Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold446
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: 3567220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 22
Found at i:3454 original size:21 final size:22
Alignment explanation
Indices: 3416--3461 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3406 ATCTGTTGAA
* **
3416 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
3437 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
3459 ACT
1 ACT
3462 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:6327 original size:21 final size:20
Alignment explanation
Indices: 6296--6339 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
6286 AATAATTTAA
*
6296 TTAATTAAATTTATTTTATT
1 TTAATTAAATTTATTTGATT
6316 TTAATATAAATTTATTTGATT
1 TTAAT-TAAATTTATTTGATT
6337 TTA
1 TTA
6340 GTTATGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTAATTAAATTTATTTGATT
Found at i:6395 original size:17 final size:16
Alignment explanation
Indices: 6371--6416 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
6361 CTAAGTAAAT
*
6371 TAAAAAAAATAAAAAGGA
1 TAAAAAAAA-GAAAA-GA
6389 TAAAAAAAAGAAAAGA
1 TAAAAAAAAGAAAAGA
*
6405 TAAAAGAAAGAA
1 TAAAAAAAAGAA
6417 GAAAAAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 13 0.50
17 4 0.15
18 9 0.35
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (16 bp):
TAAAAAAAAGAAAAGA
Found at i:8996 original size:20 final size:20
Alignment explanation
Indices: 8962--9016 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
8952 AATATAATTT
8962 TTCCATTCTATTTCTGCTCCA
1 TTCCATTC-ATTTCTGCTCCA
8983 TTCCATTCATTTCTGCTCCA
1 TTCCATTCATTTCTGCTCCA
*
9003 TTCCATTCAATTCT
1 TTCCATTCATTTCT
9017 CACTCTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 25 0.76
21 8 0.24
ACGTcount: A:0.16, C:0.33, G:0.04, T:0.47
Consensus pattern (20 bp):
TTCCATTCATTTCTGCTCCA
Found at i:9269 original size:20 final size:21
Alignment explanation
Indices: 9224--9284 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
9214 AACTAATAAG
9224 ATTTATATTAAAAATTATATT
1 ATTTATATTAAAAATTATATT
*
9245 ATTTAT-TTAAATA-TATATT
1 ATTTATATTAAAAATTATATT
9264 ATTT-TA-TAAACATATTATATT
1 ATTTATATTAAA-A-ATTATATT
9285 TAATATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 7 0.21
21 12 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTATATTAAAAATTATATT
Found at i:9273 original size:18 final size:19
Alignment explanation
Indices: 9224--9278 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
9214 AACTAATAAG
*
9224 ATTTATATTAAAAATTATATT
1 ATTTATA-TAAATA-TATATT
*
9245 ATTTATTTAAATATATATT
1 ATTTATATAAATATATATT
*
9264 ATTT-TATAAACATAT
1 ATTTATATAAATATAT
9279 TATATTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 9 0.30
19 10 0.33
20 5 0.17
21 6 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATATAAATATATATT
Found at i:10292 original size:65 final size:65
Alignment explanation
Indices: 10209--10335 Score: 209
Period size: 65 Copynumber: 2.0 Consensus size: 65
10199 CACTTGATAT
* * * *
10209 GAGTTGGCCATTCTTAATTTATATTTTTTGGTAGTACGTAATGAAATTATTGAGCTTTGAAATAA
1 GAGTGGGCCATTCTTAATTGATATTTTTTGGCAGTACCTAATGAAATTATTGAGCTTTGAAATAA
*
10274 GAGTGGGCCATTCTTAATTGATGTTTTTTGGCAGTACCTAATGAAATTATTGAGCTTTGAAA
1 GAGTGGGCCATTCTTAATTGATATTTTTTGGCAGTACCTAATGAAATTATTGAGCTTTGAAA
10336 GTTTGAAATG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.41
Consensus pattern (65 bp):
GAGTGGGCCATTCTTAATTGATATTTTTTGGCAGTACCTAATGAAATTATTGAGCTTTGAAATAA
Found at i:11637 original size:21 final size:20
Alignment explanation
Indices: 11591--11642 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
11581 TAATATTTAA
11591 TTTTTATTTAATATTAAAAT
1 TTTTTATTTAATATTAAAAT
*
11611 TATTTATTTAATATTAAAAAT
1 TTTTTATTTAATATT-AAAAT
*
11632 TTTTTAATTAA
1 TTTTTATTTAA
11643 ATAATTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTATTTAATATTAAAAT
Found at i:12809 original size:19 final size:19
Alignment explanation
Indices: 12777--12825 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
12767 CTATTTTTGC
12777 ATAATTT-A-TTATTAAAA
1 ATAATTTAATTTATTAAAA
*
12794 ATAATTTAATTTATTAAAC
1 ATAATTTAATTTATTAAAA
* *
12813 CTAATTTATTTTA
1 ATAATTTAATTTA
12826 ATATAACCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 7 0.26
18 1 0.04
19 19 0.70
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATTTAATTTATTAAAA
Found at i:14000 original size:17 final size:18
Alignment explanation
Indices: 13964--14020 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
13954 TAAATACTTA
* *
13964 TAATATTTAATTTTTATT
1 TAATATTAAAATTTTATT
13982 TAATATTAAAATTTT-TT
1 TAATATTAAAATTTTATT
* *
13999 TAAT-TAAATAATTTAATT
1 TAATATTAA-AATTTTATT
14017 TAAT
1 TAAT
14021 TGATTTGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 3 0.09
17 11 0.33
18 19 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATATTAAAATTTTATT
Found at i:15025 original size:65 final size:65
Alignment explanation
Indices: 14946--15071 Score: 198
Period size: 65 Copynumber: 1.9 Consensus size: 65
14936 CACTTGATAG
* * *
14946 GAGTTGGCCATTCTTAATTAATATTTTTTGGTAGTACGTGATGAAATTCTTGAGCTTTGAAATAA
1 GAGTTGGCCATTCTTAATTAATATTTTTTGGCAGTACGTAATGAAATTATTGAGCTTTGAAATAA
* * *
15011 GAGTTGGCCATTCTTAATTGATGTTTTTTGGCAGTATGTAATGAAATTATTGAGCTTTGAA
1 GAGTTGGCCATTCTTAATTAATATTTTTTGGCAGTACGTAATGAAATTATTGAGCTTTGAA
15072 TGTCTGAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (65 bp):
GAGTTGGCCATTCTTAATTAATATTTTTTGGCAGTACGTAATGAAATTATTGAGCTTTGAAATAA
Found at i:16341 original size:18 final size:18
Alignment explanation
Indices: 16318--16371 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 18
16308 TAAATACTTA
16318 TAATATTTAATTTTTATT
1 TAATATTTAATTTTTATT
*
16336 TAATATTAAAATTTGTTTATT
1 TAATATT-TAA-TT-TTTATT
16357 TAAATAATTTAATTT
1 T-AAT-ATTTAATTT
16372 AATTAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 7 0.24
19 2 0.07
20 3 0.10
21 9 0.31
22 5 0.17
23 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TAATATTTAATTTTTATT
Found at i:17384 original size:65 final size:65
Alignment explanation
Indices: 17304--17430 Score: 200
Period size: 65 Copynumber: 2.0 Consensus size: 65
17294 CACTTGATAT
* * *
17304 GAGTTGGCCATTCTTAATTAATATTTTTTGGTAGTACGTAATGAAATTATTGAATTTTGAAATAA
1 GAGTTGGACATTCTTAATTAATATTTTTTGGCAGTACGTAATGAAATTATTGAACTTTGAAATAA
* * *
17369 GAGTTGGACATTCTTAATTGATGTTTTTTGGCAGTACGTAATGAAATTATTGAGCTTTGAAA
1 GAGTTGGACATTCTTAATTAATATTTTTTGGCAGTACGTAATGAAATTATTGAACTTTGAAA
17431 GTGTGAAATG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (65 bp):
GAGTTGGACATTCTTAATTAATATTTTTTGGCAGTACGTAATGAAATTATTGAACTTTGAAATAA
Found at i:18719 original size:20 final size:19
Alignment explanation
Indices: 18690--18735 Score: 83
Period size: 20 Copynumber: 2.4 Consensus size: 19
18680 TATAATATTT
18690 AATTTTTATTTAATATTAA
1 AATTTTTATTTAATATTAA
18709 AATTATTTATTTAATATTAA
1 AATT-TTTATTTAATATTAA
18729 AATTTTT
1 AATTTTT
18736 TTAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTTTATTTAATATTAA
Found at i:19763 original size:65 final size:65
Alignment explanation
Indices: 19683--19809 Score: 173
Period size: 65 Copynumber: 2.0 Consensus size: 65
19673 CACTTGATAT
* * * * *
19683 GAGTTGGCCATTCTTAATTAATATTTTTGGGTAGTACGTGATGAAATTATTGAGCTTTGAAATAA
1 GAGTTGGACATTCTTAATTAATATTTTTGGGCAATACGTAATGAAAGTATTGAGCTTTGAAATAA
* * * *
19748 GAGTTGGACATTCTTAATTGATGTTTTTTGGCAATATGTAATGAAAGTATTGAGCTTTGAAA
1 GAGTTGGACATTCTTAATTAATATTTTTGGGCAATACGTAATGAAAGTATTGAGCTTTGAAA
19810 GTGTGAAATG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (65 bp):
GAGTTGGACATTCTTAATTAATATTTTTGGGCAATACGTAATGAAAGTATTGAGCTTTGAAATAA
Found at i:20235 original size:14 final size:14
Alignment explanation
Indices: 20213--20246 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20203 TTTAATATTT
20213 TTTGA-TTAAATAA
1 TTTGATTTAAATAA
*
20226 TTTGATTTAATTAA
1 TTTGATTTAAATAA
20240 TTTGATT
1 TTTGATT
20247 GATTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTGATTTAAATAA
Found at i:20251 original size:13 final size:13
Alignment explanation
Indices: 20213--20252 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
20203 TTTAATATTT
*
20213 TTTGATTAAATAA
1 TTTGATTAATTAA
20226 TTTGATTTAATTAA
1 TTTGA-TTAATTAA
*
20240 TTTGATTGATTAA
1 TTTGATTAATTAA
20253 ATAAATAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTGATTAATTAA
Found at i:20778 original size:15 final size:13
Alignment explanation
Indices: 20758--20791 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
20748 TTCATTAACA
20758 TTAATTAAAGATTAT
1 TTAATTAAA-ATT-T
20773 TTAATTAAAATTT
1 TTAATTAAAATTT
20786 TTAATT
1 TTAATT
20792 TTTTTACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 3 0.16
15 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
TTAATTAAAATTT
Found at i:24049 original size:20 final size:20
Alignment explanation
Indices: 23973--24046 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
23963 TTTTACCCAG
*
23973 ATGTATCGATATATATTTCA
1 ATGTATCGATACATATTTCA
* * * * *
23993 ATATATCAATACATGTATGA
1 ATGTATCGATACATATTTCA
24013 ATGTATCGATACAT-TCTTCA
1 ATGTATCGATACATAT-TTCA
24033 ATGTATCGATACAT
1 ATGTATCGATACAT
24047 TCTGTCTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATATTTCA
Found at i:24990 original size:20 final size:22
Alignment explanation
Indices: 24950--24997 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
24940 TAGCCTTTGA
*
24950 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
24972 CCATGCA-TTTTTAAC-ATG-T
1 CCATGCATTTTTTAACTATGTT
24991 CCA-GCAT
1 CCATGCAT
24998 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 3 0.12
21 7 0.29
22 7 0.29
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:27191 original size:14 final size:14
Alignment explanation
Indices: 27173--27227 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
27163 TATTAAAATT
* *
27173 TAATATTTTAATAT
1 TAATATTCTAATAA
*
27187 TAATATTCCAAATAA
1 TAATATT-CTAATAA
27202 TAATATTCTAATAA
1 TAATATTCTAATAA
27216 TAATATT-TAATA
1 TAATATTCTAATA
27228 CTAAAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 5 0.14
14 20 0.56
15 11 0.31
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATATTCTAATAA
Found at i:28345 original size:37 final size:37
Alignment explanation
Indices: 28295--28368 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
28285 TGAATTGGAT
28295 CAGTTTCTCTCCAACAAATAAGTGCTTGGGCCAAAAA
1 CAGTTTCTCTCCAACAAATAAGTGCTTGGGCCAAAAA
28332 CAGTTTCTCTCCAACAAATAAGTGCTTGGGCCAAAAA
1 CAGTTTCTCTCCAACAAATAAGTGCTTGGGCCAAAAA
28369 AATCCTACCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (37 bp):
CAGTTTCTCTCCAACAAATAAGTGCTTGGGCCAAAAA
Found at i:28365 original size:20 final size:20
Alignment explanation
Indices: 28305--28365 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
28295 CAGTTTCTCT
28305 CCAACAAATAAGTGCTTGGG
1 CCAACAAATAAGTGCTTGGG
* *
28325 CCAA-AAA-CAGTTTCTCT---
1 CCAACAAATAAG-TGCT-TGGG
28342 CCAACAAATAAGTGCTTGGG
1 CCAACAAATAAGTGCTTGGG
28362 CCAA
1 CCAA
28366 AAAAATCCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
17 5 0.17
18 8 0.27
19 8 0.27
20 9 0.30
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
CCAACAAATAAGTGCTTGGG
Found at i:28955 original size:23 final size:23
Alignment explanation
Indices: 28924--28972 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
28914 TTTAATAAGT
28924 TAACAATTTTTAAAATAAAAT-TA
1 TAACAATTTTTAAAA-AAAATATA
* *
28947 TAACTATTTTTTAAAAAAATATA
1 TAACAATTTTTAAAAAAAATATA
28970 TAA
1 TAA
28973 TTATATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TAACAATTTTTAAAAAAAATATA
Found at i:28984 original size:23 final size:22
Alignment explanation
Indices: 28940--28986 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
28930 TTTTTAAAAT
* *
28940 AAAATTATAACTATTTTTTAAA
1 AAAATTATAACTATATTATAAA
*
28962 AAAATATATAATTATATTATAAA
1 AAAAT-TATAACTATATTATAAA
28985 AA
1 AA
28987 TTTGAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATTATAACTATATTATAAA
Found at i:29287 original size:26 final size:28
Alignment explanation
Indices: 29249--29307 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
29239 CTTAAAATTT
*
29249 AAAAT-AATAAT-AAAATTGTTTTTTAA
1 AAAATAAATAATAAAAATTATTTTTTAA
29275 AAAATAAAT-ATAAAAATTATTTTTTAA
1 AAAATAAATAATAAAAATTATTTTTTAA
29302 AAAATA
1 AAAATA
29308 TTTTTACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
AAAATAAATAATAAAAATTATTTTTTAA
Found at i:29645 original size:14 final size:14
Alignment explanation
Indices: 29626--29653 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29616 TTTTTTTATT
29626 TTAAATATATTTTA
1 TTAAATATATTTTA
29640 TTAAATATATTTTA
1 TTAAATATATTTTA
29654 AATATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:30045 original size:19 final size:18
Alignment explanation
Indices: 30021--30073 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
30011 GATTCTAGCT
*
30021 GAAAAAGAAAGGAAGAAAG
1 GAAAAAGAAA-GAAGAAAC
30040 GAAAAA-AAA-AAGAAAC
1 GAAAAAGAAAGAAGAAAC
*
30056 AAAGAAAGAAAGAAGAAA
1 GAA-AAAGAAAGAAGAAA
30074 AAAAGGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 8 0.28
17 3 0.10
18 6 0.21
19 12 0.41
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (18 bp):
GAAAAAGAAAGAAGAAAC
Found at i:30063 original size:4 final size:4
Alignment explanation
Indices: 30024--30095 Score: 60
Period size: 4 Copynumber: 18.0 Consensus size: 4
30014 TCTAGCTGAA
* * *
30024 AAAG AAAG GAAG AAAGG AAA- AAAA AAAG AAAC AAAG AAAG AAAG -AAG
1 AAAG AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
30071 AAAA AAAGG AAAAG AAAG AAA- AAAG
1 AAAG AAA-G -AAAG AAAG AAAG AAAG
30096 TTATATATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
3 9 0.16
4 38 0.69
5 5 0.09
6 3 0.05
ACGTcount: A:0.76, C:0.01, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:30064 original size:28 final size:25
Alignment explanation
Indices: 30028--30091 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
30018 GCTGAAAAAG
*
30028 AAAGGAAGAAAGGAAAAAAAAAAGAAA
1 AAAGAAAGAAA-GAAAAAAAAAAG-AA
* *
30055 CAAAGAAAGAAAGAAGAAAAAAAGGA
1 -AAAGAAAGAAAGAAAAAAAAAAGAA
30081 AAAGAAAGAAA
1 AAAGAAAGAAA
30092 AAAGTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.33
26 1 0.03
27 11 0.33
28 10 0.30
ACGTcount: A:0.77, C:0.02, G:0.22, T:0.00
Consensus pattern (25 bp):
AAAGAAAGAAAGAAAAAAAAAAGAA
Found at i:30095 original size:28 final size:27
Alignment explanation
Indices: 30023--30095 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
30013 TTCTAGCTGA
*
30023 AAAAGAAAGGAAGAAAGGAAAAAAAAAAG
1 AAAAGAAA-GAA-AAAAGAAAAAAAAAAG
* *
30052 -AAACAAAGAAAGAAAGAAGAAAAAAAGG
1 AAAAGAAAGAAA-AAAGAA-AAAAAAAAG
30080 AAAAGAAAGAAAAAAG
1 AAAAGAAAGAAAAAAG
30096 TTATATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.03
27 8 0.22
28 18 0.49
29 10 0.27
ACGTcount: A:0.77, C:0.01, G:0.22, T:0.00
Consensus pattern (27 bp):
AAAAGAAAGAAAAAAGAAAAAAAAAAG
Found at i:30493 original size:13 final size:13
Alignment explanation
Indices: 30475--30512 Score: 62
Period size: 12 Copynumber: 3.1 Consensus size: 13
30465 GCAAGCAAAG
30475 AGAAAGATAGAAA
1 AGAAAGATAGAAA
30488 AGAAAGA-AGAAA
1 AGAAAGATAGAAA
30500 AGAAAG-TAGAAA
1 AGAAAGATAGAAA
30512 A
1 A
30513 AAATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (13 bp):
AGAAAGATAGAAA
Found at i:30553 original size:12 final size:13
Alignment explanation
Indices: 30525--30553 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30515 ATTAAAATGT
30525 TTATATTTTTTAC
1 TTATATTTTTTAC
30538 TTATATTTTTTA-
1 TTATATTTTTTAC
30550 TTAT
1 TTAT
30554 GTAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATATTTTTTAC
Found at i:31430 original size:18 final size:19
Alignment explanation
Indices: 31390--31431 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
31380 TATTTTAATA
*
31390 TGTTTATGTATTTTTATTT
1 TGTTTATGTATTTTTATTG
31409 TGTTTAT-T-TTTTGTATTG
1 TGTTTATGTATTTT-TATTG
31427 TGTTT
1 TGTTT
31432 TCTTATATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.12, C:0.00, G:0.14, T:0.74
Consensus pattern (19 bp):
TGTTTATGTATTTTTATTG
Found at i:36017 original size:21 final size:23
Alignment explanation
Indices: 35991--36044 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
35981 ATTGTTGTTT
35991 ATATTATTTTTTATAT-TTAA-A
1 ATATTATTTTTTATATATTAATA
36012 ATATTATATTTTTATATATTAATA
1 ATATTAT-TTTTTATATATTAATA
36036 AT-TTATTTT
1 ATATTATTTT
36045 ATTTTATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.23
22 12 0.40
23 8 0.27
24 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTATTTTTTATATATTAATA
Found at i:36018 original size:26 final size:26
Alignment explanation
Indices: 35988--36059 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 26
35978 TATATTGTTG
35988 TTTATATTATTTTTTATATTTAA-AA
1 TTTATATTATTTTTTATATTTAATAA
*
36013 TAT-TA-TA-TTTTTATATATTAATAA
1 TTTATATTATTTTTTATAT-TTAATAA
*
36037 TTTATTTTATTTTATGTATATTT
1 TTTATATTATTTT-T-TATATTT
36060 TTATATATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
22 9 0.24
23 6 0.16
24 6 0.16
25 3 0.08
26 2 0.05
27 3 0.08
28 3 0.08
29 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTATATTATTTTTTATATTTAATAA
Found at i:36174 original size:11 final size:11
Alignment explanation
Indices: 36157--36241 Score: 59
Period size: 12 Copynumber: 7.5 Consensus size: 11
36147 GATATTTTCG
36157 TATATTTATAT
1 TATATTTATAT
*
36168 CATATTTATAT
1 TATATTTATAT
*
36179 TATTTTTTATAT
1 TA-TATTTATAT
36191 TATATTT-TAT
1 TATATTTATAT
36201 T-T-TTTATAT
1 TATATTTATAT
*
36210 CTATCTATCTATAT
1 -TA--TATTTATAT
*
36224 ATATATATATAT
1 -TATATTTATAT
36236 ATATAT
1 -TATAT
36242 GAAATTAGCT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
8 3 0.05
9 4 0.07
10 5 0.08
11 15 0.25
12 24 0.40
13 1 0.02
14 8 0.13
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:36189 original size:23 final size:21
Alignment explanation
Indices: 36161--36205 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
36151 TTTTCGTATA
36161 TTTATATCATATTTATATTATTT
1 TTTATATCATATTT-TATT-TTT
*
36184 TTTATATTATATTTTATTTTT
1 TTTATATCATATTTTATTTTT
36205 T
1 T
36206 ATATCTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 4 0.19
23 13 0.62
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATATCATATTTTATTTTT
Found at i:36202 original size:19 final size:18
Alignment explanation
Indices: 36169--36209 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
36159 TATTTATATC
36169 ATATTTATATTATTTTTT
1 ATATTTATATTATTTTTT
*
36187 ATATTATATTTTATTTTTT
1 ATATT-TATATTATTTTTT
36206 ATAT
1 ATAT
36210 CTATCTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATATTTATATTATTTTTT
Found at i:36335 original size:11 final size:11
Alignment explanation
Indices: 36319--36356 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
36309 AGAACGGAGG
36319 AAAAAAAGGAA
1 AAAAAAAGGAA
36330 AAAAAAA-GAA
1 AAAAAAAGGAA
*
36340 AGAAAAAGAGAA
1 AAAAAAAG-GAA
36352 AAAAA
1 AAAAA
36357 TTAGATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 9 0.39
11 7 0.30
12 7 0.30
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGAA
Found at i:36353 original size:31 final size:34
Alignment explanation
Indices: 36287--36356 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
36277 TTTTTACATC
* *
36287 AAAAGGAAAAAGAGAGAAAGAAAGAACGGAGGAAA
1 AAAAGGAAAAAAAAAGAAAGAAAGAAC-GAGGAAA
36322 AAAAGGAAAAAAAAAGAAAGAAA-AA-GA-GAAA
1 AAAAGGAAAAAAAAAGAAAGAAAGAACGAGGAAA
36353 AAAA
1 AAAA
36357 TTAGATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 8 0.24
32 2 0.06
34 2 0.06
35 21 0.64
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.00
Consensus pattern (34 bp):
AAAAGGAAAAAAAAAGAAAGAAAGAACGAGGAAA
Found at i:36801 original size:22 final size:25
Alignment explanation
Indices: 36773--36829 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
36763 AGAAAGATGG
36773 AAAGAAAAAAA-A-AGAGA-AAAGA
1 AAAGAAAAAAAGAGAGAGATAAAGA
*
36795 AAAGAAAGAAAATGAGAGAGATAAATA
1 AAAGAAA-AAAA-GAGAGAGATAAAGA
36822 AAAGAAAA
1 AAAGAAAA
36830 TTTTAATGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 7 0.24
23 4 0.14
25 1 0.03
26 6 0.21
27 11 0.38
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.05
Consensus pattern (25 bp):
AAAGAAAAAAAGAGAGAGATAAAGA
Found at i:36985 original size:21 final size:22
Alignment explanation
Indices: 36942--36990 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
36932 GTCATATTCA
*
36942 TTTTTATATTATATTTTAATTAT
1 TTTTTATATCATATTTT-ATTAT
*
36965 TTTTTATGTCATATTTT-TTAT
1 TTTTTATATCATATTTTATTAT
36986 TTTTT
1 TTTTT
36991 GTATATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
23 15 0.62
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTTATATCATATTTTATTAT
Found at i:37204 original size:20 final size:22
Alignment explanation
Indices: 37153--37205 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
37143 AATGTAATTT
*
37153 TAAATAAATAAATTTTATTTAA
1 TAAATAATTAAATTTTATTTAA
* *
37175 TAAA-ATTTAATTTTTA-TTAA
1 TAAATAATTAAATTTTATTTAA
37195 -AAATAATTAAA
1 TAAATAATTAAA
37206 AATATAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 3 0.12
20 9 0.36
21 9 0.36
22 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATAATTAAATTTTATTTAA
Found at i:38154 original size:16 final size:18
Alignment explanation
Indices: 38128--38164 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
38118 TAATAATAGA
*
38128 TGAATTAATAA-TCACTT
1 TGAATTAATAAGTCACCT
38145 TGAA-TAATAAGTCACCT
1 TGAATTAATAAGTCACCT
38162 TGA
1 TGA
38165 TCAAAGTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (18 bp):
TGAATTAATAAGTCACCT
Found at i:38375 original size:15 final size:16
Alignment explanation
Indices: 38346--38381 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
38336 AATATAATTG
38346 ATTTATTATATAGTTA
1 ATTTATTATATAGTTA
*
38362 TTTTATTATA-AGTTA
1 ATTTATTATATAGTTA
38377 ATTTA
1 ATTTA
38382 ATATGTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATTTATTATATAGTTA
Found at i:38792 original size:23 final size:23
Alignment explanation
Indices: 38761--38805 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
38751 TATTTTTAAC
38761 AATTATTTTATTTAATAAAATTTA
1 AATTATTTTA-TTAATAAAATTTA
38785 AATT-TTTTATTAATAAAATTT
1 AATTATTTTATTAATAAAATTT
38806 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.57
23 5 0.24
24 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATTATTTTATTAATAAAATTTA
Found at i:39698 original size:50 final size:50
Alignment explanation
Indices: 39480--40948 Score: 1306
Period size: 49 Copynumber: 30.7 Consensus size: 50
39470 GTAATTGATA
* * * * * **
39480 ACATGCTTTGATTCTTGATGCTTTAAAAATAAAAAG-GGAATATACA-TT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * **
39528 AAATGTTTTGATTCTTGATGCTTTAAAAATAAAAA-AAGAACATACATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * *
39577 AAATGTTTTGATTCTTGATGCTTTTAAGATAAAAAG-AGGA-ACGCAGTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* *
39625 ACATGTTTTGATTATTGATACTTTTAAGATAAAAAGAAGAACACGTC-TTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACG-CATTT
* * *
39675 ATATGTTTTTATTCTTGATACTTTTAAGATAAAAAG-AGAAACACGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAG-AACACGCATTT
* * *
39725 ACATATTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACACCTTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * *
39775 ATATGTTTTTATTCTTGATGCTTTTAAGATAAAAAGAGGAACACGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * *
39825 ACATGTTTTAATTCTTGATGCTTTTAAGAGAAAAA-AGGAACACACATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * **
39874 ATATGTTTTGATTCTTGATGCTTTTAAGATAAAAA-AAGAAATACATATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAG-AACACGCATTT
* * * * **
39924 ATATGTTTTGATTCTTGATACTTTTAAGGTTAAAAG-AGAACACATATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * *
39973 ATATGTTTTGATTATTGATGCTGTTAAGATAAAAAAGAA-ATACA--CATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGAT-AAAAAGAAGA-ACACGCATTT
* *
40022 ACATATTTTGATTCTTGATGCTTTTAAGACAAAAAG-AGAACACAG-ATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACAC-GCATTT
* * * *
40071 ACATGTTTTGATTCTTGATGCTTTTAAGACAAAAAGGA-AATACACATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * * *
40120 ATATGTTTTGATTTTTAATGCTTTTAAGACAAAAAGAAGAACACGCATAT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * * *
40170 ACATGTTTTTATTCTTAATGCTTTTAAAATAAAAA-AGGAACATGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* *
40219 ACATGTTTTGATTTTTGATAC-TTT----T----AG-AGAACACGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * *
40259 ACATATTTTGATTCGTGATGCTTTTAAGATAAAAAGAGGAACATGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * ** *
40309 ACATGTTTTGGTTCTTGATGCTTTTATGATAAAAA-AAAAACACATATAT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * *
40358 ACATATTTTGA---TT-ATGCTTTTAAGACAAAAAGAA-AACACACATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * * *
40403 ACATATTTTGATTATTAATGTTTTTAAGATAAAAAG-AGAACAAGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* *
40452 ACATGTTTTGATTCTTGATG------ACA-AAAAGGAA-ATACA--CATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGA-ACACGCATTT
* * * * * *
40493 ACATGTTTTAATTATTAATGATTTTAAAATAAAAAG-AGAACATGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
*
40542 ACATG--TTGATTCTTGATG------ACA-AAAAAGAA-ATACA--CATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGA-ACACGCATTT
* * * *
40581 ACATGTTTTAATTATTAATGCTTTTAAGATAAAAAG-AGAACATGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* *
40630 ACATG--TTGATTCTT-A-G------AGACAAAAAG-AGAACACACATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * *
40669 ACATATTTTGATTTTTGATGCTTTTAAGACAAAAAGAGGAACACAGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACAC-GCATTT
* *
40720 ACATGTTTTGATTCTTGATGCTTTTAAAATAAAAAGGA-AACACGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* *
40769 ACATGTTTTGATTCTTAATGCTTTTAAGAT-AAAAGAAAAACACGCATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * *
40818 ATATGTTTTGATTCTTGATGCTTTTAACATAAAAAG-ATAACACACATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * * **
40867 ATATGTTTTGATTTTTGATACTTTTAAGAT-AAAAGAA-AACACATATTT
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
* * *
40915 ACATATTTTGATTTTTTATGC-TTTAAGATAAAAA
1 ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAA
40949 AACACATATT
Statistics
Matches: 1187, Mismatches: 154, Indels: 160
0.79 0.10 0.11
Matches are distributed among these distances:
39 34 0.03
40 36 0.03
41 49 0.04
42 7 0.01
43 7 0.01
44 1 0.00
45 38 0.03
46 5 0.00
47 41 0.03
48 147 0.12
49 468 0.39
50 310 0.26
51 44 0.04
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (50 bp):
ACATGTTTTGATTCTTGATGCTTTTAAGATAAAAAGAAGAACACGCATTT
Found at i:40283 original size:40 final size:40
Alignment explanation
Indices: 40207--40284 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
40197 AATAAAAAAG
* * **
40207 GAACATGCATTTACATGTTTTGATTTTTGATACTTTTAGA
1 GAACACGCATTTACATATTTTGATTCGTGATACTTTTAGA
*
40247 GAACACGCATTTACATATTTTGATTCGTGATGCTTTTA
1 GAACACGCATTTACATATTTTGATTCGTGATACTTTTA
40285 AGATAAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (40 bp):
GAACACGCATTTACATATTTTGATTCGTGATACTTTTAGA
Found at i:40333 original size:90 final size:89
Alignment explanation
Indices: 40157--40334 Score: 266
Period size: 89 Copynumber: 2.0 Consensus size: 89
40147 GACAAAAAGA
* * *
40157 AGAACACGCATATACATGTTTTTATTCTTAATGCTTTTAAAATAAAAAAGGAACATGCATTTACA
1 AGAACACGCATATACATATTTTGATTCGTAATGCTTTTAAAATAAAAAAGGAACATGCATTTACA
*
40222 TGTTTTGATTTTTGATACTTTTAG
66 TGTTTTGATTCTTGATACTTTTAG
* * *
40246 AGAACACGCATTTACATATTTTGATTCGTGATGCTTTTAAGATAAAAAGAGGAACATGCATTTAC
1 AGAACACGCATATACATATTTTGATTCGTAATGCTTTTAAAATAAAAA-AGGAACATGCATTTAC
* *
40311 ATGTTTTGGTTCTTGATGCTTTTA
65 ATGTTTTGATTCTTGATACTTTTA
40335 TGATAAAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
89 42 0.53
90 37 0.47
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (89 bp):
AGAACACGCATATACATATTTTGATTCGTAATGCTTTTAAAATAAAAAAGGAACATGCATTTACA
TGTTTTGATTCTTGATACTTTTAG
Found at i:40388 original size:45 final size:45
Alignment explanation
Indices: 40326--40417 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
40316 TTGGTTCTTG
* * *
40326 ATGCTTTTATGATAAAAAAAAAACACATATATACATATTTTGATT
1 ATGCTTTTAAGACAAAAAAAAAACACACATATACATATTTTGATT
* *
40371 ATGCTTTTAAGACAAAAAGAAAACACACATTTACATATTTTGATT
1 ATGCTTTTAAGACAAAAAAAAAACACACATATACATATTTTGATT
40416 AT
1 AT
40418 TAATGTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (45 bp):
ATGCTTTTAAGACAAAAAAAAAACACACATATACATATTTTGATT
Found at i:40492 original size:41 final size:41
Alignment explanation
Indices: 40447--40589 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 41
40437 AGAGAACAAG
*
40447 CATTTACATGTTTTGATTCTTGATGACAAAAAGGAAATACA
1 CATTTACATGTTTTGATTCTTGATGACAAAAAAGAAATACA
* * * * * *
40488 CATTTACATGTTTTAATTATTAATGATTTTAAAATAAAAAGAGAACA
1 CATTTACATGTTTTGATTCTTGATGA---CAAAA-AAGAA-A-TACA
40535 TGCATTTACATG--TTGATTCTTGATGACAAAAAAGAAATACA
1 --CATTTACATGTTTTGATTCTTGATGACAAAAAAGAAATACA
40576 CATTTACATGTTTT
1 CATTTACATGTTTT
40590 AATTATTAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
39 10 0.13
41 28 0.35
42 1 0.01
43 4 0.05
44 8 0.10
45 3 0.04
46 1 0.01
47 14 0.18
49 10 0.13
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (41 bp):
CATTTACATGTTTTGATTCTTGATGACAAAAAAGAAATACA
Found at i:40507 original size:90 final size:90
Alignment explanation
Indices: 40304--40927 Score: 568
Period size: 88 Copynumber: 6.7 Consensus size: 90
40294 GAGGAACATG
* * * * * * *
40304 CATTTACATGTTTTGGTTCTTGATGCTTTTATGATAAAAAAAAAAC-A-CATATATACATATTTT
1 CATTTACATGTTTTGATTATTAATGCTTTTAAGATAAAAAGAGAACAAGCAT-T-TACATGTTTT
* * *
40367 GATTATGCTTTTAAGACAAAAAGAAAACACA
64 GA-T-T-C-TTGATGACAAAAAGGAAACACA
* *
40398 CATTTACATATTTTGATTATTAATGTTTTTAAGATAAAAAGAGAACAAGCATTTACATGTTTTGA
1 CATTTACATGTTTTGATTATTAATGCTTTTAAGATAAAAAGAGAACAAGCATTTACATGTTTTGA
*
40463 TTCTTGATGACAAAAAGGAAATACA
66 TTCTTGATGACAAAAAGGAAACACA
* * * *
40488 CATTTACATGTTTTAATTATTAATGATTTTAAAATAAAAAGAGAACATGCATTTACATG--TTGA
1 CATTTACATGTTTTGATTATTAATGCTTTTAAGATAAAAAGAGAACAAGCATTTACATGTTTTGA
* *
40551 TTCTTGATGACAAAAAAGAAATACA
66 TTCTTGATGACAAAAAGGAAACACA
* *
40576 CATTTACATGTTTTAATTATTAATGCTTTTAAGATAAAAAGAGAACATGCATTTACATG--TTGA
1 CATTTACATGTTTTGATTATTAATGCTTTTAAGATAAAAAGAGAACAAGCATTTACATGTTTTGA
40639 TTCTTAGA-GACAAAAA-GAGAACACA
66 TTCTT-GATGACAAAAAGGA-AACACA
* * * *
40664 CATTTACATATTTTGATTTTTGATGCTTTTAAGACAAAAAGAGGAACACAGCATTTACATGTTTT
1 CATTTACATGTTTTGATTATTAATGCTTTTAAGATAAAAAGA-GAACA-AGCATTTACATGTTTT
* *
40729 GATTCTTGATGCTTTTAAAATAAAAAGGAAACACG
64 GATTCTTGATG--------ACAAAAAGGAAACACA
* * * *
40764 CATTTACATGTTTTGATTCTTAATGCTTTTAAGAT-AAAAGAAAAACACGCATTTATATGTTTTG
1 CATTTACATGTTTTGATTATTAATGCTTTTAAGATAAAAAG-AGAACAAGCATTTACATGTTTTG
*
40828 ATTCTTGATGCTTTTAACATAAAAAGATAACACA
65 ATTCTTGATG------ACA-AAAAGGA-AACACA
* * * * * * *
40862 CATTTATATGTTTTGATTTTTGATACTTTTAAGAT-AAAAGAAAACACA-TATTTACATATTTTG
1 CATTTACATGTTTTGATTATTAATGCTTTTAAGATAAAAAGAGAACA-AGCATTTACATGTTTTG
40925 ATT
65 ATT
40928 TTTTATGCTT
Statistics
Matches: 457, Mismatches: 51, Indels: 41
0.83 0.09 0.07
Matches are distributed among these distances:
87 2 0.00
88 144 0.32
89 7 0.02
90 83 0.18
91 3 0.01
92 11 0.02
93 1 0.00
94 49 0.11
95 2 0.00
96 8 0.02
97 27 0.06
98 66 0.14
99 9 0.02
100 43 0.09
101 2 0.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (90 bp):
CATTTACATGTTTTGATTATTAATGCTTTTAAGATAAAAAGAGAACAAGCATTTACATGTTTTGA
TTCTTGATGACAAAAAGGAAACACA
Found at i:40752 original size:139 final size:139
Alignment explanation
Indices: 40097--40900 Score: 513
Period size: 139 Copynumber: 5.8 Consensus size: 139
40087 GATGCTTTTA
* * * * * *
40097 AGACAAAAAG-GAAATACACATTTATATGTTTTGATTTTTAATGCTTTTAAGACAAAAAGAAGAA
1 AGACAAAAAGAG-AACACACATTTACATATTTTGATTCTTGATGCTTTTAAGACAAAAAGAGGAA
* * *
40161 CAC-GCATATACATGTTTTTATTCTTAATGCTTTTAAAATAAAAA-AGGAACATGCATTTACATG
65 CACAGCATTTACATGTTTTGATTCTTGATGCTTTTAAAATAAAAAGA-GAACATGCATTTACATG
*
40224 TTTTGATT-TTTG
129 --TTGATTCTTAG
* **** * * *
40236 ATACTTTTAGAGAACACGCATTTACATATTTTGATTCGTGATGCTTTTAAGATAAAAAGAGGAAC
1 AGACAAAAAGAGAACACACATTTACATATTTTGATTCTTGATGCTTTTAAGACAAAAAGAGGAAC
* * ** * *
40301 A-TGCATTTACATGTTTTGGTTCTTGATGCTTTTATGATAAAAAAAAAACA--CATATATACATA
66 ACAGCATTTACATGTTTTGATTCTTGATGCTTTTAAAATAAAAAGAGAACATGCAT-T-TAC--A
*
40363 TTTTGATTATGCTTTTA-
127 TGTTGA-T-T-C--TTAG
* * * * *
40380 AGACAAAAAGAAAACACACATTTACATATTTTGATTATTAATGTTTTTAAGATAAAAAGA-GAAC
1 AGACAAAAAGAGAACACACATTTACATATTTTGATTCTTGATGCTTTTAAGACAAAAAGAGGAAC
* * * ** *
40444 A-AGCATTTACATGTTTTGATTCTTGATGAC---AAAAAGGAAATACACATTTACATG-TTTTA-
66 ACAGCATTTACATGTTTTGATTCTTGATG-CTTTTAAAA-TAAA-A-AGA-GAACATGCATTTAC
*
40503 ATTATTAATGATT-TTA-
126 A-T-GT--TGATTCTTAG
* * ** * * *
40519 AAATAAAAAGAGAACATGCATTTAC--ATGTTGATTCTTGA------T--GACAAAAA-AGAAAT
1 AGACAAAAAGAGAACACACATTTACATATTTTGATTCTTGATGCTTTTAAGACAAAAAGAGGAAC
* * * *
40573 ACA-CATTTACATGTTTTAATTATTAATGCTTTTAAGATAAAAAGAGAACATGCATTTACATGTT
66 ACAGCATTTACATGTTTTGATTCTTGATGCTTTTAAAATAAAAAGAGAACATGCATTTACATGTT
40637 GATTCTTAG
131 GATTCTTAG
*
40646 AGACAAAAAGAGAACACACATTTACATATTTTGATTTTTGATGCTTTTAAGACAAAAAGAGGAAC
1 AGACAAAAAGAGAACACACATTTACATATTTTGATTCTTGATGCTTTTAAGACAAAAAGAGGAAC
*
40711 ACAGCATTTACATGTTTTGATTCTTGATGCTTTTAAAATAAAAAG-GAAACACGCATTTACATGT
66 ACAGCATTTACATGTTTTGATTCTTGATGCTTTTAAAATAAAAAGAG-AACATGCATTTACATG-
40775 TTTGATTCTTAATG
129 -TTGATTCTT-A-G
* * * * * * *
40789 CTTTTAAGA-TAAAAGAAAAACACGCATTTATATGTTTTGATTCTTGATGCTTTTAACATAAAAA
1 ------AGACAAAAAG-AGAACACACATTTACATATTTTGATTCTTGATGCTTTTAAGACAAAAA
* * * * *
40853 GA-TAACACA-CATTTATATGTTTTGATTTTTGATACTTTTAAGATAAAA
59 GAGGAACACAGCATTTACATGTTTTGATTCTTGATGCTTTTAAAATAAAA
40901 GAAAACACAT
Statistics
Matches: 516, Mismatches: 92, Indels: 106
0.72 0.13 0.15
Matches are distributed among these distances:
125 5 0.01
126 3 0.01
127 27 0.05
128 9 0.02
129 46 0.09
130 4 0.01
131 4 0.01
135 1 0.00
137 22 0.04
138 9 0.02
139 171 0.33
140 3 0.01
141 15 0.03
142 5 0.01
143 35 0.07
144 55 0.11
145 9 0.02
146 1 0.00
147 35 0.07
148 11 0.02
149 46 0.09
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (139 bp):
AGACAAAAAGAGAACACACATTTACATATTTTGATTCTTGATGCTTTTAAGACAAAAAGAGGAAC
ACAGCATTTACATGTTTTGATTCTTGATGCTTTTAAAATAAAAAGAGAACATGCATTTACATGTT
GATTCTTAG
Found at i:41276 original size:18 final size:17
Alignment explanation
Indices: 41255--41295 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
41245 ATATATAAAT
41255 TTTTATTTATATGTTATA
1 TTTTATTTATAT-TTATA
41273 TTTTA-TTATATTTATA
1 TTTTATTTATATTTATA
41289 TATTTAT
1 T-TTTAT
41296 GACGTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 10 0.48
18 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTATTTATATTTATA
Found at i:41283 original size:17 final size:16
Alignment explanation
Indices: 41255--41309 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 16
41245 ATATATAAAT
41255 TTTTATTTATATGTTATA
1 TTTTA-TTATAT-TTATA
41273 TTTTATTATATTTATA
1 TTTTATTATATTTATA
*
41289 TATTTATGACGTATTTATA
1 T-TTTATTA--TATTTATA
41308 TT
1 TT
41310 ATTTTTTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.18
17 12 0.36
18 6 0.18
19 9 0.27
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTATTATATTTATA
Found at i:41331 original size:28 final size:28
Alignment explanation
Indices: 41264--41333 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
41254 TTTTTATTTA
*
41264 TATGTTATATTTTATTATATTTATATATT
1 TATGTCATATTTTATTAT-TTTATATATT
* * * *
41293 TATGACGTATTTATATTATTTTTTGTA-T
1 TATGTCATATTT-TATTATTTTATATATT
41321 TATGTCATATTTT
1 TATGTCATATTTT
41334 TAATATTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
27 1 0.03
28 11 0.33
29 15 0.45
30 6 0.18
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (28 bp):
TATGTCATATTTTATTATTTTATATATT
Found at i:41349 original size:28 final size:27
Alignment explanation
Indices: 41256--41351 Score: 68
Period size: 28 Copynumber: 3.4 Consensus size: 27
41246 TATATAAATT
* * *
41256 TTTATTTA-TATGTTATATTTTATTATA
1 TTTATATATTATGTCATATTTT-TAATA
* * * *
41283 TTTATATATTTATGACGTATTTATATTA
1 TTTATATA-TTATGTCATATTTTTAATA
* *
41311 TTTTTTGTATTATGTCATATTTTTAATA
1 -TTTATATATTATGTCATATTTTTAATA
41339 TTTATCATATTAT
1 TTTAT-ATATTAT
41352 TTTCAAATAA
Statistics
Matches: 50, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
27 11 0.22
28 24 0.48
29 15 0.30
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.62
Consensus pattern (27 bp):
TTTATATATTATGTCATATTTTTAATA
Found at i:44997 original size:173 final size:170
Alignment explanation
Indices: 44711--45039 Score: 509
Period size: 173 Copynumber: 1.9 Consensus size: 170
44701 AAACTTATTT
*
44711 CATTCCATAATTCAAATAAAACTTCTTATGAGGTACTTTATTAGGTACATAATTTTTTTTATGCA
1 CATTCCATAATTCAAATAAAACTTCTTATGAGGTACTTTATTAAGTACATAATTTTTTTTATGCA
* *
44776 AAAACTTATAATAAATTTAAAATAACTTATTCGATCTTTTAAATCTATTATATATAGATATCAAA
66 AAAACTTATAACAAATTCAAAATAACTTATTCGATCTTTTAAATCTATTATATATAGATATCAAA
44841 TAAT-TGAAGTTTACACAAATTATAAAGGGAACCTATTTTC
131 TAATCT-AAGTTTACACAAATTATAAAGGGAACCTATTTTC
* * *
44881 CATTCCATAATTCAAATGAAACTTCTTATGAGGTATTTTATTAAGTATATAATTTCATTTTTTAT
1 CATTCCATAATTCAAATAAAACTTCTTATGAGGTACTTTATTAAGTACATAA-TT--TTTTTTAT
* *
44946 GCAAAGACTTATAACAAATTCAAAATAACTTATTCGATCTTTCT-AATCTATTGTATATAGATAT
63 GCAAAAACTTATAACAAATTCAAAATAACTTATTCGATCTTT-TAAATCTATTATATATAGATAT
* *
45010 CAAATAATCTAAGTTTGCATAAATTATAAA
127 CAAATAATCTAAGTTTACACAAATTATAAA
45040 ATGACCTATT
Statistics
Matches: 144, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
170 48 0.33
171 2 0.01
173 92 0.64
174 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (170 bp):
CATTCCATAATTCAAATAAAACTTCTTATGAGGTACTTTATTAAGTACATAATTTTTTTTATGCA
AAAACTTATAACAAATTCAAAATAACTTATTCGATCTTTTAAATCTATTATATATAGATATCAAA
TAATCTAAGTTTACACAAATTATAAAGGGAACCTATTTTC
Found at i:45987 original size:277 final size:277
Alignment explanation
Indices: 45493--46027 Score: 926
Period size: 277 Copynumber: 1.9 Consensus size: 277
45483 AAGGAAAATA
* *
45493 TGGTAGATGGGTGAACAGAAACGAAATATGGAATCAAGACTTCGAGATACGATGAATCACTTTCT
1 TGGTAGATGGGTGAACAGAAACAAAATATGGAATCAAGACTTCAAGATACGATGAATCACTTTCT
* *
45558 TTAAAGAGTTATTTGCCCCCACATAAAGTTTGCTAACAAGTCTAAGCAATAACACTCCCAAGATA
66 TTAAAGAGTTATTTGCCCCCACATAAAATTTGCTAACAAGTATAAGCAATAACACTCCCAAGATA
* *
45623 CAATGAAGCCTATATAAATTCTGCAACTAGTAATATTGAAAAACTCCTTAATCTCTTATTCTTTC
131 CAATGAAGCCTATATAAATTCTGCAACTAATAATATTGAAAAACCCCTTAATCTCTTATTCTTTC
*
45688 TAGTAAACTGTAATAATTTTAGAAATAATTTGAAATTGAATTGGAATGAAAATTTTAGCAATAGA
196 TAGTAAACTCTAATAATTTTAGAAATAATTTGAAATTGAATTGGAATGAAAATTTTAGCAATAGA
45753 TGTTGGTATTTATAGGT
261 TGTTGGTATTTATAGGT
*
45770 TGGTAGATGGGTGAACAGAAACAAAATATGGAATCAAGACTTCAAGATATGATGAATCACTTTCT
1 TGGTAGATGGGTGAACAGAAACAAAATATGGAATCAAGACTTCAAGATACGATGAATCACTTTCT
* *
45835 TTAAAGAGTTATTTGCCCCCACATAAAATTTGCTAACAGGTATAAGCAATAACACTTCCAAGATA
66 TTAAAGAGTTATTTGCCCCCACATAAAATTTGCTAACAAGTATAAGCAATAACACTCCCAAGATA
* * * * *
45900 CAATGAAGTCTTTATAAATTCTGCAACTAATAATATTGAAGAACCCCTTAATCTCTTATTTTTTG
131 CAATGAAGCCTATATAAATTCTGCAACTAATAATATTGAAAAACCCCTTAATCTCTTATTCTTTC
*
45965 TAGTAAACTCTAATAATTTTAGAAATGATTTGAAATTGAATTGGAATGAAAATTTTAGCAATA
196 TAGTAAACTCTAATAATTTTAGAAATAATTTGAAATTGAATTGGAATGAAAATTTTAGCAATA
46028 TGGGTTAACA
Statistics
Matches: 242, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
277 242 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (277 bp):
TGGTAGATGGGTGAACAGAAACAAAATATGGAATCAAGACTTCAAGATACGATGAATCACTTTCT
TTAAAGAGTTATTTGCCCCCACATAAAATTTGCTAACAAGTATAAGCAATAACACTCCCAAGATA
CAATGAAGCCTATATAAATTCTGCAACTAATAATATTGAAAAACCCCTTAATCTCTTATTCTTTC
TAGTAAACTCTAATAATTTTAGAAATAATTTGAAATTGAATTGGAATGAAAATTTTAGCAATAGA
TGTTGGTATTTATAGGT
Found at i:47328 original size:18 final size:19
Alignment explanation
Indices: 47307--47349 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 19
47297 AATACAGTAC
*
47307 AATATGAAAAATAAAATA-
1 AATATGAAAAATAAAAAAT
47325 AATAT--AAAATAAAAAAT
1 AATATGAAAAATAAAAAAT
47342 AATATGAA
1 AATATGAA
47350 TATACAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 5 0.24
19 1 0.05
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AATATGAAAAATAAAAAAT
Found at i:47343 original size:23 final size:22
Alignment explanation
Indices: 47313--47361 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
47303 GTACAATATG
47313 AAAAATAAAATAAATATAAAATA
1 AAAAATAAAATAAATATAAAA-A
* * *
47336 AAAAATAATATGAATATACAAA
1 AAAAATAAAATAAATATAAAAA
47358 AAAA
1 AAAA
47362 TAACACGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAAATAAAATAAATATAAAAA
Found at i:47363 original size:18 final size:16
Alignment explanation
Indices: 47314--47363 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
47304 TACAATATGA
*
47314 AAAATAAAATAAATAT
1 AAAATAAAAAAAATAT
47330 AAAATAAAAAATAATAT
1 AAAATAAAAAA-AATAT
*
47347 GAATATACAAAAAAATA
1 -AAAATA-AAAAAAATA
47364 ACACGATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 10 0.34
17 5 0.17
18 9 0.31
19 5 0.17
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAATAAAAAAAATAT
Found at i:47372 original size:20 final size:21
Alignment explanation
Indices: 47335--47373 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
47325 AATATAAAAT
* *
47335 AAAAAATAATATGAATATACA
1 AAAAAATAACACGAATATACA
47356 AAAAAATAACACG-ATATA
1 AAAAAATAACACGAATATA
47374 AAAGACAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.67, C:0.08, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAAAATAACACGAATATACA
Found at i:47435 original size:18 final size:18
Alignment explanation
Indices: 47395--47435 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
47385 GATGTAAAAA
47395 ATAAAATTAACATGACAT
1 ATAAAATTAACATGACAT
*
47413 -GAAAATATAACATGA-AT
1 ATAAAAT-TAACATGACAT
47430 ATAAAA
1 ATAAAA
47436 AAATATAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (18 bp):
ATAAAATTAACATGACAT
Found at i:47575 original size:21 final size:22
Alignment explanation
Indices: 47528--47578 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
47518 ATGTGACACG
47528 AAAAATAAAACAAATAAGATAA
1 AAAAATAAAACAAATAAGATAA
* * * *
47550 GAAAATAATACGAAT-ATATAA
1 AAAAATAAAACAAATAAGATAA
47571 AAAAATAA
1 AAAAATAA
47579 CATGATTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAAATAAAACAAATAAGATAA
Found at i:48546 original size:2 final size:2
Alignment explanation
Indices: 48539--48592 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
48529 ACTACATACA
48539 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
48581 AT AT AT AT AT AT
1 AT AT AT AT AT AT
48593 GTGATACTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49422 original size:8 final size:8
Alignment explanation
Indices: 49405--49474 Score: 56
Period size: 8 Copynumber: 8.9 Consensus size: 8
49395 AATATTGATA
49405 TAAA-TAT
1 TAAATTAT
49412 TAAATTAT
1 TAAATTAT
49420 T-AATTAT
1 TAAATTAT
*
49427 TAAAATAAT
1 T-AAATTAT
* *
49436 AAAAATAT
1 TAAATTAT
49444 T-AATTAT
1 TAAATTAT
*
49451 TAAAATAT
1 TAAATTAT
*
49459 TAAAATAT
1 TAAATTAT
49467 TAATATTA
1 TAA-ATTA
49475 ATATGTCTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
7 17 0.34
8 25 0.50
9 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TAAATTAT
Found at i:49427 original size:15 final size:15
Alignment explanation
Indices: 49386--49475 Score: 67
Period size: 15 Copynumber: 5.7 Consensus size: 15
49376 ATTTAATTTT
*
49386 TTAAATAATAATATTGA
1 TTAAATATTAA-ATT-A
49403 TATAAATATTAAATTA
1 T-TAAATATTAAATTA
* *
49419 TTAATTATTAAAATAA
1 TTAAATATT-AAATTA
*
49435 TAAAAATATT-AATTA
1 T-TAAATATTAAATTA
*
49450 TTAAAATATTAAAATA
1 TT-AAATATTAAATTA
49466 TT-AATATTAA
1 TTAAATATTAA
49476 TATGTCTAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
14 8 0.13
15 19 0.32
16 14 0.23
17 10 0.17
18 9 0.15
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (15 bp):
TTAAATATTAAATTA
Found at i:49449 original size:24 final size:23
Alignment explanation
Indices: 49406--49475 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 23
49396 ATATTGATAT
* *
49406 AAATATTAAATTATTAATTATTA
1 AAATATAAAAATATTAATTATTA
49429 AAATAATAAAAATATTAATTATTA
1 AAAT-ATAAAAATATTAATTATTA
*
49453 AAATATTAAAATATTAA-TATTA
1 AAATATAAAAATATTAATTATTA
49475 A
1 A
49476 TATGTCTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 6 0.14
23 16 0.37
24 21 0.49
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATATAAAAATATTAATTATTA
Found at i:49586 original size:28 final size:32
Alignment explanation
Indices: 49539--49596 Score: 79
Period size: 29 Copynumber: 1.9 Consensus size: 32
49529 AAAATAATAT
49539 TATTTATTATTAGAACA-TTTAATAATAAAAA
1 TATTTATTATTAGAACATTTTAATAATAAAAA
*
49570 TATTTATT-TTA-AA-ATTTTAATATTAAA
1 TATTTATTATTAGAACATTTTAATAATAAA
49597 TCTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 1 0.04
29 13 0.52
30 3 0.12
31 8 0.32
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
TATTTATTATTAGAACATTTTAATAATAAAAA
Found at i:49735 original size:33 final size:38
Alignment explanation
Indices: 49698--49781 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
49688 TTAACATGAT
* *
49698 TTTTAATAAT-TA-AATAT-ATTTTTATTA-ATA-CTA
1 TTTTAATAATATATAATATAACTTTTATTATAAATCTA
* *
49731 TTTTAAAAATATATAATATAACTTTTATTATAAATGTA
1 TTTTAATAATATATAATATAACTTTTATTATAAATCTA
49769 TTTTAATAATATA
1 TTTTAATAATATA
49782 ACAACTTTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 9 0.22
34 2 0.05
35 5 0.12
36 9 0.22
37 2 0.05
38 14 0.34
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (38 bp):
TTTTAATAATATATAATATAACTTTTATTATAAATCTA
Found at i:50488 original size:14 final size:14
Alignment explanation
Indices: 50470--50511 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
50460 TTAGTATCAC
50470 AAATTTAATTATAT
1 AAATTTAATTATAT
*
50484 TAATTTAATTA-AT
1 AAATTTAATTATAT
*
50497 AAATTTAAATATAT
1 AAATTTAATTATAT
50511 A
1 A
50512 TATATCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTATAT
Found at i:50571 original size:24 final size:25
Alignment explanation
Indices: 50520--50574 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
50510 TATATATCAA
50520 TTAAATTTTTAATATCAAATAATATT
1 TTAAATTTTTAATAT-AAATAATATT
* *
50546 TTAAATTTTTATTAT-AATAATTTT
1 TTAAATTTTTAATATAAATAATATT
50570 TTAAA
1 TTAAA
50575 AAAATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 13 0.48
26 14 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAAATTTTTAATATAAATAATATT
Found at i:51681 original size:50 final size:50
Alignment explanation
Indices: 51565--51982 Score: 418
Period size: 50 Copynumber: 8.4 Consensus size: 50
51555 GCTTTAATTT
* * * *
51565 TTGATACTTTTAAGATAAAAAAAAGAAACATACATTTACATCTTTTAATTC
1 TTGATACTTTTAAGATAAAAAGAAG-AACATGCATTTACATGTTTTGATTC
* * *
51616 TTGATGCTTTTAA-ATAAAAAGAAGAACATGCGTTTACATATTTTGATTC
1 TTGATACTTTTAAGATAAAAAGAAGAACATGCATTTACATGTTTTGATTC
* * * * *
51665 TTGATGCTTTTAAAATAAAAAGAGGAACACGTATTTACATGTTTTGATTC
1 TTGATACTTTTAAGATAAAAAGAAGAACATGCATTTACATGTTTTGATTC
** * * * * *
51715 TTGATGTTTTTAAGATAAAAAGAGGAACACGTATTTACATATTTTGATTT
1 TTGATACTTTTAAGATAAAAAGAAGAACATGCATTTACATGTTTTGATTC
* * *
51765 TTGATGCTTTTAAGATAAAAAG-GGAACATGCATTTATATGTTTTGATTC
1 TTGATACTTTTAAGATAAAAAGAAGAACATGCATTTACATGTTTTGATTC
* * ** * *
51814 TTAATACTTTTAAGATAAAAGGAAGAACACACATTTACATGTTTTAATTTT
1 TTGATACTTTTAAGATAAAAAGAAGAACATGCATTTACATGTTTTGA-TTC
* * * * *
51865 TTTATATTTTTAAGAT-AAAA-AAGAAACATGCATTTACATATTTTAATTA
1 TTGATACTTTTAAGATAAAAAGAAG-AACATGCATTTACATGTTTTGATTC
* * *
51914 TTGATATTTTTAAGATAAAAA-AAGACTCAT--ATTTACATGTTTTGATTT
1 TTGATACTTTTAAGATAAAAAGAAGA-ACATGCATTTACATGTTTTGATTC
*
51962 TTTATACTTTTAAGATAAAAA
1 TTGATACTTTTAAGATAAAAA
51983 AATATATTTT
Statistics
Matches: 317, Mismatches: 44, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
48 34 0.11
49 96 0.30
50 159 0.50
51 28 0.09
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (50 bp):
TTGATACTTTTAAGATAAAAAGAAGAACATGCATTTACATGTTTTGATTC
Found at i:51716 original size:99 final size:100
Alignment explanation
Indices: 51561--51982 Score: 467
Period size: 100 Copynumber: 4.2 Consensus size: 100
51551 ACGTGCTTTA
* * * * *
51561 ATTTTTGATACTTTTAAGATAAAAAAAAGAAACATACATTTACATCTTTTAATTCTTGATGCTTT
1 ATTTTTGATACTTTTAAGAT-AAAAAGAGGAACATGCATTTACATGTTTTAATTCTTGATACTTT
* *
51626 TAA-ATAAAAAGAAGAACATGCGTTTACATATTTTG
65 TAAGATAAAAAGAAGAACACGCATTTACATATTTTG
* * * * * * **
51661 ATTCTTGATGCTTTTAAAATAAAAAGAGGAACACGTATTTACATGTTTTGATTCTTGATGTTTTT
1 ATTTTTGATACTTTTAAGATAAAAAGAGGAACATGCATTTACATGTTTTAATTCTTGATACTTTT
* *
51726 AAGATAAAAAGAGGAACACGTATTTACATATTTTG
66 AAGATAAAAAGAAGAACACGCATTTACATATTTTG
* * * *
51761 ATTTTTGATGCTTTTAAGATAAAAAG-GGAACATGCATTTATATGTTTTGATTCTTAATACTTTT
1 ATTTTTGATACTTTTAAGATAAAAAGAGGAACATGCATTTACATGTTTTAATTCTTGATACTTTT
* * * *
51825 AAGATAAAAGGAAGAACACACATTTACATGTTTTA
66 AAGATAAAAAGAAGAACACGCATTTACATATTTTG
* * * * * *
51860 ATTTTTTTATATTTTTAAGATAAAAA-AGAAACATGCATTTACATATTTTAATTATTGATATTTT
1 A-TTTTTGATACTTTTAAGATAAAAAGAGGAACATGCATTTACATGTTTTAATTCTTGATACTTT
* ** *
51924 TAAGATAAAAA-AAG-ACTCATATTTACATGTTTTG
65 TAAGATAAAAAGAAGAACACGCATTTACATATTTTG
*
51958 ATTTTTTATACTTTTAAGATAAAAA
1 ATTTTTGATACTTTTAAGATAAAAA
51983 AATATATTTT
Statistics
Matches: 275, Mismatches: 44, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
97 23 0.08
98 18 0.07
99 104 0.38
100 130 0.47
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (100 bp):
ATTTTTGATACTTTTAAGATAAAAAGAGGAACATGCATTTACATGTTTTAATTCTTGATACTTTT
AAGATAAAAAGAAGAACACGCATTTACATATTTTG
Found at i:51813 original size:149 final size:149
Alignment explanation
Indices: 51557--51982 Score: 477
Period size: 149 Copynumber: 2.9 Consensus size: 149
51547 GATCACGTGC
* * * * *
51557 TTTAATTT-TTGATACTTTTAAGATAAAAAAAAGAA-ACATACATTTACATCTTTTAATTCTTGA
1 TTTAATTTCTTGATATTTTTAAGAT-AAAAAAGGAACACGT--ATTTACATATTTTAATTATTGA
* * * * *
51620 TGCTTTTAA-ATAAAAAGAAGAACATGCGTTTACATATTTTGATTCTTGATGCTTTTAAAATAAA
63 TGCTTTTAAGATAAAAAG-AGAACATGCATTTACATGTTTTGATTCTTAATACTTTTAAGATAAA
* **
51684 AAGAGGAACACGTATTTACATGT
127 AAGAAGAACACACATTTACATGT
* * * *
51707 TTTGA-TTCTTGATGTTTTTAAGATAAAAAGAGGAACACGTATTTACATATTTTGATTTTTGATG
1 TTTAATTTCTTGATATTTTTAAGATAAAAA-AGGAACACGTATTTACATATTTTAATTATTGATG
* * *
51771 CTTTTAAGATAAAAAGGGAACATGCATTTATATGTTTTGATTCTTAATACTTTTAAGATAAAAGG
65 CTTTTAAGATAAAAAGAGAACATGCATTTACATGTTTTGATTCTTAATACTTTTAAGATAAAAAG
51836 AAGAACACACATTTACATGT
130 AAGAACACACATTTACATGT
* * * * * **
51856 TTTAATTTTTTTATATTTTTAAGATAAAAAAGAAACATGCATTTACATATTTTAATTATTGATAT
1 TTTAATTTCTTGATATTTTTAAGATAAAAAAGGAACACGTATTTACATATTTTAATTATTGATGC
* * * *
51921 TTTTAAGATAAAAAAAGACTCAT--ATTTACATGTTTTGATTTTTTATACTTTTAAGATAAAAA
66 TTTTAAGATAAAAAGAGA-ACATGCATTTACATGTTTTGATTCTTAATACTTTTAAGATAAAAA
51983 AATATATTTT
Statistics
Matches: 233, Mismatches: 37, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
148 35 0.15
149 141 0.61
150 54 0.23
151 3 0.01
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (149 bp):
TTTAATTTCTTGATATTTTTAAGATAAAAAAGGAACACGTATTTACATATTTTAATTATTGATGC
TTTTAAGATAAAAAGAGAACATGCATTTACATGTTTTGATTCTTAATACTTTTAAGATAAAAAGA
AGAACACACATTTACATGT
Found at i:52508 original size:26 final size:26
Alignment explanation
Indices: 52479--52565 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 26
52469 ATTATTATTT
*
52479 ATTTTAAATACTTAATGAAATATTAA
1 ATTTTAAATACTTAATGTAATATTAA
* * * *
52505 ATTTTAACATAATATTAT-TATTATT-T
1 ATTTTAA-ATACT-TAATGTAATATTAA
*
52531 ATTTTAAATACTTAACGTAATATTAA
1 ATTTTAAATACTTAATGTAATATTAA
52557 ATTTTAAAT
1 ATTTTAAAT
52566 GTTATTATGT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
24 2 0.04
25 10 0.21
26 23 0.49
27 9 0.19
28 3 0.06
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTTTAAATACTTAATGTAATATTAA
Found at i:52511 original size:52 final size:52
Alignment explanation
Indices: 52455--52563 Score: 191
Period size: 52 Copynumber: 2.1 Consensus size: 52
52445 GTAGTCAACC
* *
52455 TTTAACATAATGTTATTATTATTTATTTTAAATACTTAATGAAATATTAAAT
1 TTTAACATAATATTATTATTATTTATTTTAAATACTTAACGAAATATTAAAT
*
52507 TTTAACATAATATTATTATTATTTATTTTAAATACTTAACGTAATATTAAAT
1 TTTAACATAATATTATTATTATTTATTTTAAATACTTAACGAAATATTAAAT
52559 TTTAA
1 TTTAA
52564 ATGTTATTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (52 bp):
TTTAACATAATATTATTATTATTTATTTTAAATACTTAACGAAATATTAAAT
Found at i:53209 original size:26 final size:27
Alignment explanation
Indices: 53192--53274 Score: 78
Period size: 30 Copynumber: 2.9 Consensus size: 27
53182 TATTTGGTAA
53192 TAAAATAATATATTAATATTAAATAAT
1 TAAAATAATATATTAATATTAAATAAT
*
53219 TAAAATAATATTATTTATTATTAAA-ACATT
1 TAAAATAATA-TA-TTAATATTAAATA-A-T
* *
53249 TAATAATAAAAATTTTAATATTAAAT
1 TAA-AAT-AATATATTAATATTAAAT
53275 CTAGACCTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
27 10 0.22
28 3 0.07
29 11 0.24
30 14 0.31
31 4 0.09
32 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAAATAATATATTAATATTAAATAAT
Found at i:53456 original size:19 final size:19
Alignment explanation
Indices: 53432--53468 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53422 ATTTATTTTT
53432 AATATAATTTTAATAATTA
1 AATATAATTTTAATAATTA
* *
53451 AATATATTTTTATTAATT
1 AATATAATTTTAATAATT
53469 TTTTTTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATAATTTTAATAATTA
Found at i:53893 original size:10 final size:10
Alignment explanation
Indices: 53878--53913 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
53868 TTTAAAAAAT
53878 AAATATTAAA
1 AAATATTAAA
53888 AAATA-TAAA
1 AAATATTAAA
*
53897 AAATTTTAAA
1 AAATATTAAA
53907 AAATATT
1 AAATATT
53914 TTCACAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATATTAAA
Found at i:55240 original size:2 final size:2
Alignment explanation
Indices: 55233--55266 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55223 AGTGAAATAC
55233 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
55267 GAAAGACTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57359 original size:2 final size:2
Alignment explanation
Indices: 57352--57383 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
57342 TTTTGAACAA
*
57352 AG AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
57384 TATTGCAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:57884 original size:92 final size:92
Alignment explanation
Indices: 57669--57992 Score: 489
Period size: 92 Copynumber: 3.5 Consensus size: 92
57659 TTATAATTAC
* *
57669 GCCAAGCCAAAACTCCTTAATGATGTTAGTGCGTGCTTTTCCTAACTTTTCTACCACGCGGC--A
1 GCCAAGCCAAAACTCCTTAATGATGTTAGTGCGTGCTTTTCCTAACTTTTCTAGCAAGCGGCAAA
*
57732 A-AGGATGTTAGCTCGGACAGAAGTAT
66 AGAGGATGTTAGCTCGGACAGACGTAT
*
57758 GCCAAGCCAAAACTCCTTAATGATGTTAGTGCGTGCTTTAT-CTAACTTTTCTAGCAAGTGGCAA
1 GCCAAGCCAAAACTCCTTAATGATGTTAGTGCGTGCTTT-TCCTAACTTTTCTAGCAAGCGGCAA
57822 AAGAGGATGTTAGCTCGGACAGACGTAT
65 AAGAGGATGTTAGCTCGGACAGACGTAT
* * **
57850 GCCAAGCCAAAACTCCTTAAGGATGTTATTGCGTGCTTTTCCTAACTTTTCTAGCATCCGGCAAA
1 GCCAAGCCAAAACTCCTTAATGATGTTAGTGCGTGCTTTTCCTAACTTTTCTAGCAAGCGGCAAA
57915 AGAGGATGTTAGCTCGGACAGAAC-TAT
66 AGAGGATGTTAGCTCGGACAG-ACGTAT
*
57942 GCCAAGCCAAAACTCCTCAATGATGTTTAGTGCGTGCTTTT-CTAACCTTTT
1 GCCAAGCCAAAACTCCTTAATGATG-TTAGTGCGTGCTTTTCCTAA-CTTTT
57993 GTACAGCCTA
Statistics
Matches: 215, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
89 57 0.27
90 1 0.00
91 3 0.01
92 133 0.62
93 21 0.10
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (92 bp):
GCCAAGCCAAAACTCCTTAATGATGTTAGTGCGTGCTTTTCCTAACTTTTCTAGCAAGCGGCAAA
AGAGGATGTTAGCTCGGACAGACGTAT
Found at i:58744 original size:29 final size:30
Alignment explanation
Indices: 58679--58746 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
58669 TGGGAGATTG
*
58679 ATCAAACTAATATTATTTTAAAAATTAATT
1 ATCAAAATAATATTATTTTAAAAATTAATT
* *
58709 ATTAAAATAATATTGTTTT-AAAA-TATATT
1 ATCAAAATAATATTATTTTAAAAATTA-ATT
58738 ATCAAAATA
1 ATCAAAATA
58747 CCATTGTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.06
29 15 0.45
30 16 0.48
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (30 bp):
ATCAAAATAATATTATTTTAAAAATTAATT
Found at i:59147 original size:16 final size:16
Alignment explanation
Indices: 59097--59147 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
59087 TAACATGAAT
59097 ATACAAAAAAATAACA
1 ATACAAAAAAATAACA
* *
59113 CA-ACTAAAATATTATACA
1 -ATAC-AAAAAAATA-ACA
59131 ATACAAAAAAATAACA
1 ATACAAAAAAATAACA
59147 A
1 A
59148 AAGTATGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
16 6 0.22
17 16 0.59
18 5 0.19
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.18
Consensus pattern (16 bp):
ATACAAAAAAATAACA
Found at i:59703 original size:19 final size:19
Alignment explanation
Indices: 59679--59717 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
59669 ATATTACGAG
59679 AAAT-AATTGAAAAAAAAGA
1 AAATAAATT-AAAAAAAAGA
*
59698 AAATAAATTAAGAAAAAGA
1 AAATAAATTAAAAAAAAGA
59717 A
1 A
59718 TTTGAGAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (19 bp):
AAATAAATTAAAAAAAAGA
Found at i:59890 original size:17 final size:17
Alignment explanation
Indices: 59865--59900 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
59855 AATTTAAGTT
*
59865 AAAATTAAAAAATAAAA
1 AAAAGTAAAAAATAAAA
*
59882 AAAAGTAAAAGATAAAA
1 AAAAGTAAAAAATAAAA
59899 AA
1 AA
59901 TCAAACACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAGTAAAAAATAAAA
Found at i:60493 original size:21 final size:22
Alignment explanation
Indices: 60468--60512 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
60458 TGATCATTAA
*
60468 AAAATC-AAATATTGATACTTT
1 AAAATCTAAATATCGATACTTT
*
60489 AAAATCTAAGTATCGATACTTT
1 AAAATCTAAATATCGATACTTT
60511 AA
1 AA
60513 TACTTTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAATCTAAATATCGATACTTT
Found at i:64419 original size:277 final size:277
Alignment explanation
Indices: 63891--64446 Score: 724
Period size: 277 Copynumber: 2.0 Consensus size: 277
63881 ATGAGGCAAA
* * *
63891 ATTTGAATTATGAAGTTCAAAAGGTAGGTCAACCAAGTTAAAAAGGTAAAAAGAATGGTTTTGTC
1 ATTTGAATTATGAAGTTCAAAAGATAGGTCAAACAAGTTAAAAAGGTAAAAACAATGGTTTTGTC
* * *
63956 AAGTAAATAGTATTTTGAAATATTTGAAGCTCGGGTGAATTTTTTGTGGGGTGAAGGGAGTATTA
66 AAGTAAATAATATTTTGAAATATTTAAAGCTCGGGTGAATATTTTGTGGGGTGAAGGGAGTATTA
* * ** * **
64021 AGAGTTTGATAATGCTAAATGTTACTTAGGAACAAACAGTCCTCTACACAGATGGAAAATTAGTT
131 AGAGTCTGATAATGCTAAATATTAAGTAGGAACAAACAATCCTCTACACAGATGGAAAACCAGTT
* * * * *
64086 TTTTTATTATCCCAAAACTTTCAGACTATTCGATTAGCTTCCCTAATGTAGGTGGTACTCAAATT
196 CTTTTAATATCCCAAAACTTTCAGACTATTCAATTAGCTTACCTAATATAGGTGGTACTCAAATT
64151 AAAACATGTTTTAAGGC
261 AAAACATGTTTTAAGGC
* *
64168 ATTTGGATTATGAAGTTCAAAAGATAGGTCAAACAAGTTAAAAAGGTATAAACAATGGTTTTGTC
1 ATTTGAATTATGAAGTTCAAAAGATAGGTCAAACAAGTTAAAAAGGTAAAAACAATGGTTTTGTC
* * *
64233 AAGTAAATAATATTTTGAAATA-TTAAAGGTTTGGGTGGATATTTTGTGGGGTGAAGGGGGAG-A
66 AAGTAAATAATATTTTGAAATATTTAAA-GCTCGGGTGAATATTTTGTGGGGTGAA--GGGAGTA
* * ** * ** * *
64296 TTAAGGGTCTGCTCGTGCTAAATATTAAGTAGGGACAGTCAATCTTCTACACGGATGGAAAACCA
128 TTAAGAGTCTGATAATGCTAAATATTAAGTAGGAACAAACAATCCTCTACACAGATGGAAAACCA
* *
64361 G-TCTTTTAATATCCCAAAAC-TTCAGTCTATTCAATTAGCTTACCTCATATATGGTGGTACTCA
193 GTTCTTTTAATATCCCAAAACTTTCAGACTATTCAATTAGCTTACCTAATATA-GGTGGTACTCA
* *
64424 AATTTAAATATGTTTTAAGGC
257 AATTAAAACATGTTTTAAGGC
64445 AT
1 AT
64447 GGAATACTAT
Statistics
Matches: 239, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
276 30 0.13
277 153 0.64
278 51 0.21
279 5 0.02
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (277 bp):
ATTTGAATTATGAAGTTCAAAAGATAGGTCAAACAAGTTAAAAAGGTAAAAACAATGGTTTTGTC
AAGTAAATAATATTTTGAAATATTTAAAGCTCGGGTGAATATTTTGTGGGGTGAAGGGAGTATTA
AGAGTCTGATAATGCTAAATATTAAGTAGGAACAAACAATCCTCTACACAGATGGAAAACCAGTT
CTTTTAATATCCCAAAACTTTCAGACTATTCAATTAGCTTACCTAATATAGGTGGTACTCAAATT
AAAACATGTTTTAAGGC
Found at i:70144 original size:2 final size:2
Alignment explanation
Indices: 70137--70172 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
70127 GGGTTTGTTT
* *
70137 TG TG TG TG TG TG TG TG TG TG TG CG TG TG CG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
70173 AGAAATGTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.06, G:0.50, T:0.44
Consensus pattern (2 bp):
TG
Found at i:70451 original size:41 final size:40
Alignment explanation
Indices: 70367--70464 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 40
70357 TTACGTCGAG
* * *
70367 TTAAATTTAAATTATA-TTTAAATATAAAATTTAATTTTTT
1 TTAAATTT-ATTTATATTTTAAATATAAAATTTAAATTTAT
70407 TTAAATTTATTTATATTTATAAATA-AATAATTTAAATTTAT
1 TTAAATTTATTTATATTT-TAAATATAA-AATTTAAATTTAT
*
70448 TTAAATCTATTTATATT
1 TTAAATTTATTTATATT
70465 ATATTTTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
39 6 0.12
40 12 0.24
41 33 0.65
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (40 bp):
TTAAATTTATTTATATTTTAAATATAAAATTTAAATTTAT
Found at i:71377 original size:26 final size:25
Alignment explanation
Indices: 71327--71383 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
71317 TTAATTAAAA
* *
71327 AATATATAAATTAATTAGTCAAATT
1 AATATATAAATTAATGAATCAAATT
71352 AATATATTAAATTCAATGAATC-AATT
1 AATATA-TAAATT-AATGAATCAAATT
*
71378 TATATA
1 AATATA
71384 ATATATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 15 0.56
27 6 0.22
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (25 bp):
AATATATAAATTAATGAATCAAATT
Found at i:74612 original size:17 final size:17
Alignment explanation
Indices: 74590--74623 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
74580 AACAAATTTT
74590 GAAAAGACAAATACAAG
1 GAAAAGACAAATACAAG
**
74607 GAAAAGATGAATACAAG
1 GAAAAGACAAATACAAG
74624 ATGTGATAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.09, G:0.21, T:0.09
Consensus pattern (17 bp):
GAAAAGACAAATACAAG
Found at i:75883 original size:17 final size:17
Alignment explanation
Indices: 75861--75894 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
75851 AACAAATTTT
75861 GAAAAGACAAATACAAG
1 GAAAAGACAAATACAAG
**
75878 GAAAAGATGAATACAAG
1 GAAAAGACAAATACAAG
75895 ATGTGATAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.09, G:0.21, T:0.09
Consensus pattern (17 bp):
GAAAAGACAAATACAAG
Found at i:79790 original size:8 final size:8
Alignment explanation
Indices: 79777--79867 Score: 57
Period size: 8 Copynumber: 11.4 Consensus size: 8
79767 TCATGCAATT
79777 TATATTTA
1 TATATTTA
*
79785 TATATTTT
1 TATATTTA
79793 TATATATTA
1 TATAT-TTA
79802 TA-A-TTA
1 TATATTTA
*
79808 TAT-TTAA
1 TATATTTA
*
79815 AATA-TTA
1 TATATTTA
79822 TATATTTA
1 TATATTTA
79830 TATAAATTTTAA
1 TAT--A-TTT-A
*
79842 TATATTAA
1 TATATTTA
79850 TA-ATTTA
1 TATATTTA
*
79857 TATACTTA
1 TATATTTA
79865 TAT
1 TAT
79868 TATATTTATG
Statistics
Matches: 64, Mismatches: 9, Indels: 20
0.69 0.10 0.22
Matches are distributed among these distances:
6 5 0.08
7 15 0.23
8 29 0.45
9 6 0.09
10 2 0.03
11 3 0.05
12 4 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (8 bp):
TATATTTA
Found at i:79828 original size:37 final size:35
Alignment explanation
Indices: 79780--79867 Score: 106
Period size: 37 Copynumber: 2.5 Consensus size: 35
79770 TGCAATTTAT
* *
79780 ATTTATATATTTTTATATATTATAATTATATTTAA-A
1 ATTTATATATTTATATAAATTATAA-TATA-TTAATA
*
79816 ATATTATATATTTATATAAATTTTAATATATTAATA
1 AT-TTATATATTTATATAAATTATAATATATTAATA
*
79852 ATTTATATACTTATAT
1 ATTTATATATTTATAT
79868 TATATTTATG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 17 0.37
36 9 0.20
37 20 0.43
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (35 bp):
ATTTATATATTTATATAAATTATAATATATTAATA
Found at i:79835 original size:20 final size:20
Alignment explanation
Indices: 79796--79835 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
79786 ATATTTTTAT
*
79796 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
79816 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
79836 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:79844 original size:20 final size:19
Alignment explanation
Indices: 79784--79847 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
79774 ATTTATATTT
* *
79784 ATATATTTTTATATATTATA
1 ATATA-TTTTATAAATTTTA
*
79804 AT-TATATTTA-AAATATT-
1 ATATAT-TTTATAAATTTTA
79821 ATATATTTATATAAATTTTA
1 ATATATTT-TATAAATTTTA
79841 ATATATT
1 ATATATT
79848 AATAATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 4 0.11
18 10 0.29
19 12 0.34
20 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATATTTTATAAATTTTA
Found at i:81223 original size:67 final size:68
Alignment explanation
Indices: 81137--81270 Score: 180
Period size: 67 Copynumber: 2.0 Consensus size: 68
81127 TTCAAAAATC
* * * *
81137 TTACAAGATGTAATAACTTTATATATGCAAATAAATTTATC-ATTTTTATCCGAATTTAAAATTT
1 TTACAAGATGTAATAACTTTATACATGCAAATAAATTCATCAATTTTGATCCGAATTTAAAAATT
81201 AAT
66 AAT
* * * * *
81204 TTACAAGATTTGATAACTTTATACGTGTAAATATATTCATCAATTTTGATCCGAATTTAAAAATT
1 TTACAAGATGTAATAACTTTATACATGCAAATAAATTCATCAATTTTGATCCGAATTTAAAAATT
81269 AA
66 AA
81271 CTTAATCGAT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
67 34 0.60
68 23 0.40
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (68 bp):
TTACAAGATGTAATAACTTTATACATGCAAATAAATTCATCAATTTTGATCCGAATTTAAAAATT
AAT
Found at i:82410 original size:9 final size:9
Alignment explanation
Indices: 82396--82430 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
82386 TGGAGAAATA
82396 AAAAATAAT
1 AAAAATAAT
82405 AAAAATAAT
1 AAAAATAAT
*
82414 AAAATATAAA
1 AAAA-ATAAT
82424 AAAAATA
1 AAAAATA
82431 GGGAAAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATAAT
Found at i:82412 original size:16 final size:16
Alignment explanation
Indices: 82391--82430 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
82381 ATTTTTGGAG
82391 AAATAA-AAAATAATAA
1 AAATAATAAAAT-ATAA
82407 AAATAATAAAATATAA
1 AAATAATAAAATATAA
*
82423 AAAAAATA
1 AAATAATA
82431 GGGAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAATAATAAAATATAA
Found at i:82416 original size:19 final size:19
Alignment explanation
Indices: 82392--82430 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
82382 TTTTTGGAGA
*
82392 AATAAAAAATAATAAAAAT
1 AATAAAAAATAAAAAAAAT
*
82411 AATAAAATATAAAAAAAAT
1 AATAAAAAATAAAAAAAAT
82430 A
1 A
82431 GGGAAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
AATAAAAAATAAAAAAAAT
Found at i:83716 original size:2 final size:2
Alignment explanation
Indices: 83709--83759 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
83699 TGAAAAATGC
* *
83709 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT A- AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
83751 GT AT AT AT A
1 AT AT AT AT A
83760 AATTTACGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:83869 original size:124 final size:124
Alignment explanation
Indices: 83712--83957 Score: 474
Period size: 124 Copynumber: 2.0 Consensus size: 124
83702 AAAATGCATA
*
83712 TATATATATATATATATATATATACATACATATAATCATGTATATATAAATTTACGCAATAAAAA
1 TATATATATATATATATATACATACATACATATAATCATGTATATATAAATTTACGCAATAAAAA
*
83777 TTATATATTATACAAAAATATTGTATATGTTAGTATGTGCATATTTACTTATTATAATT
66 TTATATATTATACAAAAATATTATATATGTTAGTATGTGCATATTTACTTATTATAATT
83836 TATATATATATATATATATACATACATACATATAATCATGTATATATAAATTTACGCAATAAAAA
1 TATATATATATATATATATACATACATACATATAATCATGTATATATAAATTTACGCAATAAAAA
83901 TTATATATTATACAAAAATATTATATATGTTAGTATGTGCATATTTACTTATTATAA
66 TTATATATTATACAAAAATATTATATATGTTAGTATGTGCATATTTACTTATTATAA
83958 ATTTTTAATT
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 120 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (124 bp):
TATATATATATATATATATACATACATACATATAATCATGTATATATAAATTTACGCAATAAAAA
TTATATATTATACAAAAATATTATATATGTTAGTATGTGCATATTTACTTATTATAATT
Found at i:84869 original size:12 final size:12
Alignment explanation
Indices: 84852--84901 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
84842 TTGAGTTAGA
* *
84852 TTAAATTTAAGT
1 TTAAATTAAAAT
84864 TTAAATTAAAAT
1 TTAAATTAAAAT
*
84876 TTAAATTAAAAG
1 TTAAATTAAAAT
*
84888 TTAAAGT-AAAT
1 TTAAATTAAAAT
84899 TTA
1 TTA
84902 TTTAATTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
11 6 0.18
12 27 0.82
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
TTAAATTAAAAT
Found at i:85798 original size:7 final size:7
Alignment explanation
Indices: 85788--85819 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
85778 AAAATATTAA
85788 AATTTAT
1 AATTTAT
85795 AATTTAT
1 AATTTAT
85802 AATTTAT
1 AATTTAT
85809 AATTTAT
1 AATTTAT
85816 AATT
1 AATT
85820 ATTATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTAT
Found at i:85985 original size:2 final size:2
Alignment explanation
Indices: 85978--86007 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
85968 ATTAGTTTTA
85978 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
86008 TCACTGTTTT
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:86404 original size:18 final size:18
Alignment explanation
Indices: 86381--86419 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
86371 GAAAATATAA
* *
86381 AATTTTATATTATTTTTT
1 AATTTTATAATAATTTTT
*
86399 AATTTTTTAATAATTTTT
1 AATTTTATAATAATTTTT
86417 AAT
1 AAT
86420 ATTTTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
AATTTTATAATAATTTTT
Found at i:86417 original size:10 final size:9
Alignment explanation
Indices: 86394--86428 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
86384 TTTATATTAT
86394 TTTTTAAT-
1 TTTTTAATA
86402 TTTTTAATAA
1 TTTTTAAT-A
86412 TTTTTAATA
1 TTTTTAATA
86421 TTTTTAAT
1 TTTTTAAT
86429 TATATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 9 0.36
10 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTTAATA
Found at i:86450 original size:15 final size:15
Alignment explanation
Indices: 86432--86470 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
86422 TTTTAATTAT
*
86432 ATAATATTTAAAAAA
1 ATAATATATAAAAAA
* *
86447 ATAAAATATAAAAAT
1 ATAATATATAAAAAA
86462 ATAATATAT
1 ATAATATAT
86471 GTAATTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATATATAAAAAA
Found at i:86852 original size:20 final size:20
Alignment explanation
Indices: 86827--86867 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
86817 ATTATACAAT
86827 TAAAAGGATTAATATCTTAA
1 TAAAAGGATTAATATCTTAA
* *
86847 TAAAAGTATTAATGTCTTAA
1 TAAAAGGATTAATATCTTAA
86867 T
1 T
86868 TTTTTTTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (20 bp):
TAAAAGGATTAATATCTTAA
Found at i:86978 original size:15 final size:16
Alignment explanation
Indices: 86949--86978 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
86939 TAAGTATATA
86949 TTATTAAAACATATTT
1 TTATTAAAACATATTT
86965 TTATTAAAA-ATATT
1 TTATTAAAACATATT
86979 ATATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTAAAACATATTT
Found at i:86985 original size:16 final size:17
Alignment explanation
Indices: 86945--86985 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
86935 TATATAAGTA
86945 TATATTATTAAAACATAT
1 TATA-TATTAAAACATAT
*
86963 T-TTTATTAAAA-ATAT
1 TATATATTAAAACATAT
86978 TATATATT
1 TATATATT
86986 TTTATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 5 0.25
16 13 0.65
17 1 0.05
18 1 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATATTAAAACATAT
Found at i:87050 original size:21 final size:22
Alignment explanation
Indices: 86994--87051 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
86984 TTTTTATAAT
* *
86994 TTTTATTATATTAATAATTTATA
1 TTTTATT-TTTTAATAATATATA
*
87017 TTATATATATTTTAA-AATATATA
1 TT-T-TATTTTTTAATAATATATA
87040 TTTTATTTTTTA
1 TTTTATTTTTTA
87052 TTTCATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 8 0.28
22 1 0.03
23 11 0.38
24 6 0.21
25 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTATTTTTTAATAATATATA
Found at i:87060 original size:42 final size:41
Alignment explanation
Indices: 86926--87070 Score: 113
Period size: 41 Copynumber: 3.6 Consensus size: 41
86916 TTGTTTAAAT
* * * *
86926 TTAAAAATTTATATAAGTATATATTATTAAAACATAT-TTTTA
1 TTAATAATTTATATTA-TATATATT-TTAAAATATATATTATA
* * *
86968 TTAA-AA---ATATTATATAT-TTTTATAATTTTTATTATA
1 TTAATAATTTATATTATATATATTTTAAAATATATATTATA
*
87004 TTAATAATTTATATTATATATATTTTAAAATATATATTTTA
1 TTAATAATTTATATTATATATATTTTAAAATATATATTATA
** *
87045 TTTTTTATTTCATATTATATAATATT
1 TTAATAATTT-ATATTATAT-ATATT
87071 GCCACGTCTC
Statistics
Matches: 82, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
35 7 0.09
36 10 0.12
37 7 0.09
38 5 0.06
40 11 0.13
41 24 0.29
42 13 0.16
43 5 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (41 bp):
TTAATAATTTATATTATATATATTTTAAAATATATATTATA
Found at i:88453 original size:19 final size:18
Alignment explanation
Indices: 88424--88461 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
88414 TTACAGGACT
88424 TAAGATTAGTGATGGATA
1 TAAGATTAGTGATGGATA
*
88442 TAAGAGTTAGTGTTGGATA
1 TAAGA-TTAGTGATGGATA
88461 T
1 T
88462 GGGTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (18 bp):
TAAGATTAGTGATGGATA
Found at i:89930 original size:15 final size:15
Alignment explanation
Indices: 89912--89960 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
89902 CTATTTAATC
89912 TAATTTGATTTGAAT
1 TAATTTGATTTGAAT
** *
89927 TAATCAGA-TTAAATT
1 TAATTTGATTTGAA-T
89942 TAATTTGATTTGAAT
1 TAATTTGATTTGAAT
89957 TAAT
1 TAAT
89961 CAGATTAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (15 bp):
TAATTTGATTTGAAT
Found at i:89946 original size:30 final size:30
Alignment explanation
Indices: 89912--89969 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
89902 CTATTTAATC
89912 TAATTTGATTTGAATTAATCAGATTAAATT
1 TAATTTGATTTGAATTAATCAGATTAAATT
89942 TAATTTGATTTGAATTAATCAGATTAAA
1 TAATTTGATTTGAATTAATCAGATTAAA
89970 GATAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (30 bp):
TAATTTGATTTGAATTAATCAGATTAAATT
Done.