Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 18 of 333
Found at i:5240849 original size:18 final size:17
Alignment explanation
Indices: 5240828--5240870 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
5240818 ATGATCTTAA
5240828 TGATGATGATGTTGATAC
1 TGATGATGATGTTGAT-C
*
5240846 TGATGTTGATGTTGATC
1 TGATGATGATGTTGATC
5240863 TCGATGAT
1 T-GATGAT
5240871 TATACCCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (17 bp):
TGATGATGATGTTGATC
Found at i:5241457 original size:59 final size:60
Alignment explanation
Indices: 5241317--5241495 Score: 306
Period size: 60 Copynumber: 3.0 Consensus size: 60
5241307 CCAAAATTTG
5241317 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGG--ATTTTTGTTCTGAAATGGAAAATTC
*
5241379 ATTTCTTTTTTGTCAGTTTTATGTTTGTTGTTTGGATTTTTGTTCTGAAATGGAAAATTC
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTGTTCTGAAATGGAAAATTC
*
5241439 ATTTC-TTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTTGTTTTGAAATGGAAAA
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGA-TTTTTGTTCTGAAATGGAAAA
5241496 ACTAGTTTGT
Statistics
Matches: 113, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
59 29 0.26
60 50 0.44
62 34 0.30
ACGTcount: A:0.19, C:0.07, G:0.18, T:0.56
Consensus pattern (60 bp):
ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATTTTTGTTCTGAAATGGAAAATTC
Found at i:5243960 original size:289 final size:289
Alignment explanation
Indices: 5243441--5244155 Score: 1378
Period size: 289 Copynumber: 2.5 Consensus size: 289
5243431 CCAACCTTAT
5243441 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
5243506 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
*
5243571 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGTATATTTATATAACATTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
** *
5243636 TCTGATTTACTTATAAAAATTAAACTACGATTCTTTTTTGATATTATTATATTCAAATTACTATT
196 TCCAATTTACTTATAAAAATTAAACTACAATTCTTTTTTGATATTATTATATTCAAATTACTATT
5243701 TTTTATATTAATAATGTTTGATTTTAATA
261 TTTTATATTAATAATGTTTGATTTTAATA
5243730 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
5243795 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
5243860 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
131 AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
5243925 TCCAATTTACTTATAAAAATTAAACTACAATTCTTTTTTGATATTATTATATTCAAATTACTATT
196 TCCAATTTACTTATAAAAATTAAACTACAATTCTTTTTTGATATTATTATATTCAAATTACTATT
5243990 TTTTATATTAATAATGTTTGATTTTAATA
261 TTTTATATTAATAATGTTTGATTTTAATA
*
5244019 TTTAAATATTTTAAAGATTCAAATTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
1 TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
5244084 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTT-AAAAATTCAA
66 GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
5244148 AAAGACTT
131 AAAGACTT
5244156 TTTATCACAA
Statistics
Matches: 421, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
288 18 0.04
289 403 0.96
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (289 bp):
TTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCT
GCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTCAA
AAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATATTTATATAACATTAATTTATT
TCCAATTTACTTATAAAAATTAAACTACAATTCTTTTTTGATATTATTATATTCAAATTACTATT
TTTTATATTAATAATGTTTGATTTTAATA
Found at i:5244404 original size:15 final size:15
Alignment explanation
Indices: 5244360--5244415 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
5244350 AACGACATGT
*
5244360 ATATTACTTAATTAAA
1 ATATTATTTAATT-AA
5244376 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
5244389 ATATTATTTAATTAA
1 ATATTATTTAATTAA
5244404 ATATTATTTAAT
1 ATATTATTTAAT
5244416 CCCGCTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.09
13 7 0.20
14 2 0.06
15 16 0.46
16 4 0.11
17 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:5244560 original size:9 final size:9
Alignment explanation
Indices: 5244520--5244612 Score: 96
Period size: 9 Copynumber: 10.0 Consensus size: 9
5244510 TATTTGATAT
*
5244520 CATAATTTA
1 CATAACTTA
*
5244529 TATAACTTA
1 CATAACTTA
* *
5244538 CAAAACGTA
1 CATAACTTA
5244547 CATAACTTA
1 CATAACTTA
* *
5244556 TATAAATAAATA
1 CATAACT---TA
*
5244568 TATAACTTA
1 CATAACTTA
5244577 CATAACTTA
1 CATAACTTA
5244586 CATAACTTA
1 CATAACTTA
5244595 CATAACTTA
1 CATAACTTA
5244604 CATAACTTA
1 CATAACTTA
5244613 TATGTTGTCA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
9 62 0.89
12 8 0.11
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:5244584 original size:48 final size:49
Alignment explanation
Indices: 5244516--5244608 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 49
5244506 AATATATTTG
* * *
5244516 ATATCATAATTTATATAACTTACAAAACGTACATAACTTATATAAATAA
1 ATATCATAACTTACATAACTTACAAAACGTACATAACTTACATAAATAA
* *
5244565 ATAT-ATAACTTACATAACTTACATAACTTACATAACTTACATAA
1 ATATCATAACTTACATAACTTACAAAACGTACATAACTTACATAA
5244609 CTTATATGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 35 0.90
49 4 0.10
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.34
Consensus pattern (49 bp):
ATATCATAACTTACATAACTTACAAAACGTACATAACTTACATAAATAA
Found at i:5250384 original size:31 final size:31
Alignment explanation
Indices: 5250338--5250404 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
5250328 TGGTTGTATT
* *
5250338 TTTTATGTTAAATTTGCTGTTTTTGGCTGCA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
* * * *
5250369 TTTTATATTATATTTGTTGTATTTGGTTGGA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
5250400 TTTTA
1 TTTTA
5250405 ATGCAGGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTTATATTAAATTTGCTGTATTTGGCTGCA
Found at i:5250530 original size:43 final size:43
Alignment explanation
Indices: 5250456--5250636 Score: 272
Period size: 43 Copynumber: 4.2 Consensus size: 43
5250446 ATCTGCCAAA
**** * *
5250456 TTTAGCGGCGCTTTTTTTGCAAGCGCTGCTAAAAGCCTTGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACC
5250499 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACC
* * *
5250542 TTTAGCAGTGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACC
*
5250585 TTTACCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACC
5250628 TTTAGCGGC
1 TTTAGCGGC
5250637 ATTTTTTTCC
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 124 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACC
Found at i:5262899 original size:46 final size:46
Alignment explanation
Indices: 5262839--5263112 Score: 415
Period size: 46 Copynumber: 6.0 Consensus size: 46
5262829 TTTGACATGA
* * * * * *
5262839 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* *
5262885 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5262931 TGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5262977 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
5263023 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5263069 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5263113 AGAGCACACT
Statistics
Matches: 209, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 205 0.98
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:5265574 original size:30 final size:29
Alignment explanation
Indices: 5265540--5265607 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
5265530 CACCCTTAAA
* *
5265540 ATATTTACACTATTAGTCCATCAACTTTTC
1 ATATTTACACT-TTAATCCATCAAATTTTC
* *
5265570 ATATTTACACTTTAATCCTTCAAATTTTG
1 ATATTTACACTTTAATCCATCAAATTTTC
5265599 AGTATTTAC
1 A-TATTTAC
5265608 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (29 bp):
ATATTTACACTTTAATCCATCAAATTTTC
Found at i:5267935 original size:20 final size:20
Alignment explanation
Indices: 5267894--5267936 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5267884 TTACCCCAAA
*
5267894 CCCCCAAACTTTATTACTTT
1 CCCCCAAACTTTATTACCTT
5267914 CCCCCAATACTTTATT-CCTT
1 CCCCCAA-ACTTTATTACCTT
5267934 CCC
1 CCC
5267937 ACTTTTCCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (20 bp):
CCCCCAAACTTTATTACCTT
Found at i:5268069 original size:22 final size:19
Alignment explanation
Indices: 5268044--5268092 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
5268034 TTTCCTCCCA
5268044 TTTACTTTCCCCTCAAAAACTT
1 TTTACTTTCCCC-C-AAAAC-T
* *
5268066 TTTATTTTCCCCCTAAACT
1 TTTACTTTCCCCCAAAACT
5268085 TTTACTTT
1 TTTACTTT
5268093 TCACCCTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.33
20 4 0.17
21 1 0.04
22 11 0.46
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTACTTTCCCCCAAAACT
Found at i:5268093 original size:20 final size:20
Alignment explanation
Indices: 5268060--5268099 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5268050 TTCCCCTCAA
*
5268060 AAACTTTTTATTTTCCCCCT
1 AAACTTTTTATTTTCACCCT
5268080 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTA-TTTTCACCCT
5268100 TTCCCCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
AAACTTTTTATTTTCACCCT
Found at i:5268347 original size:18 final size:18
Alignment explanation
Indices: 5268324--5268395 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
5268314 CAATTTCATA
*
5268324 TTTTATTTTTAATATAAT
1 TTTTATTTTTAATATATT
*** *
5268342 TTTTATTAAAAATCACATT
1 TTTTATTTTTAAT-ATATT
*
5268361 TTTTATATTTAATATATT
1 TTTTATTTTTAATATATT
* *
5268379 TTTTAATTTTAAAATAT
1 TTTTATTTTTAATATAT
5268396 ATAGTGACAA
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
18 28 0.70
19 12 0.30
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATTTTTAATATATT
Found at i:5277591 original size:8 final size:8
Alignment explanation
Indices: 5277578--5277642 Score: 53
Period size: 8 Copynumber: 8.1 Consensus size: 8
5277568 GGCCCATCCG
5277578 TATTATTT
1 TATTATTT
5277586 TATTATTT
1 TATTATTT
*
5277594 TA-AATATT
1 TATTAT-TT
*
5277602 TA-TATTA
1 TATTATTT
5277609 TATTATTT
1 TATTATTT
*
5277617 TAATATTT
1 TATTATTT
* *
5277625 AATAATTT
1 TATTATTT
5277633 TATATATTT
1 TAT-TATTT
5277642 T
1 T
5277643 TATATAATCA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
7 5 0.11
8 34 0.77
9 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TATTATTT
Found at i:5277607 original size:23 final size:23
Alignment explanation
Indices: 5277581--5277647 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
5277571 CCATCCGTAT
5277581 TATTTTATTATTTTAAATATTT-A
1 TATTTTATTATTTT-AATATTTAA
*
5277604 TATTATATTATTTTAATATTTAA
1 TATTTTATTATTTTAATATTTAA
*
5277627 TAATTTTATATATTTTTATAT
1 T-ATTTTAT-TATTTTAATAT
5277648 AATCATCTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 7 0.18
23 15 0.39
24 6 0.16
25 10 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTTATTATTTTAATATTTAA
Found at i:5277616 original size:31 final size:31
Alignment explanation
Indices: 5277578--5277637 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
5277568 GGCCCATCCG
* *
5277578 TATTATTTTATTATTTTA-AATATTTATATTA
1 TATTATTTTAATATTTAATAAT-TTTATATTA
5277609 TATTATTTTAATATTTAATAATTTTATAT
1 TATTATTTTAATATTTAATAATTTTATAT
5277638 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
TATTATTTTAATATTTAATAATTTTATATTA
Found at i:5279495 original size:17 final size:17
Alignment explanation
Indices: 5279462--5279511 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
5279452 AGATGACTAT
*
5279462 ATAAAAAATTTCA-AAAA
1 ATAAAAAATAT-ATAAAA
5279479 ATAAAAAATATATAAAA
1 ATAAAAAATATATAAAA
**
5279496 ATATTAAATAT-TAAAA
1 ATAAAAAATATATAAAA
5279512 TAATATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 6 0.21
17 23 0.79
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAAATATATAAAA
Found at i:5279516 original size:28 final size:29
Alignment explanation
Indices: 5279445--5279518 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 29
5279435 ACATTAAAAT
* *
5279445 AATATTAAGATGACTATATAAAAAATTTCA
1 AATATTAAAAT-AATATATAAAAAATTTCA
* *
5279475 AAAAATAAAA-AATATAT-AAAAATATT-A
1 AATATTAAAATAATATATAAAAAAT-TTCA
5279502 AATATTAAAATAATATA
1 AATATTAAAATAATATA
5279519 ATATAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
27 15 0.42
28 14 0.39
30 7 0.19
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (29 bp):
AATATTAAAATAATATATAAAAAATTTCA
Found at i:5285077 original size:21 final size:22
Alignment explanation
Indices: 5285035--5285095 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
5285025 GAACTGGTTT
*
5285035 ATTTTTTATTTAATTT-ATAAT-A
1 ATTTTTTA--TAATTTAAAAATAA
5285057 ATTTTTTATAATTTAAAAATAA
1 ATTTTTTATAATTTAAAAATAA
*
5285079 ATATTTTAT-ATTTAAAA
1 ATTTTTTATAATTTAAAA
5285096 TAGTGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 6 0.17
21 12 0.34
22 17 0.49
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTTATAATTTAAAAATAA
Found at i:5285097 original size:20 final size:20
Alignment explanation
Indices: 5285043--5285097 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
5285033 TTATTTTTTA
* *
5285043 TTTA-ATTTATAAT-AATTT
1 TTTATATTTAAAATAAATAT
5285061 TTTATAATTTAAAAATAAATAT
1 TTTAT-ATTT-AAAATAAATAT
5285083 TTTATATTTAAAATA
1 TTTATATTTAAAATA
5285098 GTGAAAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 4 0.13
20 10 0.32
21 8 0.26
22 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATATTTAAAATAAATAT
Found at i:5285749 original size:17 final size:17
Alignment explanation
Indices: 5285725--5285763 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5285715 ATCCTTCACT
*
5285725 CTTTTTTTTTGTTTT-A
1 CTTTTTTTTAGTTTTAA
5285741 CTTTATTTTTAGTTTTAA
1 CTTT-TTTTTAGTTTTAA
5285759 CTTTT
1 CTTTT
5285764 AAAAGTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 11 0.55
18 5 0.25
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTTTTTTAGTTTTAA
Found at i:5286634 original size:60 final size:60
Alignment explanation
Indices: 5286553--5286706 Score: 227
Period size: 60 Copynumber: 2.6 Consensus size: 60
5286543 ATTCTCAACG
* * * *
5286553 TTTATAAAATTGATCATTTTAGTTCGAATTCTAAAAATTTAATAAATTTAACCCTTAATA
1 TTTATAAAATTTATCAATTTAGTTCGAATTCTAAAAATTTAATAAATTAAACCCTCAATA
* * * *
5286613 TTTATAAAATTTATCAATTTAGTTTGAACTCTAAAGATTTAATAAATTAAACTCTCAATA
1 TTTATAAAATTTATCAATTTAGTTCGAATTCTAAAAATTTAATAAATTAAACCCTCAATA
*
5286673 TTTATAAAATTTATCAATTTAGTTCTAATTCTAA
1 TTTATAAAATTTATCAATTTAGTTCGAATTCTAA
5286707 GTTGACATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 83 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.44
Consensus pattern (60 bp):
TTTATAAAATTTATCAATTTAGTTCGAATTCTAAAAATTTAATAAATTAAACCCTCAATA
Found at i:5293956 original size:36 final size:36
Alignment explanation
Indices: 5293904--5293990 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
5293894 CCCAACTACT
* *
5293904 GTATACGTGAACAGTACTATATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTATATACGTAAATAGTGCC
* *
5293940 GTATATGTGAATAGTACTGTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACTATATACGTAAATAGTGCC
5293976 GTATACGTGAATAGT
1 GTATACGTGAATAGT
5293991 GCCGTAAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (36 bp):
GTATACGTGAATAGTACTATATACGTAAATAGTGCC
Found at i:5293991 original size:18 final size:18
Alignment explanation
Indices: 5293904--5293996 Score: 114
Period size: 18 Copynumber: 5.2 Consensus size: 18
5293894 CCCAACTACT
* * *
5293904 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTGCC
*
5293922 ATATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
* * *
5293940 GTATATGTGAATAGTACT
1 GTATACGTGAATAGTGCC
*
5293958 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTGCC
5293976 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
5293994 GTA
1 GTA
5293997 AACGGTCGTA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTGCC
Found at i:5303491 original size:23 final size:24
Alignment explanation
Indices: 5303448--5303497 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
5303438 TAAGATGAGT
*
5303448 ATATATAAATTTTAATAAAAAA-A
1 ATATATAAATTTAAATAAAAAAGA
*
5303471 ATAT-TAAATATTAAATTAAAAAGA
1 ATATATAAAT-TTAAATAAAAAAGA
5303495 ATA
1 ATA
5303498 AAAATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 14 0.61
24 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
ATATATAAATTTAAATAAAAAAGA
Found at i:5304631 original size:19 final size:18
Alignment explanation
Indices: 5304600--5304642 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
5304590 CTATATTTTC
*
5304600 ATAAAATAAATTTACTTA
1 ATAAAATAAATTTAATTA
*
5304618 CTAAAATGAAATTTAATTA
1 ATAAAAT-AAATTTAATTA
5304637 ATAAAA
1 ATAAAA
5304643 ATATCAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATTTAATTA
Found at i:5313021 original size:63 final size:62
Alignment explanation
Indices: 5312919--5313127 Score: 224
Period size: 63 Copynumber: 3.3 Consensus size: 62
5312909 CAGGGACACG
* * *
5312919 GGCGTGTGCCCAAGCCGTGTAACTCACTGTTTGTA-GTATAAAAACCACATGGCTAGGTATATA
1 GGCGTGTGCCCAAGCCGTGTAACTCATTGTTTG-AGGTATAAAAACCACATGGCAAGG-ACATA
* * * * * *
5312982 GGCGTGTGCCCAGGCTGTGTAACTCATTGTTTGAGGTATAAAAACCACACAGCCAAAGACACA
1 GGCGTGTGCCCAAGCCGTGTAACTCATTGTTTGAGGTATAAAAACCACA-TGGCAAGGACATA
* * * * *
5313045 GGCGTGTGCCCAGGCCGTGTATCTCATTGTTTGTGCT-TAAAAACCACATGGCCAAGGCACATG
1 GGCGTGTGCCCAAGCCGTGTAACTCATTGTTTGAGGTATAAAAACCACATGG-CAAGG-ACATA
*
5313108 GGCGTGTGCCCAAGCTGTGT
1 GGCGTGTGCCCAAGCCGTGT
5313128 TGCAGGATGT
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
61 1 0.01
62 16 0.13
63 101 0.83
64 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (62 bp):
GGCGTGTGCCCAAGCCGTGTAACTCATTGTTTGAGGTATAAAAACCACATGGCAAGGACATA
Found at i:5317194 original size:132 final size:132
Alignment explanation
Indices: 5317017--5317401 Score: 431
Period size: 132 Copynumber: 2.9 Consensus size: 132
5317007 AAAGTATGAG
* * *
5317017 TGAAGTTCTAAAGGAATC-TTCGATCATTTTG-GACAAAC-AGAAAATTGCAACCCAGCACATTA
1 TGAAATTCTAAAGGAA-CATTCGATTATTTTGAG-CAAACGAG-AAATTGCAACCCAGCACGTTA
* * * * * *
5317079 GGGTACGATTACC-CGAATTGCCTAACT-TCGAATATTACCTTCGTTTTGAA-GAGTTTTTAGAA
63 GGGCACGATT-CCGCGAATTGCC-AAATATCGAACATCACCCTCGTTTTAAAGGA-TTTTTAGAA
5317141 AACATAAA
125 AACATAAA
*
5317149 TGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGTTAGGG
1 TGAAATTCTAAAGGAACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGTTAGGG
* * * * * *
5317214 CACGATTCCGCGAATTGTCAAATATTGAACATCGCCCTCGTTTTAAAGGATTTTTAGGAGACATG
66 CACGATTCCGCGAATTGCCAAATATCGAACATCACCCTCGTTTTAAAGGATTTTTAGAAAACATA
*
5317279 AG
131 AA
* * * *
5317281 TGAAATTTTGAAGGAATATTCGATTATTTTGAGCAAACGAGAAATTGCAAGCCAGCACGTTAGGG
1 TGAAATTCTAAAGGAACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGTTAGGG
* * * * * *
5317346 CATGATTTCGCGAATTGTCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTA
66 CACGATTCCGCGAATTGCCAAATATCGAACATCACCCTCGTTTTAAAGGATTTTTA
5317402 AACGAATAAT
Statistics
Matches: 220, Mismatches: 27, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
131 6 0.03
132 209 0.95
133 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (132 bp):
TGAAATTCTAAAGGAACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGTTAGGG
CACGATTCCGCGAATTGCCAAATATCGAACATCACCCTCGTTTTAAAGGATTTTTAGAAAACATA
AA
Found at i:5318014 original size:21 final size:20
Alignment explanation
Indices: 5317974--5318014 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5317964 ATGTTGTGAA
* *
5317974 AAAATAAAAAAATAATAAAT
1 AAAATAAAAAAACAACAAAT
5317994 AAAATAAAAAAACACACAAAT
1 AAAATAAAAAAACA-ACAAAT
5318015 TTTACGTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAATAAAAAAACAACAAAT
Found at i:5322445 original size:13 final size:13
Alignment explanation
Indices: 5322427--5322451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5322417 ATTTGTGAAA
5322427 AAATAAAATAAAT
1 AAATAAAATAAAT
5322440 AAATAAAATAAA
1 AAATAAAATAAA
5322452 GAACACACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:5325485 original size:133 final size:133
Alignment explanation
Indices: 5325247--5325553 Score: 364
Period size: 133 Copynumber: 2.3 Consensus size: 133
5325237 AGGTTTGTTC
* * * * *
5325247 TCTTCGATCTTCTCCACTGGAACTTCAGGGAGACAAGATCTGCAATCTTTAGCCTACTCCTCTAC
1 TCTTCGATCTACTCCACTGGAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
* * *
5325312 AACTTTAAGGAGATAGGGTGTTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACATGATTCG
66 AACTTTAAGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACACGATTCG
5325377 CCA
131 CCA
* * * * * *
5325380 TCTTCGATCTACTCTATTGTAACTTTAGGGAAATAAGATTTACAATCTTCAGCCTACTCCACTAC
1 TCTTCGATCTACTCCACTGGAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
* * * *
5325445 AACTTT-AGGAAGCTAGGATGGTGGTTTAAATCTGCTTCACTGCAATTTTAGGAAGACACGATTC
66 AACTTTAAGG-AGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACACGATTC
* *
5325509 GTCG
130 GCCA
* ** * * *
5325513 TCGTCGATCCGCTCTACTGCAACTTCAGGGAGACAAGATCT
1 TCTTCGATCTACTCCACTGGAACTTCAGGGAAACAAGATCT
5325554 GTAGAATTCA
Statistics
Matches: 144, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
132 3 0.02
133 141 0.98
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (133 bp):
TCTTCGATCTACTCCACTGGAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
AACTTTAAGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACACGATTCG
CCA
Found at i:5336968 original size:132 final size:132
Alignment explanation
Indices: 5336806--5337191 Score: 446
Period size: 132 Copynumber: 2.9 Consensus size: 132
5336796 AAAGTATGAG
* *
5336806 TGAAATTCTAAAGGAATC-TTCGATCATTTTGGACAAAC-AGAAAATTGCAACCCAGCACATTAG
1 TGAAATTCTAAAGGAA-CATTCGATTATTTTGGACAAACGAG-AAATTGCAACCCAGCACGTTAG
* * * * * *
5336869 GGTACGATTACC-CGAATTGCCAAACT-TCGAATATTACCTTCATTTTGAAGAGTTTTT-AGAAA
64 GGCACGATT-CCGCGAATTGTCAAA-TATCGAACATCACCTTCGTTTTAAAGAGTTTTTAAG-AA
*
5336931 ACGTAAA
126 ACATAAA
* * *
5336938 TGAAATTCTAAAGGGACATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCATGTTAGGG
1 TGAAATTCTAAAGGAACATTCGATTATTTTGGACAAACGAGAAATTGCAACCCAGCACGTTAGGG
* * * *
5337003 CACAATTCCGCGAATTGTCAAATATCGAACATCGCCCTCGTTTTAAAG-GATTTTTAAGAGACAT
66 CACGATTCCGCGAATTGTCAAATATCGAACATCACCTTCGTTTTAAAGAG-TTTTTAAGAAACAT
* *
5337067 GAG
130 AAA
* * *
5337070 TGAAAATT-TGAAGGAATATTCGATTATTTT-GAGCAAACGAGAAATTGCAACTCAGCACGTTAG
1 TG-AAATTCTAAAGGAACATTCGATTATTTTGGA-CAAACGAGAAATTGCAACCCAGCACGTTAG
*
5337133 GGCACGATTCCGCGAATTGTCAAATATCGAACATCACCTTCGTTTTAAAGAATTTTTAA
64 GGCACGATTCCGCGAATTGTCAAATATCGAACATCACCTTCGTTTTAAAGAGTTTTTAA
5337192 ACGAATAATT
Statistics
Matches: 217, Mismatches: 28, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
131 6 0.03
132 202 0.93
133 9 0.04
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (132 bp):
TGAAATTCTAAAGGAACATTCGATTATTTTGGACAAACGAGAAATTGCAACCCAGCACGTTAGGG
CACGATTCCGCGAATTGTCAAATATCGAACATCACCTTCGTTTTAAAGAGTTTTTAAGAAACATA
AA
Found at i:5339872 original size:22 final size:22
Alignment explanation
Indices: 5339847--5339890 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5339837 GGGCTGTAGG
5339847 GTATTAGTTATGTAGTTGGGTT
1 GTATTAGTTATGTAGTTGGGTT
5339869 GTATTAGTTATGTAGTTGGGTT
1 GTATTAGTTATGTAGTTGGGTT
5339891 ATGTAATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (22 bp):
GTATTAGTTATGTAGTTGGGTT
Found at i:5348079 original size:363 final size:363
Alignment explanation
Indices: 5347411--5348139 Score: 1352
Period size: 363 Copynumber: 2.0 Consensus size: 363
5347401 TGTTCAAATC
* *
5347411 TCACTCTTAAAAATTGTTGCTATTTTTGTTCCTATCTTTATCTTTAATCATTTGACTTAAATTGT
1 TCACTCTTAAAAATTGTTGCTATTTTTGTTCCTATCTTTATCTTTAATCATTTGACATAAATTCT
5347476 ATTTCCCTCAATTTGTAATAGAATGAGCTTGTTGATTTAGTGGTAAGGTGTTAGCTTGCTCTTTG
66 ATTTCCCTCAATTTGTAATAGAATGAGCTTGTTGATTTAGTGGTAAGGTGTTAGCTTGCTCTTTG
5347541 GTCTTGTGTTTGAATCACTGCTTGAGCAAAATGAGATTATTTTTGCTATTTCTCATGTTTGTGCG
131 GTCTTGTGTTTGAATCACTGCTTGAGCAAAATGAGATTATTTTTGCTATTTCTCATGTTTGTGCG
* **
5347606 TCCAAGTGTCAGATATTGAATTTAATTCAAATATTGGATTAAGCTGTTAAGTGGTGGTTAGAAGA
196 TCCAAGTGTCAGATATTGAATTTAATTCAAATATTGGATTAAGCTATTAAGTGACGGTTAGAAGA
5347671 CTAGTTTGGTTAGGATTTAGTTATTTCTTAGAAAAAAAATTTGAAAATTGATTGATTGAAAATAA
261 CTAGTTTGGTTAGGATTTAGTTATTTCTTAGAAAAAAAATTTGAAAATTGATTGATTGAAAATAA
5347736 AAAGATTTTTAATCCCCACTTTTCTCTCCGACACTATT
326 AAAGATTTTTAATCCCCACTTTTCTCTCCGACACTATT
*
5347774 TCACTCTTAGAAATTGTTGCTATTTTTGTTCCTATCTTTATCTTTAAGT-ATTTGACATAAATTC
1 TCACTCTTAAAAATTGTTGCTATTTTTGTTCCTATCTTTATCTTTAA-TCATTTGACATAAATTC
*
5347838 TATTTCCCTCAATTTGTAATAGAATGAGCTTGTTGGTTTAGTGGTAAGGTGTTAGCTTGCTCTTT
65 TATTTCCCTCAATTTGTAATAGAATGAGCTTGTTGATTTAGTGGTAAGGTGTTAGCTTGCTCTTT
*
5347903 GGTCTTGTGTTTGAATCACTGCTTGAGCAAAATGAGATTATTTTTGCTGTTTCTCATGTTTGTGC
130 GGTCTTGTGTTTGAATCACTGCTTGAGCAAAATGAGATTATTTTTGCTATTTCTCATGTTTGTGC
5347968 GTCCAAGTGTCAGATATTGAATTTAATTCAAATATTGGATTAAGCTATTAAGTGACGGTTAGAAG
195 GTCCAAGTGTCAGATATTGAATTTAATTCAAATATTGGATTAAGCTATTAAGTGACGGTTAGAAG
*
5348033 ACTAGTTTGGTTAGGATTTAGTTATTTCTTAGAAAAAAATTTTGAAAATTGATTGATTGAAAATA
260 ACTAGTTTGGTTAGGATTTAGTTATTTCTTAGAAAAAAAATTTGAAAATTGATTGATTGAAAATA
*
5348098 AAAAGATTTTTAATCCCCACTTTTCTCTCTGACACTATT
325 AAAAGATTTTTAATCCCCACTTTTCTCTCCGACACTATT
5348137 TCA
1 TCA
5348140 TGTCCCTTTT
Statistics
Matches: 355, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
363 354 1.00
364 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (363 bp):
TCACTCTTAAAAATTGTTGCTATTTTTGTTCCTATCTTTATCTTTAATCATTTGACATAAATTCT
ATTTCCCTCAATTTGTAATAGAATGAGCTTGTTGATTTAGTGGTAAGGTGTTAGCTTGCTCTTTG
GTCTTGTGTTTGAATCACTGCTTGAGCAAAATGAGATTATTTTTGCTATTTCTCATGTTTGTGCG
TCCAAGTGTCAGATATTGAATTTAATTCAAATATTGGATTAAGCTATTAAGTGACGGTTAGAAGA
CTAGTTTGGTTAGGATTTAGTTATTTCTTAGAAAAAAAATTTGAAAATTGATTGATTGAAAATAA
AAAGATTTTTAATCCCCACTTTTCTCTCCGACACTATT
Found at i:5349680 original size:43 final size:43
Alignment explanation
Indices: 5349626--5349713 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
5349616 AATAACAACA
* *
5349626 TAATTTGATCCATTTCATGCAATTGAGTCCTTTTTGGTAAATT
1 TAATTTAATCCATTTCATGCAATTGAGTCCTTTTAGGTAAATT
5349669 TAATTTAATCCATTTCATGCAATTGAGTCCTTTTAGGTAAATT
1 TAATTTAATCCATTTCATGCAATTGAGTCCTTTTAGGTAAATT
5349712 TA
1 TA
5349714 CATATTTACC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.45
Consensus pattern (43 bp):
TAATTTAATCCATTTCATGCAATTGAGTCCTTTTAGGTAAATT
Found at i:5359282 original size:14 final size:15
Alignment explanation
Indices: 5359263--5359291 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5359253 TTGTTCTTTA
5359263 TTAAAA-TTCTATAT
1 TTAAAATTTCTATAT
5359277 TTAAAATTTCTATAT
1 TTAAAATTTCTATAT
5359292 CTTCTCTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAAATTTCTATAT
Found at i:5360604 original size:24 final size:26
Alignment explanation
Indices: 5360568--5360620 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
5360558 TATTTCATTA
**
5360568 TATCCTATTATTT-TTTTAGT-TTTT
1 TATCCTACCATTTATTTTAGTATTTT
*
5360592 TATCCTACCATTTATTTTATTATTTT
1 TATCCTACCATTTATTTTAGTATTTT
5360618 TAT
1 TAT
5360621 TATACTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.46
25 6 0.25
26 7 0.29
ACGTcount: A:0.21, C:0.11, G:0.02, T:0.66
Consensus pattern (26 bp):
TATCCTACCATTTATTTTAGTATTTT
Found at i:5365007 original size:21 final size:21
Alignment explanation
Indices: 5364981--5365025 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5364971 GAGGGATCAA
*
5364981 ATGCTGGAGTCCCAGAAAAAC
1 ATGCTGGAGTCACAGAAAAAC
*
5365002 ATGCTGGAGTCACAGAACAAC
1 ATGCTGGAGTCACAGAAAAAC
5365023 ATG
1 ATG
5365026 ATGAGCCAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (21 bp):
ATGCTGGAGTCACAGAAAAAC
Found at i:5368555 original size:25 final size:25
Alignment explanation
Indices: 5368521--5368572 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
5368511 GCCAGCCCAA
5368521 AGGATAACTTTTCATTGCCTCACAT
1 AGGATAACTTTTCATTGCCTCACAT
5368546 AGGATAACTTTTCATTGCCTCACAT
1 AGGATAACTTTTCATTGCCTCACAT
5368571 AG
1 AG
5368573 ACACTCTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (25 bp):
AGGATAACTTTTCATTGCCTCACAT
Found at i:5372526 original size:135 final size:135
Alignment explanation
Indices: 5372286--5372646 Score: 460
Period size: 135 Copynumber: 2.7 Consensus size: 135
5372276 GATTACAGAT
* *
5372286 ATCATCAGCCTTATCTTCACTGGGCAGGAGTGGAGCAGGCT-AA-ATACCAGATCTTATCTTCAT
1 ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* * * *
5372349 TGAGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
66 TGAGCAGGAGCGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGGACCGACAATGGAGCAGA
5372414 TTCCA
131 TTCCA
* *
5372419 ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGGTCTTATCTTCAC
1 ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* * * * *
5372484 TGAACAGGAGCGGAGCAGATCAAATTTTGGTGAATCTTATCTCCATGGATCGACAATGGAGCAGA
66 TGAGCAGGAGCGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGGACCGACAATGGAGCAGA
*
5372549 TTTCA
131 TTCCA
** * * * * *
5372554 GCCACCAG-TCTTATCTTCACTGAGCAGGAGTGAAGCA-GATCAAATTATAGCAAATCTTATCTT
1 ATCATCAGCT-TTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAA-TATACCAGATCTTATCTT
* *
5372617 CGTTGAGCAGGAGCGAAGCAGATCAGATTT
63 CATTGAGCAGGAGCGAAGCAGATCAAATTT
5372647 CAGCAGATCC
Statistics
Matches: 196, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
133 39 0.20
134 5 0.03
135 112 0.57
136 40 0.20
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (135 bp):
ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
TGAGCAGGAGCGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGGACCGACAATGGAGCAGA
TTCCA
Found at i:5379455 original size:34 final size:34
Alignment explanation
Indices: 5379412--5379480 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
5379402 GATAATATAC
*
5379412 ATGTATTCATATATCATCCATATGTTTTATTTAT
1 ATGTATTCATATATCATACATATGTTTTATTTAT
*
5379446 ATGTATTCATATATCGTACATATGTTTTATTTAT
1 ATGTATTCATATATCATACATATGTTTTATTTAT
5379480 A
1 A
5379481 CTTTCATACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.52
Consensus pattern (34 bp):
ATGTATTCATATATCATACATATGTTTTATTTAT
Found at i:5380444 original size:64 final size:64
Alignment explanation
Indices: 5380343--5380466 Score: 248
Period size: 64 Copynumber: 1.9 Consensus size: 64
5380333 TCTCCCACTA
5380343 ATAACATATATATAATCTTAATTAATTAGTTAATTAGCCTTTAATTAAATTGATCAATGGACTC
1 ATAACATATATATAATCTTAATTAATTAGTTAATTAGCCTTTAATTAAATTGATCAATGGACTC
5380407 ATAACATATATATAATCTTAATTAATTAGTTAATTAGCCTTTAATTAAATTGATCAATGG
1 ATAACATATATATAATCTTAATTAATTAGTTAATTAGCCTTTAATTAAATTGATCAATGG
5380467 CCATCATTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (64 bp):
ATAACATATATATAATCTTAATTAATTAGTTAATTAGCCTTTAATTAAATTGATCAATGGACTC
Found at i:5392266 original size:7 final size:7
Alignment explanation
Indices: 5392256--5392295 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
5392246 TTAGAGTCTG
5392256 AGGTTTA
1 AGGTTTA
5392263 AGGTTTA
1 AGGTTTA
*
5392270 GGGTTTA
1 AGGTTTA
*
5392277 AAGTTTA
1 AGGTTTA
5392284 AGGTTTA
1 AGGTTTA
5392291 AGGTT
1 AGGTT
5392296 CAGATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (7 bp):
AGGTTTA
Found at i:5392268 original size:21 final size:21
Alignment explanation
Indices: 5392244--5392290 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5392234 GAAGTTCAGA
* *
5392244 GTTTAGAGTCTGAGGTTTAAG
1 GTTTAGAGTCTAAAGTTTAAG
* *
5392265 GTTTAGGGTTTAAAGTTTAAG
1 GTTTAGAGTCTAAAGTTTAAG
5392286 GTTTA
1 GTTTA
5392291 AGGTTCAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.43
Consensus pattern (21 bp):
GTTTAGAGTCTAAAGTTTAAG
Found at i:5395257 original size:20 final size:21
Alignment explanation
Indices: 5395232--5395274 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
5395222 TACATGGAGG
* *
5395232 TTCTTTTTTTTC-CTTTTTAA
1 TTCTTTTTTCTCAATTTTTAA
5395252 TTCTTTTTTCTCAATTTTTAA
1 TTCTTTTTTCTCAATTTTTAA
5395273 TT
1 TT
5395275 TGCATTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (21 bp):
TTCTTTTTTCTCAATTTTTAA
Found at i:5397658 original size:17 final size:18
Alignment explanation
Indices: 5397626--5397660 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5397616 TTGTTTTTTT
5397626 TAAATATATAAAATTTAA
1 TAAATATATAAAATTTAA
*
5397644 TAAAT-TATAATATTTAA
1 TAAATATATAAAATTTAA
5397661 ACTAATAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATATATAAAATTTAA
Found at i:5400270 original size:11 final size:11
Alignment explanation
Indices: 5400254--5400278 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5400244 AAGAAAGGGG
5400254 GAAAGAGAAGA
1 GAAAGAGAAGA
5400265 GAAAGAGAAGA
1 GAAAGAGAAGA
5400276 GAA
1 GAA
5400279 GAAGAAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (11 bp):
GAAAGAGAAGA
Found at i:5400441 original size:27 final size:27
Alignment explanation
Indices: 5400388--5400443 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
5400378 TAATATTTTT
* *
5400388 TTTAAGGAAATAATTGTTAATTGTTAA
1 TTTAAGGAAATAAATGTTAATTATTAA
*
5400415 TTTAAGGAAATAAATGATTTA-TATTAA
1 TTTAAGGAAATAAATG-TTAATTATTAA
5400442 TT
1 TT
5400444 GTTAATGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (27 bp):
TTTAAGGAAATAAATGTTAATTATTAA
Found at i:5400643 original size:11 final size:11
Alignment explanation
Indices: 5400627--5400657 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5400617 GTACAAAAAA
5400627 TATTTTATTAT
1 TATTTTATTAT
5400638 TATTTTATTAT
1 TATTTTATTAT
5400649 TATTTTATT
1 TATTTTATT
5400658 TAATTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:5401008 original size:146 final size:146
Alignment explanation
Indices: 5400820--5402133 Score: 1796
Period size: 146 Copynumber: 9.1 Consensus size: 146
5400810 AAAAAATCCA
* * * * *
5400820 AAAATAAAATAAAAAAGGCCAAAATCAGAGTTTTTTATTAAATTAATATAAATATACTAAAATAA
1 AAAATAAAA-AAAAACGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAAACTAAAATAA
* * *
5400885 TACATATGAAACATTATGAACTAAAATAATA-AAAAAATAAAATACGAAAATAGTATATTTTGAA
65 TACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
5400949 AAATAAAATCCGAAAAT
130 AAATAAAATCCGAAAAT
*
5400966 AAAATAAAAAACAAACGACCAAAATCAGAATTTTTTACTAAATTAATAT-AAAAAACTAAAATAA
1 AAAATAAAAAA-AAACGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAAACTAAAATAA
* * *
5401030 TACCTTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATATGAAAATAGTGTATTTTAAA
65 TACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
*
5401095 AAATAAAATCCGAAAAC
130 AAATAAAATCCGAAAAT
*
5401112 AAAAT--AAAAAAA-GGCCAAAATCACAA-TTTTTACTAAATTAATATAAAAAAACTAAAATAAT
1 AAAATAAAAAAAAACGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAAACTAAAATAAT
** * * * *
5401173 ACA--TGAAACATTATGTAAAAAAATAATATAAAAAACAAAAAACG-AAATAATATATCTTAAAA
66 ACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAA
*
5401235 AATAAAAT-CTAAAA-
131 AATAAAATCCGAAAAT
* * * * *
5401249 ATAA-AAATAAAAAGGGCCAAAATCAGAGTTTTTTTCTAAATTAATATAAAAAAACTAAAATAAT
1 AAAATAAAAAAAAACGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAAACTAAAATAAT
* * * *
5401313 ACA--GGAAACATTATGTACTAAAATAATATAAAAAACAAAATACGAAAATAATAAATTTTAAAA
66 ACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAA
5401376 AATAAAATCCGAAAAT
131 AATAAAATCCGAAAAT
* * *
5401392 -AAA-AATAAAAAA-GGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAAAAACTAAAATA
1 AAAATAAAAAAAAACGGCCAAAATCAGA--ATTTTTTACTAAATTAATATAAAAAAACTAAAATA
5401454 ATACATTTGAAACATTATGTACTAAAATAATATAAAAGAATAAAATACGAAAATAGTATATTTTA
64 ATACATTTGAAACATTATGTACTAAAATAATATAAAA-AATAAAATACGAAAATAGTATATTTTA
*
5401519 AAAAATAAAATCCGAAAAC
128 AAAAATAAAATCCGAAAAT
* * *
5401538 AAAAT-AAATAAAATGGCCAAAATCACAGA-TTTTTACTAAATTAATATAAAAAAACTAAAATAA
1 AAAATAAAAAAAAACGGCCAAAATCAGA-ATTTTTTACTAAATTAATATAAAAAAACTAAAATAA
5401601 TACA--TGAAACATTATGTACTAAAATAATAT-AAAAATAAAATACGAAAATAGTATATTTTAAA
65 TACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
**
5401663 AAATAAAATCTAAAAAT
130 AAATAAAATCCGAAAAT
* * * *
5401680 -AAA-AAATAAAAAGGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAAAAACTAAAATA
1 AAAATAAAAAAAAACGGCCAAAATCAGA--ATTTTTTACTAAATTAATATAAAAAAACTAAAATA
*
5401743 ATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAATAAGAAAATAGTATATTTTA
64 ATACATTTGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTA
5401808 AAAAATAAAATCCGAAAAT
128 AAAAATAAAATCCGAAAAT
* * *
5401827 AAAATAAAAATAAACGGCCAAAATCAGAGTTTTTTATTAAATTAATATAAAAAAACTAAAATAAT
1 AAAATAAAAAAAAACGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAAACTAAAATAAT
* *
5401892 ACATTTTG-AACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAGTGTATTTTAAA
66 ACA-TTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
*
5401956 AAGTAAAATCCGAAAAT
130 AAATAAAATCCGAAAAT
* * * *
5401973 AAAATAAAAAAAAACAAACGGTCAAAATCAGAGTTTTTTTATTAAATTAATATAAAAAAATACAA
1 AAAAT---AAAAAA-AAACGGCCAAAATCAGA-ATTTTTTACTAAATTAATAT-AAAAAA-ACTA
* *
5402038 AAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAATATAT
59 AAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATAT
5402103 TTTAAAAAATAAAATCCGAAAAT
124 TTTAAAAAATAAAATCCGAAAAT
5402126 AAAATAAA
1 AAAATAAA
5402134 TACCAAAATA
Statistics
Matches: 1050, Mismatches: 82, Indels: 68
0.88 0.07 0.06
Matches are distributed among these distances:
137 3 0.00
138 11 0.01
139 35 0.03
140 110 0.10
141 76 0.07
142 87 0.08
143 82 0.08
144 30 0.03
145 98 0.09
146 223 0.21
147 115 0.11
148 19 0.02
149 25 0.02
150 19 0.02
151 19 0.02
152 10 0.01
153 88 0.08
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (146 bp):
AAAATAAAAAAAAACGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAAACTAAAATAAT
ACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAA
AATAAAATCCGAAAAT
Found at i:5401377 original size:30 final size:29
Alignment explanation
Indices: 5401341--5401397 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
5401331 TAAAATAATA
5401341 TAAAAAACAAAATACGAAAATAATAAATTT
1 TAAAAAACAAAATACGAAAATAA-AAATTT
* *
5401371 TAAAAAATAAAATCCGAAAATAAAAAT
1 TAAAAAACAAAATACGAAAATAAAAAT
5401398 AAAAAAGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.21
Consensus pattern (29 bp):
TAAAAAACAAAATACGAAAATAAAAATTT
Found at i:5401627 original size:289 final size:289
Alignment explanation
Indices: 5400812--5402136 Score: 1862
Period size: 289 Copynumber: 4.6 Consensus size: 289
5400802 TATATTTTAA
* * *
5400812 AAAATCCAAAAAT-AAAATAAAAAAGGCCAAAATCAGAG-TTTTTTAT-TAAATTAATATAAATA
1 AAAATCCGAAAATAAAAATAAAAAAGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAAA
* * *
5400874 TACTAAAATAATACATATGAAACATTATGAACTAAAATAATA-AAAAAATAAAATACGAAAATAG
66 AACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAG
* * *
5400938 TATATTTTGAAAAATAAAATCCGAAAATAAAATAAAAAACAAACGACCAAAATCAGA-ATTTTTT
131 TATATTTTAAAAAATAAAATCCGAAAATAAAAT-AAATACAAACGGCCAAAATCAGAGA-TTTTT
*
5401002 ACTAAATTAATAT-AAAAAACTAAAATAATACCTTTGAAACATTATGTACTAAAATAATATAAAA
194 ACTAAATTAATATAAAAAAACTAAAATAATA-C-ATGAAACATTATGTACTAAAATAATATAAAA
* *
5401066 AATAAAATATGAAAATAGTGTATTTTAAAAAAT
257 AATAAAATACGAAAATAGTATATTTTAAAAAAT
* * * *
5401099 AAAATCCGAAAA-CAAAATAAAAAAAGGCCAAAATCACA---ATTTTTACTAAATTAATATAAAA
1 AAAATCCGAAAATAAAAAT-AAAAAAGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAA
** * *
5401160 AAACTAAAATAATACA--TGAAACATTATGTAAAAAAATAATATAAAAAACAAAAAACG-AAATA
65 AAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATA
* * * * * * * *
5401222 ATATATCTTAAAAAATAAAAT-CTAAAA-ATAA-AAATAAAAAGGGCCAAAATCAGAGTTTTTTT
130 GTATATTTTAAAAAATAAAATCCGAAAATAAAATAAATACAAACGGCCAAAATCAGAGATTTTTA
* *
5401284 CTAAATTAATATAAAAAAACTAAAATAATACAGGAAACATTATGTACTAAAATAATATAAAAAAC
195 CTAAATTAATATAAAAAAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAT
* *
5401349 AAAATACGAAAATAATAAATTTTAAAAAAT
260 AAAATACGAAAATAGTATATTTTAAAAAAT
5401379 AAAATCCGAAAATAAAAATAAAAAAGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAAA
1 AAAATCCGAAAATAAAAATAAAAAAGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAAA
5401444 AACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAGAATAAAATACGAAAATA
66 AACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAA-AATAAAATACGAAAATA
* * *
5401509 GTATATTTTAAAAAATAAAATCCGAAAACAAAATAAATA-AAATGGCCAAAATCACAGATTTTTA
130 GTATATTTTAAAAAATAAAATCCGAAAATAAAATAAATACAAACGGCCAAAATCAGAGATTTTTA
5401573 CTAAATTAATATAAAAAAACTAAAATAATACATGAAACATTATGTACTAAAATAATAT-AAAAAT
195 CTAAATTAATATAAAAAAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAT
5401637 AAAATACGAAAATAGTATATTTTAAAAAAT
260 AAAATACGAAAATAGTATATTTTAAAAAAT
** *
5401667 AAAATCTAAAAATAAAAAATAAAAAGGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAA
1 AAAATCCGAAAAT-AAAAATAAAAAAGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAA
*
5401732 AAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAATAAGAAAAT
65 AAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAAT
* * *
5401797 AGTATATTTTAAAAAATAAAATCCGAAAATAAAATAAAAATAAACGGCCAAAATCAGAGTTTTTT
129 AGTATATTTTAAAAAATAAAATCCGAAAATAAAATAAATACAAACGGCCAAAATCAGAGATTTTT
*
5401862 ATTAAATTAATATAAAAAAACTAAAATAATACATTTTG-AACATTATGTACTAAAATAATATAAA
194 ACTAAATTAATATAAAAAAACTAAAATAATACA---TGAAACATTATGTACTAAAATAATATAAA
* * *
5401926 AAATAAAATACAAAAATAGTGTATTTTAAAAAGT
256 AAATAAAATACGAAAATAGTATATTTTAAAAAAT
* * *
5401960 AAAATCCGAAAATAAAATAAAAAAAAACAAACGGTCAAAATCAGAGTTTTTTTAT-TAAATTAAT
1 AAAATCCG-----AAAATAAAAATAAA-AAA-GGCCAAAATCAGAGTTTTTTTTTCTAAATTAAT
*
5402024 ATAAAAAAATACAAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATA
59 AT-AAAAAA-ACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATA
* *
5402089 CAAAAATAATATATTTTAAAAAATAAAATCCGAAAATAAAATAAATAC
122 CGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATAAAATAAATAC
5402137 CAAAATATAT
Statistics
Matches: 930, Mismatches: 75, Indels: 54
0.88 0.07 0.05
Matches are distributed among these distances:
280 87 0.09
281 42 0.05
282 17 0.02
283 40 0.04
284 5 0.01
285 73 0.08
286 26 0.03
287 69 0.07
288 67 0.07
289 228 0.25
290 62 0.07
292 23 0.02
293 41 0.04
297 8 0.01
298 18 0.02
299 83 0.09
300 41 0.04
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (289 bp):
AAAATCCGAAAATAAAAATAAAAAAGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAAA
AACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAG
TATATTTTAAAAAATAAAATCCGAAAATAAAATAAATACAAACGGCCAAAATCAGAGATTTTTAC
TAAATTAATATAAAAAAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAATA
AAATACGAAAATAGTATATTTTAAAAAAT
Found at i:5402083 original size:12 final size:13
Alignment explanation
Indices: 5402066--5402101 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5402056 ATTATGTACT
5402066 AAAATAATATA-A
1 AAAATAATATACA
*
5402078 AAAATAAAATACA
1 AAAATAATATACA
5402091 AAAATAATATA
1 AAAATAATATA
5402102 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAATATACA
Found at i:5402133 original size:25 final size:25
Alignment explanation
Indices: 5402066--5402133 Score: 64
Period size: 30 Copynumber: 2.5 Consensus size: 25
5402056 ATTATGTACT
*
5402066 AAAATAATATAAAAAATAAAATACA
1 AAAATAAAATAAAAAATAAAATACA
* *
5402091 AAAATAATATATTTTAAAAAATAAAATCCG
1 AAAATAA-A-A---TAAAAAATAAAATACA
5402121 AAAATAAAATAAA
1 AAAATAAAATAAA
5402134 TACCAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
25 11 0.31
27 1 0.03
28 1 0.03
29 1 0.03
30 21 0.60
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (25 bp):
AAAATAAAATAAAAAATAAAATACA
Found at i:5402169 original size:153 final size:149
Alignment explanation
Indices: 5401388--5402135 Score: 996
Period size: 147 Copynumber: 5.0 Consensus size: 149
5401378 TAAAATCCGA
* * *
5401388 AAATAAAAATAAAAAAGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAAAAACTAAAAT
1 AAATAAAAAT--AAACGGACAAAATCAGAG--TTTTTAT-TAAATTAATATAAAAAAACTAAAAT
*
5401453 AATACATTTGAAACATTATGTACTAAAATAATATAAAAGAATAAAATACGAAAATAGTATATTTT
61 AATACATTTGAAACATTATGTACTAAAATAATATAAAA-AATAAAATACAAAAATAGTATATTTT
*
5401518 AAAAAATAAAATCCGAAAACAAAAT
125 AAAAAATAAAATCCGAAAATAAAAT
* * *
5401543 AAAT-AAAAT----GGCCAAAATCACAGATTTTTACTAAATTAATATAAAAAAACTAAAATAATA
1 AAATAAAAATAAACGGACAAAATCAGAG-TTTTTATTAAATTAATATAAAAAAACTAAAATAATA
*
5401603 CA--TGAAACATTATGTACTAAAATAATAT-AAAAATAAAATACGAAAATAGTATATTTTAAAAA
65 CATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAGTATATTTTAAAAA
**
5401665 ATAAAATCTAAAAAT-AAA-
130 ATAAAATCCGAAAATAAAAT
* * *
5401683 AAAT---AA-AAAGGGCCAAAATCAGAGTTTTTTTTTCTAAATTAATATAAAAAAACTAAAATAA
1 AAATAAAAATAAACGGACAAAATCAGAG--TTTTTAT-TAAATTAATATAAAAAAACTAAAATAA
5401744 TACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAATA-AGAAAATAGTATATTTTA
63 TACATTTGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACA-AAAATAGTATATTTTA
5401808 AAAAATAAAATCCGAAAAT---A-
126 AAAAATAAAATCCGAAAATAAAAT
*
5401828 AAATAAAAATAAACGGCCAAAATCAGAGTTTTTTATTAAATTAATATAAAAAAACTAAAATAATA
1 AAATAAAAATAAACGGACAAAATCAGAG-TTTTTATTAAATTAATATAAAAAAACTAAAATAATA
*
5401893 CATTTTG-AACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAGTGTATTTTAAAA
65 CA-TTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAGTATATTTTAAAA
*
5401957 AGTAAAATCCGAAAATAAAAT
129 AATAAAATCCGAAAATAAAAT
* * * *
5401978 AAAAAAAAACAAACGGTCAAAATCAGAGTTTTTTTATTAAATTAATATAAAAAAATACAAAAATA
1 AAATAAAAATAAACGGACAAAATCAGAG--TTTTTATTAAATTAATAT-AAAAAA-ACTAAAATA
*
5402043 ATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAATATATTTTAA
62 ATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAGTATATTTTAA
5402108 AAAATAAAATCCGAAAATAAAAT
127 AAAATAAAATCCGAAAATAAAAT
5402131 AAATA
1 AAATA
5402136 CCAAAATATA
Statistics
Matches: 542, Mismatches: 26, Indels: 52
0.87 0.04 0.08
Matches are distributed among these distances:
138 2 0.00
140 4 0.01
141 16 0.03
142 48 0.09
143 34 0.06
144 26 0.05
145 31 0.06
146 77 0.14
147 105 0.19
148 26 0.05
149 18 0.03
150 25 0.05
151 19 0.04
152 10 0.02
153 92 0.17
154 5 0.01
155 4 0.01
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (149 bp):
AAATAAAAATAAACGGACAAAATCAGAGTTTTTATTAAATTAATATAAAAAAACTAAAATAATAC
ATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAGTATATTTTAAAAAA
TAAAATCCGAAAATAAAAT
Found at i:5406879 original size:18 final size:18
Alignment explanation
Indices: 5406826--5406871 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
5406816 CGTTAATGTT
5406826 TTCATCGTCATTTACATC
1 TTCATCGTCATTTACATC
5406844 TTCATCGTCATTTACATC
1 TTCATCGTCATTTACATC
5406862 TTCATCGTCA
1 TTCATCGTCA
5406872 ATATCATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.28, G:0.07, T:0.43
Consensus pattern (18 bp):
TTCATCGTCATTTACATC
Found at i:5408566 original size:22 final size:22
Alignment explanation
Indices: 5408540--5408581 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5408530 AAATTTACCT
5408540 TTTCTTTTCTTTCT-TCTTCTCC
1 TTTC-TTTCTTTCTATCTTCTCC
5408562 TTTCTTTCTTTCTATCTTCT
1 TTTCTTTCTTTCTATCTTCT
5408582 TCTTCTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTCTTTCTATCTTCTCC
Found at i:5408725 original size:27 final size:27
Alignment explanation
Indices: 5408673--5408726 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5408663 GAGAAAGGCA
* * *
5408673 CCACTGGTGCTGCCTGTGGGGCACCCT
1 CCACTGGTGCCGCCTATAGGGCACCCT
*
5408700 CCACTGGTGCCGCCTATAGGGTACCCT
1 CCACTGGTGCCGCCTATAGGGCACCCT
5408727 TCACCCTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.11, C:0.37, G:0.30, T:0.22
Consensus pattern (27 bp):
CCACTGGTGCCGCCTATAGGGCACCCT
Found at i:5409767 original size:20 final size:20
Alignment explanation
Indices: 5409729--5409768 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
5409719 ATATATTTTT
5409729 TAATTTTAATACTCTTTTAAA
1 TAATTTTAATAC-CTTTTAAA
5409750 TAATTTTAATGA-CTTTTAA
1 TAATTTTAAT-ACCTTTTAA
5409769 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 10 0.56
22 1 0.06
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (20 bp):
TAATTTTAATACCTTTTAAA
Found at i:5409790 original size:19 final size:18
Alignment explanation
Indices: 5409763--5409800 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5409753 TTTTAATGAC
5409763 TTTTAATTTTTAAAATATT
1 TTTTAATTTTTAAAA-ATT
*
5409782 TTTTTATTTTTAAAAATT
1 TTTTAATTTTTAAAAATT
5409800 T
1 T
5409801 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAATTTTTAAAAATT
Found at i:5410700 original size:17 final size:16
Alignment explanation
Indices: 5410680--5410732 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 16
5410670 AATAAAAAAA
5410680 TTATAATTTTAAAGTTT
1 TTATAATTTTAAA-TTT
5410697 TTATAATTTTATAATTTT
1 TTATAATTTTA-AA-TTT
5410715 TTAATAATTTTAAATTT
1 TT-ATAATTTTAAATTT
5410732 T
1 T
5410733 AAAAGGGCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 15 0.45
18 9 0.27
19 9 0.27
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTATAATTTTAAATTT
Found at i:5421242 original size:16 final size:17
Alignment explanation
Indices: 5421221--5421252 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5421211 TTCTCCAGAC
5421221 AAAAAGGAAAA-AAAAA
1 AAAAAGGAAAAGAAAAA
5421237 AAAAAGGAAAAGAAAA
1 AAAAAGGAAAAGAAAA
5421253 GAAAGAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGGAAAAGAAAAA
Found at i:5427567 original size:26 final size:26
Alignment explanation
Indices: 5427538--5427593 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5427528 TTATTACAAC
*
5427538 TATCATTACTATTATCTTTTAT-TTTT
1 TATCACTACTATTAT-TTTTATGTTTT
* *
5427564 TATCACTATTATTGTTTTTATGTTTT
1 TATCACTACTATTATTTTTATGTTTT
5427590 TATC
1 TATC
5427594 TATCAGCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (26 bp):
TATCACTACTATTATTTTTATGTTTT
Found at i:5427844 original size:21 final size:20
Alignment explanation
Indices: 5427820--5427886 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 20
5427810 GCATATATAT
*
5427820 ATTTTTACATATTATGTGTAC
1 ATTTTTA-ATATTATATGTAC
5427841 ATTTTCTAATATATATTATGTAC
1 ATTTT-TAATAT-TA-TATGTAC
5427864 ATACTTTTAAATATTATCATGTA
1 AT--TTTT-AATATTAT-ATGTA
5427887 TTGGTATGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 9 0.24
22 4 0.11
23 9 0.24
24 8 0.21
25 8 0.21
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (20 bp):
ATTTTTAATATTATATGTAC
Found at i:5427951 original size:18 final size:21
Alignment explanation
Indices: 5427920--5427962 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
5427910 TCTTTAATAG
5427920 TCATTTTCTAATAT-TAT-TA
1 TCATTTTCTAATATATATATA
5427939 TCATTTT-TAATATATATATA
1 TCATTTTCTAATATATATATA
5427959 TCAT
1 TCAT
5427963 ATGCATATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
19 10 0.45
20 6 0.27
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (21 bp):
TCATTTTCTAATATATATATA
Found at i:5428126 original size:26 final size:28
Alignment explanation
Indices: 5428078--5428134 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
5428068 TTATTCCTAA
*
5428078 TATATATATACATCTTTTAATATCGTAT
1 TATATATATACATCTTTTAATATCATAT
*
5428106 TATATATATATA-CTTTT-ATATCATAT
1 TATATATATACATCTTTTAATATCATAT
5428132 TAT
1 TAT
5428135 TGTTATACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 11 0.41
27 5 0.19
28 11 0.41
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.53
Consensus pattern (28 bp):
TATATATATACATCTTTTAATATCATAT
Found at i:5433159 original size:32 final size:32
Alignment explanation
Indices: 5433078--5433164 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
5433068 TTGAACAAAT
* * * *
5433078 TAATGAGAA-TTTTCTAAAAATTTTGGAGGGCT
1 TAATGAAAATTTTTC-AAAAATTTTGAAGAGCC
* *
5433110 TAAT-AAGATTTTCCAAAAATTTTGAAGAGCC
1 TAATGAAAATTTTTCAAAAATTTTGAAGAGCC
*
5433141 TAATGAAAATTTTTCAAAATTTTT
1 TAATGAAAATTTTTCAAAAATTTT
5433165 AGAGCTCAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
31 20 0.45
32 24 0.55
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (32 bp):
TAATGAAAATTTTTCAAAAATTTTGAAGAGCC
Found at i:5433160 original size:31 final size:31
Alignment explanation
Indices: 5433078--5433163 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
5433068 TTGAACAAAT
* * * * *
5433078 TAATGAGAATTTTCTAAAAATTTTGGAGGGCT
1 TAATGAAAATTTT-TCAAAATTTTGAAGAGCC
* *
5433110 TAAT-AAGATTTTCCAAAAATTTTGAAGAGCC
1 TAATGAAAATTTTTC-AAAATTTTGAAGAGCC
5433141 TAATGAAAATTTTTCAAAATTTT
1 TAATGAAAATTTTTCAAAATTTT
5433164 TAGAGCTCAG
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
31 31 0.72
32 12 0.28
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (31 bp):
TAATGAAAATTTTTCAAAATTTTGAAGAGCC
Found at i:5438523 original size:13 final size:13
Alignment explanation
Indices: 5438505--5438531 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5438495 TTGGTACCAC
5438505 ATTTATATCATCA
1 ATTTATATCATCA
5438518 ATTTATATCATCA
1 ATTTATATCATCA
5438531 A
1 A
5438532 AGCATCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTATATCATCA
Found at i:5440539 original size:14 final size:14
Alignment explanation
Indices: 5440520--5440549 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5440510 CCGTGCGTGA
5440520 CTTTCTTTTTCTTT
1 CTTTCTTTTTCTTT
*
5440534 CTTTCTTTTTTTTT
1 CTTTCTTTTTCTTT
5440548 CT
1 CT
5440550 GATTTGTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTTCTTTTTCTTT
Found at i:5441294 original size:18 final size:18
Alignment explanation
Indices: 5441284--5441320 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5441274 TGTTTTAAAG
5441284 ATAATTTTTGTATTATAA
1 ATAATTTTTGTATTATAA
5441302 ATAATTTTTGTATTATAA
1 ATAATTTTTGTATTATAA
5441320 A
1 A
5441321 CTTTTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
ATAATTTTTGTATTATAA
Found at i:5442269 original size:15 final size:16
Alignment explanation
Indices: 5442249--5442278 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5442239 GGATATAGAA
5442249 AAATA-TTTAAAAAAT
1 AAATATTTTAAAAAAT
5442264 AAATATTTTAAAAAA
1 AAATATTTTAAAAAA
5442279 GAGAGATATA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATTTTAAAAAAT
Found at i:5447276 original size:15 final size:16
Alignment explanation
Indices: 5447244--5447278 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5447234 ACCAAAATCT
*
5447244 AAATAATTCAAACTCA
1 AAATAATTCAAACCCA
5447260 AAATAATT-AAACCCA
1 AAATAATTCAAACCCA
5447275 AAAT
1 AAAT
5447279 TAGAGGACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAATTCAAACCCA
Found at i:5450584 original size:81 final size:81
Alignment explanation
Indices: 5450447--5450614 Score: 318
Period size: 81 Copynumber: 2.1 Consensus size: 81
5450437 ATAGAAACTG
5450447 AAACCATGTAATCTTTGCCATTTTAATGTGAACTTCCAGTCTATGTAGAAACTGAGTATACTAAG
1 AAACCATGTAATCTTTGCCATTTTAATGTGAACTTCCAGTCTATGTAGAAACTGAGTATACTAAG
5450512 TTTAATAGTACACAAA
66 TTTAATAGTACACAAA
* *
5450528 AGACCATGTAATCTTTGCCATTTTAATGTGAACTTCCAGTTTATGTAGAAACTGAGTATACTAAG
1 AAACCATGTAATCTTTGCCATTTTAATGTGAACTTCCAGTCTATGTAGAAACTGAGTATACTAAG
5450593 TTTAATAGTACACAAA
66 TTTAATAGTACACAAA
5450609 AAACCA
1 AAACCA
5450615 GAAATCTAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (81 bp):
AAACCATGTAATCTTTGCCATTTTAATGTGAACTTCCAGTCTATGTAGAAACTGAGTATACTAAG
TTTAATAGTACACAAA
Found at i:5457680 original size:65 final size:65
Alignment explanation
Indices: 5457566--5457696 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
5457556 GAAGCTATGA
5457566 ACAAGATTGAGGATGTGTTGTTCACAATACTAAAATAGACAATACATTCATGTTATCAACACAAT
1 ACAAGATTGAGGATGTGTTGTTCACAATACTAAAATAGACAATACATTCATGTTATCAACACAAT
* * *
5457631 ACAATATTGAGGATGTGTTGTTTACAATACTAAAA-ATGACAATATATTCATGTTATCAACACAA
1 ACAAGATTGAGGATGTGTTGTTCACAATACTAAAATA-GACAATACATTCATGTTATCAACACAA
5457695 T
65 T
5457696 A
1 A
5457697 TTTTAATAGG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 1 0.02
65 61 0.98
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (65 bp):
ACAAGATTGAGGATGTGTTGTTCACAATACTAAAATAGACAATACATTCATGTTATCAACACAAT
Found at i:5457750 original size:12 final size:12
Alignment explanation
Indices: 5457735--5457814 Score: 58
Period size: 12 Copynumber: 6.4 Consensus size: 12
5457725 ACTATTTATT
5457735 TATTTTT-TTAAA
1 TATTTTTATT-AA
5457747 TATTTTTATTAA
1 TATTTTTATTAA
5457759 TATTTATATATTATA
1 TATTT-T-TATTA-A
*
5457774 TCACTGTTTATT--
1 T-A-TTTTTATTAA
**
5457786 TATTTTTAAAAA
1 TATTTTTATTAA
5457798 TATTTTTATTAA
1 TATTTTTATTAA
5457810 TATTT
1 TATTT
5457815 ATATATTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
10 5 0.09
11 1 0.02
12 30 0.56
13 3 0.06
14 5 0.09
15 6 0.11
16 2 0.04
17 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (12 bp):
TATTTTTATTAA
Found at i:5457778 original size:51 final size:51
Alignment explanation
Indices: 5457720--5457821 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
5457710 AGTAAAAAAA
**
5457720 ATATCACTATTTATTTATTTTTTTAAATATTTTTATTAATATTTATATATT
1 ATATCACTATTTATTTATTTTTAAAAATATTTTTATTAATATTTATATATT
*
5457771 ATATCACTGTTTATTTATTTTTAAAAATATTTTTATTAATATTTATATATT
1 ATATCACTATTTATTTATTTTTAAAAATATTTTTATTAATATTTATATATT
5457822 TTAGAATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (51 bp):
ATATCACTATTTATTTATTTTTAAAAATATTTTTATTAATATTTATATATT
Found at i:5457962 original size:18 final size:17
Alignment explanation
Indices: 5457939--5457979 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
5457929 ATAACCCGAT
5457939 ATTAAATAAATTTATAAA
1 ATTAAATAAATTTA-AAA
*
5457957 ATTAAAAAAATTTAAAA
1 ATTAAATAAATTTAAAA
5457974 A-TAAAT
1 ATTAAAT
5457980 TTATCATGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAATAAATTTAAAA
Found at i:5463784 original size:14 final size:14
Alignment explanation
Indices: 5463765--5463794 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5463755 AGCACAACCG
*
5463765 TTGGGTACAAAGTT
1 TTGGGTACAAAATT
5463779 TTGGGTACAAAATT
1 TTGGGTACAAAATT
5463793 TT
1 TT
5463795 CCGGTAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (14 bp):
TTGGGTACAAAATT
Found at i:5464704 original size:22 final size:22
Alignment explanation
Indices: 5464664--5464706 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5464654 CATATATGTT
* * *
5464664 AATATAATTAATATTTTAGATA
1 AATATAATAAAAATATTAGATA
5464686 AATATAATAAAAATATTAGAT
1 AATATAATAAAAATATTAGAT
5464707 CGATTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
AATATAATAAAAATATTAGATA
Found at i:5469178 original size:16 final size:16
Alignment explanation
Indices: 5469159--5469203 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
5469149 CAAGAGTTTG
*
5469159 AAATAACTCAAAATCA
1 AAATAATTCAAAATCA
* *
5469175 AAATTATTCAAATTCA
1 AAATAATTCAAAATCA
5469191 AAATAATTCAAAA
1 AAATAATTCAAAA
5469204 AATTTATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAATTCAAAATCA
Found at i:5470518 original size:15 final size:16
Alignment explanation
Indices: 5470493--5470526 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5470483 GAGGAAAAAA
5470493 TTATGTAAAAATATAT
1 TTATGTAAAAATATAT
*
5470509 TTAT-TAAAAATTTAT
1 TTATGTAAAAATATAT
5470524 TTA
1 TTA
5470527 AAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATGTAAAAATATAT
Found at i:5472832 original size:46 final size:44
Alignment explanation
Indices: 5472775--5472889 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
5472765 ACAGGACAGA
*
5472775 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGAAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
5472821 ACAGAATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGAAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* * **
5472865 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGAAATGAGCCATGTAAGTCCAT
5472890 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 34 0.56
46 27 0.44
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.28
Consensus pattern (44 bp):
ACAGAAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:5472881 original size:44 final size:45
Alignment explanation
Indices: 5472775--5472908 Score: 137
Period size: 46 Copynumber: 3.0 Consensus size: 45
5472765 ACAGGACAGA
* * *
5472775 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGAATTAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
5472821 ACAGAATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGAATTAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * * *
5472865 ACAGGAA-TAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACA-GAATTAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5472909 CAGGGTATTG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 33 0.44
45 4 0.05
46 38 0.51
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (45 bp):
ACAGAATTAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:5478704 original size:148 final size:147
Alignment explanation
Indices: 5478401--5478712 Score: 344
Period size: 148 Copynumber: 2.1 Consensus size: 147
5478391 TTTATAAAAT
* *
5478401 ATATATACAATTGACATTATATAATTTAGGTAGATAATTAATGATATGTATCACTATATACAACT
1 ATATATACAATTGACATTATATAATTAAGATAGATAATTAATGATATGTATCACTATATACAACT
** * ** *
5478466 ATGTTATTATAATGTATATTTTTATATTAATGATATGCAAGCTTAAACCCTAAACATGTAATTAA
66 ATGACATTATAATGTACATTTTTATATTAATGATACACAAGCTTAAACCCTAAACATGTAACTAA
5478531 CTTTATGTCAAATTATA
131 CTTTATGTCAAATTATA
* * * * * *
5478548 ATACATACAGTT-ACCATTATATAGTTAAGATAGATTATTAATTATATG--TCACCTTATCTACA
1 ATATATACAATTGA-CATTATATAATTAAGATAGATAATTAATGATATGTATCA-C-TATATACA
* * * * ** *
5478610 ATTATGACATTATAATGTACATTTTTTATATTAATGATACATAATCTTAAACCTTAAATGTGTAG
63 ACTATGACATTATAATGTACA-TTTTTATATTAATGATACACAAGCTTAAACCCTAAACATGTAA
*
5478675 CTAACTTTATGGT-AGATTATA
127 CTAACTTTAT-GTCAAATTATA
*
5478696 ATATATACAATTAACAT
1 ATATATACAATTGACAT
5478713 GAGTTAAGTA
Statistics
Matches: 135, Mismatches: 24, Indels: 11
0.79 0.14 0.06
Matches are distributed among these distances:
145 3 0.02
146 2 0.01
147 63 0.47
148 64 0.47
149 3 0.02
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.41
Consensus pattern (147 bp):
ATATATACAATTGACATTATATAATTAAGATAGATAATTAATGATATGTATCACTATATACAACT
ATGACATTATAATGTACATTTTTATATTAATGATACACAAGCTTAAACCCTAAACATGTAACTAA
CTTTATGTCAAATTATA
Found at i:5479038 original size:42 final size:43
Alignment explanation
Indices: 5478976--5479057 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
5478966 TTTGCAATTG
* *
5478976 TTATGTAACATTTAATTTGTTTG-AAATTCTTATGTTTAAGTTA
1 TTATGTAACATTTAAATTG-TTGAAAATTATTATGTTTAAGTTA
*
5479019 TTATGT-ATATTTAAATTGTTGCAAAATTATTATGTTTAA
1 TTATGTAACATTTAAATTGTTG-AAAATTATTATGTTTAA
5479058 TTTGTTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 3 0.09
42 10 0.29
43 21 0.62
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (43 bp):
TTATGTAACATTTAAATTGTTGAAAATTATTATGTTTAAGTTA
Found at i:5482025 original size:10 final size:10
Alignment explanation
Indices: 5482012--5482036 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5482002 GCTTTTAGGG
5482012 CATTTTCTTC
1 CATTTTCTTC
5482022 CATTTTCTTC
1 CATTTTCTTC
5482032 CATTT
1 CATTT
5482037 GCTTTCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (10 bp):
CATTTTCTTC
Found at i:5483991 original size:25 final size:25
Alignment explanation
Indices: 5483957--5484008 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
5483947 AATCCCAAAG
5483957 TAAAATTATGGGCTTAAGTCGAAAT
1 TAAAATTATGGGCTTAAGTCGAAAT
5483982 TAAAATTATGGGCTTAAGTCGAAAT
1 TAAAATTATGGGCTTAAGTCGAAAT
5484007 TA
1 TA
5484009 TTTAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (25 bp):
TAAAATTATGGGCTTAAGTCGAAAT
Found at i:5493328 original size:17 final size:17
Alignment explanation
Indices: 5493288--5493328 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
5493278 CTAAATTGAG
5493288 TTTTAT-TTTTATTTAA
1 TTTTATATTTTATTTAA
5493304 TTTATATATTTT-TTTAA
1 TTT-TATATTTTATTTAA
5493321 TCTTTATA
1 T-TTTATA
5493329 GCGTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 6 0.27
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATATTTTATTTAA
Found at i:5504235 original size:21 final size:21
Alignment explanation
Indices: 5504211--5504261 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
5504201 TAAATTTTTG
*
5504211 ATTTAATCATTTAAAAATTACA
1 ATTTAATCA-TAAAAAATTACA
* *
5504233 TTTTTTATCATAAAAAATTACA
1 -ATTTAATCATAAAAAATTACA
5504255 ATTTAAT
1 ATTTAAT
5504262 TTTGGCCCCC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 5 0.22
22 11 0.48
23 7 0.30
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTAATCATAAAAAATTACA
Found at i:5504463 original size:27 final size:29
Alignment explanation
Indices: 5504433--5504494 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
5504423 TAAATCACAC
*
5504433 AAATTATAT-TTATAATATATTTTT-TTA
1 AAATTATATAATATAATATATTTTTGTTA
*
5504460 AAATT-TATAATATAATATTTTTTTGTTA
1 AAATTATATAATATAATATATTTTTGTTA
*
5504488 TAATTAT
1 AAATTAT
5504495 CTCAAACACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 3 0.10
27 18 0.62
28 7 0.24
29 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
AAATTATATAATATAATATATTTTTGTTA
Found at i:5506071 original size:21 final size:22
Alignment explanation
Indices: 5506037--5506077 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5506027 TATTCAACTT
*
5506037 TAAAAAATTACAAAATAATTAC
1 TAAAAAATTACAAAAAAATTAC
*
5506059 TAAAATATT-CAAAAAAATT
1 TAAAAAATTACAAAAAAATT
5506078 CATTTAAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAATTACAAAAAAATTAC
Found at i:5509670 original size:24 final size:24
Alignment explanation
Indices: 5509643--5509688 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5509633 TATTATTTAT
*
5509643 ATTTTTAAAACTTTAAATTAATAA
1 ATTTATAAAACTTTAAATTAATAA
* *
5509667 ATTTATAAAATTTTAATTTAAT
1 ATTTATAAAACTTTAAATTAAT
5509689 TTTTATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTATAAAACTTTAAATTAATAA
Found at i:5514438 original size:17 final size:17
Alignment explanation
Indices: 5514400--5514431 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5514390 AGTCGTTTTC
5514400 TCTTTGTAAGTCTCAAG
1 TCTTTGTAAGTCTCAAG
5514417 TCTTTG-AAGT-TCAAG
1 TCTTTGTAAGTCTCAAG
5514432 CTTCTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (17 bp):
TCTTTGTAAGTCTCAAG
Found at i:5516926 original size:13 final size:13
Alignment explanation
Indices: 5516893--5516947 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
5516883 TAGCCTATTC
5516893 TAAATTAAT-AAAA
1 TAAA-TAATAAAAA
5516906 TAAA-AATAAAAA
1 TAAATAATAAAAA
*
5516918 TAAATAATAAAAC
1 TAAATAATAAAAA
*
5516931 TAAATAAAACAAAA
1 TAAATAATA-AAAA
5516945 TAA
1 TAA
5516948 TATCTTCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 3 0.08
12 8 0.22
13 19 0.53
14 6 0.17
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:5520409 original size:18 final size:18
Alignment explanation
Indices: 5520366--5520415 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
5520356 GATTGTGGCA
* *
5520366 TTGGGTTTTTGG-TATTT
1 TTGGGTTTTGGGTTAATT
5520383 TATGTGGTTTTGGGTTAATT
1 T-TG-GGTTTTGGGTTAATT
5520403 TTGGG-TTTGGGTT
1 TTGGGTTTTGGGTT
5520416 CATATGGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 10 0.36
20 5 0.18
ACGTcount: A:0.08, C:0.00, G:0.34, T:0.58
Consensus pattern (18 bp):
TTGGGTTTTGGGTTAATT
Found at i:5520429 original size:17 final size:16
Alignment explanation
Indices: 5520404--5520448 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
5520394 GGGTTAATTT
5520404 TGGGTTTGGGTTCATA
1 TGGGTTTGGGTTCATA
* *
5520420 TGGGTATTGGGTTTATG
1 TGGGT-TTGGGTTCATA
5520437 TGGGTGTTGGGT
1 TGGGT-TTGGGT
5520449 GTGGTTGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.09, C:0.02, G:0.44, T:0.44
Consensus pattern (16 bp):
TGGGTTTGGGTTCATA
Found at i:5527094 original size:10 final size:10
Alignment explanation
Indices: 5527056--5527093 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5527046 TAAATTAATA
5527056 AAATAAAAAT
1 AAATAAAAAT
5527066 AAATAATAAAT
1 AAATAA-AAAT
*
5527077 -AATAAAACT
1 AAATAAAAAT
5527086 AAATAAAA
1 AAATAAAA
5527094 CAAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:5527100 original size:20 final size:20
Alignment explanation
Indices: 5527055--5527101 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5527045 CTAAATTAAT
5527055 AAAATAAAAATAAATAATAA
1 AAAATAAAAATAAATAATAA
* *
5527075 ATAATAAAACTAAATAA-AA
1 AAAATAAAAATAAATAATAA
5527094 CAAAATAA
1 -AAAATAA
5527102 TATCTTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAATAAAAATAAATAATAA
Found at i:5529490 original size:26 final size:26
Alignment explanation
Indices: 5529454--5529505 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5529444 AAATAAAGAT
5529454 AATGTATTATTTACATACAAACTTAC
1 AATGTATTATTTACATACAAACTTAC
5529480 AATGTATTATTTACATACAAACTTAC
1 AATGTATTATTTACATACAAACTTAC
5529506 CTCGGTGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.38
Consensus pattern (26 bp):
AATGTATTATTTACATACAAACTTAC
Found at i:5538034 original size:35 final size:35
Alignment explanation
Indices: 5537985--5538054 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
5537975 ACGGGGCTGT
5537985 TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
1 TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
* **
5538020 TTCTAAAATGCCGTATGAATTGTTTTGTTATGCCA
1 TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
5538055 AATATCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (35 bp):
TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
Found at i:5553099 original size:18 final size:18
Alignment explanation
Indices: 5553059--5553101 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5553049 ATTTATGTTA
5553059 TTTTATATTAACAATAAT
1 TTTTATATTAACAATAAT
* *
5553077 ATTTATATTAATTAAT-AT
1 TTTTATATTAA-CAATAAT
5553095 TTTTATA
1 TTTTATA
5553102 ACAGTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTATATTAACAATAAT
Found at i:5558647 original size:16 final size:16
Alignment explanation
Indices: 5558627--5558664 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5558617 AAATTGGTTG
5558627 AAATTTAAGA-TATTTT
1 AAATTTAA-ATTATTTT
*
5558643 GAATTTAAATTATTTT
1 AAATTTAAATTATTTT
5558659 AAATTT
1 AAATTT
5558665 TGAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
AAATTTAAATTATTTT
Found at i:5565355 original size:15 final size:16
Alignment explanation
Indices: 5565335--5565364 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5565325 CAACAAGAAC
5565335 AATTTACA-TAAAATG
1 AATTTACATTAAAATG
5565350 AATTTACATTAAAAT
1 AATTTACATTAAAAT
5565365 AGGTTCCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (16 bp):
AATTTACATTAAAATG
Found at i:5569130 original size:21 final size:21
Alignment explanation
Indices: 5569106--5569145 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5569096 ACGCGTCTGA
**
5569106 CACCAGCTGCCACCGCCCAAG
1 CACCAGCCACCACCGCCCAAG
*
5569127 CACCTGCCACCACCGCCCA
1 CACCAGCCACCACCGCCCA
5569146 TGCCCACTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.57, G:0.15, T:0.05
Consensus pattern (21 bp):
CACCAGCCACCACCGCCCAAG
Found at i:5569352 original size:18 final size:19
Alignment explanation
Indices: 5569325--5569361 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5569315 TTTCTTCTTC
*
5569325 GTTTTCTCTTA-TTTATTT
1 GTTTTATCTTATTTTATTT
5569343 GTTTTATCTTATTTTATTT
1 GTTTTATCTTATTTTATTT
5569362 TATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (19 bp):
GTTTTATCTTATTTTATTT
Found at i:5570058 original size:25 final size:23
Alignment explanation
Indices: 5570016--5570068 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
5570006 AACTTTATTT
*
5570016 TTATTATTAATTCTATTATTGCTA
1 TTATTATTAATTCCATTATT-CTA
5570040 CTTATTATT-ATTGCCATTATTCTA
1 -TTATTATTAATT-CCATTATTCTA
5570064 TTATT
1 TTATT
5570069 TCTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 6 0.23
25 15 0.58
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATTATTAATTCCATTATTCTA
Found at i:5570173 original size:23 final size:23
Alignment explanation
Indices: 5570136--5570184 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5570126 ATAATCATTA
* *
5570136 TTATTCTTTATTTGTTATTGTTG
1 TTATTCTTTATTTGTCATTATTG
5570159 TTATTCTATTA-TTGTCATTATTG
1 TTATTCT-TTATTTGTCATTATTG
5570182 TTA
1 TTA
5570185 ATATTGGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.18, C:0.06, G:0.10, T:0.65
Consensus pattern (23 bp):
TTATTCTTTATTTGTCATTATTG
Found at i:5573038 original size:17 final size:18
Alignment explanation
Indices: 5573010--5573048 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
5573000 CTTTTATTTT
5573010 CTAACGAATAAAATTAAG
1 CTAACGAATAAAATTAAG
*
5573028 CTAAC-AATAAAATTAAT
1 CTAACGAATAAAATTAAG
5573045 CTAA
1 CTAA
5573049 AGCTTCTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (18 bp):
CTAACGAATAAAATTAAG
Found at i:5573601 original size:10 final size:10
Alignment explanation
Indices: 5573583--5573642 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
5573573 GAGGAAGAGC
*
5573583 AGAAGAAAAT
1 AGAAAAAAAT
5573593 AGAAAAAAA-
1 AGAAAAAAAT
*
5573602 AGATAAAAAT
1 AGAAAAAAAT
* *
5573612 ATAAAAATAT
1 AGAAAAAAAT
* *
5573622 AAAAAAATAAA
1 AGAAAAA-AAT
5573633 AGAAAAAAAT
1 AGAAAAAAAT
5573643 TAAATTGTTC
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
9 8 0.21
10 23 0.61
11 7 0.18
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.13
Consensus pattern (10 bp):
AGAAAAAAAT
Found at i:5573617 original size:7 final size:8
Alignment explanation
Indices: 5573598--5573633 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
5573588 AAAATAGAAA
*
5573598 AAAAAGAT
1 AAAAATAT
5573606 AAAAATAT
1 AAAAATAT
5573614 AAAAATAT
1 AAAAATAT
*
5573622 AAAAAAAT
1 AAAAATAT
5573630 AAAA
1 AAAA
5573634 GAAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (8 bp):
AAAAATAT
Found at i:5573617 original size:16 final size:16
Alignment explanation
Indices: 5573598--5573646 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
5573588 AAAATAGAAA
5573598 AAAAAGATAAAAATAT
1 AAAAAGATAAAAATAT
* *
5573614 AAAAATATAAAAAAAT
1 AAAAAGATAAAAATAT
*
5573630 -AAAAGAAAAAAAT-T
1 AAAAAGATAAAAATAT
5573644 AAA
1 AAA
5573647 TTGTTCAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 1 0.04
15 12 0.44
16 14 0.52
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (16 bp):
AAAAAGATAAAAATAT
Found at i:5574284 original size:50 final size:50
Alignment explanation
Indices: 5574224--5574321 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
5574214 GATTACTTGT
*
5574224 AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAGTATTTGC
1 AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAATATTTGC
5574274 AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAATATTT
1 AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAATATTT
5574322 ATTAGTTTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (50 bp):
AAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAGATTTAATATTTGC
Found at i:5587369 original size:19 final size:20
Alignment explanation
Indices: 5587338--5587392 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 20
5587328 TTAATTTAAG
5587338 AATTTAGTTTTTTATAATT-T
1 AATTTA-TTTTTTATAATTAT
*
5587358 AATTTATTTTTTATCATTACT
1 AATTTATTTTTTATAATTA-T
5587379 AATGTTATTTTTTA
1 AAT-TTATTTTTTA
5587393 GTTTAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 11 0.35
20 6 0.19
21 4 0.13
22 10 0.32
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (20 bp):
AATTTATTTTTTATAATTAT
Found at i:5587993 original size:29 final size:30
Alignment explanation
Indices: 5587960--5588017 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
5587950 AAAGAACCCT
*
5587960 AATTTAAACTAAATTAACA-ATAAAAATTC
1 AATTTAAACTAAATTAAAATATAAAAATTC
***
5587989 AATTTATTTTAAATTAAAATATAAAAATT
1 AATTTAAACTAAATTAAAATATAAAAATT
5588018 AAATCATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (30 bp):
AATTTAAACTAAATTAAAATATAAAAATTC
Found at i:5589037 original size:24 final size:24
Alignment explanation
Indices: 5589005--5589052 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5588995 AGAGAAGAAA
5589005 CGATGCATTAATCTTAAAGGAATG
1 CGATGCATTAATCTTAAAGGAATG
5589029 CGATGCATTAATCTTAAAGGAATG
1 CGATGCATTAATCTTAAAGGAATG
5589053 ACTTGTTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (24 bp):
CGATGCATTAATCTTAAAGGAATG
Found at i:5590074 original size:19 final size:18
Alignment explanation
Indices: 5590052--5590148 Score: 58
Period size: 19 Copynumber: 5.3 Consensus size: 18
5590042 CTAAAAATAT
5590052 TAAAAATATATAAACTTTA
1 TAAAAATATATAAAC-TTA
5590071 TAAAAA-ATAATAAAACTTA
1 TAAAAATAT-AT-AAACTTA
* **
5590090 TAAATAT-TATAAAAATA
1 TAAAAATATATAAACTTA
* *
5590107 TAAAAATCTAGTAAA-TTC
1 TAAAAATATA-TAAACTTA
*
5590125 TAATAAAT-TATAAAATTAA
1 TAA-AAATATATAAACTT-A
5590144 TAAAA
1 TAAAA
5590149 CATGTTTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
17 15 0.24
18 16 0.25
19 28 0.44
20 4 0.06
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (18 bp):
TAAAAATATATAAACTTA
Found at i:5590078 original size:20 final size:19
Alignment explanation
Indices: 5590053--5590093 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
5590043 TAAAAATATT
5590053 AAAAAT-ATATAAACTTTATA
1 AAAAATAATA-AAAC-TTATA
5590073 AAAAATAATAAAACTTATA
1 AAAAATAATAAAACTTATA
5590092 AA
1 AA
5590094 TATTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 10 0.50
21 3 0.15
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATAATAAAACTTATA
Found at i:5590121 original size:28 final size:26
Alignment explanation
Indices: 5590043--5590123 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 26
5590033 TATTAAATTC
*
5590043 TAAAAATATTAAAAATATATAAACTTTA
1 TAAAAATA-TAAAAATCTATAAA-TTTA
*
5590071 TAAAAA-ATAATAAAACTTATAAATATTA
1 TAAAAATATAA-AAATC-TATAAAT-TTA
5590099 TAAAAATATAAAAATCTAGTAAATT
1 TAAAAATATAAAAATCTA-TAAATT
5590124 CTAATAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
26 3 0.07
27 8 0.18
28 30 0.67
29 4 0.09
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (26 bp):
TAAAAATATAAAAATCTATAAATTTA
Done.