Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2558
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: 129476
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5550 original size:4 final size:4
Alignment explanation
Indices: 5541--5576 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
5531 GTTATTGATT
*
5541 TTTA TTTA TTTA TTTA TTTA TTTG TTTA TATTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTT
5577 CTATGCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:7493 original size:24 final size:24
Alignment explanation
Indices: 7466--7517 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
7456 TTAGTAAGTC
*
7466 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
7490 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
7514 AAAT
1 AAAT
7518 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:9459 original size:24 final size:24
Alignment explanation
Indices: 9432--9483 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9422 TTAGTAAGTC
*
9432 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
9456 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
9480 AAAT
1 AAAT
9484 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:10297 original size:15 final size:14
Alignment explanation
Indices: 10266--10301 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
10256 ATGTTTTTCA
*
10266 GAAAATGATTTCTG
1 GAAAATAATTTCTG
10280 GAAAATAATTTACTG
1 GAAAATAATTT-CTG
10295 GAAAATA
1 GAAAATA
10302 TTTTTTAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.31
Consensus pattern (14 bp):
GAAAATAATTTCTG
Found at i:11029 original size:14 final size:14
Alignment explanation
Indices: 11010--11039 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11000 TGTCTAGAAG
11010 ATAGGAGAATCGTC
1 ATAGGAGAATCGTC
11024 ATAGGAGAATCGTC
1 ATAGGAGAATCGTC
11038 AT
1 AT
11040 CCCTCAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (14 bp):
ATAGGAGAATCGTC
Found at i:13375 original size:18 final size:18
Alignment explanation
Indices: 13354--13405 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
13344 AGGAATGAAG
13354 GAAGGGAGAAGAATGGAT
1 GAAGGGAGAAGAATGGAT
*** * *
13372 GAAGGGAGCTTACTAGAT
1 GAAGGGAGAAGAATGGAT
13390 GAAGGGAGAAGAATGG
1 GAAGGGAGAAGAATGG
13406 CTGAGAGCTT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.42, T:0.13
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:21584 original size:50 final size:50
Alignment explanation
Indices: 21516--21701 Score: 174
Period size: 50 Copynumber: 3.6 Consensus size: 50
21506 TTTCTTGTAC
* * **
21516 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * *** * *
21566 TGCCCATGCCATGTCCCAGACATGGTTTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * * *
21616 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TC---GG
*
21672 TGCCAATGCCATGTCCCAAACATGGTCTTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTA
21702 TATGGGATCT
Statistics
Matches: 107, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
50 77 0.72
53 2 0.02
56 28 0.26
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:23958 original size:72 final size:72
Alignment explanation
Indices: 23836--23979 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
23826 ATTAAGTTAA
* *
23836 GTTTTTCGAATTATTATTTAAGTAAAAAATTGAAGTTTGAAAATGTAATTAAATTAACTGGTCAT
1 GTTTTTCGAATTATTATTTAAGTAAAAAATTGAAGTTCGAAAATGAAATTAAATTAACTGGTCAT
23901 TGTGAAT
66 TGTGAAT
* *
23908 GTTTTTCGAATTATTATTTAAGTAAACAATTGAAGTTCGAAAATGAAATTAAATTAGCTGGTCAT
1 GTTTTTCGAATTATTATTTAAGTAAAAAATTGAAGTTCGAAAATGAAATTAAATTAACTGGTCAT
23973 TGTGAAT
66 TGTGAAT
23980 CCTTTGAATA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (72 bp):
GTTTTTCGAATTATTATTTAAGTAAAAAATTGAAGTTCGAAAATGAAATTAAATTAACTGGTCAT
TGTGAAT
Found at i:27438 original size:39 final size:40
Alignment explanation
Indices: 27361--27507 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
27351 TAGCTCCTCG
* * *
27361 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
27401 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
27440 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
27480 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
27508 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:27518 original size:80 final size:80
Alignment explanation
Indices: 27407--27587 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
27397 CTCATTCAAT
* * *
27407 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
27470 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
27486 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
27550 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
27567 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
27588 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:27547 original size:40 final size:40
Alignment explanation
Indices: 27404--27587 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
27394 TAACTCATTC
* *
27404 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
27444 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
27484 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
27524 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
27565 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27588 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:35265 original size:39 final size:40
Alignment explanation
Indices: 35188--35334 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
35178 TAGCTCCTCG
* * *
35188 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
35228 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
35267 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
35307 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
35335 ATTAATATCG
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:35283 original size:40 final size:39
Alignment explanation
Indices: 35231--35359 Score: 170
Period size: 40 Copynumber: 3.3 Consensus size: 39
35221 TAACTCATTC
* *
35231 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAAAACTCGCACA
* *
35271 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTA-AAACTCGCACA
* *
35311 AAGGCCTTCGGGACTTAACCCGGAATTAATA-TCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAAAACTCGCACA
*
35349 AATACCTTCGG
1 AATGCCTTCGG
35360 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
38 16 0.21
39 3 0.04
40 59 0.76
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATTAAAACTCGCACA
Found at i:35396 original size:78 final size:80
Alignment explanation
Indices: 35234--35412 Score: 208
Period size: 78 Copynumber: 2.3 Consensus size: 80
35224 CTCATTCAAT
* * *
35234 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGAATTA
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGAATTA
*
35299 GTATCTCGCACAAAG
66 GTATCTAGCACAAAG
* **
35314 GCCTTCGGGACTTAACCCGGA-ATTAATA-TCGCACAAATACCTTC-GGATCTTAGTCCGG-ATA
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGA-CTTAACCCGGAAT-
35375 TAGTCA-CTTAGCACAAA-
64 TAGT-ATC-TAGCACAAAG
*
35392 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
35413 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
77 5 0.06
78 47 0.54
79 14 0.16
80 21 0.24
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGAATTA
GTATCTAGCACAAAG
Found at i:46836 original size:40 final size:40
Alignment explanation
Indices: 46752--46935 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
46742 TTGAATGCTG
* * * *
46752 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
46791 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * **
46832 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACCAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
46872 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
46912 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
46936 GAATGAGTTA
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 110 0.91
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:46956 original size:39 final size:39
Alignment explanation
Indices: 46832--46982 Score: 117
Period size: 40 Copynumber: 3.8 Consensus size: 39
46822 AGTTATTAAT
* ** * * *
46832 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATAC-CAAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
** *
46872 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
46912 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
46952 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
46983 GAGCTATATC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 29 0.31
40 64 0.69
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:56063 original size:253 final size:253
Alignment explanation
Indices: 55615--56125 Score: 1022
Period size: 253 Copynumber: 2.0 Consensus size: 253
55605 TTCAAACCCT
55615 ATTTTCGTAAATCGTGTTCATATATATATTAATAATATTTAATGTTTATGATGCTAGTATAGAAA
1 ATTTTCGTAAATCGTGTTCATATATATATTAATAATATTTAATGTTTATGATGCTAGTATAGAAA
55680 TATATTAAAGTTTGGTTGAGTAATTTTGTTTAATTGATAGTTAATTAAGGTATAAGTGTAACGAC
66 TATATTAAAGTTTGGTTGAGTAATTTTGTTTAATTGATAGTTAATTAAGGTATAAGTGTAACGAC
55745 CCTAAAGTTAGTAGTGTCGAAAAATCAAGTATCGAGAACTCTTTTCCATAAACCAAGCCTGTAAT
131 CCTAAAGTTAGTAGTGTCGAAAAATCAAGTATCGAGAACTCTTTTCCATAAACCAAGCCTGTAAT
55810 TATTTTTATTAAGTATTTACGAAGTTATTATATAGGTGAATTGAATTTTGGATAGGTA
196 TATTTTTATTAAGTATTTACGAAGTTATTATATAGGTGAATTGAATTTTGGATAGGTA
55868 ATTTTCGTAAATCGTGTTCATATATATATTAATAATATTTAATGTTTATGATGCTAGTATAGAAA
1 ATTTTCGTAAATCGTGTTCATATATATATTAATAATATTTAATGTTTATGATGCTAGTATAGAAA
55933 TATATTAAAGTTTGGTTGAGTAATTTTGTTTAATTGATAGTTAATTAAGGTATAAGTGTAACGAC
66 TATATTAAAGTTTGGTTGAGTAATTTTGTTTAATTGATAGTTAATTAAGGTATAAGTGTAACGAC
55998 CCTAAAGTTAGTAGTGTCGAAAAATCAAGTATCGAGAACTCTTTTCCATAAACCAAGCCTGTAAT
131 CCTAAAGTTAGTAGTGTCGAAAAATCAAGTATCGAGAACTCTTTTCCATAAACCAAGCCTGTAAT
56063 TATTTTTATTAAGTATTTACGAAGTTATTATATAGGTGAATTGAATTTTGGATAGGTA
196 TATTTTTATTAAGTATTTACGAAGTTATTATATAGGTGAATTGAATTTTGGATAGGTA
56121 ATTTT
1 ATTTT
56126 GTCGAATTAA
Statistics
Matches: 258, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 258 1.00
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (253 bp):
ATTTTCGTAAATCGTGTTCATATATATATTAATAATATTTAATGTTTATGATGCTAGTATAGAAA
TATATTAAAGTTTGGTTGAGTAATTTTGTTTAATTGATAGTTAATTAAGGTATAAGTGTAACGAC
CCTAAAGTTAGTAGTGTCGAAAAATCAAGTATCGAGAACTCTTTTCCATAAACCAAGCCTGTAAT
TATTTTTATTAAGTATTTACGAAGTTATTATATAGGTGAATTGAATTTTGGATAGGTA
Found at i:64865 original size:32 final size:32
Alignment explanation
Indices: 64821--64882 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
64811 TACCTATTTT
*
64821 GCTATCTCTGAAAGGATGCCTTTATGGCTAAG
1 GCTATCTCTGAAAGGAAGCCTTTATGGCTAAG
*
64853 GCTATC-CTTGAAAGGAAGCCTTTGTGGCTA
1 GCTATCTC-TGAAAGGAAGCCTTTATGGCTA
64883 TCTCTGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (32 bp):
GCTATCTCTGAAAGGAAGCCTTTATGGCTAAG
Found at i:65251 original size:17 final size:19
Alignment explanation
Indices: 65229--65265 Score: 51
Period size: 17 Copynumber: 2.0 Consensus size: 19
65219 ATCTTCGCGG
65229 TAGTTG-TGTTTC-CAATA
1 TAGTTGATGTTTCACAATA
65246 TAGTTGATTGTTTCACAATA
1 TAGTTGA-TGTTTCACAATA
65266 ATTTGGGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
19 6 0.35
20 5 0.29
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (19 bp):
TAGTTGATGTTTCACAATA
Found at i:69689 original size:28 final size:28
Alignment explanation
Indices: 69626--69776 Score: 232
Period size: 28 Copynumber: 5.4 Consensus size: 28
69616 TATATTAATC
* *
69626 CGCACACTCAATGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
69653 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
69681 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
69709 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
69737 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
69766 CGCACACTTAG
1 CGCACACTTAG
69777 CGCCAATCTC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
27 21 0.18
28 79 0.68
29 16 0.14
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:77710 original size:28 final size:28
Alignment explanation
Indices: 77647--77800 Score: 274
Period size: 28 Copynumber: 5.5 Consensus size: 28
77637 ATATTAAGTC
* *
77647 CGCACACTCAATGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
77674 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
77702 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
77730 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
77758 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
77786 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
77801 GTACAATTTA
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 21 0.17
28 101 0.83
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:77746 original size:56 final size:56
Alignment explanation
Indices: 77648--77825 Score: 277
Period size: 56 Copynumber: 3.2 Consensus size: 56
77638 TATTAAGTCC
* *
77648 GCACACTCAATGCTATATAATC-AACTCGCACACTTAGTGCTATATAATCAAACTT
1 GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACTT
*
77703 GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACTC
1 GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACTT
* * * *
77759 GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTGTACAATTTAAACCT
1 GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAA-TCAAACTT
77816 GCACACTTAG
1 GCACACTTAG
77826 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
55 20 0.18
56 78 0.69
57 15 0.13
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (56 bp):
GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACTT
Found at i:87003 original size:10 final size:10
Alignment explanation
Indices: 86971--86996 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
86961 GCTCACTTAG
86971 TTTCCTACAT
1 TTTCCTACAT
86981 TTTCCTACAT
1 TTTCCTACAT
86991 TTTCCT
1 TTTCCT
86997 GAATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTCCTACAT
Found at i:95226 original size:23 final size:22
Alignment explanation
Indices: 95194--95245 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
95184 GATTGAGAGT
95194 GAAAAGAATT-GAAGAAAGAAGA
1 GAAAAGAATTAGAA-AAAGAAGA
95216 GAAAATGAATTAGAAAAAGAA-A
1 GAAAA-GAATTAGAAAAAGAAGA
*
95238 CAAAAGAA
1 GAAAAGAA
95246 AAAGACGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 10 0.37
23 11 0.41
24 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.21, T:0.10
Consensus pattern (22 bp):
GAAAAGAATTAGAAAAAGAAGA
Found at i:98437 original size:27 final size:27
Alignment explanation
Indices: 98364--98765 Score: 464
Period size: 27 Copynumber: 14.9 Consensus size: 27
98354 CAAGACCCCA
*
98364 AAATACCCCCATAGGGTAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
***
98391 AAATA-CCTTGTAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
** *
98417 AAATACCCCTGTAAGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
98444 AAATACCCCTATAGGGTAAAATAATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
98471 AAATACCTCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
98498 AAATAACCCCATAAGGTAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
*
98525 AAATACCCCCGTAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* ** ** *
98552 AGATACCCCCGCAATGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
98579 AAATACCCCTATAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
98606 AAATACTCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
98633 AAATACCCCCATAGGGTAAAAAGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
**
98660 AAATACCCCCATAGGGTAAAATGACAA
1 AAATACCCCCATAGGGTAAAATGACCG
** * * *
98687 AAATACCTTCGTAAGGTAAAATAACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
98714 AAATACCCCCGTAAGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
98741 AAATACCCTCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
98766 TGTTATACCC
Statistics
Matches: 316, Mismatches: 58, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
26 22 0.07
27 294 0.93
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCG
Found at i:99155 original size:28 final size:28
Alignment explanation
Indices: 99116--99318 Score: 264
Period size: 28 Copynumber: 7.3 Consensus size: 28
99106 CACTGTACTA
*
99116 GTTACTGTATTGGGCTAAGGCCCACACA
1 GTTACTGTATTGGGCTAAGGCCCACACT
* *
99144 GTTACTGTATTGGGCTAAGTCCGACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* * *
99172 GATACTATATTGGGCTAAAGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* *
99200 ATTACTGTATTGGGCTAAGGCTCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* *
99228 GTTACTGCATCGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* *
99256 GTTACTGCATCGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* **
99284 GTTACTGCATCAGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
99312 G-TACTGT
1 GTTACTGT
99319 TACTGAATAG
Statistics
Matches: 156, Mismatches: 19, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
27 5 0.03
28 151 0.97
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:100074 original size:9 final size:9
Alignment explanation
Indices: 100060--100135 Score: 100
Period size: 9 Copynumber: 8.4 Consensus size: 9
100050 TTTGGTTAAA
100060 AATTAACCG
1 AATTAACCG
100069 AATTAACCG
1 AATTAACCG
*
100078 AATTAACTG
1 AATTAACCG
*
100087 GATT-ACCGG
1 AATTAACC-G
100096 AATTAACCG
1 AATTAACCG
*
100105 AATTACCCG
1 AATTAACCG
*
100114 AATTAATCG
1 AATTAACCG
100123 AATTAACCG
1 AATTAACCG
100132 AATT
1 AATT
100136 GAATCACTAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
8 2 0.04
9 52 0.91
10 3 0.05
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:100209 original size:20 final size:20
Alignment explanation
Indices: 100180--100223 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
100170 TAGACTTTAG
100180 TTTTAGTTTTAGTT-TTAGAA
1 TTTTAGTTTTAGTTATTA-AA
* *
100200 TTTTATTTTTATTTATTAAA
1 TTTTAGTTTTAGTTATTAAA
100220 TTTT
1 TTTT
100224 TGTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTAGTTTTAGTTATTAAA
Found at i:100277 original size:18 final size:18
Alignment explanation
Indices: 100237--100280 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
100227 AATTTTTATG
**
100237 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
100255 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
100273 CTTGGGTT
1 ATTGGGTT
100281 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:100875 original size:75 final size:75
Alignment explanation
Indices: 100739--100886 Score: 210
Period size: 75 Copynumber: 2.0 Consensus size: 75
100729 GGAAAACCAA
* *
100739 GATTATTCCCTTATTAATAGAGAATGAAAATGGAAAGTTAGAAAAAGCTATTACATTCTTTCCAA
1 GATTATTCCCTTATTAATAGAGAATGAAAATGGAAAGTTAGAAAAAGCAATTACATGCTTTCCAA
*
100804 AAGAATATAG
66 AAAAATATAG
* * *
100814 GATTATTCCTTTATTAATAGAGAA-GACAAATGGAAATTTAGAAAAATG-AATTATATGCTTTCC
1 GATTATTCCCTTATTAATAGAGAATGA-AAATGGAAAGTTAGAAAAA-GCAATTACATGCTTTCC
100877 AAAAAAATAT
64 AAAAAAATAT
100887 TAATTTCCAT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
74 2 0.03
75 62 0.95
76 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (75 bp):
GATTATTCCCTTATTAATAGAGAATGAAAATGGAAAGTTAGAAAAAGCAATTACATGCTTTCCAA
AAAAATATAG
Found at i:112337 original size:683 final size:683
Alignment explanation
Indices: 111032--112397 Score: 2091
Period size: 683 Copynumber: 2.0 Consensus size: 683
111022 TAACAACTGA
*
111032 GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAAAAGGGTACCAGATGGACCATAGCCG
1 GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAAAAGGCTACCAGATGGACCATAGCCG
* * *
111097 ATATTCGCAGAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAAATGACGAAAAGGGT
66 ATATTCACAAAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAAATGACGAAAAGAGT
* * *
111162 ACGATTAATGGACAACGAAGAATGAACCCTATCTTGAAGGACGTAGTCAAGAAAGAAATCATCAA
131 ACGATTAATGGACAACAAAGAATGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATCAA
*
111227 GTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGTCTGATCCAGTGCG
196 GTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGTCAGATCCAGTGCG
* * * *
111292 TGCCAAAGAAAAGAGGTATCACGGTCATTAAGAAGAAGAATAATGAGTTGATACCGACTAGAACG
261 TGCCAAAGAAAAGAGGTATCACGGCCATTAAGAAGAAGAATAACGAGTTGATACCAAATAGAACG
*
111357 GTGACGGGATGGAGAATTTGCATCAATTACCAGAAGTTGAACAAGGCAACCAGGAAAGATCACTT
326 GTGACGGGATGGAGAATTTGCATCAATTACCAGAAGCTGAACAAGGCAACCAGGAAAGATCACTT
* * *
111422 TCCTTTGTCGTTTTTGGACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTGTTTTCTCG
391 TCCTTTGCCGTTTTTAGACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATTTTCTCG
* * * * * * *
111487 ATGGATACTTGGGGTATATTCATATTACAGTAGCATCGAAAGATCAGCACAAGACAACATTCACC
456 ATGGATACTCGGGGTATAATCAAATTACAGTAGCACCGAAAGATCAACAAAAGAAAACATTCACC
* * *
111552 TACCCGTATGGTACGCTTTCATTTAGGCGCATGCCATTTGGTTTATGTAATGCACCTGCTACATT
521 TACCCGTACGGTACGCTTGCATTTAGGCACATGCCATTTGGTTTATGTAATGCACCTGCTACATT
* *
111617 TCAAAGAACTATGATGTCTATTTTTACTGACATGGTTGAGAAATATTTGGAAGTTTTTATGGATG
586 TCAAAGAACTATAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTTTATGGATG
111682 ATTTTTCAGTATTCAGAGATACATATGATGATT
651 ATTTTTCAGTATTCAGAGATACATATGATGATT
* * * * **
111715 GCAAGAAGAGAAACTCATCCTGGTGTTGAAACAATTCAAGAAGGCTATCGGATGGACCATAGTTG
1 GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAAAAGGCTACCAGATGGACCATAGCCG
*
111780 ATATTCACAAAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAAATGGCGAAAAAGAG
66 ATATTCACAAAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAAATGACG-AAAAGAG
* * *
111845 -ACGATTGATGGTCAACAAAGACTGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATCA
130 TACGATTAATGGACAACAAAGAATGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATCA
**
111909 AGTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATGGGTAAGTCCAG-TCCAGTG
195 AGTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGT-CAGATCCAGTG
111973 CGTGCCAAAGAAAAGAGGTATCACGGCCATTGAA-AATG-AGAATAACGAGTTGATACCAAATAG
259 CGTGCCAAAGAAAAGAGGTATCACGGCCATT-AAGAA-GAAGAATAACGAGTTGATACCAAATAG
* * * *
112036 AACGGTTACGGGATGGAGAATTTGCAT-AGATTATC-GAAAGCTGAACTAGGCAACTAGGAAAGA
322 AACGGTGACGGGATGGAGAATTTGCATCA-ATTACCAG-AAGCTGAACAAGGCAACCAGGAAAGA
* * *
112099 TCACTTTCCTTTGCCGTTTTTAGACCAGATGCTGGATAGACTCGTAGGGTGAGACTATTACTATT
385 TCACTTTCCTTTGCCGTTTTTAGACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATT
*
112164 TTCTCGATGGATACTCGGGGTATAATCAAATTATAGTAGCACC-AGAAGATCAACAAAAGAAAAC
450 TTCTCGATGGATACTCGGGGTATAATCAAATTACAGTAGCACCGA-AAGATCAACAAAAGAAAAC
* * *
112228 ATTCACCTTCTCGTACGGTAC-ATCTGCATTTAGGCACATGCCATTTGGTTTATGTAATGCACCT
514 ATTCACCTACCCGTACGGTACGCT-TGCATTTAGGCACATGCCATTTGGTTTATGTAATGCACCT
* ** *
112292 GCTACATTTCAAATATGTCTAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTT
578 GCTACATTTCAAAGAACTATAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTT
* *
112357 TATGGATGATTTTTTAGTATTCGGAGATACATATGATGATT
643 TATGGATGATTTTTCAGTATTCAGAGATACATATGATGATT
112398 TCCTAAACAA
Statistics
Matches: 618, Mismatches: 57, Indels: 16
0.89 0.08 0.02
Matches are distributed among these distances:
682 4 0.01
683 603 0.98
684 11 0.02
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (683 bp):
GCAAGAAGAGAAACTCATCCTAGTGTTGAAACAATTCAAAAAGGCTACCAGATGGACCATAGCCG
ATATTCACAAAATTAGTCCATCTGTATGCATGCACAAGATTATCTTAGAAAATGACGAAAAGAGT
ACGATTAATGGACAACAAAGAATGAACCCCATCATGAAGGACGTAGTCAAGAAAGAAATCATCAA
GTGGTTAGATGCGGGTATAATTTACCCCATCTCAGATAGTTCATACGTAAGTCAGATCCAGTGCG
TGCCAAAGAAAAGAGGTATCACGGCCATTAAGAAGAAGAATAACGAGTTGATACCAAATAGAACG
GTGACGGGATGGAGAATTTGCATCAATTACCAGAAGCTGAACAAGGCAACCAGGAAAGATCACTT
TCCTTTGCCGTTTTTAGACCAGATGCTAGATAGACTCGCAGGGCGAGACTATTACTATTTTCTCG
ATGGATACTCGGGGTATAATCAAATTACAGTAGCACCGAAAGATCAACAAAAGAAAACATTCACC
TACCCGTACGGTACGCTTGCATTTAGGCACATGCCATTTGGTTTATGTAATGCACCTGCTACATT
TCAAAGAACTATAATGTCTATTTTTACTGACATGGTTGAGAAATATTTGAAAGTTTTTATGGATG
ATTTTTCAGTATTCAGAGATACATATGATGATT
Found at i:119897 original size:19 final size:19
Alignment explanation
Indices: 119856--119897 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
119846 ATTGAACTTG
* *
119856 AAAATTGGACTAGAGATCG
1 AAAATTGGACTAGAGAACC
119875 AAAATTGGAACTA-AGAACC
1 AAAATTGG-ACTAGAGAACC
119894 AAAA
1 AAAA
119898 AATGAGATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (19 bp):
AAAATTGGACTAGAGAACC
Found at i:120247 original size:17 final size:17
Alignment explanation
Indices: 120230--120262 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
120220 ATAATTTTAT
120230 TTTAA-TAAATTTAATA
1 TTTAATTAAATTTAATA
*
120246 TTTAATTTAATTTAATA
1 TTTAATTAAATTTAATA
120263 CTTATCTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTAAATTTAATA
Found at i:120330 original size:37 final size:37
Alignment explanation
Indices: 120283--120361 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
120273 TAATATTTTA
* *
120283 TTAATTTAATATTTA-AGTGATTATC-TTAATATTAAAT
1 TTAATCTAATATTTATAGTGATAATCATT-ATATT-AAT
*
120320 TTAATCTAATATTTATATTGATAATCATTATATTAAT
1 TTAATCTAATATTTATAGTGATAATCATTATATTAAT
120357 TTAAT
1 TTAAT
120362 ATTAAAGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 22 0.59
38 13 0.35
39 2 0.05
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (37 bp):
TTAATCTAATATTTATAGTGATAATCATTATATTAAT
Found at i:120330 original size:68 final size:69
Alignment explanation
Indices: 120240--120374 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 69
120230 TTTAATAAAT
* * * * *
120240 TTAATATTTAATTTAATTTAATACTTATCTTGATAAT-ATTTTATTAATTTAATATTTAAGTGAT
1 TTAATATTAAATTTAATCTAATACTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
120304 TATC
66 TATC
* *
120308 TTAATATTAAATTTAATCTAATATTTATATTGATAATCATTATATTAATTTAATATTAAAGTTAT
1 TTAATATTAAATTTAATCTAATACTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
120373 TA
66 TA
120375 AGGTTAATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
68 33 0.56
69 26 0.44
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (69 bp):
TTAATATTAAATTTAATCTAATACTTATATTGATAATCATTATATTAATTTAATATTAAAGTGAT
TATC
Found at i:121274 original size:13 final size:13
Alignment explanation
Indices: 121253--121301 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
121243 TTTAGTTTGG
121253 ATTTTTATTTT-T
1 ATTTTTATTTTCT
121265 ATTTTCTA-TTTCT
1 ATTTT-TATTTTCT
121278 ATTTTT-TTCTTCT
1 ATTTTTATT-TTCT
*
121291 ATTTTTGTTTT
1 ATTTTTATTTT
121302 GGTTTGCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 10 0.31
13 20 0.62
14 2 0.06
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (13 bp):
ATTTTTATTTTCT
Found at i:121275 original size:19 final size:19
Alignment explanation
Indices: 121253--121301 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
121243 TTTAGTTTGG
121253 ATTTTTATTTTTATT-TTCT
1 ATTTTTATTTTT-TTCTTCT
*
121272 ATTTCTATTTTTTTCTTCT
1 ATTTTTATTTTTTTCTTCT
*
121291 ATTTTTGTTTT
1 ATTTTTATTTT
121302 GGTTTGCACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (19 bp):
ATTTTTATTTTTTTCTTCT
Found at i:121581 original size:7 final size:7
Alignment explanation
Indices: 121565--121594 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
121555 AGTTTTGATG
*
121565 TTGGAGT
1 TTGGATT
121572 TTGGATT
1 TTGGATT
121579 TTGGATT
1 TTGGATT
121586 TTGGATT
1 TTGGATT
121593 TT
1 TT
121595 TTTTCTTGTA
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:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (7 bp):
TTGGATT
Found at i:121582 original size:14 final size:14
Alignment explanation
Indices: 121555--121594 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
121545 TGAATCGTTA
* *
121555 AGTTTTGATGTTGG
1 AGTTTGGATTTTGG
121569 AGTTTGGATTTTGG
1 AGTTTGGATTTTGG
*
121583 ATTTTGGATTTT
1 AGTTTGGATTTT
121595 TTTTCTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (14 bp):
AGTTTGGATTTTGG
Found at i:123250 original size:40 final size:40
Alignment explanation
Indices: 123166--123349 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
123156 TTGAATGCTG
* * * *
123166 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
123205 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
123246 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
123286 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
123326 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
123350 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:123303 original size:80 final size:81
Alignment explanation
Indices: 123166--123346 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
123156 TTGAATGCTG
* * *
123166 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
123230 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
123246 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
123307 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
123326 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
123347 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:123370 original size:39 final size:39
Alignment explanation
Indices: 123234--123396 Score: 141
Period size: 40 Copynumber: 4.1 Consensus size: 39
123224 GGTATTTGTG
* * * **
123234 CGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTG
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGG-CATTGAA
* * **
123274 CGAGATACT-AATTCCGGGTTAAGTCCCGAAGGCATTCGTG
1 CGAGTTA-TAAAATCCGGGTTAAGTCCCGAAGGCATT-GAA
*
123314 CGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
* * * *
123353 TGAGTTAATATAA-CCGGGCTATGTCCCGAAGGCACTTGAA
1 CGAGTT-ATAAAATCCGGGTTAAGTCCCGAAGGCA-TTGAA
123393 CGAG
1 CGAG
123397 GAGCTAAATC
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
39 29 0.28
40 75 0.71
41 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (39 bp):
CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
Done.