888 AATTATTATAGT
1 AATTATTATAGT
49900 AA
1 AA
49902 ATAACACTAA
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
AATTATTATAGT
Found at i:55026 original size:17 final size:17
Alignment explanation
Indices: 54990--55023 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54980 ATTTTTTTAT
*
54990 ATTTTTTTTCATTGAAA
1 ATTTTTATTCATTGAAA
55007 ATTTTTATT-ATTGAAA
1 ATTTTTATTCATTGAAA
55023 A
1 A
55024 ATTCTATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
ATTTTTATTCATTGAAA
Found at i:69132 original size:22 final size:24
Alignment explanation
Indices: 69104--69168 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 24
69094 TTTTATCTTT
*
69104 TAAAATTTTAAATTAAT-AAA-AA
1 TAAAATTTTAATTTAATCAAATAA
* *
69126 TAAAATTATATTTTAATCTCAAATAA
1 TAAAATTTTAATTTAA--TCAAATAA
69152 TAAAATTTTAATTTAAT
1 TAAAATTTTAATTTAAT
69169 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
22 13 0.38
24 2 0.06
25 3 0.09
26 16 0.47
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAATTTTAATTTAATCAAATAA
Found at i:73737 original size:2 final size:2
Alignment explanation
Indices: 73730--73762 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
73720 TGAGACTTAA
73730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73763 CAGCACCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78622 original size:38 final size:39
Alignment explanation
Indices: 78580--78656 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
78570 TATATATGTA
*
78580 TATAACAATATCAATTTT-GTTCTTTTATTAGGTATTTT
1 TATAACAATATCAATTTTAGTTATTTTATTAGGTATTTT
* *
78618 TATAACAATGTCAATTTTATTTATTTTATTAGGTATTTT
1 TATAACAATATCAATTTTAGTTATTTTATTAGGTATTTT
78657 CTTAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 17 0.49
39 18 0.51
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (39 bp):
TATAACAATATCAATTTTAGTTATTTTATTAGGTATTTT
Found at i:80597 original size:14 final size:15
Alignment explanation
Indices: 80580--80608 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
80570 AATAAAATAT
80580 ATTATT-TTAAATTA
1 ATTATTGTTAAATTA
80594 ATTATTGTTAAATTA
1 ATTATTGTTAAATTA
80609 GTGTTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTATTGTTAAATTA
Found at i:87633 original size:6 final size:6
Alignment explanation
Indices: 87622--87647 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
87612 AACCACCAGA
87622 AGAAAC AGAAAC AGAAAC AGAAAC AG
1 AGAAAC AGAAAC AGAAAC AGAAAC AG
87648 TAAAGACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.15, G:0.19, T:0.00
Consensus pattern (6 bp):
AGAAAC
Found at i:93230 original size:2 final size:2
Alignment explanation
Indices: 93223--93256 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
93213 TTAGAATGTT
*
93223 TA TA TA TA TA TA TT 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
93257 AATTACGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:96321 original size:44 final size:45
Alignment explanation
Indices: 96273--96374 Score: 147
Period size: 44 Copynumber: 2.2 Consensus size: 45
96263 ATATTAAAAG
96273 AATATTTTAAATATTATTAAAACATAA-T-ATTATTAA-AAATGAAA
1 AATATTTTAAATATTATTAAAACA-AAGTAATT-TTAAGAAATGAAA
96317 AATATTTTAAATATTATTAAAACAAAGTTAATTTTAAGAAATGAAA
1 AATATTTTAAATATTATTAAAACAAAG-TAATTTTAAGAAATGAAA
96363 AATATTATTAAA
1 AATATT-TTAAA
96375 AGAAAAACGA
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
43 2 0.04
44 24 0.45
45 5 0.09
46 17 0.32
47 5 0.09
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (45 bp):
AATATTTTAAATATTATTAAAACAAAGTAATTTTAAGAAATGAAA
Found at i:96564 original size:31 final size:31
Alignment explanation
Indices: 96529--96607 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
96519 ATTTTAAATA
*
96529 TAAATAAATATTTAAATGATTAAAACGTAAT
1 TAAATAAATATTTAAATGATTAAAACATAAT
* * *
96560 TAAATGATTATCTAAATGATTAAAACATAAT
1 TAAATAAATATTTAAATGATTAAAACATAAT
*
96591 TAAAGTATA-ATTTAAAT
1 TAAA-TAAATATTTAAAT
96608 TAAATAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (31 bp):
TAAATAAATATTTAAATGATTAAAACATAAT
Found at i:96948 original size:19 final size:20
Alignment explanation
Indices: 96923--96968 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
96913 GATCACCGTA
*
96923 ATTTTTT-AATTAA-TTTTT
1 ATTTTTTAAATTAAGTTATT
96941 AGTTTTTTAAATTAAGTTATT
1 A-TTTTTTAAATTAAGTTATT
96962 ATTTTTT
1 ATTTTTT
96969 TTTTTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.04
19 6 0.25
20 12 0.50
21 5 0.21
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
ATTTTTTAAATTAAGTTATT
Found at i:103970 original size:2 final size:2
Alignment explanation
Indices: 103965--103994 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
103955 TAAAAAAAAA
103965 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
103995 GGTAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121237 original size:17 final size:18
Alignment explanation
Indices: 121212--121246 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
121202 GCACTTTGAA
121212 ATTTCAATTTT-CCTTTT
1 ATTTCAATTTTGCCTTTT
*
121229 ATTTTAATTTTGCCTTTT
1 ATTTCAATTTTGCCTTTT
121247 CAATTAGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.17, C:0.14, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTTCAATTTTGCCTTTT
Found at i:122680 original size:21 final size:23
Alignment explanation
Indices: 122654--122777 Score: 155
Period size: 23 Copynumber: 5.4 Consensus size: 23
122644 CGGAACAAAT
* *
122654 AGAGAGTAC-CAAAGTACTAA-C
1 AGAGAGCACACAAAGTGCTAATC
*
122675 AGAGAGCACA-AACAGTGCTAAAC
1 AGAGAGCACACAA-AGTGCTAATC
122698 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAATC
122721 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAATC
* *
122744 AGAGAGCACACACAGTGTTAATAAC
1 AGAGAGCACACAAAGTGCTAAT--C
122769 AGAGAGCAC
1 AGAGAGCAC
122778 GCTGGTGTTC
Statistics
Matches: 92, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
21 10 0.11
22 7 0.08
23 63 0.68
24 2 0.02
25 10 0.11
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAATC
Found at i:123661 original size:18 final size:17
Alignment explanation
Indices: 123633--123676 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
123623 AAAAAGGTTG
123633 ATTTC-CTTCTCTTTTC
1 ATTTCTCTTCTCTTTTC
123649 ATTTGCTCTTCTCTTTTC
1 ATTT-CTCTTCTCTTTTC
*
123667 CTTTCTCTTC
1 ATTTCTCTTC
123677 AATTTGATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 7 0.28
18 14 0.56
ACGTcount: A:0.05, C:0.32, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTTCTCTTCTCTTTTC
Found at i:125813 original size:59 final size:57
Alignment explanation
Indices: 125669--125868 Score: 181
Period size: 59 Copynumber: 3.4 Consensus size: 57
125659 CAACTCATGG
* * * * *
125669 GGGTAAAATGGAAATTTT-GGAAAAGTTCGGGGTTAAAAATGAGATTTTTAGACACTCGA
1 GGGTAAAATGGTAATTTTAGGAAAA--TC-GGATAAAAAATGAGATTTTTGGACATTCGA
* ** * * *
125728 GGGTAAAATGGCAACTTTTAAAAAAATCAGGATCAAAAATGAAATTTTTGGACATTCGG
1 GGGTAAAATGGTAA-TTTTAGGAAAATC-GGATAAAAAATGAGATTTTTGGACATTCGA
*
125787 GGGTAAAATGGTAATCTTTAGGAAAATCGAGATAAAAAATG-GATTTTTGGGA-AGTTCTA
1 GGGTAAAATGGTAAT-TTTAGGAAAATCG-GATAAAAAATGAGATTTTT-GGACA-TTCGA
*
125846 GGGTAAAATGGTAATTTTTGGAA
1 GGGTAAAATGGTAATTTTAGGAA
125869 GTTTTGGGGT
Statistics
Matches: 117, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
58 16 0.14
59 93 0.79
60 4 0.03
61 4 0.03
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTAGGAAAATCGGATAAAAAATGAGATTTTTGGACATTCGA
Found at i:125863 original size:30 final size:28
Alignment explanation
Indices: 125822--125981 Score: 148
Period size: 30 Copynumber: 5.5 Consensus size: 28
125812 ATCGAGATAA
125822 AAAATGG--ATTTTTGGGAAGTTCTAGGGT
1 AAAATGGTAATTTTT-GGAAGTT-TAGGGT
*
125850 AAAATGGTAATTTTTGGAAGTTTTGGGGTT
1 AAAATGGTAATTTTTGGAAG-TTTAGGG-T
*
125880 AAAATTGG-AATTTTTAGAAGTTTAGAGGT
1 AAAA-TGGTAATTTTTGGAAGTTTAG-GGT
*
125909 AAAATGGTAATTTTTGGAGGATTTAGGGT
1 AAAATGGTAATTTTTGGAAG-TTTAGGGT
***
125938 CAAAATTAAAATTTTTGGAAGTTTAAGGGT
1 -AAAATGGTAATTTTTGGAAGTTT-AGGGT
125968 AAAAAT-GTAATTTT
1 -AAAATGGTAATTTT
125982 CAAAAGTATC
Statistics
Matches: 110, Mismatches: 12, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
28 10 0.09
29 40 0.36
30 57 0.52
31 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.39
Consensus pattern (28 bp):
AAAATGGTAATTTTTGGAAGTTTAGGGT
Found at i:125900 original size:59 final size:58
Alignment explanation
Indices: 125837--125981 Score: 184
Period size: 59 Copynumber: 2.4 Consensus size: 58
125827 GGATTTTTGG
* * * **
125837 GAAGTTCTAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAATTGGAATTTTTA
1 GAAGTT-TAGGGTAAAATGGTAATTTTTGGAAGATTTAGGGTCAAAATTAAAATTTTTA
* *
125896 GAAGTTTAGAGGTAAAATGGTAATTTTTGGAGGATTTAGGGTCAAAATTAAAATTTTTG
1 GAAGTTTAG-GGTAAAATGGTAATTTTTGGAAGATTTAGGGTCAAAATTAAAATTTTTA
125955 GAAGTTTAAGGGTAAAAAT-GTAATTTT
1 GAAGTTT-AGGGT-AAAATGGTAATTTT
125982 CAAAAGTATC
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
58 3 0.04
59 66 0.87
60 7 0.09
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.39
Consensus pattern (58 bp):
GAAGTTTAGGGTAAAATGGTAATTTTTGGAAGATTTAGGGTCAAAATTAAAATTTTTA
Found at i:127662 original size:6 final size:6
Alignment explanation
Indices: 127651--127734 Score: 104
Period size: 6 Copynumber: 14.7 Consensus size: 6
127641 ATTTTGAAAA
127651 TAAATT TAAATT TAAA-T TAAATT TAAATT TAAATT T-AATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * * *
127697 CAAATT TAAA-A TAAATC TAAATT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
127735 AGGGGCCCGA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
5 18 0.27
6 49 0.73
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:127673 original size:17 final size:17
Alignment explanation
Indices: 127651--127734 Score: 98
Period size: 17 Copynumber: 4.9 Consensus size: 17
127641 ATTTTGAAAA
127651 TAAATTTAAATTTAAA-T
1 TAAA-TTAAATTTAAATT
127668 TAAATTTAAATTTAAATT
1 TAAA-TTAAATTTAAATT
* *
127686 TAATTTAAATTCAAATT
1 TAAATTAAATTTAAATT
* *
127703 TAAAATAAATCTAAATT
1 TAAATTAAATTTAAATT
*
127720 TAAAATAAATTTAAA
1 TAAATTAAATTTAAA
127735 AGGGGCCCGA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
17 55 0.93
18 4 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTAAATTTAAATT
Found at i:127681 original size:23 final size:23
Alignment explanation
Indices: 127651--127734 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
127641 ATTTTGAAAA
127651 TAAATTTAAATTTAAATTAAATT
1 TAAATTTAAATTTAAATTAAATT
*
127674 TAAATTTAAATTTAATTTAAATT
1 TAAATTTAAATTTAAATTAAATT
* *
127697 CAAATTTAAA-ATAAATCTAAATT
1 TAAATTTAAATTTAAAT-TAAATT
*
127720 TAAA-ATAAATTTAAA
1 TAAATTTAAATTTAAA
127735 AGGGGCCCGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
22 8 0.15
23 44 0.85
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTAAATT
Found at i:127735 original size:11 final size:11
Alignment explanation
Indices: 127647--127735 Score: 55
Period size: 11 Copynumber: 8.4 Consensus size: 11
127637 TTAAATTTTG
127647 AAAATAAATTT
1 AAAATAAATTT
*
127658 AAATTTAAA-TT
1 AAA-ATAAATTT
*
127669 AAATTTAAATTT
1 AAA-ATAAATTT
* *
127681 AAATTTAATTT
1 AAAATAAATTT
*
127692 AAATTCAAATTT
1 AAAAT-AAATTT
127704 AAAATAAA--T
1 AAAATAAATTT
*
127713 ---CTAAATTT
1 AAAATAAATTT
127721 AAAATAAATTT
1 AAAATAAATTT
127732 AAAA
1 AAAA
127736 GGGGCCCGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
6 4 0.06
8 1 0.02
9 1 0.02
11 40 0.62
12 18 0.28
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATAAATTT
Found at i:128507 original size:207 final size:206
Alignment explanation
Indices: 128064--129076 Score: 1209
Period size: 206 Copynumber: 4.9 Consensus size: 206
128054 TTGACTTGGC
* * * * ** * *
128064 CTTCTTCTCAGTATCTTAACAAGAAGATGACCGCATCACTTGCTTT-GATCCACTTCTCTGTGTT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG-TTTCAATCTGCTTCTCTGTATC
* * * *
128128 TCATCAGGAAGAC-AGATTTGGTTCACTTCTCCGTTTCTCATCAGGAAGCTAACCATTTTATTGT
65 TCATCAGGAAGACGA-ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGC
* * ** ** * *
128192 TTCGACTTGCTTCTTAGTATCTCATCAATAAGCTAAGGTTCGAAGATTTGCTCACATCAAGCGCG
129 TTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTG
* *
128257 GGTTTGATTTGGT
194 GGTTTGATTAGAT
* ** ** *
128270 CTTCTTCTCAGTATCTCATCAGAAAGATGACCATATTGCTTGTTTCAATCTACTTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTGCTTCTCTGTATCT
* * * * *
128335 TATCAGAAAGACGAATTTGGTCCACTTCTTAGTATCTCTTCAGGAAGCTAACCTTTTTATTGCTT
66 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* * * *
128400 CGACCTCCTTCTCAGTATCTCATCAGGAAGTCGGGGGTTCGAAGATTTACTCACATCGAGTGTGG
131 CGACCTGCTTCTCAGTATCTCATCAGGAAG-CTGGGGTTCGAAGATTTGCTCACATCGAGCGTGG
128465 GTTTGATTAGAT
195 GTTTGATTAGAT
128477 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT-TCGCTTCTCTGTATC
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCT-GCTTCTCTGTATC
** * * * * *
128541 TCATCAGGAAGACGAATTTCATCGACTACTCAGTATCTTATCAGGAAGCTAACCTTTTTATTGTT
65 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCT
*
128606 TCG-CGCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCTCATCGAGCGTG
130 TCGAC-CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTG
* * *
128670 AAG-TTG-GTATA-
194 -GGTTTGATTAGAT
* * * *
128681 CTTC-TCT--GTATGTCATCAGGAAGATGACCGCCTTACTTGTTTCAATCTGTTTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTGCTTCTCTGTATCT
* * * *
128743 CATTAGGAAAACGAATTTTGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
66 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* * * **
128808 CGACATGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTTGAAGATTTGCTCACATCGAGCGTATG
131 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGG
* *
128873 TTTGATTTGGT
196 TTTGATTAGAT
* * * ** * *
128884 CTTCTTCTCAGTATCTCATTAGGAAGATGACTGCGTCGTTTGTTTTAATCCGCTTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTGCTTCTCTGTATCT
* * * *
128949 CATGAGGAAGACAAATTTGGTCCACTTCTTAGTATCTCATCAAGAAGCTAACCATTTTATTGCTT
66 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* *
129014 CGGCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGGTTCGAAGATTTGCTCACATCGAGCGT
131 CGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTGCTCACATCGAGCGT
129077 ATACTTCTCT
Statistics
Matches: 688, Mismatches: 104, Indels: 29
0.84 0.13 0.04
Matches are distributed among these distances:
200 1 0.00
201 164 0.24
202 3 0.00
203 7 0.01
204 7 0.01
205 6 0.01
206 294 0.43
207 206 0.30
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (206 bp):
CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTGCTTCTCTGTATCT
CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGG
TTTGATTAGAT
Found at i:129265 original size:39 final size:39
Alignment explanation
Indices: 129147--129278 Score: 129
Period size: 39 Copynumber: 3.4 Consensus size: 39
129137 TGCCCCGTGA
* * * * *
129147 TCGGGGTAGGAGTTTGGTTGACAATAATTTACCCCAAGC
1 TCGGGGTAAGAGATTGGTTGACTATAATCTACCCCAGGC
* * ** * * *
129186 TCGGCGTAAGAGATCGAATGACTATAATCTGCCTCTGGC
1 TCGGGGTAAGAGATTGGTTGACTATAATCTACCCCAGGC
* *
129225 TCGGGGTAAGAGATTGGTTGATTATGATCTACCCCAGGC
1 TCGGGGTAAGAGATTGGTTGACTATAATCTACCCCAGGC
*
129264 TCGGGGTAAAAGATT
1 TCGGGGTAAGAGATT
129279 AAATGGCTTC
Statistics
Matches: 71, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGGTTGACTATAATCTACCCCAGGC
Found at i:129293 original size:78 final size:78
Alignment explanation
Indices: 129147--129321 Score: 174
Period size: 78 Copynumber: 2.2 Consensus size: 78
129137 TGCCCCGTGA
* * * * *
129147 TCGGGGTAGGAGTTTGGTTGACAATAATTTACCCCAAGCTCGGCGTAAGAGATCGAATGACTATA
1 TCGGGGTAAGAGATTGGTTGACAATAATCTACCCCAAGCTCGGCGTAAAAGATCAAATGACTATA
**
129212 ATCTG-CCTCTGGC
66 ATCTGTCC-CAAGC
** * * * * *
129225 TCGGGGTAAGAGATTGGTTGATTATGATCTACCCCAGGCTCGGGGTAAAAGATTAAATGGCT-TC
1 TCGGGGTAAGAGATTGGTTGACAATAATCTACCCCAAGCTCGGCGTAAAAGATCAAATGACTAT-
129289 AATCTGTCCCAAGC
65 AATCTGTCCCAAGC
* *
129303 TCAGGGTACGAGATTGGTT
1 TCGGGGTAAGAGATTGGTT
129322 AACGATGTAG
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
77 1 0.01
78 76 0.96
79 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (78 bp):
TCGGGGTAAGAGATTGGTTGACAATAATCTACCCCAAGCTCGGCGTAAAAGATCAAATGACTATA
ATCTGTCCCAAGC
Found at i:129744 original size:50 final size:50
Alignment explanation
Indices: 129690--129913 Score: 138
Period size: 50 Copynumber: 4.5 Consensus size: 50
129680 CACAGTTCGT
129690 CGTTGCGACTTA-AGGCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGC
1 CGTTGCGACTTAGA-GCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGC
* * * ** * *
129740 CGTTGCGGTCTTAGATCTTTCCCTTCATG--TCTTCATGGTACTGGATTCGC
1 CGTTGC-GACTTAGAGCTTTCCCTT-TTGTATCTTTGTGGTATTGGATCCGC
* * * * * ** *
129790 CGTTGCGGCTTAAATCTTT-CCTTCT-TATCTTCTGAGGTACACGGTAT--AC
1 CGTTGCGACTTAGAGCTTTCCCTTTTGTATCTT-TGTGGTA-TTGG-ATCCGC
* * * *
129839 CATTGTGACTTAGAGTTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGT
1 CGTTGCGACTTAGAGCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGC
* * *
129889 CGTTGTGGTCTTAGATCTTTCCCTT
1 CGTTG-CGACTTAGAGCTTTCCCTT
129914 CAAATCTTTA
Statistics
Matches: 128, Mismatches: 33, Indels: 25
0.69 0.18 0.13
Matches are distributed among these distances:
47 1 0.01
48 10 0.08
49 31 0.24
50 46 0.36
51 37 0.29
52 3 0.02
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (50 bp):
CGTTGCGACTTAGAGCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGC
Found at i:129809 original size:100 final size:99
Alignment explanation
Indices: 129594--129810 Score: 222
Period size: 100 Copynumber: 2.2 Consensus size: 99
129584 GTTCGTCATC
* * *** * * * *
129594 GCGACTTAAACCTTTCCCCTTCAAATCTTCGTGGCACTGGATTCGCCGTTGCGGCTTAAATCTTT
1 GCGACTTAAAGCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGCCGTTGCGGCTTAAATCTTT
* *
129659 CCCTTCTTGCCTTCTGAGGTACACAGTTCGTCGTT
66 CCCTTCATGCCTTCT-AGGTACACAGTTCGCCGTT
* *
129694 GCGACTTAAGGCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGCCGTTGCGGTCTTAGATCTT
1 GCGACTTAAAGCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGCCGTTGCGG-CTTAAATCTT
* **
129759 TCCCTTCATGTCTTC-ATGGTAC-TGGATTCGCCGTT
65 TCCCTTCATGCCTTCTA-GGTACACAG-TTCGCCGTT
* *
129794 GCGGCTTAAATCTTTCC
1 GCGACTTAAAGCTTTCC
129811 TTCTTATCTT
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
99 2 0.02
100 71 0.75
101 22 0.23
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (99 bp):
GCGACTTAAAGCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGCCGTTGCGGCTTAAATCTTT
CCCTTCATGCCTTCTAGGTACACAGTTCGCCGTT
Found at i:130043 original size:150 final size:150
Alignment explanation
Indices: 129605--130080 Score: 616
Period size: 150 Copynumber: 3.2 Consensus size: 150
129595 CGACTTAAAC
* * *
129605 CTTTCCCCTTCAAATCTTCGTGGCACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGCC
1 CTTT-CCCTTCAAATCTTCATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTC
* * *
129670 TTCTGAGGTACACAGTTCGT--CGTTGCGACTTAAGGCTTTCCCTTTTGTATCTTTGTGGTATTG
65 TTCTGAGGTACAC-GATC-TACCGTTGTGACTTAAAGCTTTCCCTTTTGTATCTTTGTGGTATTG
129733 GATCCGCCGTTGCGGTCTTAGAT
128 GATCCGCCGTTGCGGTCTTAGAT
** *
129756 CTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTT-CCTTCTTATCT
1 CTTTCCCTTCAAATCTTCATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCT
* * * * *
129820 TCTGAGGTACACGGTATACCATTGTGACTTAGAGTTTTCCCTTTTGTATCTTTGTGGTATTGGAT
66 TCTGAGGTACACGATCTACCGTTGTGACTTAAAGCTTTCCCTTTTGTATCTTTGTGGTATTGGAT
* *
129885 CCGTCGTTGTGGTCTTAGAT
131 CCGCCGTTGCGGTCTTAGAT
* * * *
129905 CTTTCCCTTCAAATCTTTATGATACTGGATTCGTCGTTGCGGCATAAATCTTTCCCTTCTTGTCT
1 CTTTCCCTTCAAATCTTCATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCT
* * * * * *
129970 TCTGAGGTACACGATCTACCGTTGTGACTTAAACCTTTCTCTTTTGCATCTTTATGGTACTAGAT
66 TCTGAGGTACACGATCTACCGTTGTGACTTAAAGCTTTCCCTTTTGTATCTTTGTGGTATTGGAT
*
130035 CTGCCGTTGCGGTCTTAGAT
131 CCGCCGTTGCGGTCTTAGAT
* * ** *
130055 CTCTCCTTTCATGTCTTCCTGGTACT
1 CTTTCCCTTCAAATCTTCATGGTACT
130081 AATACCTATA
Statistics
Matches: 279, Mismatches: 43, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
147 1 0.00
148 2 0.01
149 127 0.46
150 145 0.52
151 4 0.01
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.41
Consensus pattern (150 bp):
CTTTCCCTTCAAATCTTCATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCT
TCTGAGGTACACGATCTACCGTTGTGACTTAAAGCTTTCCCTTTTGTATCTTTGTGGTATTGGAT
CCGCCGTTGCGGTCTTAGAT
Found at i:136520 original size:59 final size:57
Alignment explanation
Indices: 136388--136548 Score: 171
Period size: 59 Copynumber: 2.7 Consensus size: 57
136378 GTTCGAGGTT
* * * *
136388 AAAAATGTGATTTTTAGACACCTAGGGGTGAAACGGTAACTTTTAAAAAAATCGAGATC
1 AAAAATG-GATTTTTAGACATCTAGGGGTAAAATGGTAA-TTTTAAAAAAATCGAGATA
** * *
136447 AAAAATAAAATTTTTAGACATCTGGGGGTAAAATGGTAATATTTACAAAAATCGAGATA
1 AAAAAT-GGATTTTTAGACATCTAGGGGTAAAATGGTAAT-TTTAAAAAAATCGAGATA
* *
136506 AAAAATGGATTTTTTGGA-AGTTTAGGGGTAAAATGGTAATTTT
1 AAAAATGGA-TTTTTAGACA-TCTAGGGGTAAAATGGTAATTTT
136549 TAGAAGTTTC
Statistics
Matches: 85, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
58 6 0.07
59 79 0.93
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (57 bp):
AAAAATGGATTTTTAGACATCTAGGGGTAAAATGGTAATTTTAAAAAAATCGAGATA
Found at i:136549 original size:29 final size:28
Alignment explanation
Indices: 136507--136715 Score: 195
Period size: 29 Copynumber: 7.1 Consensus size: 28
136497 ATCGAGATAA
*
136507 AAAATGGATTTTTTGGAAGTTTAGGGGT
1 AAAATGGAATTTTTGGAAGTTTAGGGGT
* *
136535 AAAATGGTAATTTTTAGAAGTTTCGGGGTT
1 AAAATGG-AATTTTTGGAAGTTTAGGGG-T
* * *
136565 AAAATCAGAATTTTTGGAAGTTCAAGGGT
1 AAAAT-GGAATTTTTGGAAGTTTAGGGGT
136594 AAAATGGTAATTTTTGGAAGTTTA-GGGT
1 AAAATGG-AATTTTTGGAAGTTTAGGGGT
* *
136622 CAAAATTAGATTTTTTGGAAGTTTAGGGGT
1 -AAAA-TGGAATTTTTGGAAGTTTAGGGGT
* * * *
136652 AAAAATGAAATTTTTGAAAGTTTCGAGGTT
1 -AAAATGGAATTTTTGGAAGTTTAG-GGGT
* *
136682 AAGAATGGAATTTTGGCGAAGTTTAAGGGT
1 AA-AATGGAATTTTTG-GAAGTTTAGGGGT
136712 AAAA
1 AAAA
136716 ATATAATTTC
Statistics
Matches: 146, Mismatches: 25, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
28 12 0.08
29 76 0.52
30 51 0.35
31 7 0.05
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGT
Found at i:136579 original size:59 final size:57
Alignment explanation
Indices: 136507--136715 Score: 224
Period size: 59 Copynumber: 3.6 Consensus size: 57
136497 ATCGAGATAA
* * *
136507 AAAATGGATTTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTT
1 AAAATAGAATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTT-GAAGTTTCGGGGTT
* * *
136565 AAAATCAGAATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAGTTT-AGGGTC
1 AAAAT-AGAATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTT-GAAGTTTCGGGGTT
* * * *
136623 AAAATTAGATTTTTTGGAAGTTTAGGGGTAAAAAT-GAAATTTTTGAAAGTTTCGAGGTT
1 AAAA-TAGAATTTTTGGAAGTTTAAGGGT-AAAATGGTAATTTTTG-AAGTTTCGGGGTT
* *
136682 AAGAATGGAATTTTGGCGAAGTTTAAGGGTAAAA
1 AA-AATAGAATTTTTG-GAAGTTTAAGGGTAAAA
136716 ATATAATTTC
Statistics
Matches: 126, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
57 1 0.01
58 47 0.37
59 64 0.51
60 14 0.11
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (57 bp):
AAAATAGAATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGAAGTTTCGGGGTT
Found at i:137875 original size:3 final size:3
Alignment explanation
Indices: 137869--137908 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
137859 TTTTTTTTAT
* *
137869 TTA TTA TTA GTA TTAA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
137909 ATGCTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:137916 original size:15 final size:15
Alignment explanation
Indices: 137869--137917 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
137859 TTTTTTTTAT
* *
137869 TTATTATTAGTATTAA
1 TTATTATTAATACT-A
*
137885 TTATTATTAATATTA
1 TTATTATTAATACTA
*
137900 TTATTATTAATGCTA
1 TTATTATTAATACTA
137915 TTA
1 TTA
137918 AAACATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (15 bp):
TTATTATTAATACTA
Found at i:138622 original size:14 final size:15
Alignment explanation
Indices: 138599--138627 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
138589 AATTTGGACA
138599 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
138614 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
138628 ATAATAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:138664 original size:6 final size:6
Alignment explanation
Indices: 138653--138708 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
138643 ATTTTGAAAA
* * * *
138653 TAAATT TAAATT TAAATT CAAATT TAAA-A TAAATC TAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
138699 TAAATT TAAA
1 TAAATT TAAA
138709 AGGGGCATGG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 8 0.20
6 33 0.80
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:138685 original size:29 final size:28
Alignment explanation
Indices: 138640--138709 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
138630 AATAATCTTT
* *
138640 TAAATTTTGAAAATAAATTTAAATTTAAAT
1 TAAA-TTT-AAAATAAATCTAAATTTAAAA
138670 TCAAATTTAAAATAAATCTAAATTTAAAA
1 T-AAATTTAAAATAAATCTAAATTTAAAA
138699 TAAATTTAAAA
1 TAAATTTAAAA
138710 GGGGCATGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 10 0.27
29 20 0.54
30 4 0.11
31 3 0.08
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (28 bp):
TAAATTTAAAATAAATCTAAATTTAAAA
Found at i:138708 original size:17 final size:17
Alignment explanation
Indices: 138653--138708 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
138643 ATTTTGAAAA
*
138653 TAAATTTAAATTTAAATT
1 TAAATTTAAA-ATAAATT
* *
138671 CAAATTTAAAATAAATC
1 TAAATTTAAAATAAATT
138688 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
138705 TAAA
1 TAAA
138709 AGGGGCATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
17 24 0.73
18 9 0.27
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:143546 original size:17 final size:19
Alignment explanation
Indices: 143516--143551 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
143506 AAATAAAATG
143516 ATTTAAAAATTAAATATCA
1 ATTTAAAAATTAAATATCA
143535 ATTT-AAAA-TAAATATCA
1 ATTTAAAAATTAAATATCA
143552 TAATTTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTAAAAATTAAATATCA
Found at i:144736 original size:17 final size:15
Alignment explanation
Indices: 144688--144741 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
144678 ACATTAAAAT
144688 AATATTAAAATAATT-
1 AATATTAAAA-AATTA
*
144703 -ATA-TAAAAAATTC
1 AATATTAAAAAATTA
144716 AATAATTAAAAATATTA
1 AAT-ATTAAAAA-ATTA
144733 AATATTAAA
1 AATATTAAA
144742 TTAAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
12 4 0.12
13 5 0.15
14 5 0.15
15 1 0.03
16 12 0.36
17 6 0.18
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATTAAAAAATTA
Found at i:144757 original size:21 final size:21
Alignment explanation
Indices: 144719--144759 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
144709 AAAATTCAAT
*
144719 AATTAAAAATATTAAATATTA
1 AATTAAAAATAATAAATATTA
144740 AATT-AAAATAATATAATATT
1 AATTAAAAATAATA-AATATT
144760 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTAAAAATAATAAATATTA
Found at i:148257 original size:36 final size:36
Alignment explanation
Indices: 148210--148309 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 36
148200 TGAGGAGGGA
*
148210 TTATAAGTAATTTCAGACATTATATAAA-GAGAGAAG
1 TTATAAGTAATTTCAGACATTGTATAAAGGA-AGAAG
* *
148246 TTATAAGTAA-TTCTAGATATTGTATAAAGGAAGAGG
1 TTATAAGTAATTTC-AGACATTGTATAAAGGAAGAAG
* * *
148282 CTATAGGTAATTTCAAACATTGTATAAA
1 TTATAAGTAATTTCAGACATTGTATAAA
148310 AAGTAGCAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 3 0.06
36 46 0.85
37 5 0.09
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (36 bp):
TTATAAGTAATTTCAGACATTGTATAAAGGAAGAAG
Found at i:149036 original size:15 final size:16
Alignment explanation
Indices: 149016--149049 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
149006 AAAAAAATAA
*
149016 TAAAATA-TTTAAATT
1 TAAAATACTTTAAAAT
149031 TAAAATACTTTAAAAT
1 TAAAATACTTTAAAAT
149047 TAA
1 TAA
149050 TTTTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATACTTTAAAAT
Found at i:160500 original size:2 final size:2
Alignment explanation
Indices: 160495--160522 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
160485 TGCCAAAGAA
160495 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
160523 TAAATTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:166611 original size:23 final size:21
Alignment explanation
Indices: 166573--166617 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
166563 ATGTAAAAAA
166573 TGTAAAATTTTAAAAAAAATT
1 TGTAAAATTTTAAAAAAAATT
166594 TGTAAATATATTTAAAAAAAATT
1 TGTAAA-AT-TTTAAAAAAAATT
166617 T
1 T
166618 AAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 6 0.27
22 2 0.09
23 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TGTAAAATTTTAAAAAAAATT
Found at i:166613 original size:22 final size:22
Alignment explanation
Indices: 166567--166626 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 22
166557 TAAAAAATGT
166567 AAAAAA-TGTAAAAT-TTTAAA
1 AAAAAATTGTAAAATATTTAAA
*
166587 AAAAATTTGTAAATATATTT-AA
1 AAAAAATTGTAAA-ATATTTAAA
166609 AAAAAATT-TAAAATATTT
1 AAAAAATTGTAAAATATTT
166627 TTTTATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 11 0.31
21 10 0.29
22 11 0.31
23 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (22 bp):
AAAAAATTGTAAAATATTTAAA
Found at i:166636 original size:23 final size:23
Alignment explanation
Indices: 166610--166666 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
166600 TATATTTAAA
* **
166610 AAAAATTTAAAATATTTTTTTAT
1 AAAAATTTAAAATATATAATTAT
*
166633 AAAATTTTAAAATATATAATTAT
1 AAAAATTTAAAATATATAATTAT
166656 AAAAATTTAAA
1 AAAAATTTAAA
166667 TCGGTATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAAATTTAAAATATATAATTAT
Found at i:166758 original size:20 final size:18
Alignment explanation
Indices: 166717--166776 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
166707 TTAAATACTT
**
166717 TTTTAAATTTTTATAACAA
1 TTTT-AATTTTTATAATTA
166736 TTTTCAATTTTTATATATTA
1 TTTT-AATTTTTATA-ATTA
*
166756 TTTTGATTTTT-TAATTA
1 TTTTAATTTTTATAATTA
166773 TTTT
1 TTTT
166777 TTAAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.22
18 2 0.06
19 20 0.56
20 6 0.17
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTAATTTTTATAATTA
Found at i:166774 original size:17 final size:19
Alignment explanation
Indices: 166742--166776 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
166732 ACAATTTTCA
166742 ATTTTTATATATTATTTTG
1 ATTTTTATATATTATTTTG
166761 ATTTTT-TA-ATTATTTT
1 ATTTTTATATATTATTTT
166777 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (19 bp):
ATTTTTATATATTATTTTG
Found at i:166807 original size:24 final size:23
Alignment explanation
Indices: 166771--166816 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
166761 ATTTTTTAAT
166771 TATTTTTTAAAATTTTATAAAAAAC
1 TATTTTTTAAAA-TTTA-AAAAAAC
166796 TATTTTTT-AAATTTAAAAAAA
1 TATTTTTTAAAATTTAAAAAAA
166817 TTATCTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 4 0.19
24 3 0.14
25 8 0.38
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTTTTAAAATTTAAAAAAAC
Found at i:167772 original size:23 final size:23
Alignment explanation
Indices: 167746--167791 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
167736 GAATAATTCG
*
167746 ATGATCATTTTGTAATTAAAATT
1 ATGATCATTTTGTAACTAAAATT
167769 ATGATCATTTTGTAACTAAAATT
1 ATGATCATTTTGTAACTAAAATT
167792 GAGTAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (23 bp):
ATGATCATTTTGTAACTAAAATT
Found at i:171692 original size:18 final size:20
Alignment explanation
Indices: 171656--171694 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
171646 ATATTTTTTT
171656 TTATATTTTTTAGCATCATTA
1 TTATATTTTTTAG-ATCATTA
171677 TTAT-TTTTTTAG-TCATTA
1 TTATATTTTTTAGATCATTA
171695 AATTTCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (20 bp):
TTATATTTTTTAGATCATTA
Found at i:181670 original size:31 final size:30
Alignment explanation
Indices: 181630--181699 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 30
181620 TCAAAGTTTA
181630 AATTAAAAAATTA-TCAAAAT-TATATATAAAT
1 AATTAAAAAATTACT-AAAATAT-TAT-TAAAT
181661 AATATAAAAAATTACTAAAATATTATTAAAT
1 AAT-TAAAAAATTACTAAAATATTATTAAAT
181692 AATTAAAA
1 AATTAAAA
181700 TTAAATACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
30 5 0.14
31 11 0.31
32 18 0.50
33 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (30 bp):
AATTAAAAAATTACTAAAATATTATTAAAT
Found at i:185769 original size:30 final size:31
Alignment explanation
Indices: 185719--185787 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
185709 GGTACCTAAT
*
185719 TTTTTTGTTCAATTTGGTACTCAAACTTGACA
1 TTTTTT-TTCAATTTAGTACTCAAACTTGACA
*
185751 TTTTTTTT-AATTTAGTACTTAAACTTGACA
1 TTTTTTTTCAATTTAGTACTCAAACTTGACA
*
185781 CTTTTTT
1 TTTTTTT
185788 AAGTTGATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 26 0.76
31 2 0.06
32 6 0.18
ACGTcount: A:0.25, C:0.13, G:0.09, T:0.54
Consensus pattern (31 bp):
TTTTTTTTCAATTTAGTACTCAAACTTGACA
Found at i:185801 original size:29 final size:30
Alignment explanation
Indices: 185735--185805 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
185725 GTTCAATTTG
* * *
185735 GTACTCAAACTTGACATTTTTTTTAATTTA
1 GTACTTAAACTTGACATCTTTTTTAATTGA
185765 GTACTTAAACTTGACA-CTTTTTTAAGTTGA
1 GTACTTAAACTTGACATCTTTTTTAA-TTGA
*
185795 -TATTTAAACTT
1 GTACTTAAACTT
185806 TTTGGGATCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (30 bp):
GTACTTAAACTTGACATCTTTTTTAATTGA
Found at i:186118 original size:27 final size:28
Alignment explanation
Indices: 186055--186132 Score: 90
Period size: 27 Copynumber: 2.8 Consensus size: 28
186045 AAAAATTATC
*
186055 AAGTTCACGTATCAAATTAAATAAAAAG
1 AAGTTCAAGTATCAAATTAAATAAAAAG
*
186083 AA-TTTAAGTATCAAATTAAA-AAAAA-
1 AAGTTCAAGTATCAAATTAAATAAAAAG
*
186108 AAGTATCAAGTTATCATATTAAATA
1 AAGT-TCAAG-TATCAAATTAAATA
186133 CATTTTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 2 0.05
26 6 0.14
27 20 0.48
28 13 0.31
29 1 0.02
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (28 bp):
AAGTTCAAGTATCAAATTAAATAAAAAG
Found at i:205839 original size:13 final size:13
Alignment explanation
Indices: 205823--205848 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
205813 ATTGGACTTG
205823 TTTTTATTTTATT
1 TTTTTATTTTATT
205836 TTTTTATTTTATT
1 TTTTTATTTTATT
205849 GGGCACACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:218534 original size:31 final size:32
Alignment explanation
Indices: 218489--218548 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
218479 AATCAAGTAA
* * *
218489 ATTAATTGATTTTCT-TAATTAATTAAAAAAT
1 ATTAATTGAATTTCTCAAAATAATTAAAAAAT
*
218520 ATTAATTTAATTTCTCAAAATAATTAAAA
1 ATTAATTGAATTTCTCAAAATAATTAAAA
218549 CCAATGCATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 13 0.54
32 11 0.46
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (32 bp):
ATTAATTGAATTTCTCAAAATAATTAAAAAAT
Found at i:220412 original size:24 final size:23
Alignment explanation
Indices: 220384--220443 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 23
220374 CCATGTGAAA
*
220384 TTTAAATTTTT-TTACTTTCTTTAT
1 TTTAAATTTTTCTT-CTAT-TTTAT
220408 TTTAACCATTTTTCTTCTATTTTAT
1 TTTAA--ATTTTTCTTCTATTTTAT
220433 TTCTAAATTTT
1 TT-TAAATTTT
220444 GTCCTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
24 10 0.32
25 7 0.23
26 12 0.39
27 2 0.06
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAAATTTTTCTTCTATTTTAT
Found at i:228673 original size:2 final size:2
Alignment explanation
Indices: 228666--228690 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
228656 TTAAAAACAC
228666 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
228691 ATAAAGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:263995 original size:18 final size:18
Alignment explanation
Indices: 263952--264006 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
263942 TTTTATAATT
*
263952 TTATTTTCT-TTTTTAAA
1 TTATTTTATATTTTTAAA
*
263969 ATATTTTTATATTTTTAAA
1 TTA-TTTTATATTTTTAAA
263988 TTATTTTA-ATTTATTAAA
1 TTATTTTATATTT-TTAAA
264006 T
1 T
264007 AAAATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.19
18 16 0.50
19 10 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTTATATTTTTAAA
Found at i:265348 original size:33 final size:33
Alignment explanation
Indices: 265302--265368 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
265292 TGAAATGTAT
*
265302 CCTCCCAATTCATGGTCAATTTAATAATTCAAA
1 CCTCCCAAATCATGGTCAATTTAATAATTCAAA
265335 CCTCCCAAATCATGGTCAATTTAATAATTCAAA
1 CCTCCCAAATCATGGTCAATTTAATAATTCAAA
265368 C
1 C
265369 AATGTCGTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (33 bp):
CCTCCCAAATCATGGTCAATTTAATAATTCAAA
Found at i:267388 original size:29 final size:33
Alignment explanation
Indices: 267356--267418 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 33
267346 AATTTGATAC
*
267356 ATGAATTTTG-ATT-TGGTGCA-AT-TATACAT
1 ATGAAATTTGAATTGTGGTGCATATGTATACAT
*
267385 ATGAAATTTGAATTGTGGTTCATATGTATACAT
1 ATGAAATTTGAATTGTGGTGCATATGTATACAT
267418 A
1 A
267419 AAATTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.32
30 3 0.11
31 6 0.21
32 2 0.07
33 8 0.29
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.43
Consensus pattern (33 bp):
ATGAAATTTGAATTGTGGTGCATATGTATACAT
Found at i:267625 original size:29 final size:30
Alignment explanation
Indices: 267571--267627 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
267561 AAACTGAATT
267571 AAATCAAAATTTCATATATAAAATTACAAA
1 AAATCAAAATTTCATATATAAAATTACAAA
* *
267601 AAATCAAAA-TTCATATATGATATTACA
1 AAATCAAAATTTCATATATAAAATTACA
267628 TATTGAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTACAAA
Found at i:285208 original size:28 final size:28
Alignment explanation
Indices: 285168--285225 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
285158 GTTTTTTCTG
285168 TTTTCCTCCCACAATTTTCATGTTATCA
1 TTTTCCTCCCACAATTTTCATGTTATCA
* *
285196 TTTTCGTCCCACAGTTTTCATGTTATCA
1 TTTTCCTCCCACAATTTTCATGTTATCA
285224 TT
1 TT
285226 CTCATGGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.48
Consensus pattern (28 bp):
TTTTCCTCCCACAATTTTCATGTTATCA
Found at i:287762 original size:24 final size:24
Alignment explanation
Indices: 287730--287786 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
287720 AAATTGACTT
287730 CTGCAGCTGTTGCAATA-GCAGCGG
1 CTGCAGCTGTTGCAA-AGGCAGCGG
* *
287754 CTGCTGCTGTTGCAAAGGCTGCGG
1 CTGCAGCTGTTGCAAAGGCAGCGG
*
287778 CTGCGGCTG
1 CTGCAGCTG
287787 CCAATGTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.14, C:0.26, G:0.37, T:0.23
Consensus pattern (24 bp):
CTGCAGCTGTTGCAAAGGCAGCGG
Found at i:300738 original size:17 final size:17
Alignment explanation
Indices: 300716--300751 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
300706 TAAATTTTAA
300716 ATCAAAGAAATAAATGT
1 ATCAAAGAAATAAATGT
300733 ATCAAAGAAATAAATGT
1 ATCAAAGAAATAAATGT
300750 AT
1 AT
300752 ATTCAAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (17 bp):
ATCAAAGAAATAAATGT
Found at i:304476 original size:58 final size:56
Alignment explanation
Indices: 304365--304511 Score: 152
Period size: 58 Copynumber: 2.5 Consensus size: 56
304355 TAAATTTGAT
* * * *
304365 ATTTTTTTAATTTGGTACTTAAATATTTTTTACCTAAATTGGTACCTGAACTTGACA
1 ATTTTTTTAATTTGGTTCCT-AATTTTTTTTACCTAAATTGATACCTGAACTTGACA
* * *
304422 ATTTTTTTAATTTGGTTCCTAATTTTTTTTGAATCTAATTTGATACCTGAACTTGGCA
1 ATTTTTTTAATTTGGTTCCTAATTTTTTTT--ACCTAAATTGATACCTGAACTTGACA
* *
304480 TTTTTTCTTAAATTGGTAT-CTAAGTTTTTTTT
1 ATTTTT-TTAATTTGGT-TCCTAA-TTTTTTTT
304512 TAGATTCAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
56 9 0.12
57 18 0.24
58 27 0.36
59 13 0.17
60 9 0.12
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (56 bp):
ATTTTTTTAATTTGGTTCCTAATTTTTTTTACCTAAATTGATACCTGAACTTGACA
Found at i:304768 original size:32 final size:33
Alignment explanation
Indices: 304711--304788 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 33
304701 CCCCAAAAAA
** *
304711 TTTAAGTACCAATTTCAAAAAAAAAGTGTCAAG
1 TTTAAGTACCAAAATCAAAAAAAAAGTATCAAG
304744 TTTAAGTACCAAAAT-AAAAAAAAAGTATCAAG
1 TTTAAGTACCAAAATCAAAAAAAAAGTATCAAG
*
304776 TTCAAGTACCAAA
1 TTTAAGTACCAAA
304789 TATTATATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 28 0.68
33 13 0.32
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (33 bp):
TTTAAGTACCAAAATCAAAAAAAAAGTATCAAG
Found at i:305559 original size:31 final size:32
Alignment explanation
Indices: 305519--305583 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
305509 TATGTATTAT
* *
305519 AATTAATTAATTTTAATT-TTTATATTTTTTA
1 AATTAATTAATTTTAATTCTTTAAACTTTTTA
*
305550 AATTGATTAATTTTAATTCTTTAAACTTTTTA
1 AATTAATTAATTTTAATTCTTTAAACTTTTTA
305582 AA
1 AA
305584 ATTTGAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (32 bp):
AATTAATTAATTTTAATTCTTTAAACTTTTTA
Found at i:307485 original size:59 final size:58
Alignment explanation
Indices: 307409--307847 Score: 153
Period size: 59 Copynumber: 7.4 Consensus size: 58
307399 AGACATCCGG
* * * ** *
307409 GGGTAAATTGGTAATTTTGGGAAGAATC-GGGATCGAAAATGGAATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTCGGAA-AATCAAGG-TAAAAAATGGAATTTTTGAAAGTTCGA
* * *
307468 GGGTAAAATGGTCATTTTTCGGAAAATCAAGGTAAAAAATGGAATTTTTGAAAGTTTGG
1 GGGTAAAATGGT-AATTTTCGGAAAATCAAGGTAAAAAATGGAATTTTTGAAAGTTCGA
* * * ** * * * * * *
307527 GGGTAAAATGGTTATTTTTTGAAAAAAAAAATTGAGGTCAAAAAT-AAAATTTGGAAAGTTTGG
1 GGGTAAAATGG-TAATTTTCG-----GAAAATCAAGGTAAAAAATGGAATTTTTGAAAGTTCGA
** * ** * *
307590 GGGTAAAAAAAGTAATTTTGGGAAAAATCGGGGT-TAAAATGGATTTTTTGAAAGCTT-G-
1 GGGT-AAAATGGTAATTTTCGG-AAAATCAAGGTAAAAAATGGAATTTTTGAAAG-TTCGA
** * * * * *
307648 GGGTAAAAAAAGTAATTTTGGGAAAAATCGATGT-TAAAATGGAATTTTTGGAAGCTT-G-
1 GGGT-AAAATGGTAATTTTCGG-AAAATCAAGGTAAAAAATGGAATTTTTGAAAG-TTCGA
* * * * * * *
307706 GGGTTAAAATGGTAATTTTTGGTGAAATCATGGTTAAAAATGGAAATTTGGAAAGTT-TA
1 GGG-TAAAATGGTAATTTTCGG-AAAATCAAGGTAAAAAATGGAATTTTTGAAAGTTCGA
* * * * * * * * *
307765 GTGGTAAAATTGTAATTTTTGGAAAAATTAGGGT-CAATATAGAATTTTGGAAAGTTTGA
1 G-GGTAAAATGGTAATTTTCGG-AAAATCAAGGTAAAAAATGGAATTTTTGAAAGTTCGA
* *
307824 GGGCAAAAAT-GTAATTTTTGGAAA
1 GGG-TAAAATGGTAATTTTCGGAAA
307848 GTTTGGGGTT
Statistics
Matches: 305, Mismatches: 57, Indels: 38
0.76 0.14 0.09
Matches are distributed among these distances:
57 3 0.01
58 116 0.38
59 124 0.41
60 16 0.05
63 26 0.09
64 20 0.07
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTCGGAAAATCAAGGTAAAAAATGGAATTTTTGAAAGTTCGA
Found at i:307610 original size:30 final size:29
Alignment explanation
Indices: 307576--307668 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
307566 AAAAATAAAA
*
307576 TTTGGAAAGTTTGGGGGTAAAAAAAGTAAT
1 TTTGGAAAGATT-GGGGTAAAAAAAGTAAT
* * * * * *
307606 TTTGGGAAAAATCGGGGT-TAAAATGGATT
1 TTT-GGAAAGATTGGGGTAAAAAAAGTAAT
* *
307635 TTTTGAAAGCTTGGGGTAAAAAAAGTAAT
1 TTTGGAAAGATTGGGGTAAAAAAAGTAAT
307664 TTTGG
1 TTTGG
307669 GAAAAATCGA
Statistics
Matches: 45, Mismatches: 16, Indels: 5
0.68 0.24 0.08
Matches are distributed among these distances:
28 10 0.22
29 21 0.47
30 8 0.18
31 6 0.13
ACGTcount: A:0.37, C:0.02, G:0.29, T:0.32
Consensus pattern (29 bp):
TTTGGAAAGATTGGGGTAAAAAAAGTAAT
Found at i:307628 original size:29 final size:29
Alignment explanation
Indices: 307596--307700 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 29
307586 TTGGGGGTAA
307596 AAAAAGTAATTTTGGGAAAAATCGGGGTT
1 AAAAAGTAATTTTGGGAAAAATCGGGGTT
* * ** ** * *
307625 AAAATG-GATTTTTTGAAAGCTTGGGGTAA
1 AAAAAGTAATTTTGGGAAAAATCGGGGT-T
**
307654 AAAAAGTAATTTTGGGAAAAATCGATGTT
1 AAAAAGTAATTTTGGGAAAAATCGGGGTT
* * *
307683 AAAATGGAATTTTTGGAA
1 AAAAAGTAATTTTGGGAA
307701 GCTTGGGGTT
Statistics
Matches: 53, Mismatches: 21, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
28 15 0.28
29 25 0.47
30 13 0.25
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (29 bp):
AAAAAGTAATTTTGGGAAAAATCGGGGTT
Found at i:307659 original size:58 final size:58
Alignment explanation
Indices: 307580--307792 Score: 214
Period size: 58 Copynumber: 3.6 Consensus size: 58
307570 ATAAAATTTG
* * *
307580 GAAAGTTTGGGGGTAAAAAAAGTAATTTTGGGAAAAATCGGGGTTAAAATGGATTTTTT
1 GAAAGCTT-GGGGTAAAAAAAGTAATTTTGGGAAAAATCGAGGTTAAAATGGAATTTTT
*
307639 GAAAGCTTGGGGTAAAAAAAGTAATTTTGGGAAAAATCGATGTTAAAATGGAATTTTT
1 GAAAGCTTGGGGTAAAAAAAGTAATTTTGGGAAAAATCGAGGTTAAAATGGAATTTTT
* * ** * ** * *
307697 GGAAGCTTGGGGTTAAAATGGTAATTTTTGGTGAAATC-ATGGTTAAAAATGGAAATTTG
1 GAAAGCTTGGGGTAAAAAAAGTAATTTTGGGAAAAATCGA-GGTT-AAAATGGAATTTTT
* * ** *
307756 GAAAGTTTAGTGGT-AAAATTGTAATTTTTGGAAAAAT
1 GAAAGCTT-GGGGTAAAAAAAGTAATTTTGGGAAAAAT
307793 TAGGGTCAAT
Statistics
Matches: 131, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
57 1 0.01
58 81 0.62
59 45 0.34
60 4 0.03
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (58 bp):
GAAAGCTTGGGGTAAAAAAAGTAATTTTGGGAAAAATCGAGGTTAAAATGGAATTTTT
Found at i:307722 original size:29 final size:28
Alignment explanation
Indices: 307619--307727 Score: 92
Period size: 29 Copynumber: 3.8 Consensus size: 28
307609 GGGAAAAATC
* *
307619 GGGGTTAAAATGGATTTTTTGAAAGCTT
1 GGGGTTAAAATGGAATTTTTGGAAGCTT
* * * * ** *
307647 GGGGTAAAAAAAGTAATTTTGGGAAAAATC
1 GGGGT-TAAAATGGAATTTTTGG-AAGCTT
**
307677 GATGTTAAAATGGAATTTTTGGAAGCTT
1 GGGGTTAAAATGGAATTTTTGGAAGCTT
307705 GGGGTTAAAATGGTAATTTTTGG
1 GGGGTTAAAATGG-AATTTTTGG
307728 TGAAATCATG
Statistics
Matches: 58, Mismatches: 20, Indels: 5
0.70 0.24 0.06
Matches are distributed among these distances:
28 19 0.33
29 33 0.57
30 6 0.10
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
GGGGTTAAAATGGAATTTTTGGAAGCTT
Found at i:307772 original size:29 final size:29
Alignment explanation
Indices: 307683--307862 Score: 118
Period size: 29 Copynumber: 6.2 Consensus size: 29
307673 AATCGATGTT
* * *
307683 AAAATGGAATTTTTGG-AAGCTTGGGGTT
1 AAAATGGAATTTTTGGAAAGTTTAGGGTA
* *
307711 AAAATGGTAATTTTTGGTGAAA--TCATGGTTA
1 AAAATGG-AATTTTT-G-GAAAGTTTA-GGGTA
*
307742 AAAATGGAA-ATTTGGAAAGTTTAGTGGTA
1 AAAATGGAATTTTTGGAAAGTTTAG-GGTA
* * ** *
307771 AAATTGTAATTTTTGGAAAAATTAGGGTC
1 AAAATGGAATTTTTGGAAAGTTTAGGGTA
* * *
307800 AATATAGAA-TTTTGGAAAGTTTGAGGGCA
1 AAAATGGAATTTTTGGAAAGTTT-AGGGTA
* * *
307829 AAAATGTAATTTTTGGAAAGTTTGGGGTT
1 AAAATGGAATTTTTGGAAAGTTTAGGGTA
307858 AAAAT
1 AAAAT
307863 ATAATTTTAG
Statistics
Matches: 114, Mismatches: 27, Indels: 21
0.70 0.17 0.13
Matches are distributed among these distances:
27 4 0.04
28 20 0.18
29 48 0.42
30 29 0.25
31 11 0.10
32 2 0.02
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAGTTTAGGGTA
Found at i:307788 original size:30 final size:29
Alignment explanation
Indices: 307752--307883 Score: 110
Period size: 30 Copynumber: 4.5 Consensus size: 29
307742 AAAATGGAAA
307752 TTTGGAAAGTTTAGTGGTAAAATTGTAATT
1 TTTGGAAAGTTTAG-GGTAAAATTGTAATT
** * *
307782 TTTGGAAAAATTAGGGTCAATATAG-AA-T
1 TTTGGAAAGTTTAGGGT-AAAATTGTAATT
* *
307810 TTTGGAAAGTTTGAGGGCAAAAATGTAATT
1 TTTGGAAAGTTT-AGGGTAAAATTGTAATT
* *
307840 TTTGGAAAGTTTGGGGTTAAAA-TATAA-T
1 TTTGGAAAGTTTAGGG-TAAAATTGTAATT
*
307868 TTTAGAGAAGTTTAGG
1 TTTGGA-AAGTTTAGG
307884 TTTCAAAATA
Statistics
Matches: 81, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
28 21 0.26
29 26 0.32
30 34 0.42
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTGGAAAGTTTAGGGTAAAATTGTAATT
Found at i:307869 original size:58 final size:58
Alignment explanation
Indices: 307742--307882 Score: 158
Period size: 58 Copynumber: 2.4 Consensus size: 58
307732 ATCATGGTTA
* * * *
307742 AAAATGGAAATTTGGAAAGTTTAGTGGTAAAATTGTAATTTTTGGAAAAATTAGGGTC
1 AAAATAGAATTTTGGAAAGTTTAGTGGCAAAAATGTAATTTTTGGAAAAATTAGGGTC
* ** * *
307800 AATATAGAATTTTGGAAAGTTTGAG-GGCAAAAATGTAATTTTTGGAAAGTTTGGGGTT
1 AAAATAGAATTTTGGAAAGTTT-AGTGGCAAAAATGTAATTTTTGGAAAAATTAGGGTC
* *
307858 AAAATATAATTTTAGAGAAGTTTAG
1 AAAATAGAATTTTGGA-AAGTTTAG
307883 GTTTCAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 61 0.88
59 8 0.12
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.35
Consensus pattern (58 bp):
AAAATAGAATTTTGGAAAGTTTAGTGGCAAAAATGTAATTTTTGGAAAAATTAGGGTC
Found at i:308602 original size:12 final size:12
Alignment explanation
Indices: 308580--308619 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
308570 CTTTCAACTT
308580 TTATT-TTATTA
1 TTATTGTTATTA
308591 TTATTGTTATTA
1 TTATTGTTATTA
* *
308603 ATATTGTCATTA
1 TTATTGTTATTA
308615 TTATT
1 TTATT
308620 ATTAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (12 bp):
TTATTGTTATTA
Found at i:309365 original size:17 final size:16
Alignment explanation
Indices: 309345--309405 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
309335 TTTTATCTTC
309345 AATTTAAATTTAGAATA
1 AATTTAAATTTA-AATA
* *
309362 AATTTTAGTTTAAATTA
1 AATTTAAATTTAAA-TA
* *
309379 AATTTGAATTTAAAAA
1 AATTTAAATTTAAATA
309395 TAATTTAAATT
1 -AATTTAAATT
309406 CAAACTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 3 0.08
17 33 0.92
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:310087 original size:20 final size:18
Alignment explanation
Indices: 310062--310133 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 18
310052 AAAAATAATT
310062 TAAAAAGTATTTAAAAAGTA
1 TAAAAA-TATTTAAAAA-TA
* *
310082 TAAAAATAATTAATTAATA
1 TAAAAATATTTAA-AAATA
*
310101 TAAAAACCATTTAAAAAATA
1 TAAAAA-TATTT-AAAAATA
*
310121 TAAAAATAATTAA
1 TAAAAATATTTAA
310134 TTACTAATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.05
19 17 0.40
20 21 0.50
21 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAAATATTTAAAAATA
Found at i:319274 original size:21 final size:22
Alignment explanation
Indices: 319228--319288 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
319218 CGATCTAAGG
**
319228 AAAAATAAAAG-AACCAGAATT
1 AAAAATAAAAGAAAATAGAATT
319249 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
319271 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
319289 GGAAGTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:319279 original size:15 final size:16
Alignment explanation
Indices: 319254--319283 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
319244 GAATTAAAAA
319254 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
319270 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
319284 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:320113 original size:19 final size:19
Alignment explanation
Indices: 320089--320131 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
320079 AAACATAAAT
320089 TAAATACACAT-TTAAATAA
1 TAAATA-ACATCTTAAATAA
* *
320108 TAAATAATATCTTAAATAT
1 TAAATAACATCTTAAATAA
320127 TAAAT
1 TAAAT
320132 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAACATCTTAAATAA
Found at i:339453 original size:28 final size:28
Alignment explanation
Indices: 339422--339478 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
339412 CATTCGTTTT
339422 TCTCTTTTCTCTTATATGAGATTTTAGG
1 TCTCTTTTCTCTTATATGAGATTTTAGG
339450 TCTCTTTTCTCTTATATGAGATTTTAGG
1 TCTCTTTTCTCTTATATGAGATTTTAGG
339478 T
1 T
339479 TAAGGACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.54
Consensus pattern (28 bp):
TCTCTTTTCTCTTATATGAGATTTTAGG
Found at i:341403 original size:31 final size:31
Alignment explanation
Indices: 341351--341411 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
341341 AATTATAAAT
*
341351 TGGTGCAATTATATACGTGAAACTCTAATTG
1 TGGTGCAAATATATACGTGAAACTCTAATTG
* * *
341382 TGGTTCAAATATATACTTGAAACTTTAATT
1 TGGTGCAAATATATACGTGAAACTCTAATT
341412 TTGATTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (31 bp):
TGGTGCAAATATATACGTGAAACTCTAATTG
Found at i:341837 original size:22 final size:20
Alignment explanation
Indices: 341812--341860 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
341802 AAAATAATTT
341812 ATGAAATAGATCTTAAATTATA
1 ATGAAATA-ATCTTAAA-TATA
* *
341834 ATGAGATAATTTTAAATATA
1 ATGAAATAATCTTAAATATA
341854 ATGAAAT
1 ATGAAAT
341861 TGTTTAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.42
21 7 0.29
22 7 0.29
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (20 bp):
ATGAAATAATCTTAAATATA
Found at i:344729 original size:249 final size:247
Alignment explanation
Indices: 344282--344778 Score: 888
Period size: 249 Copynumber: 2.0 Consensus size: 247
344272 ACGTACTACT
*
344282 GGACTTTTTCTAATTGTCATCATTTCTTATTTTAATTGACTGACCAAATCTCATCAACGTAATTA
1 GGACTTTTTCTAATTGTCATCATTTCTCATTTTAATTGACTGACCAAATCTCATCAACGTAATTA
344347 TCATGAACATTTCTAAGAGTATATTATAGAAATTATCCCGTTTATTAACCATGAAATTATCATTA
66 TCATGAACATTTCTAAGAGTATATTATAGAAATTATCCCGTTTATTAACCATGAAATTATCATTA
344412 AACTCCAAAAAAAATAAAATTAAAAGGATGATATATCTTTCTTAACGTATGGTAAAAAGTAAAAA
131 AACTCCAAAAAAAATAAAATTAAAAGGATGATATATCTTTCTTAACGTATGGTAAAAAGT-AAAA
344477 AAAAAAAGAAAAGAAAAATGAAACAATTGACAAATTTTTAAGTTGTTCGAGGAA
195 AAAAAAA-AAAAGAAAAATGAAACAATTGACAAATTTTTAAGTTGTTCGAGGAA
* *
344531 GGACTTTTTCTAGTTGTCATCATTTCTCATTTTAATTGACTGACCAAATCTCATCAACTTAATTA
1 GGACTTTTTCTAATTGTCATCATTTCTCATTTTAATTGACTGACCAAATCTCATCAACGTAATTA
*
344596 TCATGAACATTTCTAAGAGTATATTATAGAAATTATCCCGTTTATTAACCATGGAATTATCATTA
66 TCATGAACATTTCTAAGAGTATATTATAGAAATTATCCCGTTTATTAACCATGAAATTATCATTA
344661 AACTCCAAAAAAAAAGTAAAATTAAAAGGATGATATATCTTTCTTAACGTATGGTAAAAAGT-AA
131 AACTCC-AAAAAAAA-TAAAATTAAAAGGATGATATATCTTTCTTAACGTATGGTAAAAAGTAAA
* * *
344725 AAAAAAGAAAAAGAAAAATGAAATAATTGACAAATTTTTAAGTTGTTTGAGGAA
194 AAAAAAAAAAAAGAAAAATGAAACAATTGACAAATTTTTAAGTTGTTCGAGGAA
344779 TCAGTGTATA
Statistics
Matches: 239, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
248 44 0.18
249 141 0.59
250 8 0.03
251 46 0.19
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (247 bp):
GGACTTTTTCTAATTGTCATCATTTCTCATTTTAATTGACTGACCAAATCTCATCAACGTAATTA
TCATGAACATTTCTAAGAGTATATTATAGAAATTATCCCGTTTATTAACCATGAAATTATCATTA
AACTCCAAAAAAAATAAAATTAAAAGGATGATATATCTTTCTTAACGTATGGTAAAAAGTAAAAA
AAAAAAAAAAGAAAAATGAAACAATTGACAAATTTTTAAGTTGTTCGAGGAA
Found at i:347295 original size:9 final size:9
Alignment explanation
Indices: 347277--347329 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
347267 GTCAGTAAAT
347277 AATT-TTAA
1 AATTATTAA
347285 AATTATTAA
1 AATTATTAA
347294 AATTA-T--
1 AATTATTAA
347300 -ATT-TTAA
1 AATTATTAA
347307 AA-TA-TAA
1 AATTATTAA
347314 AATTATTAA
1 AATTATTAA
347323 AATTATT
1 AATTATT
347330 GTTTGAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
5 4 0.11
7 6 0.16
8 8 0.22
9 19 0.51
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTATTAA
Found at i:347314 original size:20 final size:22
Alignment explanation
Indices: 347278--347319 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
347268 TCAGTAAATA
347278 ATTTTAAAATTATTAAAATTAT
1 ATTTTAAAATTATTAAAATTAT
347300 ATTTTAAAA-TA-TAAAATTAT
1 ATTTTAAAATTATTAAAATTAT
347320 TAAAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTAAAATTATTAAAATTAT
Found at i:347324 original size:29 final size:30
Alignment explanation
Indices: 347282--347353 Score: 112
Period size: 29 Copynumber: 2.4 Consensus size: 30
347272 TAAATAATTT
347282 TAAAATTATTAAAATTATAT-TTTAAAAT-A
1 TAAAATTATTAAAATTAT-TGTTTAAAATAA
*
347311 TAAAATTATTAAAATTATTGTTTGAAATAA
1 TAAAATTATTAAAATTATTGTTTAAAATAA
347341 TAAAATTATTAAA
1 TAAAATTATTAAA
347354 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 1 0.03
29 25 0.62
30 14 0.35
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTGTTTAAAATAA
Found at i:350348 original size:30 final size:29
Alignment explanation
Indices: 350283--350356 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
350273 GTTTGTTATG
* *
350283 TTTATTATTTTTAAAGAATTAAATTAAAT
1 TTTATTATTTTTAAAGAATCAAAGTAAAT
**
350312 TATTATTATTTTTAAAGTCTCAAAGTATAAT
1 T-TTATTATTTTTAAAGAATCAAAGTA-AAT
350343 TTTATT-TTTATTAA
1 TTTATTATTT-TTAA
350357 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 4 0.11
30 30 0.79
31 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTATTATTTTTAAAGAATCAAAGTAAAT
Found at i:355704 original size:17 final size:18
Alignment explanation
Indices: 355684--355720 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
355674 ATAGAATTAT
*
355684 TAAATA-TTAAAATAAAA
1 TAAATATTTAAAAAAAAA
355701 TAAATATTTAAAAAAAAA
1 TAAATATTTAAAAAAAAA
355719 TA
1 TA
355721 TGGACGGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAATATTTAAAAAAAAA
Found at i:356141 original size:7 final size:7
Alignment explanation
Indices: 356131--356160 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
356121 ATAAAATAAA
*
356131 AAATCTT
1 AAATTTT
356138 AAATTTT
1 AAATTTT
356145 AAATTTT
1 AAATTTT
356152 AAATTTT
1 AAATTTT
356159 AA
1 AA
356161 CCTCAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTT
Found at i:382281 original size:3 final size:3
Alignment explanation
Indices: 382273--382315 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
382263 TATAGACGAC
382273 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
382316 AAAAGATTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:389734 original size:2 final size:2
Alignment explanation
Indices: 389727--389757 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
389717 AAGGTTACCG
*
389727 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
389758 TTGTAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:391406 original size:46 final size:46
Alignment explanation
Indices: 391350--391444 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
391340 AATATTTTCA
* * *
391350 TATATTCCAAAGAAAAGAGGGTTTAGACTTCAATTGTTAGTGCTTT
1 TATATGCCAAAGAAAAGAGGGCTTAGACATCAATTGTTAGTGCTTT
391396 TATATGCCAAAGAAAAGAGGGCTTAGACATCAATTGTTAGTGCTTT
1 TATATGCCAAAGAAAAGAGGGCTTAGACATCAATTGTTAGTGCTTT
391442 TAT
1 TAT
391445 TTACTTCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.35
Consensus pattern (46 bp):
TATATGCCAAAGAAAAGAGGGCTTAGACATCAATTGTTAGTGCTTT
Found at i:400819 original size:84 final size:86
Alignment explanation
Indices: 400653--400889 Score: 252
Period size: 84 Copynumber: 2.8 Consensus size: 86
400643 ATCCACATAT
* *
400653 TTAAGGGTTTGAAAGGTATATGAATAATAATAATAATAATTGTATAAAAAATAATAAA-AGATCA
1 TTAAGGGTTTGAAAGGTATATGAATAATAACAACAAT--TTGTATAAAAAATAATAAAGAGATCA
* *
400717 AATAGAAATATTTATCTTTCGAC
64 AATAGAAACATCTATCTTTCGAC
* * * * *
400740 TTAAAGGTTTGAAAGATATATGAATAATAACAA-AATTTGTACAAAAAATAACAAAGA-ATGAAA
1 TTAAGGGTTTGAAAGGTATATGAATAATAACAACAATTTGTATAAAAAATAATAAAGAGATCAAA
* *
400803 TAGAAACA-CTAGTCTTTCTAT
66 TAGAAACATCTA-TCTTTCGAC
** * * * *
400824 TTAAGGGGGTAAAAGGTATATGAATAATAGCAACAA-TGGTATAAAAAATAATAAAG-GACCAAA
1 TTAAGGGTTTGAAAGGTATATGAATAATAACAACAATTTGTATAAAAAATAATAAAGAGATCAAA
400887 TAG
66 TAG
400890 TATTATATAA
Statistics
Matches: 125, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
83 2 0.02
84 87 0.70
85 3 0.02
86 3 0.02
87 30 0.24
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (86 bp):
TTAAGGGTTTGAAAGGTATATGAATAATAACAACAATTTGTATAAAAAATAATAAAGAGATCAAA
TAGAAACATCTATCTTTCGAC
Found at i:404398 original size:6 final size:6
Alignment explanation
Indices: 404387--404421 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
404377 ACATGTTATG
404387 GATGGT GATGGT GATGGT GATGGT GATGGT GATGG
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGG
404422 GGAGGGGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.51, T:0.31
Consensus pattern (6 bp):
GATGGT
Found at i:408860 original size:5 final size:5
Alignment explanation
Indices: 408804--408847 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
408794 CCCTCTTACT
408804 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
408848 AGTGTATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:409138 original size:241 final size:239
Alignment explanation
Indices: 408856--409405 Score: 639
Period size: 234 Copynumber: 2.3 Consensus size: 239
408846 ATAGTGTATA
** * *
408856 ATATATTAATAGTTTATATATATATATCAATTATTAAACATTATAATATCATGTAATAATATATC
1 ATATATTAATAGTTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATC
* * *
408921 TTTTTTATTATGATCTATAATATAATAATAGTTATATATAATAGTAGTACATTAATTATATATTA
66 --CTTTATTATAATCTATAATATAAT-ATAGTTATATATAATAGAAGTACATT-A-T-T-TATTA
* * * * * *
408986 ATTATTATATATTATTGTTTATTATTATGCTGGTTGAAATA-TGTTTTA-AGTCCCTATATTTTT
124 ATTATTATATATTATTGTTTATGATTATACTAGTTGAAA-AGTG-CTCAGAGTCCCTATACTTTT
* *
409049 CATATATGT-GAA-T-G-CCTTCCTACTATATTATATAATGCTATATC-ATATC
187 CATACATGTAAAATTAGTCC-TCCTACTATATTATATAATGCTATATCTATATC
* * *
409098 GTATATTAATAG-TTATATATATGCATAAATGATTAAACATTATAATATCATGTAATACTCTATC
1 ATATATTAATAGTTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATC
* * * *
409162 CTTTATTATAATTTATATTATAATATAGTTATATATAATAGAAGTACATTATTTATTACTTATTG
66 CTTTATTATAATCTATAATATAATATAGTTATATATAATAGAAGTACATTATTTATTAATTATTA
** * *
409227 TATATTATTGTTTATGATTATACTAGTTGAAAAGTGCTCAGAGTCTTTATACTTTTCGTACATTT
131 TATATTATTGTTTATGATTATACTAGTTGAAAAGTGCTCAGAGTCCCTATACTTTTCATACATGT
* *
409292 AAAATTAGTCCTCCTACTATGTTATATAATGTTATATCATATTATATC
196 AAAATTAGTCCTCCTACTATATTATATAATGCTATATC----TATATC
*
409340 ATATATTAATAGTTTATATATACATGCATCGATGATTAAACATTATAATATCATGTAATACTATA
1 ATATATTAATAGTTTATATAT--ATGCATCAATGATTAAACATTATAATATCATGTAATACTATA
409405 T
64 T
409406 AATATACTAA
Statistics
Matches: 262, Mismatches: 32, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
233 3 0.01
234 59 0.23
235 3 0.01
236 2 0.01
237 27 0.10
238 27 0.10
239 20 0.08
241 46 0.18
242 27 0.10
243 8 0.03
245 40 0.15
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (239 bp):
ATATATTAATAGTTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATC
CTTTATTATAATCTATAATATAATATAGTTATATATAATAGAAGTACATTATTTATTAATTATTA
TATATTATTGTTTATGATTATACTAGTTGAAAAGTGCTCAGAGTCCCTATACTTTTCATACATGT
AAAATTAGTCCTCCTACTATATTATATAATGCTATATCTATATC
Found at i:409541 original size:2 final size:2
Alignment explanation
Indices: 409534--409572 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
409524 AATTATTAAT
* *
409534 TA TA TA TA TA TA TA TA TA TA TA TT TA T- TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
409573 ATTATAGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:412130 original size:14 final size:14
Alignment explanation
Indices: 412111--412140 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
412101 ATTTATAAAC
412111 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
*
412125 AAAAAAGAAAAGAA
1 AAAAAAAAAAAGAA
412139 AA
1 AA
412141 TGTTCGAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:436509 original size:2 final size:2
Alignment explanation
Indices: 436502--436553 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
436492 CCAATTTTTA
436502 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
436544 AT AT AT AT AT
1 AT AT AT AT AT
436554 TTAAGAAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:439825 original size:17 final size:17
Alignment explanation
Indices: 439792--439840 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
439782 TATAAATCTA
* *
439792 AAATAAATAATAGAAATT
1 AAATAAA-AATAAAAATG
439810 AAATAAAAATAAAAATG
1 AAATAAAAATAAAAATG
*
439827 AAGTAAAAGATAAA
1 AAATAAAA-ATAAA
439841 CAAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.20
Consensus pattern (17 bp):
AAATAAAAATAAAAATG
Found at i:444526 original size:2 final size:2
Alignment explanation
Indices: 444521--444549 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
444511 TTTTTTCTTT
444521 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
444550 TACATTTTGT
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:448907 original size:31 final size:31
Alignment explanation
Indices: 448869--449007 Score: 133
Period size: 31 Copynumber: 4.5 Consensus size: 31
448859 TTAATATAAC
* *
448869 ATTTGGTACTTGAACTTGACATTTTTTACTA
1 ATTTGGTACTTAAACTTGACATTTTTTTCTA
*
448900 ATTTGGTACGTAAACTT----TTTTTTGTCTA
1 ATTTGGTACTTAAACTTGACATTTTTT-TCTA
* * *
448928 ATTTCGTACTCAAACTTGACATTTTTTCCTA
1 ATTTGGTACTTAAACTTGACATTTTTTTCTA
* * *
448959 ATTTGGTACCTAAACTTGACGCTTTTTTTTTA
1 ATTTGGTACTTAAACTTGAC-ATTTTTTTCTA
* *
448991 AGTTGGTACTTCAACTT
1 ATTTGGTACTTAAACTT
449008 TTTGGGGTCC
Statistics
Matches: 86, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
27 6 0.07
28 17 0.20
31 35 0.41
32 28 0.33
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACATTTTTTTCTA
Done.