Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 13 of 325
Found at i:3977277 original size:21 final size:21
Alignment explanation
Indices: 3977239--3977279 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3977229 TTGTTAAGGG
*
3977239 TTTAGGGTTCATGGTTCATGA
1 TTTAGGGTTCATGATTCATGA
3977260 TTTAGGGTTCGA-GATTCATG
1 TTTAGGGTTC-ATGATTCATG
3977280 GTTCAAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (21 bp):
TTTAGGGTTCATGATTCATGA
Found at i:3977549 original size:17 final size:17
Alignment explanation
Indices: 3977498--3977557 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 17
3977488 CAATCAATTT
3977498 AAATTTTCAATATTTATA
1 AAATTTTCAAT-TTTATA
3977516 AAATTTATCACATTTTATA
1 AAATTT-TCA-ATTTTATA
3977535 ATAATTTT-AATTTTAATA
1 A-AATTTTCAATTTT-ATA
3977553 AAATT
1 AAATT
3977558 AAATAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.24
18 11 0.29
19 11 0.29
20 7 0.18
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTTCAATTTTATA
Found at i:3977825 original size:43 final size:44
Alignment explanation
Indices: 3977767--3977851 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
3977757 CATTTGATTG
3977767 TTTTTTATATTATTGTA-TCACATTACAATAATATTATATATGT
1 TTTTTTATATTATTGTATTCACATTACAATAATATTATATATGT
3977810 TTTTTTATATTATTGTATTCACATTACAATAATATTATATAT
1 TTTTTTATATTATTGTATTCACATTACAATAATATTATATAT
3977852 TAGTAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 17 0.41
44 24 0.59
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (44 bp):
TTTTTTATATTATTGTATTCACATTACAATAATATTATATATGT
Found at i:3977910 original size:23 final size:21
Alignment explanation
Indices: 3977884--3977927 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
3977874 ATTAAAGATG
*
3977884 AAATTATATTTTGTATTTACATT
1 AAATTATACTTT-TA-TTACATT
3977907 AAATTATACTTTTATTACATT
1 AAATTATACTTTTATTACATT
3977928 TTCAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATTATACTTTTATTACATT
Found at i:3980050 original size:39 final size:39
Alignment explanation
Indices: 3979996--3980074 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3979986 TTGAATTTTC
3979996 TATTATCCTACTTATTTCTTTTTCTTTGCTTTGATTTGT
1 TATTATCCTACTTATTTCTTTTTCTTTGCTTTGATTTGT
3980035 TATTATCCTACTTATTTCTTTTTCTTTGCTTTGATTTGT
1 TATTATCCTACTTATTTCTTTTTCTTTGCTTTGATTTGT
3980074 T
1 T
3980075 CTTTTTATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.13, C:0.15, G:0.08, T:0.65
Consensus pattern (39 bp):
TATTATCCTACTTATTTCTTTTTCTTTGCTTTGATTTGT
Found at i:3981006 original size:19 final size:19
Alignment explanation
Indices: 3980984--3981045 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
3980974 CCTTCAAAAA
3980984 ATTATTTTAATTTTATAAT
1 ATTATTTTAATTTTATAAT
* *
3981003 ATTATTATATATTGATATAAT
1 ATTATTTTA-ATT-TTATAAT
* *
3981024 -TT-TCTTAATTTTATAAG
1 ATTATTTTAATTTTATAAT
3981041 ATTAT
1 ATTAT
3981046 AAATATTTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 5 0.15
18 5 0.15
19 12 0.36
20 5 0.15
21 6 0.18
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (19 bp):
ATTATTTTAATTTTATAAT
Found at i:3981037 original size:38 final size:38
Alignment explanation
Indices: 3980990--3981064 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
3980980 AAAAATTATT
* *
3980990 TTAATTTTATAATATTAT-TATATATTGATATAATTTTC
1 TTAATTTTATAAGATTATAAATAT-TTGATATAATTTTC
*
3981028 TTAATTTTATAAGATTATAAATATTTGATTTAATTTT
1 TTAATTTTATAAGATTATAAATATTTGATATAATTTT
3981065 TTTTTGGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 29 0.88
39 4 0.12
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (38 bp):
TTAATTTTATAAGATTATAAATATTTGATATAATTTTC
Found at i:3986519 original size:21 final size:21
Alignment explanation
Indices: 3986476--3986521 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3986466 AAAAAATTGT
* *
3986476 AAAATTTTATAAAAACCATCA
1 AAAAATTTATAAAAACCAACA
**
3986497 AAAAATTTATAAAATGCAACA
1 AAAAATTTATAAAAACCAACA
3986518 AAAA
1 AAAA
3986522 GACCCTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAATTTATAAAAACCAACA
Found at i:3986653 original size:10 final size:10
Alignment explanation
Indices: 3986640--3986675 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3986630 ATGATAAAAA
3986640 ATAAAAATTT
1 ATAAAAATTT
*
3986650 ATAAAAGTTT
1 ATAAAAATTT
*
3986660 AAAAAAATTT
1 ATAAAAATTT
3986670 ATAAAA
1 ATAAAA
3986676 TGCTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:3986733 original size:10 final size:10
Alignment explanation
Indices: 3986718--3986747 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
3986708 TTTTACAAAT
3986718 TTTACATTTC
1 TTTACATTTC
3986728 TTTACATTTC
1 TTTACATTTC
3986738 TTTATCATTT
1 TTTA-CATTT
3986748 TCTTATGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTACATTTC
Found at i:3986819 original size:20 final size:20
Alignment explanation
Indices: 3986785--3986838 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
3986775 TTTTTCTATA
* *
3986785 TTTCTAATATTTTATATTTTT
1 TTTCTAAT-TTTTATAATCTT
3986806 TTTAC-AATTTTTATAATCTT
1 TTT-CTAATTTTTATAATCTT
3986826 TTTCTAATTTTTA
1 TTTCTAATTTTTA
3986839 ACAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 1 0.03
20 21 0.72
21 6 0.21
22 1 0.03
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTCTAATTTTTATAATCTT
Found at i:3992356 original size:15 final size:16
Alignment explanation
Indices: 3992336--3992370 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3992326 CTTTTAATAT
3992336 TATTTAATATTA-TTA
1 TATTTAATATTATTTA
*
3992351 TATTTACTATTATTTA
1 TATTTAATATTATTTA
3992367 TATT
1 TATT
3992371 ATTCTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTAATATTATTTA
Found at i:3992521 original size:24 final size:24
Alignment explanation
Indices: 3992478--3992541 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
3992468 TTCTAACATG
* * *
3992478 TATATACTATGTAAATATTT-TAA
1 TATATATTATGTATACATTTCTAA
*
3992501 TACTATATTATGTATACATTTCTTA
1 TA-TATATTATGTATACATTTCTAA
*
3992526 TATATATTACGTATAC
1 TATATATTATGTATAC
3992542 GTATCTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.06
24 28 0.82
25 4 0.12
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (24 bp):
TATATATTATGTATACATTTCTAA
Found at i:3993822 original size:28 final size:28
Alignment explanation
Indices: 3993790--3993847 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
3993780 CCTTTTTAGT
*
3993790 AAAATCGCAAGTCGATTTTCAAATTTTC
1 AAAATCGCAAGTCGATATTCAAATTTTC
*
3993818 AAAATCGCAAGTCGGTATTCAAATTTTC
1 AAAATCGCAAGTCGATATTCAAATTTTC
3993846 AA
1 AA
3993848 TAAATCGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (28 bp):
AAAATCGCAAGTCGATATTCAAATTTTC
Found at i:4001803 original size:21 final size:20
Alignment explanation
Indices: 4001775--4001816 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
4001765 AAAGAGAGCA
4001775 TGTTGAGA-ACCTCAGGAAGT
1 TGTTGAGAGA-CTCAGGAAGT
*
4001795 TGTTCGAGAGACTGAGGAAGT
1 TGTT-GAGAGACTCAGGAAGT
4001816 T
1 T
4001817 CCAGCTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 14 0.74
22 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (20 bp):
TGTTGAGAGACTCAGGAAGT
Found at i:4005342 original size:76 final size:76
Alignment explanation
Indices: 4005255--4005444 Score: 310
Period size: 76 Copynumber: 2.5 Consensus size: 76
4005245 TTCTGTTTTC
* *
4005255 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCATGACACGTTAAGG-AATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTTCAATTT
*
4005319 CTTTCTTTAAAA
66 CTATCTTT-AAA
* *
4005331 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCTGAGGTAATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTTCAATTT
*
4005396 CTATCTTTCAA
66 CTATCTTTAAA
4005407 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
4005445 GGGCCACATG
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
76 88 0.82
77 19 0.18
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (76 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTTCAATTT
CTATCTTTAAA
Found at i:4005466 original size:77 final size:77
Alignment explanation
Indices: 4005255--4005469 Score: 301
Period size: 76 Copynumber: 2.8 Consensus size: 77
4005245 TTCTGTTTTC
* * ***
4005255 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCATGACACGTTAAGG-AATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCCGAGGTAATTTTCAATTT
*
4005319 CTTTCTTTAAAA
66 CTATCTTTAAAA
*
4005331 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCTGAGGTAATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCCGAGGTAATTTTCAATTT
*
4005396 CTATCTTT-CAA
66 CTATCTTTAAAA
**
4005407 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACATGCCGAGGT-ATTTTCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACATGCCGAGGTAATTTTCAA
4005470 AATTCCGTTT
Statistics
Matches: 127, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
76 89 0.70
77 27 0.21
78 11 0.09
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (77 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGCCGAGGTAATTTTCAATTT
CTATCTTTAAAA
Found at i:4005545 original size:92 final size:89
Alignment explanation
Indices: 4005386--4005799 Score: 412
Period size: 88 Copynumber: 4.6 Consensus size: 89
4005376 GCTGAGGTAA
*
4005386 TTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGC-C
1 TTTTCAATTTCTGT-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTC
* *
4005450 ACATGCCGAGGTATTTTCAAAATTCCGT
62 ACATGCTGAGGTATTTTCAAAATTCTGT
*
4005478 TTTTCAATTTCTGTTTCTTCTAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCA
1 TTTTCAATTTCTG-TT-TTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCA
*
4005543 CATGCTGAGGTATTTTC--AATTGATGTT
63 CATGCTGAGGTATTTTCAAAATT-CTG-T
* * * * *
4005570 TTTTCAGTTTATGCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTTAGG-TTAC
1 TTTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCGGCTCAC
*
4005634 ATGTTGAGGTATTTTCAAAA-TCTGT
64 ATGCTGAGGTATTTTCAAAATTCTGT
* * * * * * *
4005659 TTTTCAAATTCTGTTGTCAAAAGTCAACTCATATTGCAAGAAGTGAGTTGAGCCTTGGCTCACGT
1 TTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
* * * *
4005724 GTTGAGCTATTTTC-AATTTCTAT
66 GCTGAGGTATTTTCAAAATTCTGT
* * * **
4005747 TTTT-AATGTT-TGTTTTTAAAGATTCAATTCATATTGCGAGAAATGAGTTGAGC
1 TTTTCAAT-TTCTGTTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGC
4005800 TCAGGATCAC
Statistics
Matches: 274, Mismatches: 36, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
87 15 0.05
88 91 0.33
89 11 0.04
90 58 0.21
91 11 0.04
92 84 0.31
93 4 0.01
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (89 bp):
TTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
GCTGAGGTATTTTCAAAATTCTGT
Found at i:4007504 original size:15 final size:16
Alignment explanation
Indices: 4007484--4007518 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4007474 CTTTTAATAT
4007484 TATTTAATATTA-TTA
1 TATTTAATATTATTTA
*
4007499 TATTTACTATTATTTA
1 TATTTAATATTATTTA
4007515 TATT
1 TATT
4007519 ATTCTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTAATATTATTTA
Found at i:4008148 original size:25 final size:24
Alignment explanation
Indices: 4008094--4008161 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
4008084 ATATATTTTT
* *
4008094 ACTATCTTATGTATATATTTTGAAT
1 ACTATC-TATGTATATATTTTAAAC
*
4008119 GCTATGCTATGTATATATTTTAAAC
1 ACTAT-CTATGTATATATTTTAAAC
* *
4008144 ACTATTTATATATATATT
1 ACTATCTATGTATATATT
4008162 ATATGCATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 11 0.31
25 24 0.67
26 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (24 bp):
ACTATCTATGTATATATTTTAAAC
Found at i:4010139 original size:15 final size:15
Alignment explanation
Indices: 4010099--4010127 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4010089 TTTGGTAAAT
4010099 TAAAAAATTAAGTGC
1 TAAAAAATTAAGTGC
4010114 TAAAAAATTAAGTG
1 TAAAAAATTAAGTG
4010128 TTGAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.14, T:0.28
Consensus pattern (15 bp):
TAAAAAATTAAGTGC
Found at i:4014294 original size:12 final size:12
Alignment explanation
Indices: 4014277--4014303 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4014267 AGTTTTTGTG
4014277 AAAAATAAAATA
1 AAAAATAAAATA
4014289 AAAAATAAAATA
1 AAAAATAAAATA
4014301 AAA
1 AAA
4014304 TAAAGAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:4017010 original size:28 final size:27
Alignment explanation
Indices: 4016979--4017072 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 27
4016969 CCCGATCTCA
4016979 CACACATAGTGCTCGGTTAATAATTTCG
1 CACACATAGTGCTC-GTTAATAATTTCG
* ** * *
4017007 CACACATATTGC-C-TTACACCCGATCTAG
1 CACACATAGTGCTCGTTA-A--TAATTTCG
*
4017035 CATACATAGTGCTCGATTAATAATTTCG
1 CACACATAGTGCTCG-TTAATAATTTCG
4017063 CACACATAGT
1 CACACATAGT
4017073 ACATATATTA
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 1 0.02
28 38 0.79
29 1 0.02
30 1 0.02
31 3 0.06
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (27 bp):
CACACATAGTGCTCGTTAATAATTTCG
Found at i:4017027 original size:56 final size:56
Alignment explanation
Indices: 4016939--4017072 Score: 198
Period size: 56 Copynumber: 2.4 Consensus size: 56
4016929 ATATTCCCTA
* *
4016939 AATAATTTCGCACACACACAGTGCCTTACACCCGATCTCA-CACACATAGTGCTCGGTT
1 AATAATTTCG--CACACATAGTGCCTTACACCCGATCT-AGCACACATAGTGCTCGATT
* *
4016997 AATAATTTCGCACACATATTGCCTTACACCCGATCTAGCATACATAGTGCTCGATT
1 AATAATTTCGCACACATAGTGCCTTACACCCGATCTAGCACACATAGTGCTCGATT
4017053 AATAATTTCGCACACATAGT
1 AATAATTTCGCACACATAGT
4017073 ACATATATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
55 1 0.01
56 59 0.84
58 10 0.14
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (56 bp):
AATAATTTCGCACACATAGTGCCTTACACCCGATCTAGCACACATAGTGCTCGATT
Found at i:4030195 original size:25 final size:24
Alignment explanation
Indices: 4030165--4030231 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
4030155 GCTACAGTTA
4030165 ATGGTTTTGATATGATGGTTGATTT
1 ATGGTTTTGAT-TGATGGTTGATTT
4030190 ATGGTTTTGATT--TGGTTGATTT
1 ATGGTTTTGATTGATGGTTGATTT
* *
4030212 ATGATTTTAATCTGATGGTT
1 ATGGTTTTGAT-TGATGGTT
4030232 TATGGTCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 19 0.51
23 1 0.03
24 1 0.03
25 16 0.43
ACGTcount: A:0.19, C:0.01, G:0.25, T:0.54
Consensus pattern (24 bp):
ATGGTTTTGATTGATGGTTGATTT
Found at i:4038755 original size:3 final size:3
Alignment explanation
Indices: 4038747--4038775 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4038737 TAGAAATTTA
4038747 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4038776 GATGCAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4039907 original size:20 final size:21
Alignment explanation
Indices: 4039870--4039908 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
4039860 TATTTTTCGA
4039870 TAAAATATTAAGAATATTATT
1 TAAAATATTAAGAATATTATT
4039891 TAAAAT-TTAA-AATTATTA
1 TAAAATATTAAGAA-TATTA
4039909 CTAATGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TAAAATATTAAGAATATTATT
Found at i:4041060 original size:30 final size:30
Alignment explanation
Indices: 4040975--4041060 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 30
4040965 TATTTTATTA
* * *
4040975 TTAATTTTGTTATTATTTTAAAAGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCACTTG
4041005 TTAATTTTGTTATTATTTTAAAGGCACTTG
1 TTAATTTTGTTATTATTTTAAAGGCACTTG
*
4041035 TTAATTTTGTTATTATTTTAGAGGCA
1 TTAATTTTGTTATTATTTTAAAGGCA
4041061 TTTGCTTGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.56
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCACTTG
Found at i:4045367 original size:34 final size:31
Alignment explanation
Indices: 4045329--4045397 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 31
4045319 AGTAGTTGTA
*
4045329 TTATAAAGACGTAATTTTTGTACGTAAAATTATC
1 TTATAAAGACATAA--TTT-TACGTAAAATTATC
* *
4045363 TTATAAAGATATAATTTTATGTAAAATTATC
1 TTATAAAGACATAATTTTACGTAAAATTATC
4045394 TTAT
1 TTAT
4045398 TAAACAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 17 0.53
32 3 0.09
34 12 0.38
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (31 bp):
TTATAAAGACATAATTTTACGTAAAATTATC
Found at i:4047750 original size:13 final size:13
Alignment explanation
Indices: 4047732--4047756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4047722 TCTAACTTGA
4047732 TTAAGCTTATATT
1 TTAAGCTTATATT
4047745 TTAAGCTTATAT
1 TTAAGCTTATAT
4047757 ATATTTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TTAAGCTTATATT
Found at i:4055629 original size:45 final size:45
Alignment explanation
Indices: 4055557--4055653 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
4055547 CATGTCCATT
* *
4055557 TCCATTTTGAGAAAACCACATTTATTTCTAAATG-ATTCCATTTC
1 TCCATTTTGAGAAAACCACAATCATTTCTAAATGTATTCCATTTC
* * * *
4055601 TCCATTTTGGAGAAAACCATAATCATTTCTGAATGTTTTCTATTTC
1 TCCATTTT-GAGAAAACCACAATCATTTCTAAATGTATTCCATTTC
*
4055647 TCTATTT
1 TCCATTT
4055654 CTATTCATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 8 0.18
45 22 0.50
46 14 0.32
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (45 bp):
TCCATTTTGAGAAAACCACAATCATTTCTAAATGTATTCCATTTC
Found at i:4057115 original size:25 final size:25
Alignment explanation
Indices: 4057076--4057129 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
4057066 TGTTATACTT
*
4057076 CATGAATGCAAGAAAACCCCATTTG
1 CATGAATACAAGAAAACCCCATTTG
* *
4057101 CATGAATACATGAAAACCTCATTTG
1 CATGAATACAAGAAAACCCCATTTG
4057126 CATG
1 CATG
4057130 CATGCAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (25 bp):
CATGAATACAAGAAAACCCCATTTG
Found at i:4059342 original size:43 final size:44
Alignment explanation
Indices: 4059281--4059373 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
4059271 TCCTAATTGG
4059281 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
4059324 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
4059368 -AAAATA
1 GAAAATA
4059374 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:4059417 original size:19 final size:18
Alignment explanation
Indices: 4059395--4059434 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
4059385 TGAATAAAAC
4059395 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
*
4059414 TTATCTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
4059432 TTA
1 TTA
4059435 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:4066200 original size:43 final size:44
Alignment explanation
Indices: 4066139--4066231 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
4066129 TCCTAATTGG
4066139 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
4066182 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
4066226 -AAAATA
1 GAAAATA
4066232 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:4066275 original size:19 final size:18
Alignment explanation
Indices: 4066253--4066292 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
4066243 TGAATAAAAC
4066253 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
*
4066272 TTATCTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
4066290 TTA
1 TTA
4066293 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:4067312 original size:17 final size:18
Alignment explanation
Indices: 4067292--4067329 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4067282 TTAGAATCGG
*
4067292 ATTG-GAAAAATAATTTA
1 ATTGAGAAAAATAATTAA
*
4067309 ATTGAGAGAAATAATTAA
1 ATTGAGAAAAATAATTAA
4067327 ATT
1 ATT
4067330 AAATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (18 bp):
ATTGAGAAAAATAATTAA
Found at i:4068396 original size:61 final size:61
Alignment explanation
Indices: 4068287--4068408 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
4068277 AGAATAAAAA
* * *
4068287 TATATGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGGGGGGTGGAAACTTTATAGTTT
1 TATAAGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
4068348 TATAAGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
1 TATAAGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
4068409 AGAGCCATAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (61 bp):
TATAAGGGGATAAGGGATCTCTTTGCCTGATGCCTCGAGAGGGATGGAAACTTTATAGTTT
Found at i:4075162 original size:17 final size:17
Alignment explanation
Indices: 4075140--4075174 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4075130 AAACTGTTTG
4075140 ACAAAGTTTATAACATT
1 ACAAAGTTTATAACATT
4075157 ACAAAGTTTATAACATT
1 ACAAAGTTTATAACATT
4075174 A
1 A
4075175 AATACTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (17 bp):
ACAAAGTTTATAACATT
Found at i:4076677 original size:17 final size:18
Alignment explanation
Indices: 4076657--4076692 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
4076647 TTTATATATA
4076657 TTATATTAA-TTTTTACT
1 TTATATTAATTTTTTACT
4076674 TTATATTAATTTTTTACT
1 TTATATTAATTTTTTACT
4076692 T
1 T
4076693 CTTTCTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTAATTTTTTACT
Found at i:4081207 original size:2 final size:2
Alignment explanation
Indices: 4081200--4081226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4081190 GCTCTTGCAT
4081200 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
4081227 TAGAAACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4081462 original size:6 final size:6
Alignment explanation
Indices: 4081451--4081497 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
4081441 ATCCGAAGAG
* * * *
4081451 GAGGAA GAGGAA GAGGAA GAGGAA GGGGAC GAGGAT GAGGAT GAGGA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGA
4081498 GACTAAAGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.40, C:0.02, G:0.53, T:0.04
Consensus pattern (6 bp):
GAGGAA
Found at i:4082345 original size:2 final size:2
Alignment explanation
Indices: 4082338--4082393 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
4082328 AATAATCCTT
4082338 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4082380 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
4082394 ACATACGAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4085621 original size:9 final size:9
Alignment explanation
Indices: 4085607--4085819 Score: 87
Period size: 9 Copynumber: 22.3 Consensus size: 9
4085597 TTTTATCATA
4085607 AAAAATTAT
1 AAAAATTAT
4085616 AAAAATATCAT
1 AAAAAT-T-AT
4085627 AAAAA--AT
1 AAAAATTAT
* *
4085634 AAATATTAAC
1 AAAAATT-AT
4085644 ATAAAATTAT
1 A-AAAATTAT
*
4085654 AGAAATTAT
1 AAAAATTAT
*
4085663 AGAAAAATTAG
1 --AAAAATTAT
** *
4085674 AGTACTTAT
1 AAAAATTAT
*
4085683 AAAAAATAT
1 AAAAATTAT
4085692 AAAAATTCAT
1 AAAAATT-AT
*
4085702 AAAAGGTTAT
1 AAAA-ATTAT
*
4085712 AAATATTAT
1 AAAAATTAT
*
4085721 AAAATTTTAT
1 AAAA-ATTAT
*
4085731 AAAAATTCT
1 AAAAATTAT
4085740 AATAAATTAT
1 AA-AAATTAT
*
4085750 AAAAA-AAT
1 AAAAATTAT
4085758 AAAACA-TAT
1 AAAA-ATTAT
4085767 AAAAGCA-TATT
1 AAAA--ATTA-T
* *
4085778 CAAAATTTTT
1 -AAAAATTAT
4085788 AAAAGATTAT
1 AAAA-ATTAT
4085798 -AAAATTCAT
1 AAAAATT-AT
4085807 AAAAACTTAT
1 AAAAA-TTAT
4085817 AAA
1 AAA
4085820 TAATATGATA
Statistics
Matches: 153, Mismatches: 30, Indels: 41
0.68 0.13 0.18
Matches are distributed among these distances:
7 6 0.04
8 9 0.06
9 60 0.39
10 49 0.32
11 25 0.16
12 4 0.03
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:4085669 original size:20 final size:19
Alignment explanation
Indices: 4085604--4085750 Score: 72
Period size: 19 Copynumber: 7.7 Consensus size: 19
4085594 TATTTTTATC
*
4085604 ATAAAAAATTATAAAAATAT
1 ATAAAAAATTATAGAAAT-T
*
4085624 CATAAAAAA-TA-A-ATATT
1 -ATAAAAAATTATAGAAATT
4085641 A-ACATAAAATTATAGAAATT
1 ATA-A-AAAATTATAGAAATT
* * *
4085661 ATAGAAAAATTAGAGTACTT
1 ATA-AAAAATTATAGAAATT
*
4085681 ATAAAAAA-TATAAAAATT
1 ATAAAAAATTATAGAAATT
**
4085699 CATAAAAGGTTATA-AATATT
1 -ATAAAAAATTATAGAA-ATT
** *
4085719 ATAAAATTTTATAAAAATT
1 ATAAAAAATTATAGAAATT
* *
4085738 CTAATAAATTATA
1 ATAAAAAATTATA
4085751 AAAAAATAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
15 1 0.01
16 2 0.02
17 5 0.05
18 11 0.11
19 38 0.39
20 31 0.32
21 10 0.10
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (19 bp):
ATAAAAAATTATAGAAATT
Found at i:4085711 original size:29 final size:29
Alignment explanation
Indices: 4085679--4085734 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4085669 ATTAGAGTAC
4085679 TTATAAAAAATATAAAAATTCATAAAAGG
1 TTATAAAAAATATAAAAATTCATAAAAGG
* * * *
4085708 TTATAAATATTATAAAATTTTATAAAA
1 TTATAAAAAATATAAAAATTCATAAAA
4085735 ATTCTAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (29 bp):
TTATAAAAAATATAAAAATTCATAAAAGG
Found at i:4089605 original size:20 final size:21
Alignment explanation
Indices: 4089582--4089632 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
4089572 TCGTGTCAGT
*
4089582 AAAAAAAAGTTTGAAAAAG-A
1 AAAAAAAAGGTTGAAAAAGCA
* *
4089602 AAAACAAAGGTTGGAAAAGCA
1 AAAAAAAAGGTTGAAAAAGCA
4089623 AAAAAAAAGG
1 AAAAAAAAGG
4089633 GGAGCCCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.67, C:0.04, G:0.20, T:0.10
Consensus pattern (21 bp):
AAAAAAAAGGTTGAAAAAGCA
Found at i:4091819 original size:116 final size:116
Alignment explanation
Indices: 4091610--4091839 Score: 295
Period size: 116 Copynumber: 2.0 Consensus size: 116
4091600 AGCGTTATCC
* *
4091610 TTTTAGCACCCTGATTGATGACTGTTTGATTTTATTTGATGGAGGTTGGGTGATTGAGATTAAAC
1 TTTTAGCACCCTGATTGATGACTGGTTGACTTTATTTGATGGAGGTTGGGTGATTGAGATTAAAC
** * *
4091675 ATATTATTTGTAAGGGCAAAAAGCGTACAAATCAC-TAGGATTCTTTAACAG
66 ATATTATTTCCAAGGACAAAAAGCGTACAAATCACTTA-AATTCTTTAACAG
* * *
4091726 TTTTAGCACCCTGATTGATGATTGGTTGACTTTGTTTGAT-GAGGGTTGGGTGATTGAGATTAGA
1 TTTTAGCACCCTGATTGATGACTGGTTGACTTTATTTGATGGA-GGTTGGGTGATTGAGATTAAA
* * * *
4091790 CATATTCTTTCCAAGGACAATGAA-TGTACAAATGACTTAAATTCTTTAAC
65 CATATTATTTCCAAGGACAA-AAAGCGTACAAATCACTTAAATTCTTTAAC
4091840 GTAAGGATCC
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
115 2 0.02
116 92 0.94
117 4 0.04
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (116 bp):
TTTTAGCACCCTGATTGATGACTGGTTGACTTTATTTGATGGAGGTTGGGTGATTGAGATTAAAC
ATATTATTTCCAAGGACAAAAAGCGTACAAATCACTTAAATTCTTTAACAG
Found at i:4094553 original size:15 final size:16
Alignment explanation
Indices: 4094533--4094569 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4094523 TGGAATCGGC
4094533 TTTTTTA-TA-AAAAT
1 TTTTTTAGTAGAAAAT
4094547 ATTTTTTAGTAGAAAAT
1 -TTTTTTAGTAGAAAAT
4094564 TTTTTT
1 TTTTTT
4094570 TGGACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 8 0.40
17 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTTTAGTAGAAAAT
Found at i:4094881 original size:18 final size:18
Alignment explanation
Indices: 4094858--4094892 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4094848 ATTTCCATAC
4094858 ATTTTTCATA-ATTAATTA
1 ATTTTT-ATATATTAATTA
4094876 ATTTTTATATATTAATT
1 ATTTTTATATATTAATT
4094893 GGGTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATATATTAATTA
Found at i:4097150 original size:139 final size:143
Alignment explanation
Indices: 4096946--4097220 Score: 326
Period size: 139 Copynumber: 1.9 Consensus size: 143
4096936 ATATCGTTAA
*
4096946 TATAAAAATGTACATTATAATATCATCCATAATGGTACATAAGATTACATATCATTAATAATCTA
1 TATAAAAATGTACATTATAATA-CAT-CATAATGGTACATAAGATTACATATCATCAATAATCTA
* * * * * *
4097011 CATTGATTACGTAATGATAA-C-TGTATATATTATAATCTATCATAAAGTTAGTTACATGTTTTA
64 CATTGATTACATAATGATAACCGTATATATATTATAATCTACCATAAAATTAGTTACATATTTAA
4097074 GGTTTAAGCTTGCGG
129 GGTTTAAGCTTGCGG
* * * * *
4097089 TATAAAAATGTACATTTTAATA-AT-ATAGTTGTATATAAGGA-TACATATCATCAATTATCTAC
1 TATAAAAATGTACATTATAATACATCATAATGGTACATAA-GATTACATATCATCAATAATCTAC
* * * * * *
4097151 TTTTATTATATAATGTTAACCGTATATATATTATAATGTACCATAAAATTAGTTTCATATTTAAG
65 ATTGATTACATAATGATAACCGTATATATATTATAATCTACCATAAAATTAGTTACATATTTAAG
4097216 GTTTA
130 GTTTA
4097221 GGTTGCATAT
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
139 44 0.40
140 3 0.03
141 43 0.39
143 21 0.19
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (143 bp):
TATAAAAATGTACATTATAATACATCATAATGGTACATAAGATTACATATCATCAATAATCTACA
TTGATTACATAATGATAACCGTATATATATTATAATCTACCATAAAATTAGTTACATATTTAAGG
TTTAAGCTTGCGG
Found at i:4120137 original size:64 final size:64
Alignment explanation
Indices: 4120058--4120184 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
4120048 AGGTTTTAAC
4120058 TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAAT
1 TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAAT
*
4120122 TTGACCATAATCTGTTTTATGTTCTCTCATGTAGGTTTGAAGTCCATCTCGAGATGTTCAAAA
1 TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAA
4120185 CTATCTATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (64 bp):
TTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAAAAT
Found at i:4121248 original size:16 final size:16
Alignment explanation
Indices: 4121227--4121258 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4121217 CATCTAAAAG
4121227 GAAACCATGATTTTTC
1 GAAACCATGATTTTTC
4121243 GAAACCATGATTTTTC
1 GAAACCATGATTTTTC
4121259 AGGGATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
GAAACCATGATTTTTC
Found at i:4126540 original size:21 final size:21
Alignment explanation
Indices: 4126502--4126544 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
4126492 AAAAAATTAA
*
4126502 AAATATATTTTTATAATTTTT
1 AAATATATTTTAATAATTTTT
*
4126523 AAATA-ATTTTAATAAATTTT
1 AAATATATTTTAATAATTTTT
4126543 AA
1 AA
4126545 CTTTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATATATTTTAATAATTTTT
Found at i:4127577 original size:25 final size:25
Alignment explanation
Indices: 4127531--4127600 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
4127521 GGTTTATTTT
4127531 ATTTAATATTAATA-TAATTATATTC
1 ATTTAATATTAATATTAA-TATATTC
*
4127556 ATTTAATATTAATATTAATATA-AC
1 ATTTAATATTAATATTAATATATTC
*
4127580 ATTTAA-ATT--TATTATTATATT
1 ATTTAATATTAATATTAATATATT
4127601 TTTTTGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.22
23 3 0.08
24 7 0.17
25 18 0.45
26 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTAATATTAATATTAATATATTC
Found at i:4127611 original size:24 final size:23
Alignment explanation
Indices: 4127584--4127651 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 23
4127574 TATAACATTT
*
4127584 AAATTTATTATTATATTTTTTTGAA
1 AAATTTATTATTATA-TATTTT-AA
*
4127609 AATATTTATTGTTATATATTTTAA
1 AA-ATTTATTATTATATATTTTAA
*
4127633 AATTTTATATATTAT-TATT
1 AAATTTAT-TATTATATATT
4127652 CCTTGTCAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
23 9 0.24
24 9 0.24
25 7 0.19
26 12 0.32
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (23 bp):
AAATTTATTATTATATATTTTAA
Found at i:4127639 original size:23 final size:26
Alignment explanation
Indices: 4127586--4127707 Score: 80
Period size: 25 Copynumber: 4.8 Consensus size: 26
4127576 TAACATTTAA
*
4127586 ATTTATTATTATATTTTTTTGAAAAT
1 ATTTATTATTATATTATTTTGAAAAT
*
4127612 ATTTATTGTTATA-TATTTT-AAAAT
1 ATTTATTATTATATTATTTTGAAAAT
* * *
4127636 -TTTATATATTATTATTCCTTGTCAACAAT
1 ATTTAT-TATTA-TATT-ATTTTGAA-AAT
*
4127665 -TTT-TTAAATATATT-TTTTGAAAAT
1 ATTTATT-ATTATATTATTTTGAAAAT
4127689 ATTTA-TATT-TATATATTTT
1 ATTTATTATTATAT-TATTTT
4127708 TTATATATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
23 8 0.11
24 15 0.20
25 20 0.26
26 13 0.17
27 8 0.11
28 6 0.08
29 6 0.08
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (26 bp):
ATTTATTATTATATTATTTTGAAAAT
Found at i:4127681 original size:13 final size:12
Alignment explanation
Indices: 4127663--4127718 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
4127653 CTTGTCAACA
4127663 ATTTTTTAAATAT
1 ATTTTTT-AATAT
*
4127676 ATTTTTTGAAAAT
1 ATTTTTT-AATAT
*
4127689 ATTTATATTTATAT
1 ATTT-T-TTAATAT
4127703 ATTTTTT-ATAT
1 ATTTTTTAATAT
4127714 ATTTT
1 ATTTT
4127719 AAACTCAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 9 0.24
12 2 0.05
13 16 0.43
14 8 0.22
15 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
ATTTTTTAATAT
Found at i:4127702 original size:27 final size:27
Alignment explanation
Indices: 4127586--4127709 Score: 97
Period size: 27 Copynumber: 4.8 Consensus size: 27
4127576 TAACATTTAA
4127586 ATTTATTATTATAT-TTTTTTGAAAAT
1 ATTTATTATTATATATTTTTTGAAAAT
*
4127612 ATTTATTGTTATATA--TTTT-AAAAT
1 ATTTATTATTATATATTTTTTGAAAAT
* *
4127636 -TTTATATATTAT-TATTCCTTGTCAACAAT
1 ATTTAT-TATTATATATT--TTTTGAA-AAT
*
4127665 -TTT-TTA-AATATATTTTTTGAAAAT
1 ATTTATTATTATATATTTTTTGAAAAT
4127689 ATTTA-TATTTATATATTTTTT
1 ATTTATTA-TTATATATTTTTT
4127710 ATATATTTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
23 7 0.09
24 13 0.17
25 14 0.18
26 15 0.19
27 20 0.26
28 3 0.04
29 6 0.08
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (27 bp):
ATTTATTATTATATATTTTTTGAAAAT
Found at i:4133510 original size:22 final size:22
Alignment explanation
Indices: 4133475--4133516 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4133465 TTAATTTTGT
*
4133475 TTTTATACTGTAAAATTAAATA
1 TTTTATACTGTAAAAATAAATA
* *
4133497 TTTTATATTTTAAAAATAAA
1 TTTTATACTGTAAAAATAAA
4133517 ATAATTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTATACTGTAAAAATAAATA
Found at i:4134517 original size:18 final size:18
Alignment explanation
Indices: 4134485--4134526 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
4134475 TAAAATTTCA
4134485 TAAAAATAATAAAAA-TT
1 TAAAAATAATAAAAACTT
*
4134502 TAAAATATATTAAAAACTT
1 TAAAA-ATAATAAAAACTT
4134521 TAAAAA
1 TAAAAA
4134527 CCGGTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 10 0.45
19 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATAATAAAAACTT
Found at i:4134588 original size:22 final size:21
Alignment explanation
Indices: 4134551--4134592 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
4134541 TCAATTGTTG
4134551 GATTTTTTTTGTTTTGGTTTCT
1 GATTTTTTTTGTTTT-GTTTCT
4134573 GATTTTTTTT-TATTTGTTTC
1 GATTTTTTTTGT-TTTGTTTC
4134593 GAGTGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.07, C:0.05, G:0.14, T:0.74
Consensus pattern (21 bp):
GATTTTTTTTGTTTTGTTTCT
Found at i:4137042 original size:17 final size:18
Alignment explanation
Indices: 4137022--4137058 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
4137012 TAACCAAAAC
*
4137022 TTTATTTTTATGA-GTAT
1 TTTATTTTTAAGATGTAT
4137039 TTTATTTTTAAGATGTAT
1 TTTATTTTTAAGATGTAT
4137057 TT
1 TT
4137059 AGTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (18 bp):
TTTATTTTTAAGATGTAT
Found at i:4148929 original size:13 final size:13
Alignment explanation
Indices: 4148911--4148944 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4148901 CTTAAACCAA
4148911 AATTTTCAAAAGT
1 AATTTTCAAAAGT
* *
4148924 ACTTTTCAAAATT
1 AATTTTCAAAAGT
4148937 AATTTTCA
1 AATTTTCA
4148945 CAAACACTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (13 bp):
AATTTTCAAAAGT
Found at i:4148953 original size:26 final size:26
Alignment explanation
Indices: 4148911--4148960 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4148901 CTTAAACCAA
* *
4148911 AATTTTCAAAAGTACTTTTCAAAATT
1 AATTTTCAAAAGCACTTCTCAAAATT
4148937 AATTTTCACAAA-CACTTCTCAAAA
1 AATTTTCA-AAAGCACTTCTCAAAA
4148961 GCAATGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (26 bp):
AATTTTCAAAAGCACTTCTCAAAATT
Found at i:4154296 original size:15 final size:17
Alignment explanation
Indices: 4154275--4154315 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
4154265 TAATTATTTA
4154275 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
4154291 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
4154307 AAAATTATA
1 AAAATTATA
4154316 TTTCTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:4154316 original size:26 final size:26
Alignment explanation
Indices: 4154266--4154315 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
4154256 AATTTGGTTT
*
4154266 AATTATTTAAAAATTATAAAAATATA
1 AATTATTTAAAAATGATAAAAATATA
*
4154292 AATTA-TT-AAAATGATAAAATTATA
1 AATTATTTAAAAATGATAAAAATATA
4154316 TTTCTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 2 0.09
26 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AATTATTTAAAAATGATAAAAATATA
Found at i:4164977 original size:31 final size:27
Alignment explanation
Indices: 4164925--4164982 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 27
4164915 TAAGTTGGAA
*
4164925 TTTTTTTATTTTCGAAAATGAAGAATT
1 TTTTTTTATTTTCGAAAATGAAAAATT
4164952 TTTTTATTATTTTCTTGAAAAATGAAAAATT
1 TTTTT-TTATTTTC--G-AAAATGAAAAATT
4164983 AGTTTGATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 5 0.19
28 8 0.31
30 1 0.04
31 12 0.46
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (27 bp):
TTTTTTTATTTTCGAAAATGAAAAATT
Found at i:4167991 original size:29 final size:29
Alignment explanation
Indices: 4167934--4168017 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 29
4167924 ATATTAAAAT
* * *
4167934 TATATATAAATTTTAATTTAATGTGTAATAA
1 TATACATAAATTTTAATTT--GGTATAATAA
*
4167965 TATACATAAATTTTAATTTGGTATAATTA
1 TATACATAAATTTTAATTTGGTATAATAA
* *
4167994 TATACGTGAAATTATAATTGTGGT
1 TATACAT-AAATTTTAATT-TGGT
4168018 TTGAATGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 13 0.29
30 10 0.22
31 22 0.49
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.46
Consensus pattern (29 bp):
TATACATAAATTTTAATTTGGTATAATAA
Found at i:4168943 original size:17 final size:18
Alignment explanation
Indices: 4168923--4168963 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
4168913 AAATAAAGTT
4168923 AAAATAACAT-AAAA-GAA
1 AAAATAAC-TCAAAACGAA
*
4168940 AAAATTACTCAAAACGAA
1 AAAATAACTCAAAACGAA
4168958 AAAATA
1 AAAATA
4168964 TGGGGACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.55
18 8 0.40
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAATAACTCAAAACGAA
Found at i:4170916 original size:14 final size:14
Alignment explanation
Indices: 4170899--4170926 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4170889 TTGCATCCCA
4170899 AAACTTAAAGTTGG
1 AAACTTAAAGTTGG
4170913 AAACTTAAAGTTGG
1 AAACTTAAAGTTGG
4170927 GTTTTGGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
AAACTTAAAGTTGG
Found at i:4175155 original size:15 final size:15
Alignment explanation
Indices: 4175135--4175165 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4175125 ACACCAAATG
4175135 ATATCAATTTATGCC
1 ATATCAATTTATGCC
4175150 ATATCAATTTATGCC
1 ATATCAATTTATGCC
4175165 A
1 A
4175166 AAACATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (15 bp):
ATATCAATTTATGCC
Found at i:4181082 original size:33 final size:33
Alignment explanation
Indices: 4181040--4181106 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
4181030 ACCGAAATGA
4181040 CATAGAAAATTTTAAAACCCGATTTGATCTAAT
1 CATAGAAAATTTTAAAACCCGATTTGATCTAAT
4181073 CATAGAAAATTTTAAAACCCGATTTGATCTAAT
1 CATAGAAAATTTTAAAACCCGATTTGATCTAAT
4181106 C
1 C
4181107 TAAAACCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (33 bp):
CATAGAAAATTTTAAAACCCGATTTGATCTAAT
Found at i:4182931 original size:20 final size:20
Alignment explanation
Indices: 4182908--4182970 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
4182898 CTTTTTAAAT
*
4182908 AATTACACAAGATATTACCC
1 AATTACACAAAATATTACCC
* * **
4182928 AATTACAAAAAACATTACTA
1 AATTACACAAAATATTACCC
*
4182948 AATTATACAAAATATTACCC
1 AATTACACAAAATATTACCC
4182968 AAT
1 AAT
4182971 AATGAAAAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (20 bp):
AATTACACAAAATATTACCC
Found at i:4183046 original size:48 final size:49
Alignment explanation
Indices: 4182953--4183049 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 49
4182943 TACTAAATTA
* * * *
4182953 TACAAAATATTACCCAATAATGAAAAATTATTACAATATTTGTAATGTT
1 TACAAAACATTAACCAATAATGAAAAATTATTACAATACTCGTAATGTT
* *
4183002 TACAAAACATTAACCAATTAT-ACAAATTATTACAACT-CTCGTAATGTT
1 TACAAAACATTAACCAATAATGAAAAATTATTACAA-TACTCGTAATGTT
4183050 GTGTAACAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 22 0.54
49 19 0.46
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.35
Consensus pattern (49 bp):
TACAAAACATTAACCAATAATGAAAAATTATTACAATACTCGTAATGTT
Found at i:4187562 original size:44 final size:44
Alignment explanation
Indices: 4187514--4187603 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
4187504 GCTTGATTGA
*
4187514 TACTAATATTTTAAAATTTGCCAATGGGACTTCAACATTGTTGG
1 TACTAATATTTTAAAATTTGCCAATGAGACTTCAACATTGTTGG
4187558 TACTAATATTTTAAAATTTGCCAATGAGACTTCAACATTGTTGG
1 TACTAATATTTTAAAATTTGCCAATGAGACTTCAACATTGTTGG
4187602 TA
1 TA
4187604 ACATACTAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (44 bp):
TACTAATATTTTAAAATTTGCCAATGAGACTTCAACATTGTTGG
Found at i:4196139 original size:6 final size:6
Alignment explanation
Indices: 4196128--4196155 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4196118 TTTATGTTGT
4196128 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
4196156 CATATAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:4201902 original size:19 final size:20
Alignment explanation
Indices: 4201870--4201912 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
4201860 GACATGTAGC
4201870 AAAA-AAATATAAATAAATA
1 AAAATAAATATAAATAAATA
**
4201889 AAAATAAATA-AAATTTATA
1 AAAATAAATATAAATAAATA
4201908 AAAAT
1 AAAAT
4201913 TATTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAAATATAAATAAATA
Found at i:4201911 original size:10 final size:10
Alignment explanation
Indices: 4201898--4201996 Score: 55
Period size: 10 Copynumber: 10.3 Consensus size: 10
4201888 AAAAATAAAT
4201898 AAAATTTATA
1 AAAATTTATA
4201908 AAAA-TTATTA
1 AAAATTTA-TA
*** *
4201918 ATTTTTTTTA
1 AAAATTTATA
* *
4201928 AAATTTTTTA
1 AAAATTTATA
4201938 AAAATTT-TA
1 AAAATTTATA
4201947 AAAA--TATA
1 AAAATTTATA
* *
4201955 AAAAATTGTA
1 AAAATTTATA
**
4201965 AACTTTTATA
1 AAAATTTATA
*
4201975 AAAA-TCATA
1 AAAATTTATA
4201984 AAAATTTATA
1 AAAATTTATA
4201994 AAA
1 AAA
4201997 TGCATCAAAA
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
7 1 0.01
8 6 0.09
9 17 0.25
10 41 0.61
11 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (10 bp):
AAAATTTATA
Found at i:4201979 original size:37 final size:37
Alignment explanation
Indices: 4201926--4201997 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
4201916 TAATTTTTTT
* **
4201926 TAAAATTTTTTAAAAATTTTAAAAATATAAAAAATTG
1 TAAAATTTTATAAAAATCATAAAAATATAAAAAATTG
* * *
4201963 TAAACTTTTATAAAAATCATAAAAATTTATAAAAT
1 TAAAATTTTATAAAAATCATAAAAATATAAAAAAT
4201998 GCATCAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (37 bp):
TAAAATTTTATAAAAATCATAAAAATATAAAAAATTG
Found at i:4202331 original size:28 final size:30
Alignment explanation
Indices: 4202267--4202337 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
4202257 TTTATATATA
*
4202267 TTTATAATTTTTAACATAAAATTTTACAGTTT
1 TTTAT-ATTTTT-ACATAAAATTTAACAGTTT
*
4202299 CTTATATTTTTA-ATAAAATTTAAC-GTTT
1 TTTATATTTTTACATAAAATTTAACAGTTT
4202327 TTTAT-TTTTTA
1 TTTATATTTTTA
4202338 TTTTTTACCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.17
28 8 0.22
29 11 0.31
30 1 0.03
31 6 0.17
32 4 0.11
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTATATTTTTACATAAAATTTAACAGTTT
Found at i:4204656 original size:22 final size:21
Alignment explanation
Indices: 4204595--4204659 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
4204585 GCATTTATCT
* *
4204595 AAATATTTAATTAGACAGTTAA
1 AAATATTTAATT-GAAAATTAA
* * *
4204617 ATATAATTAATT-ATAATTAA
1 AAATATTTAATTGAAAATTAA
4204637 AAATATTTAATTCGAAAATTAA
1 AAATATTTAATT-GAAAATTAA
4204659 A
1 A
4204660 GTTTAACTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 16 0.47
22 18 0.53
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (21 bp):
AAATATTTAATTGAAAATTAA
Found at i:4204659 original size:42 final size:43
Alignment explanation
Indices: 4204595--4204686 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 43
4204585 GCATTTATCT
* * * *
4204595 AAATATTTAATTAGACAGTTAAA-TATAATTAATTATAATTAA
1 AAATATTTAATTAGAAAATTAAAGTATAACTAACTATAATTAA
* * *
4204637 AAATATTTAATTCGAAAATTAAAGTTTAACTAACTGTAATTAA
1 AAATATTTAATTAGAAAATTAAAGTATAACTAACTATAATTAA
4204680 AATATAT
1 AA-ATAT
4204687 ATGAAGGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 20 0.49
43 17 0.41
44 4 0.10
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.39
Consensus pattern (43 bp):
AAATATTTAATTAGAAAATTAAAGTATAACTAACTATAATTAA
Found at i:4217381 original size:15 final size:15
Alignment explanation
Indices: 4217361--4217390 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4217351 AACTTTTGTA
4217361 CATTATTTCACATAT
1 CATTATTTCACATAT
*
4217376 CATTATTTCAGATAT
1 CATTATTTCACATAT
4217391 TTCTCTTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (15 bp):
CATTATTTCACATAT
Found at i:4223965 original size:20 final size:20
Alignment explanation
Indices: 4223928--4223966 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4223918 AATTAATTTT
* * *
4223928 TTTTTATATTTTATAACAAC
1 TTTTTATATATAAGAACAAC
4223948 TTTTTATATATAAGAACAA
1 TTTTTATATATAAGAACAA
4223967 TGACCAACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (20 bp):
TTTTTATATATAAGAACAAC
Found at i:4227076 original size:80 final size:80
Alignment explanation
Indices: 4226982--4227138 Score: 287
Period size: 80 Copynumber: 2.0 Consensus size: 80
4226972 TTATATAATT
* *
4226982 TTTTAAAATAAAAAGTATCATTTGATAATTATGTAATAAATTTAAATTTACTATGAAAATTTTAA
1 TTTTAAAATAAAAAGTATCACTTGATAATTATGTAATAAACTTAAATTTACTATGAAAATTTTAA
4227047 TGATGTTAACAAATA
66 TGATGTTAACAAATA
*
4227062 TTTTAAAATAAAAAGTATCACTTGATAATTATGTAATAAACTTAAATTTATTATGAAAATTTTAA
1 TTTTAAAATAAAAAGTATCACTTGATAATTATGTAATAAACTTAAATTTACTATGAAAATTTTAA
4227127 TGATGTTAACAA
66 TGATGTTAACAA
4227139 TTAAATTAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (80 bp):
TTTTAAAATAAAAAGTATCACTTGATAATTATGTAATAAACTTAAATTTACTATGAAAATTTTAA
TGATGTTAACAAATA
Found at i:4229260 original size:21 final size:21
Alignment explanation
Indices: 4229236--4229279 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
4229226 GATTGATATT
4229236 ATTCAATTTTAAATAAAATTA
1 ATTCAATTTTAAATAAAATTA
4229257 ATTCAATTTTAAATAAAATTA
1 ATTCAATTTTAAATAAAATTA
4229278 AT
1 AT
4229280 CGATAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTCAATTTTAAATAAAATTA
Found at i:4230063 original size:29 final size:29
Alignment explanation
Indices: 4230003--4230058 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
4229993 AATAATAGCG
*
4230003 TAAGTGACTAAAATGTAATATTTCAAACA
1 TAAGTGACTAAAATGTAATACTTCAAACA
4230032 TAAGTGACTAAAATGTAAT-CTT-AAACA
1 TAAGTGACTAAAATGTAATACTTCAAACA
4230059 AATAAAAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 5 0.19
28 2 0.08
29 19 0.73
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (29 bp):
TAAGTGACTAAAATGTAATACTTCAAACA
Found at i:4230071 original size:31 final size:29
Alignment explanation
Indices: 4230004--4230071 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
4229994 ATAATAGCGT
* *
4230004 AAGTGACTAAAATGTAATATTTCAAACAT
1 AAGTGACTAAAATGTAATATTACAAACAA
* *
4230033 AAGTGACTAAAATGTAATCTTAAACAAATAA
1 AAGTGACTAAAATGTAATATT--ACAAACAA
4230064 AAGTGACT
1 AAGTGACT
4230072 GTTTTGTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 20 0.61
31 13 0.39
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (29 bp):
AAGTGACTAAAATGTAATATTACAAACAA
Found at i:4245651 original size:11 final size:11
Alignment explanation
Indices: 4245637--4245664 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4245627 TATTTAAATA
4245637 ATAATAACAAT
1 ATAATAACAAT
4245648 ATAATAACAAT
1 ATAATAACAAT
4245659 ATAATA
1 ATAATA
4245665 GCAAAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATAACAAT
Found at i:4253278 original size:12 final size:12
Alignment explanation
Indices: 4253261--4253291 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4253251 TTATTTTACC
4253261 CAATTTCTTCAA
1 CAATTTCTTCAA
4253273 CAATTTCTTCAA
1 CAATTTCTTCAA
*
4253285 TAATTTC
1 CAATTTC
4253292 ATTTTCTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (12 bp):
CAATTTCTTCAA
Found at i:4259148 original size:29 final size:30
Alignment explanation
Indices: 4259089--4259146 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4259079 TCCGAGCCTT
*
4259089 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
4259119 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
4259147 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:4259376 original size:13 final size:13
Alignment explanation
Indices: 4259358--4259389 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4259348 TTTCCAGCAA
4259358 TTATGAATTTATT
1 TTATGAATTTATT
4259371 TTATGAATTTATT
1 TTATGAATTTATT
*
4259384 TGATGA
1 TTATGA
4259390 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:4259597 original size:50 final size:50
Alignment explanation
Indices: 4259484--4259725 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
4259474 ATTTGGGTAA
* * *
4259484 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
4259540 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
4259590 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
4259640 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
4259690 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
4259726 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:4259673 original size:100 final size:103
Alignment explanation
Indices: 4259484--4259733 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
4259474 ATTTGGGTAA
4259484 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
4259549 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
4259590 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
4259652 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
4259690 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
4259734 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:4266401 original size:29 final size:30
Alignment explanation
Indices: 4266342--4266399 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4266332 TCCGAGCCTT
*
4266342 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
4266372 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
4266400 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:4266629 original size:13 final size:13
Alignment explanation
Indices: 4266611--4266642 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4266601 TTTCCAGCAA
4266611 TTATGAATTTATT
1 TTATGAATTTATT
4266624 TTATGAATTTATT
1 TTATGAATTTATT
*
4266637 TGATGA
1 TTATGA
4266643 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:4266850 original size:50 final size:50
Alignment explanation
Indices: 4266737--4266978 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
4266727 ATTTGGGTAA
* * *
4266737 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
4266793 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
4266843 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
4266893 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
4266943 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
4266979 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:4266926 original size:100 final size:103
Alignment explanation
Indices: 4266737--4266986 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
4266727 ATTTGGGTAA
4266737 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
4266802 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
4266843 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
4266905 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
4266943 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
4266987 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:4271083 original size:12 final size:12
Alignment explanation
Indices: 4271066--4271098 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
4271056 TTATTTTACC
4271066 CAATTTCTTCAA
1 CAATTTCTTCAA
4271078 CAATTTCTTCAA
1 CAATTTCTTCAA
*
4271090 TAATTTCTT
1 CAATTTCTT
4271099 TTTCTAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (12 bp):
CAATTTCTTCAA
Found at i:4280787 original size:19 final size:20
Alignment explanation
Indices: 4280763--4280809 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
4280753 AGTGAAAGTT
4280763 TAATGCAAATGT-TGCAATG
1 TAATGCAAATGTATGCAATG
*
4280782 TAATGCAAATGTATGGAATG
1 TAATGCAAATGTATGCAATG
4280802 -AATGCAAA
1 TAATGCAAA
4280810 AGAAAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGTATGCAATG
Found at i:4283508 original size:12 final size:13
Alignment explanation
Indices: 4283493--4283545 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 13
4283483 AATAGGGGTG
4283493 ATAATAATA-ATA
1 ATAATAATACATA
4283505 ATAATAATACA-A
1 ATAATAATACATA
*
4283517 ACAATAATACAT-
1 ATAATAATACATA
*
4283529 AT-AT-ATAGATA
1 ATAATAATACATA
4283540 ATAATA
1 ATAATA
4283546 GTAGTCAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
10 5 0.15
11 4 0.12
12 23 0.70
13 1 0.03
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (13 bp):
ATAATAATACATA
Found at i:4283633 original size:3 final size:3
Alignment explanation
Indices: 4283620--4283710 Score: 57
Period size: 3 Copynumber: 30.3 Consensus size: 3
4283610 GAGGGCATAT
**
4283620 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GGA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A ATA ATA ATA
* * *
4283667 ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA A-A ATA AAA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4283710 A
1 A
4283711 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
2 10 0.15
3 48 0.71
4 9 0.13
5 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:4283644 original size:12 final size:12
Alignment explanation
Indices: 4283620--4283700 Score: 69
Period size: 12 Copynumber: 6.8 Consensus size: 12
4283610 GAGGGCATAT
4283620 ATAATAT-AATA
1 ATAATATAAATA
4283631 ATAATATAAATA
1 ATAATATAAATA
*
4283643 ATAATATATACATG
1 ATAATATA-A-ATA
**
4283657 AGGA-AT-AATA
1 ATAATATAAATA
4283667 ATAATATAAATA
1 ATAATATAAATA
* *
4283679 ATAGTAAAAATA
1 ATAATATAAATA
*
4283691 ATAAAATAAA
1 ATAATATAAA
4283701 ATAAAAATAA
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
10 4 0.07
11 10 0.19
12 33 0.61
13 3 0.06
14 4 0.07
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:4284137 original size:13 final size:13
Alignment explanation
Indices: 4284119--4284178 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
4284109 GGGTGGTTTA
4284119 GGTGGCCAAGGTG
1 GGTGGCCAAGGTG
***
4284132 GGTGGCCAACAAG
1 GGTGGCCAAGGTG
*** *
4284145 GGTGGTGGA-GTA
1 GGTGGCCAAGGTG
4284157 GGTGGCCAAGGTG
1 GGTGGCCAAGGTG
4284170 GGTGGCCAA
1 GGTGGCCAA
4284179 CAAGGGTGGT
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
12 6 0.18
13 27 0.82
ACGTcount: A:0.20, C:0.15, G:0.50, T:0.15
Consensus pattern (13 bp):
GGTGGCCAAGGTG
Found at i:4284159 original size:38 final size:38
Alignment explanation
Indices: 4284117--4284237 Score: 233
Period size: 38 Copynumber: 3.2 Consensus size: 38
4284107 TGGGGTGGTT
4284117 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
4284155 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
*
4284193 TAGGTGGCCAAGGTGGATGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
4284231 TAGGTGG
1 TAGGTGG
4284238 GATTAGGGTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 82 1.00
ACGTcount: A:0.21, C:0.12, G:0.50, T:0.17
Consensus pattern (38 bp):
TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
Found at i:4289540 original size:27 final size:26
Alignment explanation
Indices: 4289510--4289571 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
4289500 CAAAACAAAG
*
4289510 TGGACAAAACAAAAACCACGAAAAATA
1 TGGACAAAACAAAAACCA-AAAAAATA
* * *
4289537 TGGACAAAA-TAAAACTAAAAAAATG
1 TGGACAAAACAAAAACCAAAAAAATA
4289562 TGGACAAAAC
1 TGGACAAAAC
4289572 CACAATGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 15 0.50
26 6 0.20
27 9 0.30
ACGTcount: A:0.61, C:0.15, G:0.13, T:0.11
Consensus pattern (26 bp):
TGGACAAAACAAAAACCAAAAAAATA
Found at i:4293005 original size:10 final size:10
Alignment explanation
Indices: 4292990--4293017 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
4292980 AAAGCTTAAA
4292990 TATGAAATAG
1 TATGAAATAG
4293000 TATGAAATAG
1 TATGAAATAG
4293010 TATGAAAT
1 TATGAAAT
4293018 CAAGACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (10 bp):
TATGAAATAG
Found at i:4297182 original size:39 final size:39
Alignment explanation
Indices: 4297136--4297236 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
4297126 GCTCTAATGA
* *
4297136 GCTTCAGTTAGCTTTTGGGCTTCCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTTGGGCTTCCGTTTAACACTTATGT
*
4297175 GCTTCAGTTAGCCTTTGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTTGGGCTTCCGTTTAACACTTATGT
* * *
4297214 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTTGGGCTTC
4297237 AAATCACGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.40
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTTGGGCTTCCGTTTAACACTTATGT
Found at i:4297218 original size:21 final size:20
Alignment explanation
Indices: 4297149--4297218 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
4297139 TCAGTTAGCT
* *
4297149 TTTGGGCTTCCGTTTAACAC
1 TTTGTGCTTCCGTTTAGCAC
*
4297169 TTGTGTGCTTCAG-TTAGC-C
1 TT-TGTGCTTCCGTTTAGCAC
*
4297188 TTTGGGCTTCCGTTTAGCAC
1 TTTGTGCTTCCGTTTAGCAC
4297208 TTATGTGCTTC
1 TT-TGTGCTTC
4297219 AGCTAGACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
18 8 0.20
19 8 0.20
20 9 0.22
21 15 0.38
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (20 bp):
TTTGTGCTTCCGTTTAGCAC
Found at i:4300168 original size:12 final size:13
Alignment explanation
Indices: 4300153--4300182 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
4300143 AGTGTATCAA
4300153 ATAATTTTCTA-T
1 ATAATTTTCTATT
4300165 ATAATTTTCTATT
1 ATAATTTTCTATT
4300178 ATAAT
1 ATAAT
4300183 AAATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (13 bp):
ATAATTTTCTATT
Found at i:4301072 original size:16 final size:17
Alignment explanation
Indices: 4301039--4301077 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4301029 GAAACATTTA
*
4301039 TTTTAATGTTTTAGTAT
1 TTTTAATGTATTAGTAT
*
4301056 TTTTGATGTATTA-TAT
1 TTTTAATGTATTAGTAT
4301072 TTTTAA
1 TTTTAA
4301078 AATTTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (17 bp):
TTTTAATGTATTAGTAT
Found at i:4313398 original size:25 final size:25
Alignment explanation
Indices: 4313356--4313413 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
4313346 CCATGAATAA
* * *
4313356 TATGAACAAAATAAAACTATGAAAC
1 TATGGACAGAATAAAACTATAAAAC
4313381 -AGTGGACAGAATAAAACTATAAAAC
1 TA-TGGACAGAATAAAACTATAAAAC
4313406 TATGGACA
1 TATGGACA
4313414 TGTGGATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.04
25 26 0.93
26 1 0.04
ACGTcount: A:0.55, C:0.12, G:0.14, T:0.19
Consensus pattern (25 bp):
TATGGACAGAATAAAACTATAAAAC
Found at i:4314304 original size:19 final size:20
Alignment explanation
Indices: 4314260--4314305 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
4314250 GGCAATACCA
* *
4314260 AAAATTTTAAAGATTTATAG
1 AAAATTTTAAAGAGTTATAC
*
4314280 AAAATTTTAAATAGTTAT-C
1 AAAATTTTAAAGAGTTATAC
4314299 AAAATTT
1 AAAATTT
4314306 CTCAGGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (20 bp):
AAAATTTTAAAGAGTTATAC
Found at i:4314565 original size:120 final size:120
Alignment explanation
Indices: 4314298--4314562 Score: 259
Period size: 120 Copynumber: 2.2 Consensus size: 120
4314288 AAATAGTTAT
* * * *
4314298 CAAAATTTCTCAGG-TTATATAAAAAACTTC-AAGGCTTTACCAAAATTTCTAAGAATTTATCAA
1 CAAAATTTCTAAGGATT-TAT-CAAAATTTCTAAGGCTTTACCAAAATTTCGAAGAATTTATCAA
* * * * *
4314361 TATTTTTAAAGATTTCCTTAGTTTCCCATACCCAAACAACTCAACATTTTGACATAT
64 TATTTCTAAAGATTTCCTTAGATTCCCAGACCCAAACAACACAACATTTTGACATAC
* * * * **
4314418 CAAAGTTTCTAATGATTTATCAAAATTTCTAAGGCTTTGCCATAATTTCGAAGGGTTTATCAATA
1 CAAAATTTCTAAGGATTTATCAAAATTTCTAAGGCTTTACCAAAATTTCGAAGAATTTATCAATA
* * ** *
4314483 TTTCTACAGATTTTCTTAGATTCTTAGACTCC-ACCAACACAACATTTTTTG-CATAC
66 TTTCTAAAGATTTCCTTAGATTCCCAGAC-CCAAACAACACAACA--TTTTGACATAC
* *
4314539 CAAAATTTCTTAGGATTTCTCAAA
1 CAAAATTTCTAAGGATTTATCAAA
4314563 TTTTTTAGGA
Statistics
Matches: 116, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
119 7 0.06
120 76 0.66
121 28 0.24
122 5 0.04
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (120 bp):
CAAAATTTCTAAGGATTTATCAAAATTTCTAAGGCTTTACCAAAATTTCGAAGAATTTATCAATA
TTTCTAAAGATTTCCTTAGATTCCCAGACCCAAACAACACAACATTTTGACATAC
Found at i:4314655 original size:20 final size:19
Alignment explanation
Indices: 4314593--4314660 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
4314583 TATCTAAAGA
*
4314593 TTTACCAAAAATTTTAAGGT
1 TTTACC-AAAATTTTAATGT
* *
4314613 TCTACCAAAATTTTCAATAT
1 TTTACCAAAATTTT-AATGT
*
4314633 TTTATCAAAATTTCTAATGT
1 TTTACCAAAATTT-TAATGT
4314653 TTTACCAA
1 TTTACCAA
4314661 TATGATCATC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 8 0.21
20 30 0.77
21 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (19 bp):
TTTACCAAAATTTTAATGT
Found at i:4314745 original size:20 final size:20
Alignment explanation
Indices: 4314685--4314745 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
4314675 CATTTTCGTG
* * *
4314685 TACTAATATTTCTAAAAATT
1 TACTAAAATTTTTAAAGATT
*
4314705 TAC-CAAA-TTTTATAAGAATT
1 TACTAAAATTTTTA-AAG-ATT
4314725 TACTAAAATTTTTAAAGATT
1 TACTAAAATTTTTAAAGATT
4314745 T
1 T
4314746 CATTAGTGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 13 0.41
21 6 0.19
22 5 0.16
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
TACTAAAATTTTTAAAGATT
Found at i:4319255 original size:15 final size:15
Alignment explanation
Indices: 4319230--4319287 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
4319220 TCATATATAT
4319230 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
*
4319246 TATAAATTCAATAAA
1 TATAAATTCAATCAA
* *
4319261 AATAATTTCAATCAA
1 TATAAATTCAATCAA
4319276 TATAAATTCAAT
1 TATAAATTCAAT
4319288 AAATTCATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
15 32 0.89
16 4 0.11
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:4319272 original size:30 final size:29
Alignment explanation
Indices: 4319233--4319290 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
4319223 TATATATTAT
4319233 ATAATTCAATCAATATAAATTCAATAAAA
1 ATAATTCAATCAATATAAATTCAATAAAA
4319262 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
4319291 TTCATCGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (29 bp):
ATAATTCAATCAATATAAATTCAATAAAA
Found at i:4321413 original size:33 final size:33
Alignment explanation
Indices: 4321323--4321448 Score: 148
Period size: 33 Copynumber: 3.8 Consensus size: 33
4321313 TTCTAAGTGG
** *
4321323 TATACACAAAGTATACCTTTCCTTTTCATATGG
1 TATACACAAAGTATACCTAACCTTTTCATATGT
**
4321356 TATACACAAAGTATACCTTTCCTTTTCATATGT
1 TATACACAAAGTATACCTAACCTTTTCATATGT
*
4321389 TATACACAAAGTATACCTAACC-TTTC-TAAGT
1 TATACACAAAGTATACCTAACCTTTTCATATGT
* * *
4321420 GTACACACAAAGTGTACATAACCTTTTCA
1 -TATACACAAAGTATACCTAACCTTTTCA
4321449 AGTTGTACCA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
31 4 0.05
32 23 0.28
33 56 0.67
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (33 bp):
TATACACAAAGTATACCTAACCTTTTCATATGT
Done.