Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 183 of 211
Found at i:54279732 original size:25 final size:24
Alignment explanation
Indices: 54279704--54279766 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
54279694 TTTATGAGCA
*
54279704 TCCTGATATAGGCTCCTTGTGAACT
1 TCCTGATATAGGCTCATT-TGAACT
54279729 TCCTGATAT-GGCTCATTTGAACT
1 TCCTGATATAGGCTCATTTGAACT
*
54279752 TCCTGTTATATGGCT
1 TCCTGATATA-GGCT
54279767 ATCAGGAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 14 0.41
24 7 0.21
25 13 0.38
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (24 bp):
TCCTGATATAGGCTCATTTGAACT
Found at i:54279753 original size:23 final size:24
Alignment explanation
Indices: 54279704--54279766 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 24
54279694 TTTATGAGCA
*
54279704 TCCTGATATAGGCTCCTTGTGAACT
1 TCCTGATAT-GGCTCATTGTGAACT
54279729 TCCTGATATGGCTCATT-TGAACT
1 TCCTGATATGGCTCATTGTGAACT
54279752 TCCTGTTATATGGCT
1 TCCTG--ATATGGCT
54279767 ATCAGGAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 11 0.31
24 7 0.20
25 17 0.49
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (24 bp):
TCCTGATATGGCTCATTGTGAACT
Found at i:54295468 original size:19 final size:18
Alignment explanation
Indices: 54295423--54295476 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 18
54295413 TGATGAATAA
54295423 AATAAAATAA-AATAATT
1 AATAAAATAATAATAATT
* *
54295440 -TTAAAATAATAATTATT
1 AATAAAATAATAATAATT
54295457 AATAAAATTAATAATAATT
1 AATAAAA-TAATAATAATT
54295476 A
1 A
54295477 TTTAAAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 8 0.27
17 6 0.20
18 5 0.17
19 11 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAAATAATAATAATT
Found at i:54297313 original size:20 final size:21
Alignment explanation
Indices: 54297266--54297313 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
54297256 ATATAAAATA
*
54297266 ATTAATTTTATAATAATATTT
1 ATTAATTTTATAAAAATATTT
54297287 ATT-ATTTTA-AAAAATAATTT
1 ATTAATTTTATAAAAAT-ATTT
54297307 -TTAATTT
1 ATTAATTT
54297314 ATTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTAATTTTATAAAAATATTT
Found at i:54298954 original size:88 final size:88
Alignment explanation
Indices: 54298805--54298968 Score: 256
Period size: 88 Copynumber: 1.9 Consensus size: 88
54298795 TGATTCCACC
* * * *
54298805 GTTCCTAGTACTAACATTCCGTGCGGACTTCAGGCCTGCTGGACATGTGTTTCATTCTAGGTTGC
1 GTTCCTAGTACTAACATTCCGTGCGGACTTCAAGCATGCTGGACACGTGTTTCACTCTAGGTTGC
*
54298870 CTGCGGAGCACGCGGTCCTTTCT
66 CTACGGAGCACGCGGTCCTTTCT
** *
54298893 GTTCCTAGTACTAACATTTTGTGTGGACTTCAAGCATGCTGGACACGTGTTTCACTCTAGGTTGC
1 GTTCCTAGTACTAACATTCCGTGCGGACTTCAAGCATGCTGGACACGTGTTTCACTCTAGGTTGC
54298958 CTACGGAGCAC
66 CTACGGAGCAC
54298969 AAGGCCCCCC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 68 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.32
Consensus pattern (88 bp):
GTTCCTAGTACTAACATTCCGTGCGGACTTCAAGCATGCTGGACACGTGTTTCACTCTAGGTTGC
CTACGGAGCACGCGGTCCTTTCT
Found at i:54300053 original size:105 final size:101
Alignment explanation
Indices: 54299880--54300076 Score: 270
Period size: 105 Copynumber: 1.9 Consensus size: 101
54299870 ACACTCGTAA
** * *
54299880 TGCCATAACCCAGTTATGGTCTTATCATCAGGATGCCATAGCCCAGCTATGGTCTTACACGTATA
1 TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAACTATGGTCTTACACGTAAA
54299945 CATTTACTGCCATGGTCCAACCATGGTCTTACGTTTAAGG
66 CA--T--TGCCATGGTCCAACCATGGTCTTACGTTTAAGG
* * * *
54299985 TGCCATAACCCAGTTATGGTCTTTTCATTAAAATGCCATAGCCCAACTATGGTCTTATA-TTCAA
1 TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAACTATGGTCTTACACGT-AA
54300049 ACATTGCCATGGTCCAACCATGGTCTTA
65 ACATTGCCATGGTCCAACCATGGTCTTA
54300077 TCCGTCAATT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
101 24 0.29
103 1 0.01
104 1 0.01
105 57 0.69
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (101 bp):
TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAACTATGGTCTTACACGTAAA
CATTGCCATGGTCCAACCATGGTCTTACGTTTAAGG
Found at i:54306372 original size:42 final size:42
Alignment explanation
Indices: 54306320--54306443 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 42
54306310 AGGCTGCACA
* * *
54306320 GAAGCACATAAGTA-CTAAACAAAAACCCGTAATGGTTAAACG
1 GAAGCTCATAAG-AGCTAAACAAAAACCCATAAGGGTTAAACG
* *
54306362 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAACT
1 GAAGCTCATAAGAGCTAAACAAAAACCCATAAGGGTTAAACG
* * ** * *
54306404 GAAGCTCAAAAGAGCTGAACTGAAACTCAGAAGGGTTAAA
1 GAAGCTCATAAGAGCTAAACAAAAACCCATAAGGGTTAAA
54306444 TTGAAACTCA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
41 1 0.01
42 69 0.99
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACAAAAACCCATAAGGGTTAAACG
Found at i:54306380 original size:21 final size:21
Alignment explanation
Indices: 54306356--54306490 Score: 103
Period size: 21 Copynumber: 6.5 Consensus size: 21
54306346 CCGTAATGGT
* *
54306356 TAAACGGAAGCTCATAAGAGC
1 TAAACTGAAACTCATAAGAGC
* * *
54306377 TAAAC-GAAAACCCATAAGGGT
1 TAAACTG-AAACTCATAAGAGC
* *
54306398 TAAACTGAAGCTCAAAAGAGC
1 TAAACTGAAACTCATAAGAGC
* * * *
54306419 TGAACTGAAACTCAGAAGGGT
1 TAAACTGAAACTCATAAGAGC
* *
54306440 TAAATTGAAACTCATATGAG-
1 TAAACTGAAACTCATAAGAGC
* * *
54306460 TTAATTGAAGCTCATAAGAGC
1 TAAACTGAAACTCATAAGAGC
54306481 TAAACTGAAA
1 TAAACTGAAA
54306491 GAAAACACGG
Statistics
Matches: 86, Mismatches: 25, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
20 18 0.21
21 67 0.78
22 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (21 bp):
TAAACTGAAACTCATAAGAGC
Found at i:54315604 original size:40 final size:40
Alignment explanation
Indices: 54315488--54315615 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 40
54315478 AAGATTTTCA
*
54315488 CCCAACACTAGTCAGATTAACTGACGATATTAATTGTGTG
1 CCCAGCACTAGTCAGATTAACTGACGATATTAATTGTGTG
* * * *
54315528 CCCAGGACTAGT-TGAATAAATCGAC-A-A--AGATT-TGTG
1 CCCAGCACTAGTCAGATTAACT-GACGATATTA-ATTGTGTG
* *
54315564 CCTAGCCCTAGTCAGATTAACTGACGATATTAATTGTGTG
1 CCCAGCACTAGTCAGATTAACTGACGATATTAATTGTGTG
*
54315604 CCCAACACTAGT
1 CCCAGCACTAGT
54315616 TGAATAAATT
Statistics
Matches: 66, Mismatches: 14, Indels: 16
0.69 0.15 0.17
Matches are distributed among these distances:
36 17 0.26
37 10 0.15
38 2 0.03
39 10 0.15
40 27 0.41
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (40 bp):
CCCAGCACTAGTCAGATTAACTGACGATATTAATTGTGTG
Found at i:54315643 original size:76 final size:76
Alignment explanation
Indices: 54315448--54315663 Score: 306
Period size: 76 Copynumber: 2.8 Consensus size: 76
54315438 CGATAGTAGA
* * * * * *
54315448 TGTGCCCTGCACTAGTCGAATAAATTGACAAAGATTTTCACCCAACACTAGTCAGATTAACTGAC
1 TGTGCCCAGCACTAGTTGAATAAATTGACAAAGATTTGCGCCTAGCACTAGTCAGATTAACTGAC
54315513 GATATTAATTG
66 GATATTAATTG
* * * *
54315524 TGTGCCCAGGACTAGTTGAATAAATCGACAAAGATTTGTGCCTAGCCCTAGTCAGATTAACTGAC
1 TGTGCCCAGCACTAGTTGAATAAATTGACAAAGATTTGCGCCTAGCACTAGTCAGATTAACTGAC
54315589 GATATTAATTG
66 GATATTAATTG
* * * *
54315600 TGTGCCCAACACTAGTTGAATAAATTGACAAAGACTTGCGCCTAGCACTAGTCGGATAAACTGA
1 TGTGCCCAGCACTAGTTGAATAAATTGACAAAGATTTGCGCCTAGCACTAGTCAGATTAACTGA
54315664 TGATCACATA
Statistics
Matches: 122, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 122 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (76 bp):
TGTGCCCAGCACTAGTTGAATAAATTGACAAAGATTTGCGCCTAGCACTAGTCAGATTAACTGAC
GATATTAATTG
Found at i:54331068 original size:21 final size:21
Alignment explanation
Indices: 54331042--54331083 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54331032 TATAATAATT
54331042 TAAAAATTACT-AAAATAAAAA
1 TAAAAA-TACTAAAAATAAAAA
*
54331063 TAAAAATATTAAAAATAAAAA
1 TAAAAATACTAAAAATAAAAA
54331084 ATTAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAATACTAAAAATAAAAA
Found at i:54331075 original size:15 final size:15
Alignment explanation
Indices: 54331057--54331108 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
54331047 ATTACTAAAA
54331057 TAAAAATAAAAATAT
1 TAAAAATAAAAATAT
54331072 TAAAAATAAAAA-AT
1 TAAAAATAAAAATAT
54331086 TAAATAATATATAAATAT
1 TAAA-AATA-A-AAATAT
54331104 ATAAA
1 -TAAA
54331109 TTTATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.19
15 16 0.50
16 1 0.03
17 3 0.09
18 2 0.06
19 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAATAAAAATAT
Found at i:54331282 original size:25 final size:21
Alignment explanation
Indices: 54331229--54331269 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
54331219 TAAAATAAAG
54331229 GGGGCGAAGCCAGAACAATTA
1 GGGGCGAAGCCAGAACAATTA
54331250 GGGGCGAAGCCAGAACAATT
1 GGGGCGAAGCCAGAACAATT
54331270 TTTTAGGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.34, T:0.10
Consensus pattern (21 bp):
GGGGCGAAGCCAGAACAATTA
Found at i:54331918 original size:21 final size:21
Alignment explanation
Indices: 54331871--54331918 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
54331861 ACAATAATTT
*
54331871 TTAAAAAATTCTTAAAATATC
1 TTAAAAAATTCTTAAAATAAC
**
54331892 AAAAAAAATTCTTTAAAA-AAC
1 TTAAAAAATTC-TTAAAATAAC
54331913 TTAAAA
1 TTAAAA
54331919 TTCGTAATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAAAAATTCTTAAAATAAC
Found at i:54332759 original size:15 final size:16
Alignment explanation
Indices: 54332722--54332768 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
54332712 AAATAATAGA
* *
54332722 AAATACAATATTTAA-
1 AAATATAATATATAAT
54332737 AAATATAATATATAAT
1 AAATATAATATATAAT
54332753 AAA-ATAATATA-AAT
1 AAATATAATATATAAT
54332767 AA
1 AA
54332769 TATTTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 5 0.17
15 21 0.72
16 3 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATAATATATAAT
Found at i:54334646 original size:14 final size:14
Alignment explanation
Indices: 54334627--54334654 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54334617 CATATTGTAA
54334627 CATGATTAACATTT
1 CATGATTAACATTT
54334641 CATGATTAACATTT
1 CATGATTAACATTT
54334655 ATAGTTAAAA
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:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
CATGATTAACATTT
Found at i:54335214 original size:33 final size:33
Alignment explanation
Indices: 54335172--54335239 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
54335162 GTATACAAGT
*
54335172 TGAGACCGTGGCCATCCCTAGGTTCTTGGGAGC
1 TGAGACCGTGGCCATCCCTAGGTTCTTGCGAGC
*
54335205 TGAGACCGTGGCCATCCCTGGGTTCTTGCGAGC
1 TGAGACCGTGGCCATCCCTAGGTTCTTGCGAGC
54335238 TG
1 TG
54335240 GATCTGCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.13, C:0.28, G:0.34, T:0.25
Consensus pattern (33 bp):
TGAGACCGTGGCCATCCCTAGGTTCTTGCGAGC
Found at i:54338304 original size:57 final size:57
Alignment explanation
Indices: 54338173--54338312 Score: 147
Period size: 57 Copynumber: 2.5 Consensus size: 57
54338163 CCACGAGTCG
* * * * *
54338173 TTTTAGTCTTAAGAAATTTTCTAAAATAATCGGCTGGAAATATCAATCTGCAAACTG
1 TTTTAGACTTGAGAAATTTTCTAAAATAATCAGCTGGAAATATCAATCAGCAAACTA
* * * * * *
54338230 TTTTAGATTTG-GAAAATTTTCTAAAATAATCAGCTGGGAGTATTAATCAGTAAGCTA
1 TTTTAGACTTGAG-AAATTTTCTAAAATAATCAGCTGGAAATATCAATCAGCAAACTA
* *
54338287 TTTTATACTTGAGAAATTTTCAAAAA
1 TTTTAGACTTGAGAAATTTTCTAAAA
54338313 AAAATTGACT
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
56 1 0.01
57 65 0.97
58 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (57 bp):
TTTTAGACTTGAGAAATTTTCTAAAATAATCAGCTGGAAATATCAATCAGCAAACTA
Found at i:54338505 original size:69 final size:69
Alignment explanation
Indices: 54338403--54339046 Score: 551
Period size: 69 Copynumber: 9.3 Consensus size: 69
54338393 GAGTTTGTAA
* * * * * *
54338403 CTCTCACTAACTATGTTGAAGGCTAC-GATTTTAATCCCT-CGAGCCTTATTATGATAGCTGGGA
1 CTCTCGCTAACTATGTTGGAGGCTACAG-TTTTAAT-CCTGCAAGCCTTAGTATGACAGTTGGGA
54338466 GCTTTG
64 GCTTTG
* * * * * ** **
54338472 CTCTTGCTAACTGTGTTGGAGGATACAGTTTTAATCTTGCAAGCCTTAGTATGAAAACTAAGAGC
1 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
54338537 ATTT-
66 -TTTG
54338541 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
1 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
54338606 TTTG
66 TTTG
* * * *** * *
54338610 CTCTCGCTAACTGTGTTAGAGGTTGTGGTTTTAATCCTGCAAGTCTTTA-TATGATAGTTGGGAG
1 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAG-CCTTAGTATGACAGTTGGGAG
54338674 CTTTG
65 CTTTG
* * * * * ** * *
54338679 TTCTCCCTAACTATGTTGAAGGCTTCGGTTTTAATCCTGTGAGCCTTAGTATGGCAGCTGGGAGC
1 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
54338744 TTTG
66 TTTG
* * * * * * * * ** * *
54338748 CTCTTGCTAACCATATTGGAGGTTATGAATTTTTATCCTACAAATCTTATTATGACAATTGGGAG
1 CTCTCGCTAACTATGTTGGAGGCTA-CAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAG
54338813 CTTTG
65 CTTTG
* ** ** **** * *
54338818 CTCTCACTAACTATGTTGGAGGCTGGAACTTTAATCCTATGTGCCTTAGTATGATAATTGGGAGC
1 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
54338883 TTTG
66 TTTG
* * * * * * * * * *
54338887 CACTCGCTGACTATGTTGGAGGCT-CCGATTTTAATCTTACGAGTCTTAATATGATAGCTGGGAG
1 CTCTCGCTAACTATGTTGGAGGCTACAG-TTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAG
54338951 CTTTG
65 CTTTG
* * * *
54338956 CTCTCGCTAACTGTGTTGGAGGCTGCTGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAAC
1 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
*
54339021 TTTA
66 TTTG
* *
54339025 CTCTTGCTAACTGTGTTGGAGG
1 CTCTCGCTAACTATGTTGGAGG
54339047 TTGCGATTTT
Statistics
Matches: 459, Mismatches: 107, Indels: 18
0.79 0.18 0.03
Matches are distributed among these distances:
68 9 0.02
69 390 0.85
70 60 0.13
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (69 bp):
CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
TTTG
Found at i:54338651 original size:138 final size:138
Alignment explanation
Indices: 54338403--54339077 Score: 631
Period size: 138 Copynumber: 4.9 Consensus size: 138
54338393 GAGTTTGTAA
* * * *
54338403 CTCTCACTAACTATGTTGAAGGCTAC-GATTTTAATCCCT-CGAGCCTTATTATGATAGCTGGGA
1 CTCTCACTAACTATGTTGGAGGCTACAG-TTTTAAT-CCTGCGAGCCTTAGTATGACAGTTGGGA
* * * *
54338466 GCTTTGCTCTTGCTAACTGTGTTGGAGGATAC-AGTTTTAATCTTGCAAGCCTTAGTATGAAAAC
64 GCTTTGCTCTTGCTAACTGTGTTGGAGGTTACGA-TTTTAATCCTACAAGCCTTAGTATGATAAC
**
54338530 TAAGAGCATTT-
128 TGGGAGC-TTTG
* *
54338541 CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGC
1 CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
* * ** * * * **
54338606 TTTGCTCTCGCTAACTGTGTTAGAGGTTGTGGTTTTAATCCTGCAAGTCTTTA-TATGATAGTTG
66 TTTGCTCTTGCTAACTGTGTTGGAGGTTACGATTTTAATCCTACAAG-CCTTAGTATGATAACTG
54338670 GGAGCTTTG
130 GGAGCTTTG
* * * * * * * *
54338679 TTCTCCCTAACTATGTTGAAGGCTTCGGTTTTAATCCTGTGAGCCTTAGTATGGCAGCTGGGAGC
1 CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
** * * * ** * * *
54338744 TTTGCTCTTGCTAACCATATTGGAGGTTATGAATTTTTATCCTACAAATCTTATTATGACAATTG
66 TTTGCTCTTGCTAACTGTGTTGGAGGTTACG-ATTTTAATCCTACAAGCCTTAGTATGATAACTG
54338809 GGAGCTTTG
130 GGAGCTTTG
** ** ** * * *
54338818 CTCTCACTAACTATGTTGGAGGCTGGAACTTTAATCCTATGTGCCTTAGTATGATAATTGGGAGC
1 CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
* * * * * * * * * * *
54338883 TTTGCACTCGCTGACTATGTTGGAGGCTCCGATTTTAATCTTACGAGTCTTAATATGATAGCTGG
66 TTTGCTCTTGCTAACTGTGTTGGAGGTTACGATTTTAATCCTACAAGCCTTAGTATGATAACTGG
54338948 GAGCTTTG
131 GAGCTTTG
* * * * * *
54338956 CTCTCGCTAACTGTGTTGGAGGCTGCTGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAAC
1 CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
* * * *
54339021 TTTACTCTTGCTAACTGTGTTGGAGGTTGCGATTTTTAATCCTACGATCCTTAGTAT
66 TTTGCTCTTGCTAACTGTGTTGGAGGTTACGA-TTTTAATCCTACAAGCCTTAGTAT
54339078 TCACAGAATA
Statistics
Matches: 433, Mismatches: 96, Indels: 15
0.80 0.18 0.03
Matches are distributed among these distances:
137 6 0.01
138 298 0.69
139 129 0.30
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (138 bp):
CTCTCACTAACTATGTTGGAGGCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGTTGGGAGC
TTTGCTCTTGCTAACTGTGTTGGAGGTTACGATTTTAATCCTACAAGCCTTAGTATGATAACTGG
GAGCTTTG
Found at i:54338873 original size:208 final size:205
Alignment explanation
Indices: 54338403--54339064 Score: 610
Period size: 207 Copynumber: 3.2 Consensus size: 205
54338393 GAGTTTGTAA
* * * * *
54338403 CTCTCACTAACTATGTTGAAGGCTACGATTTTAATCCCT-CGAGCCTTATTATGATAGCTGGGAG
1 CTCTCACTAACTATGTTGGAGGCT-GGATTTTAAT-CCTAAGTGCCTTA-TATGATAGTTGGGAG
* * * * * * *
54338467 CTTTGCTCTTGCTAACTGTGTTGGAGGATACAGTTTTAATCTTGCAAGCCTTAGTATGAAAACTA
63 CTTTGCTCTCGCTAACTATGTTGGAGGCTACGGTTTTAATCTTGCGAGCCTTAGTATGAAAGCTG
* * * * * *
54338532 AGAGCATTT-CTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGAC
128 GGAGC-TTTGCTCTCGCTAACCATATTGGAGGCTACAATTTTAATCCTACAAACCTTAGTATGAC
*
54338596 AGTTGGGAGCTTTG
192 AATTGGGAGCTTTG
* * * * * *
54338610 CTCTCGCTAACTGTGTTAGAGGTTGTGGTTTTAATCCTGCAAGT-CTTTATATGATAGTTGGGAG
1 CTCTCACTAACTATGTTGGAGGCTG-GATTTTAATCCT--AAGTGCCTTATATGATAGTTGGGAG
* * * * * * **
54338674 CTTTGTTCTCCCTAACTATGTTGAAGGCTTCGGTTTTAATCCTGTGAGCCTTAGTATGGCAGCTG
63 CTTTGCTCTCGCTAACTATGTTGGAGGCTACGGTTTTAATCTTGCGAGCCTTAGTATGAAAGCTG
* * * * * *
54338739 GGAGCTTTGCTCTTGCTAACCATATTGGAGGTTATGAATTTTTATCCTACAAATCTTATTATGAC
128 GGAGCTTTGCTCTCGCTAACCATATTGGAGGCTA-CAATTTTAATCCTACAAACCTTAGTATGAC
54338804 AATTGGGAGCTTTG
192 AATTGGGAGCTTTG
* * *
54338818 CTCTCACTAACTATGTTGGAGGCTGGAACTTTAATCCTATGTGCCTTAGTATGATAATTGGGAGC
1 CTCTCACTAACTATGTTGGAGGCTGG-ATTTTAATCCTAAGTGCCTTA-TATGATAGTTGGGAGC
* * * * * * * *
54338883 TTTGCACTCGCTGACTATGTTGGAGGCTCCGATTTTAATCTTACGAGTCTTAATATGATAGCTGG
64 TTTGCTCTCGCTAACTATGTTGGAGGCTACGGTTTTAATCTTGCGAGCCTTAGTATGAAAGCTGG
** * * ** * * *
54338948 GAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCTGTTTTAATCCTGCAAGCCTTAGTATGACAG
129 GAGCTTTGCTCTCGCTAACCATATTGGAGGCTACAATTTTAATCCTACAAACCTTAGTATGACAA
* *
54339013 TTGGGAACTTTA
194 TTGGGAGCTTTG
** * *
54339025 CTCTTGCTAACTGTGTTGGAGGTTGCGATTTTTAATCCTA
1 CTCTCACTAACTATGTTGGAGGCTG-GA-TTTTAATCCTA
54339065 CGATCCTTAG
Statistics
Matches: 360, Mismatches: 84, Indels: 21
0.77 0.18 0.05
Matches are distributed among these distances:
206 9 0.03
207 176 0.49
208 174 0.48
209 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (205 bp):
CTCTCACTAACTATGTTGGAGGCTGGATTTTAATCCTAAGTGCCTTATATGATAGTTGGGAGCTT
TGCTCTCGCTAACTATGTTGGAGGCTACGGTTTTAATCTTGCGAGCCTTAGTATGAAAGCTGGGA
GCTTTGCTCTCGCTAACCATATTGGAGGCTACAATTTTAATCCTACAAACCTTAGTATGACAATT
GGGAGCTTTG
Found at i:54338941 original size:277 final size:276
Alignment explanation
Indices: 54338403--54339077 Score: 715
Period size: 277 Copynumber: 2.4 Consensus size: 276
54338393 GAGTTTGTAA
* * *
54338403 CTCTCACTAACTATGTTGAAGGCTACGATTTTAATCCCT-CGAGCCTTATTATGATAGCTGGGAG
1 CTCTCACTAACTATGTTGAAGGCTACGGTTTTAAT-CCTGCGAGCCTTAGTATGACAGCTGGGAG
** * * * * *
54338467 CTTTGCTCTTGCTAACTGTGTTGGAGGATACAGTTTTAATCTTGCAAGCCTTAGTATGAAAACTA
65 CTTTGCTCTTGCTAACCATATTGGAGGATACAATTTTAATCCTACAAACCTTAGTATGAAAACTA
* ** *
54338532 AGAGCATTTCTCTCGCTAACTATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACA
130 AGAGCATTTCTCTCACTAACTATGTTGGAGGCTACAACTTTAATCCTACAAGCCTTAGTATGACA
* * * * ** * * *
54338597 GTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTGTGGTTTTAATCCTGCAAGTCTTTATAT
195 ATTGGGAGCTTTGCACTCGCTAACTATGTTAGAGGCTCCGATTTTAATCCTACAAGTCTTAATAT
*
54338662 GATAGTTGGGAGCTTTG
260 GATAGCTGGGAGCTTTG
* * * * *
54338679 TTCTCCCTAACTATGTTGAAGGCTTCGGTTTTAATCCTGTGAGCCTTAGTATGGCAGCTGGGAGC
1 CTCTCACTAACTATGTTGAAGGCTACGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGC
* * * * * * * *
54338744 TTTGCTCTTGCTAACCATATTGGAGGTTATGAATTTTTATCCTACAAATCTTATTATGACAATTG
66 TTTGCTCTTGCTAACCATATTGGAGGATA-CAATTTTAATCCTACAAACCTTAGTATGAAAACTA
* ** *** *
54338809 GGAGC-TTTGCTCTCACTAACTATGTTGGAGGCTGGAACTTTAATCCTATGTGCCTTAGTATGAT
130 AGAGCATTT-CTCTCACTAACTATGTTGGAGGCTACAACTTTAATCCTACAAGCCTTAGTATGAC
* * * *
54338873 AATTGGGAGCTTTGCACTCGCTGACTATGTTGGAGGCTCCGATTTTAATCTTACGAGTCTTAATA
194 AATTGGGAGCTTTGCACTCGCTAACTATGTTAGAGGCTCCGATTTTAATCCTACAAGTCTTAATA
54338938 TGATAGCTGGGAGCTTTG
259 TGATAGCTGGGAGCTTTG
* * * * * * * *
54338956 CTCTCGCTAACTGTGTTGGAGGCTGCTGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAAC
1 CTCTCACTAACTATGTTGAAGGCTACGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGC
* ** * * * * * *
54339021 TTTACTCTTGCTAACTGTGTTGGAGGTTGCGATTTTTAATCCTACGATCCTTAGTAT
66 TTTGCTCTTGCTAACCATATTGGAGGATAC-AATTTTAATCCTACAAACCTTAGTAT
54339078 TCACAGAATA
Statistics
Matches: 324, Mismatches: 71, Indels: 7
0.81 0.18 0.02
Matches are distributed among these distances:
275 3 0.01
276 81 0.25
277 240 0.74
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (276 bp):
CTCTCACTAACTATGTTGAAGGCTACGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGC
TTTGCTCTTGCTAACCATATTGGAGGATACAATTTTAATCCTACAAACCTTAGTATGAAAACTAA
GAGCATTTCTCTCACTAACTATGTTGGAGGCTACAACTTTAATCCTACAAGCCTTAGTATGACAA
TTGGGAGCTTTGCACTCGCTAACTATGTTAGAGGCTCCGATTTTAATCCTACAAGTCTTAATATG
ATAGCTGGGAGCTTTG
Found at i:54346371 original size:38 final size:38
Alignment explanation
Indices: 54346250--54346364 Score: 194
Period size: 38 Copynumber: 3.0 Consensus size: 38
54346240 TCCCTATCCA
*
54346250 TACTTCAAATCTGTCTTATTTTTTAGACTTAATATTTT
1 TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
*
54346288 TACTTTAAATCTGTCTCATTTTTTAGACTTAATATTTT
1 TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
* *
54346326 TACTTCAAATCTGTCTCATTTTTTAAATTTAATATTTT
1 TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
54346364 T
1 T
54346365 TATTCAAGCC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (38 bp):
TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
Found at i:54351215 original size:18 final size:18
Alignment explanation
Indices: 54351194--54351228 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
54351184 TAATATTATA
54351194 AAATA-AAATAATTATTTC
1 AAATATAAAT-ATTATTTC
54351212 AAATATAAATATTATTT
1 AAATATAAATATTATTT
54351229 TTATATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATAAATATTATTTC
Found at i:54354342 original size:25 final size:25
Alignment explanation
Indices: 54354314--54354426 Score: 122
Period size: 25 Copynumber: 4.5 Consensus size: 25
54354304 AGAGTCATTA
* *
54354314 ATCGGGAAACTCATAAGAGCCAATT
1 ATCGGGAAGCTCATGAGAGCCAATT
*
54354339 ATCGAGAAGCTCCA-GAGAGCC-ATT
1 ATCGGGAAGCT-CATGAGAGCCAATT
*
54354363 AATCAGGAAGCTCATGAGAGCCAATT
1 -ATCGGGAAGCTCATGAGAGCCAATT
* * *
54354389 ATTGGGAAGCTCGTGAGAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCCAATT
*
54354414 AGCGGGAAGCTCA
1 ATCGGGAAGCTCA
54354427 AAAGAGATGC
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
24 5 0.07
25 62 0.86
26 5 0.07
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCCAATT
Found at i:54354377 original size:50 final size:50
Alignment explanation
Indices: 54354302--54354410 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 50
54354292 GAAAAGCCTG
* *
54354302 AGAGAGTCATTAATCGGGAAACTCATAAGAGCCAATTATCGAGAAGCTCC
1 AGAGAGCCATTAATCAGGAAACTCATAAGAGCCAATTATCGAGAAGCTCC
* * * * *
54354352 AGAGAGCCATTAATCAGGAAGCTCATGAGAGCCAATTATTGGGAAGCTCG
1 AGAGAGCCATTAATCAGGAAACTCATAAGAGCCAATTATCGAGAAGCTCC
*
54354402 TGAGAGCCA
1 AGAGAGCCA
54354411 AATAGCGGGA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (50 bp):
AGAGAGCCATTAATCAGGAAACTCATAAGAGCCAATTATCGAGAAGCTCC
Found at i:54354422 original size:50 final size:49
Alignment explanation
Indices: 54354302--54354432 Score: 138
Period size: 50 Copynumber: 2.6 Consensus size: 49
54354292 GAAAAGCCTG
* *
54354302 AGAGAGTCATTAATCGGGAAACTCATAAGAGCCAATTATCGAGAAGCTCC
1 AGAGAGCCA-TAATCGGGAAGCTCATAAGAGCCAATTATCGAGAAGCTCC
* * * * *
54354352 AGAGAGCCATTAATCAGGAAGCTCATGAGAGCCAATTATTGGGAAGCTCG
1 AGAGAGCCA-TAATCGGGAAGCTCATAAGAGCCAATTATCGAGAAGCTCC
* *
54354402 TGAGAGCCA-AATAGCGGGAAGCTCAAAAGAG
1 AGAGAGCCATAAT--CGGGAAGCTCATAAGAG
54354433 ATGCGGTGTG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
48 3 0.04
50 65 0.96
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (49 bp):
AGAGAGCCATAATCGGGAAGCTCATAAGAGCCAATTATCGAGAAGCTCC
Found at i:54354894 original size:21 final size:22
Alignment explanation
Indices: 54354864--54354908 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
54354854 CTCCTCACTT
*
54354864 TTTTTTATTTTTAT-TTTAAAA
1 TTTTTAATTTTTATATTTAAAA
*
54354885 TTTTTAATTTTTATATTTCAAA
1 TTTTTAATTTTTATATTTAAAA
54354907 TT
1 TT
54354909 AAAAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTAATTTTTATATTTAAAA
Found at i:54354953 original size:22 final size:22
Alignment explanation
Indices: 54354914--54354956 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54354904 AAATTAAAAA
*
54354914 TTTTGAGAAACTTTGAGAAACT
1 TTTTGAGAAAATTTGAGAAACT
54354936 TTTTG-GAAAATTTGGAGAAAC
1 TTTTGAGAAAATTT-GAGAAAC
54354957 AACTCAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (22 bp):
TTTTGAGAAAATTTGAGAAACT
Found at i:54355238 original size:35 final size:34
Alignment explanation
Indices: 54355153--54355299 Score: 138
Period size: 34 Copynumber: 4.3 Consensus size: 34
54355143 TTTTCTTGTT
* * * *
54355153 TTTTCTTGTAGTGAATATTTCCTGTTCACACATC
1 TTTTCTTGCAGAGAATCTTTCCTGTTCACTCATC
* * *
54355187 ATTTCTT-CAAAGGAATCTTTCCTGTTCACCTCGTC
1 TTTTCTTGCAGA-GAATCTTTCCTGTTCA-CTCATC
54355222 TTTTCTTGCAGAGAATCTTTCCTGTTCA-TGCATC
1 TTTTCTTGCAGAGAATCTTTCCTGTTCACT-CATC
* * **
54355256 -ATTCTTTGCAGGGAATCTTTCCTGTTCACAAATC
1 TTTTC-TTGCAGAGAATCTTTCCTGTTCACTCATC
54355290 TTTTCTTGCA
1 TTTTCTTGCA
54355300 TCATTTCTTC
Statistics
Matches: 91, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
33 5 0.05
34 54 0.59
35 29 0.32
36 3 0.03
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (34 bp):
TTTTCTTGCAGAGAATCTTTCCTGTTCACTCATC
Found at i:54355271 original size:69 final size:69
Alignment explanation
Indices: 54355153--54355284 Score: 178
Period size: 69 Copynumber: 1.9 Consensus size: 69
54355143 TTTTCTTGTT
* *
54355153 TTTTCTTGTAGTGAATATTTCCTGTTCACACATCATTTCTTCAAAGGAATCTTTCCTGTTCACCT
1 TTTTCTTGCAGAGAATATTTCCTGTTCACACATCATTTCTTCAAAGGAATCTTTCCTGTTCACCT
54355218 CGTC
66 CGTC
* ** *
54355222 TTTTCTTGCAGAGAATCTTTCCTGTTCATGCATCA-TTCTTTGC-AGGGAATCTTTCCTGTTCAC
1 TTTTCTTGCAGAGAATATTTCCTGTTCACACATCATTTC-TT-CAAAGGAATCTTTCCTGTTCAC
54355285 AAATCTTTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
68 3 0.05
69 51 0.93
70 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (69 bp):
TTTTCTTGCAGAGAATATTTCCTGTTCACACATCATTTCTTCAAAGGAATCTTTCCTGTTCACCT
CGTC
Found at i:54358113 original size:20 final size:23
Alignment explanation
Indices: 54358078--54358122 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
54358068 GAACAAATTA
54358078 TTGATTCTATTTCTTTTTTG-AT
1 TTGATTCTATTTCTTTTTTGTAT
54358100 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTCTTTTTTGTAT
54358121 TT
1 TT
54358123 CTCTTATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (23 bp):
TTGATTCTATTTCTTTTTTGTAT
Found at i:54358178 original size:21 final size:23
Alignment explanation
Indices: 54358154--54358196 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
54358144 TTAATTTTTT
*
54358154 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTGTTTAG
*
54358175 AAAAGAGATTTGCTTCTGTTTA
1 AAAACAGATTTGCTTCTGTTTA
54358197 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTGTTTAG
Found at i:54369513 original size:12 final size:12
Alignment explanation
Indices: 54369496--54369550 Score: 67
Period size: 12 Copynumber: 4.5 Consensus size: 12
54369486 TGTTCATTTA
54369496 TTCATCAAGTCT
1 TTCATCAAGTCT
*
54369508 TTCATCAAGTGTTT
1 TTCATCAA--GTCT
*
54369522 TTCATCAAGTTT
1 TTCATCAAGTCT
54369534 TTCATCAAG-CT
1 TTCATCAAGTCT
54369545 TTCATC
1 TTCATC
54369551 TTCTGAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 7 0.18
12 21 0.54
14 11 0.28
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (12 bp):
TTCATCAAGTCT
Found at i:54369720 original size:54 final size:54
Alignment explanation
Indices: 54369661--54369772 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
54369651 ACCTTACGTC
*
54369661 ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGCGCA
1 ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGCCCA
54369715 ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGCCCA
1 ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGCCCA
54369769 ACTC
1 ACTC
54369773 CAACATGCCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.26, C:0.35, G:0.03, T:0.37
Consensus pattern (54 bp):
ACTCACATCCATCTACTTTCATTTCTTTTATTCAACCCTCTCCAAATATGCCCA
Found at i:54384412 original size:16 final size:16
Alignment explanation
Indices: 54384391--54384423 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54384381 TTCGCTGTAT
54384391 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
54384407 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
54384423 T
1 T
54384424 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:54384683 original size:18 final size:17
Alignment explanation
Indices: 54384662--54384696 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54384652 TTATTATTAA
*
54384662 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54384680 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54384697 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54384803 original size:18 final size:17
Alignment explanation
Indices: 54384782--54384816 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54384772 TTATTATTAA
*
54384782 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54384800 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54384817 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54384814 original size:59 final size:57
Alignment explanation
Indices: 54384642--54384937 Score: 206
Period size: 59 Copynumber: 5.0 Consensus size: 57
54384632 TTAATCATAT
* *
54384642 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
* * * * ** * * *
54384699 TTAATAATCA-ATATTCTTATATGAATTTACTCAAATCATAATATATGATACT-ATAAAATATAA
1 TT--TAA-CATA-ATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAAT-T-A
* *
54384762 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
* * * * ** * * *
54384819 TTAATAATCA-ATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT-ATAAAATATAA
1 TT--TAA-CATA-ATTATTATTA-AATATATTTTAATTAAAATATATGAT-TTAATAAAAT-T-A
54384882 TTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
54384938 TAAAATAATT
Statistics
Matches: 176, Mismatches: 42, Indels: 41
0.68 0.16 0.16
Matches are distributed among these distances:
57 4 0.02
58 4 0.02
59 62 0.35
60 37 0.21
61 59 0.34
62 6 0.03
63 4 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (57 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
Found at i:54384875 original size:61 final size:61
Alignment explanation
Indices: 54384690--54384877 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
54384680 ATATAATTTA
* *
54384690 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
* * * * * ** * * * *
54384751 ATAAAA-T-ATAATTTAA-C-ATAATTATTATTA-AATATATTTTAATTAAAATATATAAT-TT
1 ATAAAATTCTTAA--TAATCAAT-ATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
54384809 AATAAAATTCTTAATAATCAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
54384871 ATAAAAT
1 ATAAAAT
54384878 ATAATTTGAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 1 0.01
59 33 0.35
60 19 0.20
61 40 0.43
62 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACT
Found at i:54384923 original size:18 final size:17
Alignment explanation
Indices: 54384900--54384936 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
54384890 AATTATTATT
54384900 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
54384916 AAATATATGATTTAATA
1 AAATATATGATTTAATA
54384933 AAAT
1 AAAT
54384937 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:54384946 original size:120 final size:120
Alignment explanation
Indices: 54384642--54384937 Score: 549
Period size: 120 Copynumber: 2.5 Consensus size: 120
54384632 TTAATCATAT
54384642 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* *
54384707 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
54384762 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
54384827 CAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
*
54384882 TTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
54384938 TAAAATAATT
Statistics
Matches: 172, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
120 170 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATAAGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:54384972 original size:47 final size:46
Alignment explanation
Indices: 54384919--54385159 Score: 175
Period size: 47 Copynumber: 5.3 Consensus size: 46
54384909 TTAATTAAAA
*
54384919 TATATG-ATTTAATAAAATTTAAAATAATTATTACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATTA-TAATAAATTTTCT
* *
54384966 TATATGAATTTGTATAATTTAAAATAATTATTAT--TAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT
* * *
54385011 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT
* *
54385057 TATATGAATTTATATAATTTAAAATAATTA--ATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT
* * * *
54385102 TA-AT-AATAATATATAATTTCATAA-AATTCTTAATAATAAATATTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT
54385148 TATATGAATTTA
1 TATATGAATTTA
54385160 CTAAAATCAT
Statistics
Matches: 152, Mismatches: 20, Indels: 44
0.70 0.09 0.20
Matches are distributed among these distances:
43 6 0.04
44 46 0.30
45 18 0.12
46 13 0.09
47 59 0.39
48 10 0.07
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATTATAATAAATTTTCT
Found at i:54384993 original size:101 final size:98
Alignment explanation
Indices: 54384876--54385159 Score: 321
Period size: 91 Copynumber: 3.0 Consensus size: 98
54384866 ATACTATAAA
* *
54384876 ATATAATTTGAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTT-A
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAA-TAAAATATAT-ATTT-ATAAAATTTCA
54384940 AAATAATTATT-ACTAATAAATTTTCTTATATGAATTT
63 AAA-AATTATTGA-TAATAAATTTTCTTATATGAATTT
* *
54384977 GTATAATTTAAAATAATTATTATTAAATATAATTTAAT--AATA-ATA--TAT--AATTTCATAA
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAATATATATTTATAAAATTTCAAAA
*
54385035 AATTCTTGATAATAAATTTTCTTATATGAATTT
66 AATTATTGATAATAAATTTTCTTATATGAATTT
* *
54385068 ATATAATTTAAAATAATTAATATTAAATATAATTTAAT--AATA-ATA--TAT--AATTTCATAA
1 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAATATATATTTATAAAATTTCAAAA
* * *
54385126 AATTCTTAATAATAAATATTCTTATATGAATTT
66 AATTATTGATAATAAATTTTCTTATATGAATTT
54385159 A
1 A
54385160 CTAAAATCAT
Statistics
Matches: 172, Mismatches: 9, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
91 123 0.72
92 4 0.02
93 2 0.01
94 1 0.01
96 1 0.01
97 2 0.01
98 4 0.02
100 1 0.01
101 34 0.20
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (98 bp):
ATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAATATATATTTATAAAATTTCAAAA
AATTATTGATAATAAATTTTCTTATATGAATTT
Found at i:54385028 original size:44 final size:44
Alignment explanation
Indices: 54384978--54385120 Score: 150
Period size: 44 Copynumber: 3.2 Consensus size: 44
54384968 TATGAATTTG
54384978 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATA
* * * *
54385022 TATAATTTCATAA-AATTCTTGATAATAAAT-T-TTCTTATATGAAT-TTA
1 TATAATTT-AAAATAATTATT-AT--TAAATATAAT-TTA-AT-AATAATA
*
54385069 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATA
54385113 TATAATTT
1 TATAATTT
54385121 CATAAAATTC
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
43 3 0.04
44 31 0.39
45 10 0.13
46 10 0.13
47 22 0.28
48 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (44 bp):
TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATA
Found at i:54385049 original size:91 final size:91
Alignment explanation
Indices: 54384944--54385159 Score: 378
Period size: 91 Copynumber: 2.4 Consensus size: 91
54384934 AATTTAAAAT
* * * *
54384944 AATTATTACTAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
54385009 TTTAATAATAATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
*
54385035 AATTCTTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
54385100 TTTAATAATAATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
*
54385126 AATTCTTAATAATAAATATTCTTATATGAATTTA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTA
54385160 CTAAAATCAT
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 118 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (91 bp):
AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
TTTAATAATAATATATAATTTCATAA
Found at i:54385101 original size:16 final size:16
Alignment explanation
Indices: 54385071--54385119 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
54385061 TGAATTTATA
54385071 TAAT-TTAAA-ATAAT
1 TAATATTAAATATAAT
54385085 TAATATTAAATATAATT
1 TAATATTAAATATAA-T
*
54385102 TAATAATAATATATAAT
1 TAATATTAA-ATATAAT
54385119 T
1 T
54385120 TCATAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.13
15 5 0.17
16 4 0.13
17 11 0.37
18 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATTAAATATAAT
Found at i:54385117 original size:18 final size:17
Alignment explanation
Indices: 54385076--54385125 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
54385066 TTATATAATT
*
54385076 TAAA-ATAA-TTAATAT
1 TAAATATAATTTAATAA
54385091 TAAATATAATTTAATAA
1 TAAATATAATTTAATAA
*
54385108 TAATATATAATTTCATAA
1 TAA-ATATAATTTAATAA
54385126 AATTCTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 9 0.30
18 13 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATATAATTTAATAA
Found at i:54389257 original size:23 final size:23
Alignment explanation
Indices: 54389197--54389271 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
54389187 TCTACTCACT
*
54389197 AACAAATCAAGAACAATCTCCAGCA
1 AACAAATCAAGAACAATATCCA--A
* * *
54389222 GAC-TATCAA-AACAATTTCCAA
1 AACAAATCAAGAACAATATCCAA
54389243 AACAAATCAAGAACAATAT-CAA
1 AACAAATCAAGAACAATATCCAA
54389265 AACAAAT
1 AACAAAT
54389272 GCAACAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
21 3 0.07
22 15 0.36
23 17 0.40
24 5 0.12
25 2 0.05
ACGTcount: A:0.56, C:0.23, G:0.05, T:0.16
Consensus pattern (23 bp):
AACAAATCAAGAACAATATCCAA
Found at i:54389265 original size:22 final size:22
Alignment explanation
Indices: 54389226--54389271 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
54389216 CCAGCAGACT
*
54389226 ATCAAAACAATTTCCAAAACAA
1 ATCAAAACAATATCCAAAACAA
54389248 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
54389270 AT
1 AT
54389272 GCAACAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.17
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:54389293 original size:107 final size:107
Alignment explanation
Indices: 54389170--54389629 Score: 796
Period size: 107 Copynumber: 4.3 Consensus size: 107
54389160 CTATACTTGT
*
54389170 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATCTCCAGCAGACTATCAAAACA
1 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACA
*
54389235 ATTTCCAAAACAAATCAAGAACAATATCAAAACAAATGCAAC
66 ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
* * * *
54389277 AATTTCCAGCTTCATCTTCCT-CTCACAAACAAATCAAGAACAGTTTCCAACAGACTATCAAAAC
1 AATTTCCAGTTTCATCTT-CTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
54389341 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
65 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
* *
54389384 AATTTCCAATTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCTAGCAGACTATCAAAACA
1 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACA
* *
54389449 ATTGCCAGAACAAATCAAGAACAATATCAAAACAAATGTAAC
66 ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
* *
54389491 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAGGAACAATTTCCAGCAGACTATCAAAATA
1 AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACA
54389556 ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
66 ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
54389598 AATTTCCAGTTTCATCTTCTACTCACTAACAA
1 AATTTCCAGTTTCATCTTCTACTCACTAACAA
54389630 CGAGAAACTA
Statistics
Matches: 331, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
106 2 0.01
107 327 0.99
108 2 0.01
ACGTcount: A:0.45, C:0.25, G:0.06, T:0.24
Consensus pattern (107 bp):
AATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACA
ATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAAC
Found at i:54389364 original size:23 final size:21
Alignment explanation
Indices: 54389304--54389366 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 21
54389294 TCCTCTCACA
*
54389304 AACAAATCAAGAACAGTTTCC
1 AACAAATCAAGAACAATTTCC
54389325 AACAGACTATCAA-AACAATTTCC
1 AACA-A--ATCAAGAACAATTTCC
54389348 AGAACAAATCAAGAACAAT
1 --AACAAATCAAGAACAAT
54389367 ATCAAAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
21 4 0.11
22 6 0.17
23 15 0.43
24 6 0.17
25 4 0.11
ACGTcount: A:0.52, C:0.22, G:0.08, T:0.17
Consensus pattern (21 bp):
AACAAATCAAGAACAATTTCC
Found at i:54389375 original size:22 final size:22
Alignment explanation
Indices: 54389333--54389378 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54389323 CCAACAGACT
* *
54389333 ATCAAAACAATTTCCAGAACAA
1 ATCAAAACAATATCCAAAACAA
54389355 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
54389377 AT
1 AT
54389379 GCAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:54389471 original size:23 final size:24
Alignment explanation
Indices: 54389411--54389473 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
54389401 TCTACTCACT
* *
54389411 AACAAATCAAGAACAATTTCTAGC
1 AACAAATCAAGAACAATTGCCAGC
*
54389435 AGAC-TATCAA-AACAATTGCCAG-
1 A-ACAAATCAAGAACAATTGCCAGC
54389457 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
54389474 ATCAAAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.19
23 16 0.50
24 6 0.19
25 2 0.06
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (24 bp):
AACAAATCAAGAACAATTGCCAGC
Found at i:54389733 original size:19 final size:18
Alignment explanation
Indices: 54389691--54389735 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
54389681 GTAAACTCTT
* *
54389691 TCAAAAAACGGCAGATTA
1 TCAAAAAACAGCAGACTA
54389709 TCAAAAAACAGCAGACTA
1 TCAAAAAACAGCAGACTA
54389727 TCAAAAAAC
1 TCAAAAAAC
54389736 TGTCTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (18 bp):
TCAAAAAACAGCAGACTA
Found at i:54392166 original size:25 final size:25
Alignment explanation
Indices: 54392138--54392201 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
54392128 TTAGCCCTCT
54392138 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATGGTTCTTG
54392163 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATGGTTCTTG
54392188 CGAGCTTCCCGTTA
1 CGAGCTTCCCGTTA
54392202 ATAGCTCTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATGGTTCTTG
Found at i:54394245 original size:132 final size:132
Alignment explanation
Indices: 54394008--54394271 Score: 519
Period size: 132 Copynumber: 2.0 Consensus size: 132
54393998 AATGATATTA
54394008 AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACGGATATGG
1 AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACGGATATGG
*
54394073 GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATCTTTCAT
66 GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATATTTCAT
54394138 TG
131 TG
54394140 AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACGGATATGG
1 AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACGGATATGG
54394205 GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATATTTCAT
66 GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATATTTCAT
54394270 TG
131 TG
54394272 CTTCTCCATC
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 131 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (132 bp):
AATGTCTATATCTGATCTGTAAATTCTAGTAATGCTCCATAACCTTGTTCTAGTGACGGATATGG
GTTAGGGGTGTTACATGTGCACCTAAGGAGATACTTAACATGCTTCTCTTGCCTATATATTTCAT
TG
Found at i:54397436 original size:93 final size:93
Alignment explanation
Indices: 54397277--54397452 Score: 325
Period size: 93 Copynumber: 1.9 Consensus size: 93
54397267 AGAATCAGTA
54397277 ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
1 ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
54397342 ATGCATGAATCCTGAATCTGATTTCACG
66 ATGCATGAATCCTGAATCTGATTTCACG
* *
54397370 ATTTCTTTGACTGAAGTTATAAGCAACTCGACTCATTCGATAAGTTCTGCTACACCAGAAAATGA
1 ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
*
54397435 ATGCATGTATCCTGAATC
66 ATGCATGAATCCTGAATC
54397453 CGGTTTCGCT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (93 bp):
ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
ATGCATGAATCCTGAATCTGATTTCACG
Found at i:54398558 original size:32 final size:31
Alignment explanation
Indices: 54398522--54398588 Score: 111
Period size: 29 Copynumber: 2.2 Consensus size: 31
54398512 CAATGGAAAC
54398522 ATGTGAGAAAACTGCTGATAACAACTTTTTGT
1 ATGTGAG-AAACTGCTGATAACAACTTTTTGT
54398554 ATGT--GAAACTGCTGATAACAACTTTTTGT
1 ATGTGAGAAACTGCTGATAACAACTTTTTGT
54398583 ATGTGA
1 ATGTGA
54398589 TTATACATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 28 0.85
30 1 0.03
32 4 0.12
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (31 bp):
ATGTGAGAAACTGCTGATAACAACTTTTTGT
Found at i:54398564 original size:29 final size:29
Alignment explanation
Indices: 54398530--54398588 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
54398520 ACATGTGAGA
54398530 AAACTGCTGATAACAACTTTTTGTATGTG
1 AAACTGCTGATAACAACTTTTTGTATGTG
54398559 AAACTGCTGATAACAACTTTTTGTATGTG
1 AAACTGCTGATAACAACTTTTTGTATGTG
54398588 A
1 A
54398589 TTATACATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (29 bp):
AAACTGCTGATAACAACTTTTTGTATGTG
Found at i:54406658 original size:51 final size:50
Alignment explanation
Indices: 54406595--54406783 Score: 227
Period size: 51 Copynumber: 3.7 Consensus size: 50
54406585 AATGCTATCT
*
54406595 GGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATATCATCC
1 GGTACACATAGTAGCCTACACATAGTACTACACATGTGACCAA-ATCATCC
* * * *
54406646 GGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCTATCC
1 GGTACACATAGTAGCCTACACATAGTACTACACATGTGACCAAATC-ATCC
* * *
54406697 GGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAAAT-ATCT
1 GGTACACATAGTAGCCTACACATAGTACTACACATGTGACC--AAATCATCC
** * *
54406748 TATACTCATAGTATCCTACACATAGTACTACACATG
1 GGTACACATAGTAGCCTACACATAGTACTACACATG
54406784 AGTTCACATG
Statistics
Matches: 119, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
50 2 0.02
51 114 0.96
53 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (50 bp):
GGTACACATAGTAGCCTACACATAGTACTACACATGTGACCAAATCATCC
Found at i:54406760 original size:102 final size:102
Alignment explanation
Indices: 54406579--54406781 Score: 282
Period size: 102 Copynumber: 2.0 Consensus size: 102
54406569 CACCACCCTT
* * * *
54406579 GTGATCAATGCTATCTGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATATCAT
1 GTGACCAAAGCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAAAATCAT
* * *
54406644 CCGGTACACGTAGTAGCCTGCACATAGTACTACACAC
66 CCGATACACATAGTAGCCTACACATAGTACTACACAC
*
54406681 GTGACCAAAGCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAAAT-A
1 GTGACCAAAGCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCA-AAATCA
** * *
54406745 TCTTATACTCATAGTATCCTACACATAGTACTACACA
65 TCCGATACACATAGTAGCCTACACATAGTACTACACA
54406782 TGAGTTCACA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
102 85 0.97
103 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (102 bp):
GTGACCAAAGCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAAAATCAT
CCGATACACATAGTAGCCTACACATAGTACTACACAC
Found at i:54418111 original size:18 final size:18
Alignment explanation
Indices: 54418088--54418123 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54418078 TTGGGTCAGT
54418088 GGATTGTGTTTGATGCTA
1 GGATTGTGTTTGATGCTA
54418106 GGATTGTGTTTGATGCTA
1 GGATTGTGTTTGATGCTA
54418124 CTTACCAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.44
Consensus pattern (18 bp):
GGATTGTGTTTGATGCTA
Found at i:54425765 original size:18 final size:18
Alignment explanation
Indices: 54425742--54425780 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54425732 CTATTCAAAT
*
54425742 ATTTATTATTGGAATTT-A
1 ATTTATT-TTGAAATTTGA
54425760 ATTTATTTTGAAATTTGA
1 ATTTATTTTGAAATTTGA
54425778 ATT
1 ATT
54425781 CACATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (18 bp):
ATTTATTTTGAAATTTGA
Found at i:54427264 original size:3 final size:3
Alignment explanation
Indices: 54427249--54427302 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
54427239 AAAATAAAAT
* * * *
54427249 TAA TAA TAG TAA TAA TAA TGA TAA TAA CAC TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54427297 TAA TAA
1 TAA TAA
54427303 ACTAAATAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:54429322 original size:17 final size:16
Alignment explanation
Indices: 54429294--54429331 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
54429284 TTGAATCGAT
54429294 TTTTTTATTTTTAATATA
1 TTTTTTATTTTT-ATA-A
54429312 TTTTTTA-TTTTATAA
1 TTTTTTATTTTTATAA
54429327 TTTTT
1 TTTTT
54429332 AACAATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 3 0.15
17 4 0.20
18 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTTTATAA
Found at i:54431316 original size:16 final size:17
Alignment explanation
Indices: 54431295--54431328 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
54431285 AATAATTAGG
54431295 GCAAAAGTAT-AATTTT
1 GCAAAAGTATGAATTTT
54431311 GCAAAAGTATGAATTTT
1 GCAAAAGTATGAATTTT
54431328 G
1 G
54431329 GACCGAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
GCAAAAGTATGAATTTT
Found at i:54435323 original size:12 final size:12
Alignment explanation
Indices: 54435304--54435361 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
54435294 AAATTATGGA
54435304 TCACACGGCCTG
1 TCACACGGCCTG
** *
54435316 GGACACGGGCTG
1 TCACACGGCCTG
54435328 TCACACGGCCTG
1 TCACACGGCCTG
** *
54435340 AGACACGGGCTG
1 TCACACGGCCTG
54435352 TCACACGGCC
1 TCACACGGCC
54435362 GTGTGTCCCT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.19, C:0.36, G:0.33, T:0.12
Consensus pattern (12 bp):
TCACACGGCCTG
Found at i:54435336 original size:24 final size:24
Alignment explanation
Indices: 54435304--54435361 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
54435294 AAATTATGGA
*
54435304 TCACACGGCCTGGGACACGGGCTG
1 TCACACGGCCTGAGACACGGGCTG
54435328 TCACACGGCCTGAGACACGGGCTG
1 TCACACGGCCTGAGACACGGGCTG
54435352 TCACACGGCC
1 TCACACGGCC
54435362 GTGTGTCCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.36, G:0.33, T:0.12
Consensus pattern (24 bp):
TCACACGGCCTGAGACACGGGCTG
Found at i:54436928 original size:375 final size:372
Alignment explanation
Indices: 54436241--54436992 Score: 1423
Period size: 375 Copynumber: 2.0 Consensus size: 372
54436231 GGGTGAAACG
54436241 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
1 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
54436306 ATCATTTAAAACGGACTCTTAAAAGTATAAAACATTACAACTTAAATATTTGATAAAATAGACAT
66 ATCATTTAAAACGGACTCTTAAAAGTATAAAACATTACAACTTAAATATTTGATAAAATAGACAT
*
54436371 ATTCGCGACATATAATACTATTCACCATTTGAAAACATGTTCTAAAAAATGTCCCCCTGTATGCA
131 ATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTATGCA
54436436 TAACATCGCACTACAATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTAGTT
196 TAACATCGCACTACAATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTAGTT
*
54436501 CAACTCAAGAACTTGTATTACAAATAAAATCCATAATTTCAATGGAACTTAATGAGTCTCAACCA
261 CAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAACCA
54436566 ATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
326 ATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
54436613 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
1 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
54436678 ATCATTTAAAACGGACTCTTAAAAGTAGTACAAAACATTACAACTTAAATATTTGATAAAATAGA
66 ATCATTTAAAACGGACTCTTAAAAGTA-T--AAAACATTACAACTTAAATATTTGATAAAATAGA
*
54436743 CATATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCTTGTAT
128 CATATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTAT
* *
54436808 GCATAACATCGCACTACGATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTG
193 GCATAACATCGCACTACAATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTA
54436873 GTTCAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAA
258 GTTCAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAA
54436938 CCAATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
323 CCAATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
*
54436988 CTACT
1 ATACT
54436993 TCTTTTTAGA
Statistics
Matches: 371, Mismatches: 6, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
372 92 0.25
373 1 0.00
375 278 0.75
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (372 bp):
ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
ATCATTTAAAACGGACTCTTAAAAGTATAAAACATTACAACTTAAATATTTGATAAAATAGACAT
ATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTATGCA
TAACATCGCACTACAATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTAGTT
CAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAACCA
ATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
Found at i:54437627 original size:25 final size:25
Alignment explanation
Indices: 54437566--54437628 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
54437556 TACGTCATAT
*
54437566 AGGCTTTACAGGTAAACTGCCACAA
1 AGGCTTTACAAGTAAACTGCCACAA
** *
54437591 AGGCTTCCCAAGTAAATTGCCACAA
1 AGGCTTTACAAGTAAACTGCCACAA
54437616 AGGCTTTACAAGT
1 AGGCTTTACAAGT
54437629 GACTCATCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (25 bp):
AGGCTTTACAAGTAAACTGCCACAA
Found at i:54438532 original size:151 final size:152
Alignment explanation
Indices: 54438277--54438567 Score: 521
Period size: 151 Copynumber: 1.9 Consensus size: 152
54438267 ATCCAGTAGC
* *
54438277 AGTAACTGCGTACAAGATCACAAAATTTCTATTAGAATCTTCATTAATAGATAGTTTACTAATGT
1 AGTAACTGCGTACAAGATCACAAAATTTCTATTAGAATCTTCAGTAATAGATAGTTTACTAACGT
*
54438342 TTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACGTTTCAA
66 TTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCAA
54438407 TATCCTTACTTCATTAATAGAT
131 TATCCTTACTTCATTAATAGAT
**
54438429 AGTAACT-CGTACAAGATCATGAAATTTCTATTAGAATCTTCAGTAATAGATAGTTTACTAACGT
1 AGTAACTGCGTACAAGATCACAAAATTTCTATTAGAATCTTCAGTAATAGATAGTTTACTAACGT
*
54438493 TTCAACTACATGCAACCCCTATGTAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCAA
66 TTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCAA
54438558 TATCCTTACT
131 TATCCTTACT
54438568 CATCAACAAT
Statistics
Matches: 133, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
151 126 0.95
152 7 0.05
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (152 bp):
AGTAACTGCGTACAAGATCACAAAATTTCTATTAGAATCTTCAGTAATAGATAGTTTACTAACGT
TTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCAA
TATCCTTACTTCATTAATAGAT
Found at i:54442979 original size:24 final size:23
Alignment explanation
Indices: 54442938--54443000 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
54442928 CTCATCTTCT
* * *
54442938 TCATCTTCACCTCGACCCTTGTAC
1 TCATCTTCATCTCCACCCTCGT-C
*
54442962 TCATCTTCATTTCCACCCTCGTC
1 TCATCTTCATCTCCACCCTCGTC
54442985 TACATCTTCATCTCCA
1 T-CATCTTCATCTCCA
54443001 GCCATTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 2 0.06
24 31 0.94
ACGTcount: A:0.17, C:0.41, G:0.05, T:0.37
Consensus pattern (23 bp):
TCATCTTCATCTCCACCCTCGTC
Found at i:54444488 original size:8 final size:8
Alignment explanation
Indices: 54444475--54444503 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
54444465 TTTAAGAATT
54444475 AAAAAATA
1 AAAAAATA
54444483 AAAAAAT-
1 AAAAAATA
54444490 AAAAAATA
1 AAAAAATA
54444498 AAAAAA
1 AAAAAA
54444504 ACGAAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:54444494 original size:15 final size:15
Alignment explanation
Indices: 54444474--54444503 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54444464 TTTTAAGAAT
54444474 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
54444489 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
54444504 ACGAAGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
TAAAAAATAAAAAAA
Found at i:54445164 original size:20 final size:20
Alignment explanation
Indices: 54445139--54445193 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
54445129 TGTGGTTCAA
*
54445139 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
54445159 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
54445179 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
54445194 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:54450282 original size:32 final size:31
Alignment explanation
Indices: 54450226--54450286 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
54450216 TAGAGAAAAT
54450226 AGAAAGACTTGGATTTAAGTGAAAAAAATGA
1 AGAAAGACTTGGATTTAAGTGAAAAAAATGA
54450257 AGAAAGA-TCTGGTATTTATAG-GAAAAAAAT
1 AGAAAGACT-TGG-ATTTA-AGTGAAAAAAAT
54450287 TACAATTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 1 0.04
31 10 0.37
32 14 0.52
33 2 0.07
ACGTcount: A:0.51, C:0.03, G:0.21, T:0.25
Consensus pattern (31 bp):
AGAAAGACTTGGATTTAAGTGAAAAAAATGA
Found at i:54452242 original size:18 final size:18
Alignment explanation
Indices: 54452219--54452255 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54452209 GAGGAGGAGC
54452219 AAGCGGA-GATGGCGAAGA
1 AAGCGGAGGA-GGCGAAGA
54452237 AAGCGGAGGAGGCGAAGA
1 AAGCGGAGGAGGCGAAGA
54452255 A
1 A
54452256 GAGACAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.41, C:0.11, G:0.46, T:0.03
Consensus pattern (18 bp):
AAGCGGAGGAGGCGAAGA
Found at i:54459864 original size:5 final size:5
Alignment explanation
Indices: 54459854--54459883 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
54459844 CTTTGAAGCA
*
54459854 TGAGC TGAGC TGAGC TGAGC TGAAC TGAGC
1 TGAGC TGAGC TGAGC TGAGC TGAGC TGAGC
54459884 GGAGGTGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (5 bp):
TGAGC
Found at i:54461701 original size:15 final size:15
Alignment explanation
Indices: 54461659--54461704 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
54461649 TATATATATT
54461659 ATTTAAAAT-AA-AA
1 ATTTAAAATAAATAA
* *
54461672 ACTTAAAAAATAATAA
1 ATTTAAAATA-AATAA
54461688 ATTTAAAATAAATAA
1 ATTTAAAATAAATAA
54461703 AT
1 AT
54461705 ATAAGCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.27
15 9 0.35
16 10 0.38
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTTAAAATAAATAA
Found at i:54467582 original size:25 final size:25
Alignment explanation
Indices: 54467553--54467607 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
54467543 TGTAAACAGT
* *
54467553 AAGCTCTTCCAAGCTGAATAACGAG
1 AAGCTCATCCAAGCCGAATAACGAG
* * *
54467578 AAGCTCATGCGAGCCGAATATCGAG
1 AAGCTCATCCAAGCCGAATAACGAG
54467603 AAGCT
1 AAGCT
54467608 TATAAGAGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (25 bp):
AAGCTCATCCAAGCCGAATAACGAG
Found at i:54467616 original size:25 final size:25
Alignment explanation
Indices: 54467568--54467616 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
54467558 CTTCCAAGCT
**
54467568 GAATAACGAGAAGCTCATGCGAGCC
1 GAATAACGAGAAGCTCATAAGAGCC
* *
54467593 GAATATCGAGAAGCTTATAAGAGC
1 GAATAACGAGAAGCTCATAAGAGC
54467617 TGTTGTGTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.16
Consensus pattern (25 bp):
GAATAACGAGAAGCTCATAAGAGCC
Found at i:54470037 original size:12 final size:11
Alignment explanation
Indices: 54470015--54470087 Score: 64
Period size: 12 Copynumber: 6.6 Consensus size: 11
54470005 ACCCTTTTAA
*
54470015 TATATAAAAAT
1 TATAAAAAAAT
54470026 TATTAAAAAAAT
1 TA-TAAAAAAAT
*
54470038 CAT---AAAAT
1 TATAAAAAAAT
54470046 TATAAACAAAATT
1 TATAAA-AAAA-T
54470059 TATAAAAAAAGT
1 TATAAAAAAA-T
54470071 TATAAAAAAAT
1 TATAAAAAAAT
54470082 T-TAAAA
1 TATAAAA
54470088 TTATAAACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 7 0.13
10 5 0.10
11 5 0.10
12 28 0.54
13 7 0.13
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
TATAAAAAAAT
Found at i:54470043 original size:21 final size:22
Alignment explanation
Indices: 54470018--54470095 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 22
54470008 CTTTTAATAT
54470018 ATAAAAATTATTAAA-AAAA-TC
1 ATAAAAATTA-TAAACAAAATTC
*
54470039 AT-AAAATTATAAACAAAATTT
1 ATAAAAATTATAAACAAAATTC
54470060 ATAAAAAAAGTTATAAA-AAAATT-
1 AT--AAAAA-TTATAAACAAAATTC
54470083 -T-AAAATTATAAAC
1 ATAAAAATTATAAAC
54470096 TTTTATTAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
18 7 0.14
19 8 0.16
20 11 0.22
21 5 0.10
22 1 0.02
24 10 0.20
25 7 0.14
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (22 bp):
ATAAAAATTATAAACAAAATTC
Found at i:54480586 original size:15 final size:15
Alignment explanation
Indices: 54480568--54480600 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54480558 TTGTACAATT
54480568 TTAATT-TGATAAATA
1 TTAATTATGAT-AATA
54480583 TTAATTATGATAATA
1 TTAATTATGATAATA
54480598 TTA
1 TTA
54480601 TTCATTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TTAATTATGATAATA
Found at i:54482249 original size:7 final size:7
Alignment explanation
Indices: 54482237--54482264 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
54482227 AGTTGAGAGG
54482237 CCACTCT
1 CCACTCT
54482244 CCACTCT
1 CCACTCT
54482251 CCACTCT
1 CCACTCT
54482258 CCACTCT
1 CCACTCT
54482265 TTCTCTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.57, G:0.00, T:0.29
Consensus pattern (7 bp):
CCACTCT
Found at i:54486959 original size:60 final size:61
Alignment explanation
Indices: 54486872--54487002 Score: 201
Period size: 60 Copynumber: 2.2 Consensus size: 61
54486862 AACAAAGCAA
* * ** *
54486872 AGCAGCAAGGGTTACAGAGAGATGTGAAGAGGCAGTAAAGCAGTTGCC-AGAAAAAATAAT
1 AGCAGCAAGGGTTACAAAGAGACGTGAAGAGGCAACAAAGCAGTTGCCAAAAAAAAATAAT
*
54486932 AGCAGCAAGGGTTGCAAAGAGACGTGAAGAGGCAACAAAGCAGTTGCCAAAAAAAAATAAT
1 AGCAGCAAGGGTTACAAAGAGACGTGAAGAGGCAACAAAGCAGTTGCCAAAAAAAAATAAT
54486993 AGCAGCAAGG
1 AGCAGCAAGG
54487003 CAGAGACGTG
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
60 43 0.67
61 21 0.33
ACGTcount: A:0.45, C:0.14, G:0.29, T:0.12
Consensus pattern (61 bp):
AGCAGCAAGGGTTACAAAGAGACGTGAAGAGGCAACAAAGCAGTTGCCAAAAAAAAATAAT
Found at i:54487255 original size:60 final size:60
Alignment explanation
Indices: 54487176--54487320 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 60
54487166 GCAAATTAGT
* * * ** *
54487176 AGGGGTTACAGAGAAATGTGAAGAGATAGCTAAGTA-GTTGTCGAAAAAAA-TAATAGCAGC
1 AGGGGTTGCAGAGAGATGTGAAGAGACAGC-AACAAGGTTG-CCAAAAAAAGTAATAGCAGC
* *
54487236 AGGGGTTGCAGAGAGATGTGAAGAGGCAGCAACAAGGTTGCCAAAAAAAGTAATAGCAGT
1 AGGGGTTGCAGAGAGATGTGAAGAGACAGCAACAAGGTTGCCAAAAAAAGTAATAGCAGC
* *
54487296 AGGGGTTGCAAAGAGACGTGAAGAG
1 AGGGGTTGCAGAGAGATGTGAAGAG
54487321 GCAACAAAGC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 11 0.15
60 62 0.85
ACGTcount: A:0.41, C:0.10, G:0.33, T:0.17
Consensus pattern (60 bp):
AGGGGTTGCAGAGAGATGTGAAGAGACAGCAACAAGGTTGCCAAAAAAAGTAATAGCAGC
Found at i:54487336 original size:60 final size:59
Alignment explanation
Indices: 54487219--54487405 Score: 179
Period size: 60 Copynumber: 3.4 Consensus size: 59
54487209 GTAGTTGTCG
* * *
54487219 AAAAAAATAATAGCAGCAGGGGTTGCAGAGAGATGTGAAGAGGCAGCAACAAGGTTGCC
1 AAAAAAATAATAGCAGCAGGGGTTGCAAAGAGACGTGAAGAGGCAACAACAAGGTTGCC
*
54487278 AAAAAAAGTAATAGCAGTAGGGGTTGCAAAGAGACGTGAAGAGGCAAC-A-AAGCAGTTGCC
1 AAAAAAA-TAATAGCAGCAGGGGTTGCAAAGAGACGTGAAGAGGCAACAACAAG--GTTGCC
* *
54487338 --GAAAA-AATAGCAGCA-GGG-T----AGAGACGTG-A-A-GCAACAA-AACAGTTGCC
1 AAAAAAATAATAGCAGCAGGGGTTGCAAAGAGACGTGAAGAGGCAACAACAA-GGTTGCC
54487385 AAAAAAATAATAGCAGCAGGG
1 AAAAAAATAATAGCAGCAGGG
54487406 TAGAGACGTG
Statistics
Matches: 111, Mismatches: 8, Indels: 26
0.77 0.06 0.18
Matches are distributed among these distances:
47 11 0.10
48 4 0.04
49 5 0.05
50 19 0.17
51 2 0.02
54 1 0.01
55 3 0.03
56 9 0.08
58 7 0.06
59 8 0.07
60 42 0.38
ACGTcount: A:0.44, C:0.14, G:0.29, T:0.12
Consensus pattern (59 bp):
AAAAAAATAATAGCAGCAGGGGTTGCAAAGAGACGTGAAGAGGCAACAACAAGGTTGCC
Found at i:54487381 original size:47 final size:49
Alignment explanation
Indices: 54487307--54487418 Score: 156
Period size: 50 Copynumber: 2.2 Consensus size: 49
54487297 GGGGTTGCAA
* *
54487307 AGAGACGTGAAGAGGCAACAAAGCAGTTGCC-GAAAA-AATAGCAGCAGGGT
1 AGAGACGTG-A-A-GCAACAAAACAGTTGCCAAAAAATAATAGCAGCAGGGT
54487357 AGAGACGTGAAGCAACAAAACAGTTGCCAAAAAAATAATAGCAGCAGGGT
1 AGAGACGTGAAGCAACAAAACAGTTGCC-AAAAAATAATAGCAGCAGGGT
54487407 AGAGACGTGAAG
1 AGAGACGTGAAG
54487419 ATAGAATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
47 16 0.28
48 1 0.02
49 5 0.09
50 35 0.61
ACGTcount: A:0.45, C:0.15, G:0.29, T:0.11
Consensus pattern (49 bp):
AGAGACGTGAAGCAACAAAACAGTTGCCAAAAAATAATAGCAGCAGGGT
Found at i:54491036 original size:58 final size:58
Alignment explanation
Indices: 54490933--54491101 Score: 187
Period size: 58 Copynumber: 2.9 Consensus size: 58
54490923 TGAATCCGCA
* * * * * * * *
54490933 AGTTGTTTT-AAGTTTAGACTTATTTTCTGATATAATCAACAGAGAATATAAATCCTTG
1 AGTTGTTTTGAAG-TTAGGCATATTTTCTGAAATACTCAGCTGAGAATGTAAATCCTCG
* *
54490991 AGTTGTTTTGAAGTTAGGCATATTTTCTGAAACACTCAGCTGAGAATGTGAATCCTCG
1 AGTTGTTTTGAAGTTAGGCATATTTTCTGAAATACTCAGCTGAGAATGTAAATCCTCG
* * * * *
54491049 AGCTATTTTGAACTTAGGCATATTTTCTGAGATACTCAGCTGGGAATGTAAAT
1 AGTTGTTTTGAAGTTAGGCATATTTTCTGAAATACTCAGCTGAGAATGTAAAT
54491102 TCGCGAGCTA
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 90 0.97
59 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (58 bp):
AGTTGTTTTGAAGTTAGGCATATTTTCTGAAATACTCAGCTGAGAATGTAAATCCTCG
Found at i:54491109 original size:58 final size:58
Alignment explanation
Indices: 54490996--54491114 Score: 175
Period size: 58 Copynumber: 2.1 Consensus size: 58
54490986 CCTTGAGTTG
* * *
54490996 TTTTGAAGTTAGGCATATTTTCTGAAACACTCAGCTGAGAATGTGAATCCTCGAGCTA
1 TTTTGAACTTAGGCATATTTTCTGAAACACTCAGCTGAGAATGTAAATCCGCGAGCTA
* * * *
54491054 TTTTGAACTTAGGCATATTTTCTGAGATACTCAGCTGGGAATGTAAATTCGCGAGCTA
1 TTTTGAACTTAGGCATATTTTCTGAAACACTCAGCTGAGAATGTAAATCCGCGAGCTA
54491112 TTT
1 TTT
54491115 AAGGGCTACG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (58 bp):
TTTTGAACTTAGGCATATTTTCTGAAACACTCAGCTGAGAATGTAAATCCGCGAGCTA
Found at i:54491247 original size:70 final size:70
Alignment explanation
Indices: 54491128--54491600 Score: 284
Period size: 70 Copynumber: 6.8 Consensus size: 70
54491118 GGCTACGATA
* * * * * *
54491128 AACCTGTGAGCCTTAAAAAAACAACTAGGAGCTTTTGACTCTCGTTAACTATTTGGGTGGTGTGG
1 AACCTGCGAGCCTTAAAATAACAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGGGTGGTATGG
54491193 TATTG
66 TATTG
* ** *
54491198 AACCTGCGAGCCTTAAAATAAGAGCTAGGAGCTTTTAACTCTTTCTAACTATTT-GATGGCTATG
1 AACCTGCGAGCCTTAAAATAACAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGGGTGG-TATG
*
54491262 ATATTG
65 GTATTG
* * * * * * * * *
54491268 AACCTACAAGCATTAGAATGACAGCTAGGAGCTTTTAACTCTCGCTAATTGTTTGGG-GACTACG
1 AACCTGCGAGCCTTAAAATAACAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGGGTG-GTATG
54491332 GTATTG
65 GTATTG
* * * * * * * * *
54491338 AGCATGCGAGCCATAGAATGATAGTTAAGAGCTTTTAACTCTCGCTAACTATTTGGG-GCT-TGC
1 AACCTGCGAGCCTTAAAATAACAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGGGTGGTATG-
54491401 AGTATTG
65 -GTATTG
* * * * * * * * *
54491408 AGCCTGCGAGTCTTAGAATGATAGCT-GAGAACTTTTAACTCTCGCTAACTGTTTGCG-GG-CT-
1 AACCTGCGAGCCTTAAAATAACAGCTAG-GAGCTTTTAACTCTCGCTAACTATTTGGGTGGTATG
*
54491469 GCATTG
65 GTATTG
** * * * * * * * *
54491475 AACCTATGAGCCTTAGAATGATATCTAGGAGTTTTTAACTCTCACTAAATATTTAGG-GG-ATGC
1 AACCTGCGAGCCTTAAAATAACAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGGGTGGTAT--
*
54491538 GGTATTA
64 GGTATTG
* * * * * * *
54491545 AACTTGTGAGCC-AAAAGATGACAACTGGGAGCTTTTAACTCTCGCTAACTGTTTGG
1 AACCTGCGAGCCTTAAA-ATAACAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGG
54491601 ATTTTCGATG
Statistics
Matches: 317, Mismatches: 74, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
67 51 0.16
68 2 0.01
69 8 0.03
70 255 0.80
71 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (70 bp):
AACCTGCGAGCCTTAAAATAACAGCTAGGAGCTTTTAACTCTCGCTAACTATTTGGGTGGTATGG
TATTG
Found at i:54491581 original size:207 final size:209
Alignment explanation
Indices: 54491148--54491600 Score: 479
Period size: 207 Copynumber: 2.2 Consensus size: 209
54491138 CCTTAAAAAA
* * *
54491148 ACAACTAGGAGCTTTTGACTCTCGTTAACTATTTGGGTGGTGTGGTATTGAACCTGCGAGCCTTA
1 ACAACTAGGAGCTTTTAACTCTCGCTAACTATTTGGGTGCTGTGGTATTGAACCTGCGAGCCTTA
* ** * *
54491213 AAATAAGAGCTAGGAGCTTTTAACTCTTTCTAACTATTTGATGGCTATGATATTGAACCTACAAG
66 AAATAAGAGCTAGGAACTTTTAACTCTCGCTAACTATTTGAGGGC-ATGACATTGAACCTACAAG
* * * * *
54491278 CATTAGAATGACAGCTAGGAGCTTTTAACTCTCGCTAATTGTTTGGGGACTACGGTATTGAGCAT
130 CATTAGAATGACAGCTAGGAGCTTTTAACTCTCACTAAATATTTGGGGACTACGGTATTAAACAT
*
54491343 GCGAGCCATAGAATG
195 GCGAGCCAAAGAATG
* ** * * *
54491358 ATAGTTAAGAGCTTTTAACTCTCGCTAACTATTTGGG-GCT-TGCAGTATTGAGCCTGCGAGTCT
1 ACAACTAGGAGCTTTTAACTCTCGCTAACTATTTGGGTGCTGTG--GTATTGAACCTGCGAGCCT
* * * * * **
54491421 TAGAATGATAGCT-GAGAACTTTTAACTCTCGCTAACTGTTTGCGGGC-TG-CATTGAACCTATG
64 TAAAATAAGAGCTAG-GAACTTTTAACTCTCGCTAACTATTTGAGGGCATGACATTGAACCTACA
* * * * *
54491483 AGCCTTAGAATGATATCTAGGAGTTTTTAACTCTCACTAAATATTTAGGGGA-TGCGGTATTAAA
128 AGCATTAGAATGACAGCTAGGAGCTTTTAACTCTCACTAAATATTT-GGGGACTACGGTATTAAA
* *
54491547 CTTGTGAGCCAAA-AGATG
192 CATGCGAGCCAAAGA-ATG
* *
54491565 ACAACTGGGAGCTTTTAACTCTCGCTAACTGTTTGG
1 ACAACTAGGAGCTTTTAACTCTCGCTAACTATTTGG
54491601 ATTTTCGATG
Statistics
Matches: 198, Mismatches: 40, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
206 1 0.01
207 101 0.51
208 9 0.05
209 3 0.02
210 84 0.42
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (209 bp):
ACAACTAGGAGCTTTTAACTCTCGCTAACTATTTGGGTGCTGTGGTATTGAACCTGCGAGCCTTA
AAATAAGAGCTAGGAACTTTTAACTCTCGCTAACTATTTGAGGGCATGACATTGAACCTACAAGC
ATTAGAATGACAGCTAGGAGCTTTTAACTCTCACTAAATATTTGGGGACTACGGTATTAAACATG
CGAGCCAAAGAATG
Found at i:54496599 original size:43 final size:43
Alignment explanation
Indices: 54496541--54496687 Score: 165
Period size: 43 Copynumber: 3.4 Consensus size: 43
54496531 TTCTAAAGAT
*
54496541 GGTTGCTAAGTGCTGATTCCACCGTATATTTGACTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATATTTGAATGTGAAAGG
* * * * *
54496584 GGTTGCTATGTGCTGATTCC-CCGTATCA-CTAAATAT-AAACGT
1 GGTTGCTAAGTGCTGATTCCACCGTAT-ATTTGAATGTGAAA-GG
* *
54496626 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATATTTGAATGTGAAAGG
* *
54496669 GGTTGCTATGTACTGATTC
1 GGTTGCTAAGTGCTGATTC
54496688 TCAGTATCAC
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
41 3 0.04
42 30 0.36
43 48 0.57
44 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGTATATTTGAATGTGAAAGG
Found at i:54496639 original size:85 final size:84
Alignment explanation
Indices: 54496540--54496733 Score: 280
Period size: 85 Copynumber: 2.3 Consensus size: 84
54496530 ATTCTAAAGA
*
54496540 TGGTTGCTAAGTGCTGATTCCACCGTATATTTGACTGTGAAAGGGGTTGCTATGTGCTGATTCCC
1 TGGTTGCTAAGTGCTGATTCCACCGTATATTTGACTGTGAAAGGGGTTGCTATGTACTGATTCCC
*
54496605 CGTATCACTAAATATAAACG
66 AGTATCACTAAAT-TAAACG
* * *
54496625 TGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATGTACTGATTCTC
1 TGGTTGCTAAGTGCTGATTCCACCGTATATTTGACTGTGAAAGGGGTTGCTATGTACTGATTCCC
* * *
54496690 AGTATCACTGAATTTAAGG
66 AGTATCACTAAATTAAACG
* * *
54496709 TGGTCGCTAAGTGTTGAATCCACCG
1 TGGTTGCTAAGTGCTGATTCCACCG
54496734 AGTAACGGAT
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 26 0.27
85 72 0.73
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (84 bp):
TGGTTGCTAAGTGCTGATTCCACCGTATATTTGACTGTGAAAGGGGTTGCTATGTACTGATTCCC
AGTATCACTAAATTAAACG
Found at i:54499892 original size:51 final size:49
Alignment explanation
Indices: 54499768--54499954 Score: 214
Period size: 51 Copynumber: 3.7 Consensus size: 49
54499758 AGTGAAAGTG
* *
54499768 ATGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATG-
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAATGT
* * *
54499817 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT-GT
* * * * *
54499868 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT-GT
*
54499919 AATGGTCACATGTATAGTACTATGTGCAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
54499955 TATGAACCAA
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 6 0.05
50 37 0.32
51 71 0.62
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (49 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATGT
Found at i:54499892 original size:101 final size:102
Alignment explanation
Indices: 54499772--54499955 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 102
54499762 AAAGTGATGG
* * *
54499772 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGATAATGGTCACATGTATAGT
54499835 ACTATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
* *
54499873 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTATAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGGTCACATGTATAGTA
54499938 CTATGTGCAGGCTACTAT
66 CTATGTGCAGGCTACTAT
54499956 ATGAACCAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.53
102 32 0.42
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGGTCACATGTATAGTA
CTATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
Found at i:54500016 original size:45 final size:45
Alignment explanation
Indices: 54499965--54500051 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
54499955 TATGAACCAA
* *
54499965 ACATCATTAATTAGTAAGGTGGTTGCTATATGTTGATTCCACTGG
1 ACATCATTAATTAATAAGGTGGTTGCTATATGTTGAATCCACTGG
* *
54500010 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCCAC
1 ACATCATTAATTAATAAGGTGGTTGCTATATGTTGAATCCAC
54500052 CGAGTATCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (45 bp):
ACATCATTAATTAATAAGGTGGTTGCTATATGTTGAATCCACTGG
Found at i:54504872 original size:32 final size:33
Alignment explanation
Indices: 54504794--54504872 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
54504784 AAGAACAATA
* * * *
54504794 AAACACCACAAAAAGTAGCACCAAAATAGCACC
1 AAACAACACAAAAAGTAGCACAAAAAAAACACC
*
54504827 AAACAACATAAAAA-TAGCACAAAAAAAACACC
1 AAACAACACAAAAAGTAGCACAAAAAAAACACC
**
54504859 AAACAGTACAAAAA
1 AAACAACACAAAAA
54504873 ACAACATCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 26 0.68
33 12 0.32
ACGTcount: A:0.63, C:0.24, G:0.06, T:0.06
Consensus pattern (33 bp):
AAACAACACAAAAAGTAGCACAAAAAAAACACC
Found at i:54508188 original size:30 final size:30
Alignment explanation
Indices: 54508152--54508210 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
54508142 CCAGCTTAAG
54508152 TAAGTAAATAATAATAAAGAAAGACCGAGC
1 TAAGTAAATAATAATAAAGAAAGACCGAGC
54508182 TAAGTAAATAATAATAAAGAAAGACCGAG
1 TAAGTAAATAATAATAAAGAAAGACCGAG
54508211 AGTCCAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.08, G:0.17, T:0.17
Consensus pattern (30 bp):
TAAGTAAATAATAATAAAGAAAGACCGAGC
Found at i:54508333 original size:3 final size:3
Alignment explanation
Indices: 54508318--54508466 Score: 226
Period size: 3 Copynumber: 49.7 Consensus size: 3
54508308 TGATAAAGTT
*
54508318 AAG AAG GAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * *
54508366 GAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAA AAG GAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
54508414 GAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAA AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
54508462 AAG AA
1 AAG AA
54508467 AAATTGAAAT
Statistics
Matches: 130, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 130 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:54511970 original size:21 final size:21
Alignment explanation
Indices: 54511945--54511984 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54511935 ATGTGAATTA
* *
54511945 TAAAATATATATAATATATTT
1 TAAAATATAAAGAATATATTT
54511966 TAAAATATAAAGAATATAT
1 TAAAATATAAAGAATATAT
54511985 AAATATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TAAAATATAAAGAATATATTT
Found at i:54512148 original size:12 final size:12
Alignment explanation
Indices: 54512131--54512172 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
54512121 AAAGCATATT
54512131 TATATATGTAAG
1 TATATATGTAAG
* **
54512143 TATATATATATT
1 TATATATGTAAG
54512155 TATATATGTAAG
1 TATATATGTAAG
54512167 TATATA
1 TATATA
54512173 ATAAAGGCGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
TATATATGTAAG
Found at i:54512153 original size:24 final size:24
Alignment explanation
Indices: 54512126--54512172 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
54512116 GTATGAAAGC
54512126 ATATTTATATATGTAAGTATATAT
1 ATATTTATATATGTAAGTATATAT
54512150 ATATTTATATATGTAAGTATATA
1 ATATTTATATATGTAAGTATATA
54512173 ATAAAGGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
ATATTTATATATGTAAGTATATAT
Found at i:54512176 original size:65 final size:63
Alignment explanation
Indices: 54512077--54512201 Score: 196
Period size: 65 Copynumber: 2.0 Consensus size: 63
54512067 TATTTTTTGA
* * *
54512077 AAGTATATATATATATGTGTGTGTATATATAATAAAGGCGTATGAAAGCATATTTATATATGT
1 AAGTATATATATATATATATATGTATATATAATAAAGGCGTATGAAAGCATATTTATATATGT
*
54512140 AAGTATATATATATTTATATATGTAAGTATATAATAAAGGCGTATGAAAGCATATTTATATA
1 AAGTATATATATATATATATATGT-A-TATATAATAAAGGCGTATGAAAGCATATTTATATA
54512202 CATGTATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
63 20 0.36
64 1 0.02
65 35 0.62
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (63 bp):
AAGTATATATATATATATATATGTATATATAATAAAGGCGTATGAAAGCATATTTATATATGT
Found at i:54514035 original size:43 final size:43
Alignment explanation
Indices: 54513902--54514037 Score: 107
Period size: 43 Copynumber: 3.2 Consensus size: 43
54513892 GTTCTTAGGA
* *
54513902 AGGCAATATCTGCTTCTTTAACTAGCTCCACTGCAACCGATGG
1 AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
* *** * * * * * * *
54513945 AGGCAAGACTTTG-TT-TTTGGTCTGCTTCGCTGTTAA-TGTAAGA
1 AGGCAAGA-TCTGCTTCTTTAACCAGCTCCACTG-CAACCG-ATGG
54513988 AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
1 AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
54514031 AGGCAAG
1 AGGCAAG
54514038 GCTTTGTTTT
Statistics
Matches: 63, Mismatches: 24, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
42 14 0.22
43 34 0.54
44 15 0.24
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (43 bp):
AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
Found at i:54514045 original size:86 final size:88
Alignment explanation
Indices: 54513898--54514532 Score: 675
Period size: 88 Copynumber: 7.3 Consensus size: 88
54513888 GCTAGTTCTT
* * * * * *
54513898 AGGAAGGCAATATCTGCT-TCTTTAACTAGCTCCACTGCAACCGATG-GAGGCAAGACTTTGT-T
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAG-GTTTGTGT
* * * **
54513960 -TTTGGTCTGCTTCGCTGTTAATGT
64 CTTCGATCTGCTTCGCTGTCAATAC
* * * *
54513984 AAGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCGATG-GAGGCAAGGCTTTGT-T
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTGT
* * *
54514046 -TTCGATCTGCTTCGTTGTTAATGC
64 CTTCGATCTGCTTCGCTGTCAATAC
* * ** * * *
54514070 AAGAAGGCAAGACCTACT-TCTTTAACCATCTCCACTGCAACCGATG-GAGGCAAGGCTTTGT-T
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTGT
* * * **
54514132 -TTTGGTCTGCTTCGCTGTTAATGT
64 CTTCGATCTGCTTCGCTGTCAATAC
* * * *
54514156 AGGAAGGCAAGACCTTTTGTCTTCAACCAGCTCCA-TCACAACTGAGAGAAGCAAGGTTTGTGTC
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACT-ACAACCGAGAGAGGCAAGGTTTGTGTC
* *
54514220 TTCCACCTGCTTCGCTGTCAATAC
65 TTCGATCTGCTTCGCTGTCAATAC
* * *
54514244 AGGAAGGCAAGATCTGTTGTCTTCAACCAGGTCCGCTACAACTGAGAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCT
* * *
54514309 TTGACCTACTTCGCTGTCAATAC
66 TCGATCTGCTTCGCTGTCAATAC
* *
54514332 AGGAAGACAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCT
*
54514397 TCGACCTGCTTCGCTGTCAATAC
66 TCGATCTGCTTCGCTGTCAATAC
* * *
54514420 AGGAAGGCAAGATCTATTGTCTTCAACCAGCTGCACCACAACCGAGAGAGGCAAGGTTTGTGTCT
1 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCT
*
54514485 TCGATCTGCTTCGCTGTCAATTC
66 TCGATCTGCTTCGCTGTCAATAC
54514508 AGGAAGGCAAGATCTGTTGTCTTCA
1 AGGAAGGCAAGATCTGTTGTCTTCA
54514533 TTGATCTGTT
Statistics
Matches: 491, Mismatches: 51, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
86 178 0.36
87 29 0.06
88 283 0.58
89 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (88 bp):
AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCT
TCGATCTGCTTCGCTGTCAATAC
Found at i:54514296 original size:44 final size:44
Alignment explanation
Indices: 54514160--54514532 Score: 160
Period size: 44 Copynumber: 8.5 Consensus size: 44
54514150 TAATGTAGGA
* * *
54514160 AGGCAAGACCTTTTGTCTTCAACCAGCTCC-ATCACAACTGAGAG
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCT-ACAACTGAGAG
* * * * * * * *
54514204 AAGCAAGGTTTG-TGTCTTCCACCTGCTTCGCTGTCAA-T-ACAGG
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCT-ACAACTGAGA-G
*
54514247 AAGGCAAGATCTGTTGTCTTCAACCAGGTCCGCTACAACTGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACTGAGAG
* * ** * * *
54514292 AGGCAAGGTTTG-TGTCTTTGACCTA-CTTCGCTGTCAA-T-ACAGG
1 AGGCAAGATCTGTTGTCTTCAACC-AGCTCCGCT-ACAACTGAGA-G
* *
54514335 AAGACAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACTGAGAG
* * * * * * *
54514380 AGGCAAGGTTTG-TGTCTTCGACCTGCTTCGCTGTCAA-T-ACAGG
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCT-ACAACTGAGA-G
* * * * *
54514423 AAGGCAAGATCTATTGTCTTCAACCAGCTGCACCACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACTGAGAG
* * * * * * * * *
54514468 AGGCAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTCAATTCAG-G
1 AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCT-ACAACTGAGAG
54514511 AAGGCAAGATCTGTTGTCTTCA
1 -AGGCAAGATCTGTTGTCTTCA
54514533 TTGATCTGTT
Statistics
Matches: 232, Mismatches: 74, Indels: 45
0.66 0.21 0.13
Matches are distributed among these distances:
42 6 0.03
43 65 0.28
44 98 0.42
45 57 0.25
46 6 0.03
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (44 bp):
AGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACTGAGAG
Found at i:54515793 original size:6 final size:6
Alignment explanation
Indices: 54515784--54515828 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
54515774 TTGGCCTCTC
*
54515784 CTTTTT CTTTTT CTTTTT TTCTTTT C-TTTT C-TTTT CTTTTT -TTTT
1 CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT CTTTTT CTTTTT CTTTT
54515829 GAAATATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 14 0.40
6 17 0.49
7 4 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
CTTTTT
Found at i:54515828 original size:5 final size:5
Alignment explanation
Indices: 54515786--54515827 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
54515776 GGCCTCTCCT
54515786 TTTTC TTTT- TCTTT- TTTTC TTTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
54515828 TGAAATATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.23
5 27 0.77
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (5 bp):
TTTTC
Found at i:54520642 original size:21 final size:20
Alignment explanation
Indices: 54520605--54520643 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54520595 ATGTGAATTA
*
54520605 TAAAATATATAAATATATTT
1 TAAAATATAAAAATATATTT
54520625 TAAAATATAAAGAATATAT
1 TAAAATATAAA-AATATAT
54520644 AAATATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TAAAATATAAAAATATATTT
Found at i:54520803 original size:12 final size:12
Alignment explanation
Indices: 54520786--54520827 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
54520776 AAAGCATATT
54520786 TATATATGTAAG
1 TATATATGTAAG
* **
54520798 TATATATATATT
1 TATATATGTAAG
54520810 TATATATGTAAG
1 TATATATGTAAG
54520822 TATATA
1 TATATA
54520828 ATAAAGGCGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
TATATATGTAAG
Found at i:54520808 original size:24 final size:24
Alignment explanation
Indices: 54520781--54520827 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
54520771 GTATGAAAGC
54520781 ATATTTATATATGTAAGTATATAT
1 ATATTTATATATGTAAGTATATAT
54520805 ATATTTATATATGTAAGTATATA
1 ATATTTATATATGTAAGTATATA
54520828 ATAAAGGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
ATATTTATATATGTAAGTATATAT
Found at i:54522459 original size:25 final size:24
Alignment explanation
Indices: 54522410--54522477 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 24
54522400 ATACGACGAA
* *
54522410 CATGTAATTGGGAAGCCCTTCTGAG
1 CATGTAA-TGGGAAGCTCATCTGAG
*
54522435 TCATGTAATGGGAAGCTCATGTGAG
1 -CATGTAATGGGAAGCTCATCTGAG
54522460 C-TGTATAATGGGAAGCTC
1 CATG--TAATGGGAAGCTC
54522478 TTACGAGCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 2 0.05
24 1 0.03
25 27 0.73
26 7 0.19
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.28
Consensus pattern (24 bp):
CATGTAATGGGAAGCTCATCTGAG
Found at i:54522525 original size:24 final size:25
Alignment explanation
Indices: 54522469--54522527 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
54522459 GCTGTATAAT
* * * *
54522469 GGGAAGCTCTTACGAGCCAATTATC
1 GGGAAGCTCATACAAGCCAATAAAC
54522494 GGGAAGCTCATACAAGCC-ATAAAC
1 GGGAAGCTCATACAAGCCAATAAAC
54522518 GGGAAGCTCA
1 GGGAAGCTCA
54522528 AGAGAGCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (25 bp):
GGGAAGCTCATACAAGCCAATAAAC
Found at i:54522535 original size:24 final size:25
Alignment explanation
Indices: 54522493--54522561 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
54522483 AGCCAATTAT
*
54522493 CGGGAAGCTCATACA-AGCCA-TAAA
1 CGGGAAGCTCA-AGAGAGCCATTAAA
*
54522517 CGGGAAGCTCAAGAGAGCCATTAAT
1 CGGGAAGCTCAAGAGAGCCATTAAA
* * *
54522542 TGGAAAGCTCATGAGAGCCA
1 CGGGAAGCTCAAGAGAGCCA
54522562 AATATCGGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
23 2 0.05
24 16 0.42
25 20 0.53
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (25 bp):
CGGGAAGCTCAAGAGAGCCATTAAA
Found at i:54523731 original size:15 final size:15
Alignment explanation
Indices: 54523707--54523738 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54523697 TATGCATGTA
*
54523707 AAATATAAAAGACAT
1 AAATACAAAAGACAT
54523722 AAATACAAAAGACAT
1 AAATACAAAAGACAT
54523737 AA
1 AA
54523739 TAGTTGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:54528088 original size:114 final size:114
Alignment explanation
Indices: 54527752--54528335 Score: 500
Period size: 114 Copynumber: 5.1 Consensus size: 114
54527742 AATATCTGGC
* * * * *
54527752 ATTAGCGGCGCTT-CAAGCAAAACGCCG-TAAAAGAACA-TAATTAGCGGCGTTTTTG-GTTATG
1 ATTAGTGGCGCTTACAA-TAAAACGCCGCT-AAATAACAGT-ATTAGCGGCG-CTTTGAGTTAAG
* * * ** * *
54527813 CGCCGCAAAATCTCAAGACCAAAACGCATCGTTTTTGTATTGATGTATACAATA
62 CGCCGCAAGATATCTA-ACCAAAACGCAGAGTTTTGGTATTGATGTATACTATA
* ** * * * **
54527867 ATTAGTGGCGATTATGATAAAACGCCGCTAAAGT-A-AGTAATAGCGGCGCATTGTGGGAAGCGC
1 ATTAGTGGCGCTTACAATAAAACGCCGCTAAA-TAACAGTATTAGCGGCGCTTTGAGTTAAGCGC
* * *
54527930 CGCAA-AAATCTTAACCAAAACGCAGCGTTTTGGTATCGATGTATACTATA
65 CGCAAGATATC-TAACCAAAACGCAGAGTTTTGGTATTGATGTATACTATA
*
54527980 ATTAGTGGCGCTTACAATAAAACGCCGCTAAATAACAGTATTAGCGGCGCTTTCAGTTAAGCGCC
1 ATTAGTGGCGCTTACAATAAAACGCCGCTAAATAACAGTATTAGCGGCGCTTTGAGTTAAGCGCC
* * *
54528045 GCAAGATATGC-ACACCAAAACGCAGAG-TTTGGTATTGAGGTATATTAGA
66 GCAAGATAT-CTA-ACCAAAACGCAGAGTTTTGGTATTGATGTATACTATA
* ** * *
54528094 ATTAGTGGCGCTTA-TAGGAAACGCCGCTAAAGTATAC--TATTAGCGGCGCTTATGA-TAAAGT
1 ATTAGTGGCGCTTACAATAAAACGCCGCTAAA-TA-ACAGTATTAGCGGCGCTT-TGAGTTAAGC
* * * * *
54528155 GCCGCTATATTTCTTAACCAAAACTCA-ACGTTTTGGTCTTGATGTATACTATA
63 GCCGCAAGATATC-TAACCAAAACGCAGA-GTTTTGGTATTGATGTATACTATA
* * * * *
54528208 ATTAGTGGCGTTTACAATAAAACGCCACTACATAACAGTATTAGCGGCAC-TTAACGTTAAGCGC
1 ATTAGTGGCGCTTACAATAAAACGCCGCTAAATAACAGTATTAGCGGCGCTTTGA-GTTAAGCGC
* *
54528272 CGCAAGATATGC-ACACCAAAACGCAGAG-TTTGGTATTGATGTATATTAGA
65 CGCAAGATAT-CTA-ACCAAAACGCAGAGTTTTGGTATTGATGTATACTATA
54528322 ATTAGTGGCGCTTA
1 ATTAGTGGCGCTTA
54528336 TTGAAAAACG
Statistics
Matches: 377, Mismatches: 66, Indels: 53
0.76 0.13 0.11
Matches are distributed among these distances:
112 3 0.01
113 125 0.33
114 154 0.41
115 90 0.24
116 5 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (114 bp):
ATTAGTGGCGCTTACAATAAAACGCCGCTAAATAACAGTATTAGCGGCGCTTTGAGTTAAGCGCC
GCAAGATATCTAACCAAAACGCAGAGTTTTGGTATTGATGTATACTATA
Found at i:54528172 original size:228 final size:229
Alignment explanation
Indices: 54527938--54528373 Score: 723
Period size: 228 Copynumber: 1.9 Consensus size: 229
54527928 GCCGCAAAAA
*
54527938 TCTTAACCAAAACGCAGCGTTTTGGTATCGATGTATACTATAATTAGTGGCGCTTACAATAAAAC
1 TCTTAACCAAAACGCAACGTTTTGGTATCGATGTATACTATAATTAGTGGCGCTTACAATAAAAC
* * *
54528003 GCCGCTAAATAACAGTATTAGCGGCGCTT-TCAGTTAAGCGCCGCAAGATATGCACACCAAAACG
66 GCCACTAAATAACAGTATTAGCGGCACTTAAC-GTTAAGCGCCGCAAGATATGCACACCAAAACG
*
54528067 CAGAGTTTGGTATTGAGGTATATTAGAATTAGTGGCGCTTATAG-GAAACGCCGCTAAAGTATAC
130 CAGAGTTTGGTATTGAGGTATATTAGAATTAGTGGCGCTTATAGAAAAACGCCGCTAAAGTATAC
*
54528131 TATTAGCGGCGCTTATGATAAAGTGCCGCTATATT
195 TATTAGCAGCGCTTATGATAAAGTGCCGCTATATT
* * * *
54528166 TCTTAACCAAAACTCAACGTTTTGGTCTTGATGTATACTATAATTAGTGGCGTTTACAATAAAAC
1 TCTTAACCAAAACGCAACGTTTTGGTATCGATGTATACTATAATTAGTGGCGCTTACAATAAAAC
*
54528231 GCCACTACATAACAGTATTAGCGGCACTTAACGTTAAGCGCCGCAAGATATGCACACCAAAACGC
66 GCCACTAAATAACAGTATTAGCGGCACTTAACGTTAAGCGCCGCAAGATATGCACACCAAAACGC
* * *
54528296 AGAGTTTGGTATTGATGTATATTAGAATTAGTGGCGCTTATTGAAAAACGCCGTTAAAGTATACT
131 AGAGTTTGGTATTGAGGTATATTAGAATTAGTGGCGCTTATAGAAAAACGCCGCTAAAGTATACT
54528361 ATTAGCAGCGCTT
196 ATTAGCAGCGCTT
54528374 TCCTAGAAGC
Statistics
Matches: 192, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
228 160 0.83
229 32 0.17
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (229 bp):
TCTTAACCAAAACGCAACGTTTTGGTATCGATGTATACTATAATTAGTGGCGCTTACAATAAAAC
GCCACTAAATAACAGTATTAGCGGCACTTAACGTTAAGCGCCGCAAGATATGCACACCAAAACGC
AGAGTTTGGTATTGAGGTATATTAGAATTAGTGGCGCTTATAGAAAAACGCCGCTAAAGTATACT
ATTAGCAGCGCTTATGATAAAGTGCCGCTATATT
Done.