Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 22 of 45
Found at i:4048967 original size:11 final size:13
Alignment explanation
Indices: 4048938--4048969 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4048928 ATCAAATAAA
4048938 TATTTTATATATT
1 TATTTTATATATT
4048951 TATTTTATA-ATT
1 TATTTTATATATT
4048963 T-TTTTAT
1 TATTTTAT
4048970 TAAAGTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 6 0.32
12 4 0.21
13 9 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTTATATATT
Found at i:4054512 original size:212 final size:212
Alignment explanation
Indices: 4054140--4054561 Score: 720
Period size: 212 Copynumber: 2.0 Consensus size: 212
4054130 AGAGATAACA
* *
4054140 CTGTCGACTTTTGCCATTGCTATTTGACATATATAGCAGTGATTTTAAGAATGTCTTTGGAATCT
1 CTGTAGACTTTTGCCATTGCTATTTGACATATATAGCAGTGATTTTAAGAATATCTTTGGAATCT
* * * * *
4054205 GATTGCTGCACCGGAAATTTTGTTTAAGGGGCTGTAAACAATCTGATCTTGAGCAAACAGAGCAG
66 GATTGCTGCACCGGAAATTTTGTTTAAGGCGCCGTAAACAAGCTGATCTTGAACAAACAGAACAG
*
4054270 ACCTATGTTCATGTTTGTTTAACCCTGTTTGAGATCGGCTTGTGTTTGTTATGGATTGTTAGGGT
131 ACCTATGTTCATGTTTGTTTAACCCTGTTTGAGATCGGCTTGTGTTTGTTAAGGATTGTTAGGGT
4054335 ATTCTTCGAGCTCAGGT
196 ATTCTTCGAGCTCAGGT
4054352 CTGTAGACTTTTGCCATTGCTATTTGACATATATAGCAGTGATTTTAAGAATATCTTTGGAATCT
1 CTGTAGACTTTTGCCATTGCTATTTGACATATATAGCAGTGATTTTAAGAATATCTTTGGAATCT
* * *
4054417 TATTGCTGCACTGGAATTTTTGTCTTAA-GCGCCGTAAACAAGCTGATCTTGAACAAACAGAACA
66 GATTGCTGCACCGGAAATTTTGT-TTAAGGCGCCGTAAACAAGCTGATCTTGAACAAACAGAACA
*
4054481 GACCTATGTTCATGTTTGTTTAACCCTGTTTGAGATCGGCTTGTGTTTGTTAAGGATTTTTAGGG
130 GACCTATGTTCATGTTTGTTTAACCCTGTTTGAGATCGGCTTGTGTTTGTTAAGGATTGTTAGGG
4054546 TATTCTTCGAGCTCAG
195 TATTCTTCGAGCTCAG
4054562 CTCGTTTAAA
Statistics
Matches: 197, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
212 193 0.98
213 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (212 bp):
CTGTAGACTTTTGCCATTGCTATTTGACATATATAGCAGTGATTTTAAGAATATCTTTGGAATCT
GATTGCTGCACCGGAAATTTTGTTTAAGGCGCCGTAAACAAGCTGATCTTGAACAAACAGAACAG
ACCTATGTTCATGTTTGTTTAACCCTGTTTGAGATCGGCTTGTGTTTGTTAAGGATTGTTAGGGT
ATTCTTCGAGCTCAGGT
Found at i:4054646 original size:23 final size:23
Alignment explanation
Indices: 4054616--4054679 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
4054606 CTTGTTTAAG
4054616 TTAAATGAACTTGTTTATGAACA
1 TTAAATGAACTTGTTTATGAACA
*
4054639 TTAAATGAAATTG--T-T--A-A
1 TTAAATGAACTTGTTTATGAACA
4054656 TTAAATGAACTTGTTTATGAACA
1 TTAAATGAACTTGTTTATGAACA
4054679 T
1 T
4054680 ATTCATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 13 0.39
18 1 0.03
19 1 0.03
20 2 0.06
21 1 0.03
22 1 0.03
23 14 0.42
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (23 bp):
TTAAATGAACTTGTTTATGAACA
Found at i:4054660 original size:17 final size:17
Alignment explanation
Indices: 4054638--4054670 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4054628 GTTTATGAAC
4054638 ATTAAATGAAATTGTTA
1 ATTAAATGAAATTGTTA
*
4054655 ATTAAATGAACTTGTT
1 ATTAAATGAAATTGTT
4054671 TATGAACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (17 bp):
ATTAAATGAAATTGTTA
Found at i:4054699 original size:15 final size:15
Alignment explanation
Indices: 4054675--4054708 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4054665 CTTGTTTATG
4054675 AACATATTCATGAAA
1 AACATATTCATGAAA
* *
4054690 AACATGTTCATGAAC
1 AACATATTCATGAAA
4054705 AACA
1 AACA
4054709 AACAAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (15 bp):
AACATATTCATGAAA
Found at i:4054840 original size:31 final size:31
Alignment explanation
Indices: 4054793--4054854 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
4054783 AATTAGCATC
4054793 AAAAATTACATAATCATAGAAGTCCAAAATT
1 AAAAATTACATAATCATAGAAGTCCAAAATT
* * *
4054824 AAAAGTTACATGATCATAGAAGTCTAAAATT
1 AAAAATTACATAATCATAGAAGTCCAAAATT
4054855 TCTTAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (31 bp):
AAAAATTACATAATCATAGAAGTCCAAAATT
Found at i:4061060 original size:19 final size:18
Alignment explanation
Indices: 4061036--4061072 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4061026 TTAAATATAA
*
4061036 AAAAATATTTATATTAATT
1 AAAAAT-TTTAAATTAATT
4061055 AAAAATTTTAAATTAATT
1 AAAAATTTTAAATTAATT
4061073 TTTTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAAATTTTAAATTAATT
Found at i:4061088 original size:28 final size:26
Alignment explanation
Indices: 4061062--4061123 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 26
4061052 ATTAAAAATT
*
4061062 TTAAA-TTAATTTTTTAAATTATTAAA
1 TTAAATTTAATTTTTAAAATT-TTAAA
4061088 TTAAATTTTAATTTTTAAAATTTTAAA
1 TTAAA-TTTAATTTTTAAAATTTTAAA
*
4061115 AT-AATTTAA
1 TTAAATTTAA
4061124 CTCAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 5 0.16
26 7 0.22
27 6 0.19
28 14 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAAATTTAATTTTTAAAATTTTAAA
Found at i:4061467 original size:14 final size:14
Alignment explanation
Indices: 4061443--4061486 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
4061433 TGAATATAAT
4061443 TTTAATA-TTTTAA
1 TTTAATATTTTTAA
4061456 TTTAATATTTTTAA
1 TTTAATATTTTTAA
*
4061470 TATAAATATATTTTAA
1 T-TTAATAT-TTTTAA
4061486 T
1 T
4061487 AAAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.26
14 7 0.26
15 6 0.22
16 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATATTTTTAA
Found at i:4061477 original size:28 final size:29
Alignment explanation
Indices: 4061446--4061589 Score: 84
Period size: 29 Copynumber: 4.9 Consensus size: 29
4061436 ATATAATTTT
4061446 AATATTTTAATTTAATATTTTTAATATAA
1 AATATTTTAATTTAATATTTTTAATATAA
* *
4061475 ATATATTTTAA-TAAAAATTTTT-ATATAA
1 A-ATATTTTAATTTAATATTTTTAATATAA
* *
4061503 AA-A-TATATTTTAAT-TGTTATTAATATAAA
1 AATATTTTAATTTAATAT-TT-TTAATAT-AA
** **
4061532 AATAATTTTAATAATTTTTATTATTTCTTAT-A
1 AAT-ATTTTAAT--TTAATATT-TTTAATATAA
* *
4061564 TATATTTTAATATAATATTTTTAATA
1 AATATTTTAATTTAATATTTTTAATA
4061590 ATAATTTTTT
Statistics
Matches: 84, Mismatches: 18, Indels: 27
0.65 0.14 0.21
Matches are distributed among these distances:
25 4 0.05
26 6 0.07
27 3 0.04
28 16 0.19
29 19 0.23
30 9 0.11
31 9 0.11
32 7 0.08
34 9 0.11
35 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (29 bp):
AATATTTTAATTTAATATTTTTAATATAA
Found at i:4061478 original size:39 final size:35
Alignment explanation
Indices: 4061407--4061487 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 35
4061397 AACCTATTTA
* *
4061407 TTTAATTTTTTAATTTATTTTGTATATGAATATAAT
1 TTTAATATTTTAATTTATTTTGTATATAAATAT-AT
*
4061443 TTTAATATTTTAATTTAATATTTTTAATATAAATATAT
1 TTTAATATTTTAATTT-AT-TTTGT-ATATAAATATAT
4061481 TTTAATA
1 TTTAATA
4061488 AAAATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
36 15 0.38
37 2 0.05
38 13 0.33
39 9 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.59
Consensus pattern (35 bp):
TTTAATATTTTAATTTATTTTGTATATAAATATAT
Found at i:4061483 original size:30 final size:31
Alignment explanation
Indices: 4061447--4061517 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 31
4061437 TATAATTTTA
* * *
4061447 ATATTTTAATTTAATATTTTTA-ATATAAAT
1 ATATTTTAATTAAAAATTTTTATATAAAAAT
4061477 ATATTTTAA-TAAAAATTTTTATATAAAAAT
1 ATATTTTAATTAAAAATTTTTATATAAAAAT
4061507 ATATTTTAATT
1 ATATTTTAATT
4061518 GTTATTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.28
30 25 0.69
31 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATATTTTAATTAAAAATTTTTATATAAAAAT
Found at i:4061488 original size:14 final size:14
Alignment explanation
Indices: 4061447--4061516 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 14
4061437 TATAATTTTA
*
4061447 ATATTTTAATTTAAT
1 ATATTTTAA-TAAAT
4061462 AT-TTTTAATATAAAT
1 ATATTTT-A-ATAAAT
*
4061477 ATATTTTAATAAAA
1 ATATTTTAATAAAT
4061491 AT-TTTTATATAAAAAT
1 ATATTTTA-AT--AAAT
4061507 ATATTTTAAT
1 ATATTTTAAT
4061517 TGTTATTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
13 5 0.11
14 13 0.29
15 10 0.22
16 12 0.27
17 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATTTTAATAAAT
Found at i:4061554 original size:30 final size:28
Alignment explanation
Indices: 4061446--4061550 Score: 94
Period size: 28 Copynumber: 3.7 Consensus size: 28
4061436 ATATAATTTT
4061446 AATATTTTAATTTAATATTTTTAATATAAA
1 AATATTTTAA--TAATATTTTTAATATAAA
* *
4061476 TATATTTTAATAAAAATTTTT-ATATAAA
1 AATATTTTAAT-AATATTTTTAATATAAA
4061504 AATATATTT--TAAT-TGTTATTAATATAAA
1 AATAT-TTTAATAATAT-TT-TTAATATAAA
4061532 AATAATTTTAATAAT-TTTT
1 AAT-ATTTTAATAATATTTT
4061551 ATTATTTCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
25 1 0.02
26 4 0.06
27 3 0.05
28 26 0.41
29 15 0.24
30 14 0.22
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
AATATTTTAATAATATTTTTAATATAAA
Found at i:4061585 original size:14 final size:15
Alignment explanation
Indices: 4061563--4061600 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
4061553 TATTTCTTAT
4061563 ATATATTTTAAT-ATA
1 ATAT-TTTTAATAATA
4061578 ATATTTTTAATAATA
1 ATATTTTTAATAATA
4061593 AT-TTTTTA
1 ATATTTTTA
4061601 TTTTTATCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTTTAATAATA
Found at i:4061590 original size:12 final size:13
Alignment explanation
Indices: 4061553--4061598 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
4061543 TAATTTTTAT
4061553 TATTTCTTATAT-A
1 TATTT-TTATATAA
*
4061566 TATTTTAATATAA
1 TATTTTTATATAA
4061579 TATTTTTA-ATAA
1 TATTTTTATATAA
4061591 TAATTTTT
1 T-ATTTTT
4061599 TATTTTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTTTATATAA
Found at i:4063715 original size:25 final size:25
Alignment explanation
Indices: 4063665--4063715 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
4063655 TTTTCAAATA
**
4063665 AAATATAAATTTTATTATTATTAAC
1 AAATATAAATTTTATTATTACAAAC
*
4063690 AAATATTAA-TTTATTATTAACAAAC
1 AAATATAAATTTTATTATT-ACAAAC
4063715 A
1 A
4063716 TTTCATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATATAAATTTTATTATTACAAAC
Found at i:4063827 original size:35 final size:35
Alignment explanation
Indices: 4063788--4063858 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
4063778 TATTTACTTC
* *
4063788 AAATTTAATATATAATTAAATTAAAA-ATAAATTTA
1 AAATTTAATAGATAATTAAACTAAAATAT-AATTTA
* *
4063823 AAATTTAATAGATACTTGAACTAAAATATAATTTA
1 AAATTTAATAGATAATTAAACTAAAATATAATTTA
4063858 A
1 A
4063859 TTAAAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 29 0.94
36 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (35 bp):
AAATTTAATAGATAATTAAACTAAAATATAATTTA
Found at i:4064926 original size:6 final size:6
Alignment explanation
Indices: 4064915--4064948 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
4064905 TTTAAAATTT
*
4064915 TAAATA TAAATA TAATATA TACATA TAAATA TAA
1 TAAATA TAAATA TAA-ATA TAAATA TAAATA TAA
4064949 CCAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:4064976 original size:22 final size:22
Alignment explanation
Indices: 4064951--4065001 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
4064941 AAATATAACC
*
4064951 AATTATTTTTATACCAACCTAA
1 AATTATTTTTAAACCAACCTAA
* *
4064973 AATTATTTTTAAACCTACTTAA
1 AATTATTTTTAAACCAACCTAA
4064995 AATTATT
1 AATTATT
4065002 AGTCAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTATTTTTAAACCAACCTAA
Found at i:4065996 original size:18 final size:19
Alignment explanation
Indices: 4065955--4065996 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
4065945 TTTATTTAAA
4065955 TTTAATTATAAAATAAAAT
1 TTTAATTATAAAATAAAAT
*
4065974 ATTAATTA-AAAATAAAAT
1 TTTAATTATAAAATAAAAT
4065992 TTTAA
1 TTTAA
4065997 AATTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTAATTATAAAATAAAAT
Found at i:4066624 original size:3 final size:3
Alignment explanation
Indices: 4066616--4066650 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4066606 TATTGTATCA
*
4066616 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4066651 ATACTACATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4077776 original size:165 final size:163
Alignment explanation
Indices: 4077506--4077824 Score: 593
Period size: 165 Copynumber: 1.9 Consensus size: 163
4077496 CTTTCAGTTG
4077506 TATATTCCTTTGAATGTTGTCATTGAAAAGTAGAGTAATATATCAACAATTCAATGTTGGAATCT
1 TATATTCCTTTGAATGTTGTCATTGAAAAGTAGAGTAATATATCAACAATTCAATGTTGGAATCT
*
4077571 AACTTTGCCATTGACATATTTCCCAGACGGAAGGCAGAAAGCAAACTTGGTGAGCCAAGTGTCTT
66 AACTTTGCCACTGACATATTTCCCAGACGGAAGGCAGAAAGCAAACTTGGTGAGCCAAGTGTCTT
4077636 AACAAGTAGCAGATCACAAGACTTTGCCATTGA
131 AACAAGTAGCAGATCACAAGACTTTGCCATTGA
*
4077669 TATATTCCTTTGAATGTCGTGTCCTTGAAAAGTAGAGTAATATATCAACAATTCAATGTTGGAAT
1 TATATTCCTTTGAATGT--TGTCATTGAAAAGTAGAGTAATATATCAACAATTCAATGTTGGAAT
*
4077734 CTAACTTTGCCACTGACATATTTCCCAGACGGAAGGCAGAAAGCACACTTGGTGAGCCAAGTGTC
64 CTAACTTTGCCACTGACATATTTCCCAGACGGAAGGCAGAAAGCAAACTTGGTGAGCCAAGTGTC
4077799 TTAACAAGTAGCAGATCACAAGACTT
129 TTAACAAGTAGCAGATCACAAGACTT
4077825 ATGATTTGCT
Statistics
Matches: 151, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
163 17 0.11
165 134 0.89
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (163 bp):
TATATTCCTTTGAATGTTGTCATTGAAAAGTAGAGTAATATATCAACAATTCAATGTTGGAATCT
AACTTTGCCACTGACATATTTCCCAGACGGAAGGCAGAAAGCAAACTTGGTGAGCCAAGTGTCTT
AACAAGTAGCAGATCACAAGACTTTGCCATTGA
Found at i:4079050 original size:16 final size:16
Alignment explanation
Indices: 4079031--4079075 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
4079021 AATCAATTAG
4079031 AAATAATTTAAATTTA
1 AAATAATTTAAATTTA
* *
4079047 AAATAATTTTAATTTG
1 AAATAATTTAAATTTA
* *
4079063 AATTAATTAAAAT
1 AAATAATTTAAAT
4079076 AATTAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
AAATAATTTAAATTTA
Found at i:4079181 original size:16 final size:16
Alignment explanation
Indices: 4079162--4079192 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4079152 AATTGATTCA
*
4079162 AATTTAAAATTATTTG
1 AATTTAAAATAATTTG
4079178 AATTTAAAATAATTT
1 AATTTAAAATAATTT
4079193 AAATATGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
AATTTAAAATAATTTG
Found at i:4079211 original size:69 final size:69
Alignment explanation
Indices: 4079129--4079261 Score: 198
Period size: 69 Copynumber: 1.9 Consensus size: 69
4079119 TTTAATTAAT
* * *
4079129 TGATTAATTTAAATATTAAATTAAATTGAT-TCAAATTTAAAATTATT-TGAATTTAAAATAATT
1 TGATTAATTTAAATATTAAATTAAATTAATAT-AAATTT-AAATTATTATAAAATTAAAATAATT
4079192 TAAATA
64 TAAATA
*
4079198 TGATTAATTTAAATATTAAATTTAATTAATATAAATTTAAATTATTATAAAATTAAAATAATTT
1 TGATTAATTTAAATATTAAATTAAATTAATATAAATTTAAATTATTATAAAATTAAAATAATTT
4079262 TAAAATTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
68 8 0.14
69 49 0.84
70 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (69 bp):
TGATTAATTTAAATATTAAATTAAATTAATATAAATTTAAATTATTATAAAATTAAAATAATTTA
AATA
Found at i:4079225 original size:22 final size:22
Alignment explanation
Indices: 4079131--4079240 Score: 98
Period size: 22 Copynumber: 4.9 Consensus size: 22
4079121 TAATTAATTG
*
4079131 ATTAATTTAAATATTAAATTAA
1 ATTAATTTAAATATTAAATTTA
* * *
4079153 ATTGATTCAAAT-TTAAAATTA
1 ATTAATTTAAATATTAAATTTA
* * *
4079174 TTTGAATTTAAAATAATTTAAATATG
1 ATT-AATTT-AAAT-A-TTAAATTTA
4079200 ATTAATTTAAATATTAAATTTA
1 ATTAATTTAAATATTAAATTTA
*
4079222 ATTAATATAAAT-TTAAATT
1 ATTAATTTAAATATTAAATT
4079241 ATTATAAAAT
Statistics
Matches: 69, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
21 16 0.23
22 31 0.45
23 5 0.07
24 4 0.06
25 5 0.07
26 8 0.12
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (22 bp):
ATTAATTTAAATATTAAATTTA
Found at i:4079240 original size:16 final size:16
Alignment explanation
Indices: 4079209--4079259 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
4079199 GATTAATTTA
4079209 AATATTAAATTT-AATT
1 AATA-TAAATTTAAATT
4079225 AATATAAATTTAAATT
1 AATATAAATTTAAATT
* * *
4079241 ATTATAAAATTAAAAT
1 AATATAAATTTAAATT
4079257 AAT
1 AAT
4079260 TTTAAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 7 0.23
16 23 0.77
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATAAATTTAAATT
Found at i:4079256 original size:17 final size:17
Alignment explanation
Indices: 4079221--4079269 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
4079211 TATTAAATTT
* *
4079221 AATTAATAT-AAATTTA
1 AATTATTATAAAATTAA
4079237 AATTATTATAAAATTAA
1 AATTATTATAAAATTAA
* *
4079254 AATAATTTTAAAATTA
1 AATTATTATAAAATTA
4079270 TAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTATTATAAAATTAA
Found at i:4079258 original size:27 final size:25
Alignment explanation
Indices: 4079221--4079280 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 25
4079211 TATTAAATTT
*
4079221 AATTAATATAAATTTAAATTATTATAA
1 AATTAAAATAAATTTAAA--ATTATAA
*
4079248 AATTAAAATAATTTTAAAATTATAA
1 AATTAAAATAAATTTAAAATTATAA
4079273 AATTAAAA
1 AATTAAAA
4079281 ATAATTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 15 0.48
27 16 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AATTAAAATAAATTTAAAATTATAA
Found at i:4079268 original size:8 final size:8
Alignment explanation
Indices: 4079241--4079282 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
4079231 AATTTAAATT
4079241 ATTATAAA
1 ATTATAAA
*
4079249 ATTAAAATA
1 ATTATAA-A
*
4079258 ATTTTAAA
1 ATTATAAA
4079266 ATTATAAA
1 ATTATAAA
4079274 ATTA-AAA
1 ATTATAAA
4079281 AT
1 AT
4079283 AATTTGACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 5 0.17
8 18 0.62
9 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTATAAA
Found at i:4079279 original size:69 final size:69
Alignment explanation
Indices: 4079137--4079279 Score: 175
Period size: 69 Copynumber: 2.1 Consensus size: 69
4079127 ATTGATTAAT
* * *
4079137 TTAAATATTAAATTAAATTGATTCAAATTTAAAATTATTTGAATTTAAAATAATTTAAATATGAT
1 TTAAATATTAAATTAAATTAATTCAAATTTAAAATTATTTAAAATTAAAATAATTTAAATATGAT
* *
4079202 TAAT
66 AAAA
*
4079206 TTAAATATTAAATTTAATTAATAT-AAATTT-AAATTATTATAAAATTAAAATAATTTTAAA-AT
1 TTAAATATTAAATTAAATTAAT-TCAAATTTAAAATTATT-TAAAATTAAAATAA-TTTAAATAT
*
4079268 TATAAAA
63 GATAAAA
4079275 TTAAA
1 TTAAA
4079280 AATAATTTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
68 8 0.12
69 49 0.77
70 7 0.11
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (69 bp):
TTAAATATTAAATTAAATTAATTCAAATTTAAAATTATTTAAAATTAAAATAATTTAAATATGAT
AAAA
Found at i:4087438 original size:14 final size:14
Alignment explanation
Indices: 4087419--4087448 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4087409 ATTCACTGCA
4087419 CTCGACGAAACCGG
1 CTCGACGAAACCGG
4087433 CTCGACGAAACCGG
1 CTCGACGAAACCGG
4087447 CT
1 CT
4087449 AAAAGTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.37, G:0.27, T:0.10
Consensus pattern (14 bp):
CTCGACGAAACCGG
Found at i:4089521 original size:94 final size:94
Alignment explanation
Indices: 4089423--4089594 Score: 208
Period size: 95 Copynumber: 1.8 Consensus size: 94
4089413 CTAAGCCTTA
* * *
4089423 CAGTTTGTTAAGCTTTTTTTTCG-ATTT-TCCTTTTTTAAATGTCTAAAAG-TTGACTTA-AGCA
1 CAGTTTGCTAAGC-TTTTCTT-GAATTTATCCTTTTTTAAATGTCT-AAAGCCTGACTTAGA-CA
*
4089484 TACAAAGAAGTAATTTTCAAGTCTAAGATAGTG
62 TACAAAAAAGTAATTTTCAAGTCTAAGATAGTG
* * *
4089517 CAGTTTGCTAGGCTTTTCTTGAATTTAGTCTTTTTTTAAATGTCTAAAGCCTGACTTTGACATAC
1 CAGTTTGCTAAGCTTTTCTTGAATTTA-TCCTTTTTTAAATGTCTAAAGCCTGACTTAGACATAC
4089582 AAAAAAGTAATTT
65 AAAAAAGTAATTT
4089595 CTAAATTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
92 1 0.02
93 10 0.15
94 15 0.23
95 39 0.59
96 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (94 bp):
CAGTTTGCTAAGCTTTTCTTGAATTTATCCTTTTTTAAATGTCTAAAGCCTGACTTAGACATACA
AAAAAGTAATTTTCAAGTCTAAGATAGTG
Found at i:4089758 original size:48 final size:48
Alignment explanation
Indices: 4089653--4089762 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 48
4089643 GTTTATAAGC
* * **
4089653 TAAAGTTTT-AACTTGTGACACCATAGTTGATTTAGGTATATAAAATAA
1 TAAA-TTTTAAACTTGTGACACCAAAGTTAATTTAGACATATAAAATAA
* *
4089701 TAAACTTTAAACTTGTGACACTAAAGATTAATTTAGACATATCAAAA-AA
1 TAAATTTTAAACTTGTGACACCAAAG-TTAATTTAGACATAT-AAAATAA
4089750 -AAATTTTAAACTT
1 TAAATTTTAAACTT
4089763 AAGATCGTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
47 3 0.06
48 31 0.60
49 14 0.27
50 4 0.08
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (48 bp):
TAAATTTTAAACTTGTGACACCAAAGTTAATTTAGACATATAAAATAA
Found at i:4089865 original size:25 final size:25
Alignment explanation
Indices: 4089816--4089867 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
4089806 AGTAAGTGAT
*
4089816 ATATCCATGAAAAGATTTGATGCGA
1 ATATCCATGAAAAGATTTGACGCGA
* * *
4089841 ATATCCATGGAAGGATTTGGCGCGA
1 ATATCCATGAAAAGATTTGACGCGA
4089866 AT
1 AT
4089868 CCCTTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (25 bp):
ATATCCATGAAAAGATTTGACGCGA
Found at i:4093350 original size:19 final size:19
Alignment explanation
Indices: 4093314--4093352 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4093304 AAAAGCCGGT
* *
4093314 AAGGGAAGGGAACCAAAAA
1 AAGGAAAGGGAAACAAAAA
*
4093333 AAGGAAAGGGAAAGAAAAA
1 AAGGAAAGGGAAACAAAAA
4093352 A
1 A
4093353 TAGAACTTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.05, G:0.31, T:0.00
Consensus pattern (19 bp):
AAGGAAAGGGAAACAAAAA
Found at i:4097813 original size:15 final size:17
Alignment explanation
Indices: 4097793--4097827 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
4097783 TTTTTAAGAT
4097793 TTTCTCTGC-AATG-TC
1 TTTCTCTGCTAATGCTC
4097808 TTTCTCTGCTAATGCTC
1 TTTCTCTGCTAATGCTC
4097825 TTT
1 TTT
4097828 AAGGTCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 4 0.22
17 5 0.28
ACGTcount: A:0.11, C:0.26, G:0.11, T:0.51
Consensus pattern (17 bp):
TTTCTCTGCTAATGCTC
Found at i:4097887 original size:2 final size:2
Alignment explanation
Indices: 4097880--4097911 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4097870 GAAACTTTTG
4097880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4097912 TTACATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4102130 original size:47 final size:44
Alignment explanation
Indices: 4102079--4102183 Score: 106
Period size: 47 Copynumber: 2.3 Consensus size: 44
4102069 AAATTTTAAC
4102079 TTTTTT-ATAAAGAAAAAA-AATTTCTTAAGAAATTATAATCTGAAAT
1 TTTTTTAATAAAGAAAAAATAA-TT-TTAA-AAATTA-AATCTGAAAT
*
4102125 TTTTTTAATAATCAGAAAAAATTAATTTTCAAAATTAAATCTGAAAT
1 TTTTTTAATAA--AGAAAAAA-TAATTTTAAAAATTAAATCTGAAAT
* *
4102172 TCTTTTCATAAA
1 TTTTTTAATAAA
4102184 AAAGGTCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
45 1 0.02
46 6 0.12
47 23 0.45
48 6 0.12
49 11 0.22
50 2 0.04
51 2 0.04
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (44 bp):
TTTTTTAATAAAGAAAAAATAATTTTAAAAATTAAATCTGAAAT
Found at i:4102525 original size:14 final size:15
Alignment explanation
Indices: 4102491--4102522 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4102481 CCTAAAAATG
*
4102491 TAATTTTTTACAAAA
1 TAATTTTTTAAAAAA
4102506 TAATTTTTTAAAAAA
1 TAATTTTTTAAAAAA
4102521 TA
1 TA
4102523 TTTCAAATTT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTTTTTAAAAAA
Found at i:4102653 original size:73 final size:73
Alignment explanation
Indices: 4102522--4102696 Score: 221
Period size: 74 Copynumber: 2.4 Consensus size: 73
4102512 TTTAAAAAAT
* * * *
4102522 ATTTCAAA-TTTTAAAATAAAAATAATTAATTTTATGTTTTAAAAATAATTTTTA-TTTTTCTAA
1 ATTTTAAATTTTTAAAAGAAAAATAATT-ATCTTATCTTTTAAAAATAATTTTTATTTTTTCTAA
* *
4102585 ATGTTTCGA
65 ATATTTCAA
* * *
4102594 ATTTTAAATTTTTCAAAGAAAAATAATTA-CTTATCTTTTAAAATATAATTTTATGTTTTTTTTA
1 ATTTTAAATTTTTAAAAGAAAAATAATTATCTTATCTTTTAAAA-ATAATTTT-TATTTTTTCTA
4102658 AATATTTCAA
64 AATATTTCAA
4102668 ATTTTAAATTTTTAAAAGAAAAATAATTA
1 ATTTTAAATTTTTAAAAGAAAAATAATTA
4102697 ATTTTGTTAT
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
71 12 0.13
72 16 0.18
73 18 0.20
74 43 0.48
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (73 bp):
ATTTTAAATTTTTAAAAGAAAAATAATTATCTTATCTTTTAAAAATAATTTTTATTTTTTCTAAA
TATTTCAA
Found at i:4103245 original size:12 final size:12
Alignment explanation
Indices: 4103228--4103252 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4103218 CAGTAATTTG
4103228 AAAAAAAAAAGA
1 AAAAAAAAAAGA
4103240 AAAAAAAAAAGA
1 AAAAAAAAAAGA
4103252 A
1 A
4103253 GCAAACAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:4109453 original size:2 final size:2
Alignment explanation
Indices: 4109446--4109476 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4109436 AAATACAAGG
4109446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4109477 CTAGTTGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4117355 original size:34 final size:34
Alignment explanation
Indices: 4117299--4117516 Score: 287
Period size: 34 Copynumber: 6.4 Consensus size: 34
4117289 TTTGTTGGTT
4117299 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGTTTACCA
* *
4117332 TTATTGATTAAATGGGTGATTTGGTGGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGTTTACCA
* * *
4117366 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGTTTACCA
* **
4117400 TTGTTGATTAAATGAGAAATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGTTTACCA
* * *
4117434 TTATTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGTTTACCA
* * *
4117468 TTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGTTTACCA
4117502 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
4117517 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
33 15 0.09
34 143 0.90
35 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGTTTACCA
Found at i:4117474 original size:102 final size:101
Alignment explanation
Indices: 4117299--4117516 Score: 373
Period size: 102 Copynumber: 2.1 Consensus size: 101
4117289 TTTGTTGGTT
** *
4117299 TTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTAC
1 TTGTTGATTAAATGGAAATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
4117364 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
66 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
4117400 TTGTTGATTAAATGAGAAATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1 TTGTTGATTAAATG-GAAATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
* * *
4117465 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCA
65 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
4117502 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
4117517 TGGTTTTTAC
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 15 0.14
102 95 0.86
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (101 bp):
TTGTTGATTAAATGGAAATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
Found at i:4121973 original size:34 final size:34
Alignment explanation
Indices: 4121916--4122134 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 34
4121906 AAGTGGGAGA
*
4121916 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
4121949 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
4121983 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
****
4122017 ATTGTTGATTAAATGAAAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
4122051 ATTATTGATTAAATGGGTGATTTAGT-GACTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAG-CTTACC
* * *
4122085 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
4122119 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
4122135 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
33 18 0.11
34 140 0.88
35 2 0.01
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:4122059 original size:102 final size:101
Alignment explanation
Indices: 4121916--4122133 Score: 328
Period size: 102 Copynumber: 2.1 Consensus size: 101
4121906 AAGTGGGAGA
*** * * * **
4121916 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTA
1 ATTGTTGATTAAATGAAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTAGTGACTTA
4121981 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
4122017 ATTGTTGATTAAATGAAAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTAGTGACTT
1 ATTGTTGATTAAATG-AAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTAGTGACTT
* * *
4122082 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
4122119 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
4122134 GTGGTTTTTA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGAAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTAGTGACTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:4122984 original size:94 final size:94
Alignment explanation
Indices: 4122838--4123025 Score: 322
Period size: 94 Copynumber: 2.0 Consensus size: 94
4122828 TAGTCCTAGC
* * *
4122838 TTTCAGTCTTATCTCATGCCTTATGAAGGGCCTAAGGAAGGAGGAAGTAAGAGCCAAGAAGGATG
1 TTTCAGTCTTATCTCATGCCTTATGAAGGGCCCAAGGAAGAAGGAAGCAAGAGCCAAGAAGGATG
*
4122903 AAGGCAGAAATTAGAGAAGAAGCAGAGAA
66 AAGGCAGAAATTAGAGAAGAAGCACAGAA
*
4122932 TTTCAGTCTTATCTCATGCCTTATGTAGGGCCCAAGGAAGAAGGAAGCAAGAGCCAAGAAGGATG
1 TTTCAGTCTTATCTCATGCCTTATGAAGGGCCCAAGGAAGAAGGAAGCAAGAGCCAAGAAGGATG
*
4122997 AAGGCAGAAATTAGAGAAGATGCACAGAA
66 AAGGCAGAAATTAGAGAAGAAGCACAGAA
4123026 CCAGTCCTAG
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 88 1.00
ACGTcount: A:0.39, C:0.14, G:0.29, T:0.18
Consensus pattern (94 bp):
TTTCAGTCTTATCTCATGCCTTATGAAGGGCCCAAGGAAGAAGGAAGCAAGAGCCAAGAAGGATG
AAGGCAGAAATTAGAGAAGAAGCACAGAA
Found at i:4125155 original size:21 final size:21
Alignment explanation
Indices: 4125112--4125157 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4125102 AATTATTTGA
*
4125112 ATAATTATTTAATTTTAATTT
1 ATAATTATTTAATTTTAAATT
*
4125133 ATAATT-TTTTATTTTAAGATT
1 ATAATTATTTAATTTTAA-ATT
4125154 ATAA
1 ATAA
4125158 AAATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATAATTATTTAATTTTAAATT
Found at i:4125238 original size:5 final size:6
Alignment explanation
Indices: 4125230--4125380 Score: 61
Period size: 7 Copynumber: 25.2 Consensus size: 6
4125220 CATTATAAAA
* *
4125230 AAAT-T AAATAT AAATAT -AATAT -GATAT AAA-A- AAATAAT AAAAAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAAT-AT AAATAT
* * * *
4125274 ATAATAT AATAAAT AATTAT -ATTAT AATTTAT ATAATAT AAATTAT AAATAT
1 A-AATAT AA-ATAT AAATAT AAATAT AA-ATAT A-AATAT AAA-TAT AAATAT
* * *
4125326 -ATTAA AATATAT AATATATT AAATAT -AATAAT AAA-AT AAAAAT AAA-AT
1 AAATAT AA-ATAT AA-ATA-T AAATAT AAAT-AT AAATAT AAATAT AAATAT
4125374 AAATAT A
1 AAATAT A
4125381 TAAATTACGT
Statistics
Matches: 116, Mismatches: 12, Indels: 35
0.71 0.07 0.21
Matches are distributed among these distances:
4 3 0.03
5 35 0.30
6 33 0.28
7 41 0.35
8 4 0.03
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.36
Consensus pattern (6 bp):
AAATAT
Found at i:4125273 original size:29 final size:31
Alignment explanation
Indices: 4125223--4125280 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
4125213 TTAATTACAT
*
4125223 TATAAAAAAATTAAATATAAATATAATATGA
1 TATAAAAAAATTAAATAAAAATATAATATGA
4125254 TATAAAAAAA-T-AATAAAAATATAATAT
1 TATAAAAAAATTAAATAAAAATATAATAT
4125281 AATAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 15 0.58
30 1 0.04
31 10 0.38
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (31 bp):
TATAAAAAAATTAAATAAAAATATAATATGA
Found at i:4125313 original size:32 final size:30
Alignment explanation
Indices: 4125243--4125387 Score: 106
Period size: 29 Copynumber: 4.9 Consensus size: 30
4125233 TTAAATATAA
*
4125243 ATATAATATGATATAAA-AAA-ATAATAAAA-
1 ATATAATAT-A-ATAAATAAATATATTAAAAT
* *
4125272 ATATAATATAATAAATAATTATATTATAATTT
1 ATATAATATAATAAATAAATATATTA-AA-AT
*
4125304 ATATAATATAA-ATTATAAATATATTAAAAT
1 ATATAATATAATA-AATAAATATATTAAAAT
*
4125334 ATATAATATATTAAATATAATA-A-TAAAAT
1 ATATAATATAATAAATA-AATATATTAAAAT
* * * *
4125363 A-AAAATAAAATAAATATATAAATTA
1 ATATAATATAATAAATAAATATATTA
4125388 CGTAATTAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 20
0.75 0.10 0.16
Matches are distributed among these distances:
27 8 0.09
28 16 0.17
29 23 0.24
30 17 0.18
31 8 0.09
32 22 0.23
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.37
Consensus pattern (30 bp):
ATATAATATAATAAATAAATATATTAAAAT
Found at i:4125365 original size:17 final size:17
Alignment explanation
Indices: 4125330--4125376 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
4125320 AAATATATTA
* *
4125330 AAATAT-ATAATATATT
1 AAATATAATAATAAAAT
4125346 AAATATAATAATAAAAT
1 AAATATAATAATAAAAT
*
4125363 AAAAATAA-AATAAA
1 AAATATAATAATAAA
4125377 TATATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATATAATAATAAAAT
Found at i:4126064 original size:18 final size:18
Alignment explanation
Indices: 4126026--4126113 Score: 76
Period size: 19 Copynumber: 4.8 Consensus size: 18
4126016 TTTAAAAATC
* *
4126026 AAATAAATTAAATTAAATT
1 AAATAAATT-ATTTAATTT
4126045 AAATAAA-TATTTTAATTT
1 AAATAAATTA-TTTAATTT
4126063 AAAATAAATTATTTAATTT
1 -AAATAAATTATTTAATTT
*
4126082 AAAT-TATTATTT-ATTAAT
1 AAATAAATTATTTAATT--T
4126100 AAA-AAATTATTTAA
1 AAATAAATTATTTAA
4126114 AAATATATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
16 3 0.05
17 8 0.14
18 22 0.38
19 23 0.40
20 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATAAATTATTTAATTT
Found at i:4129693 original size:21 final size:21
Alignment explanation
Indices: 4129664--4129721 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
4129654 ATTATTATTT
* * *
4129664 AATAATAATAATAAATTATTTA
1 AATATTAATATTAAA-TATATA
4129686 AAT-TTAATTATTAAATATATA
1 AATATTAA-TATTAAATATATA
4129707 AATATTAATATTAAA
1 AATATTAATATTAAA
4129722 AATAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATTAATATTAAATATATA
Found at i:4130750 original size:120 final size:120
Alignment explanation
Indices: 4130537--4130769 Score: 349
Period size: 120 Copynumber: 1.9 Consensus size: 120
4130527 ATGTTTCCTA
* * * *
4130537 ACATCCCATCACCATTTTGTAGGAGGAGATTTAAATTAGCTCCTGAGACCTCAGCAAGATTGCTT
1 ACATCCCACCACCATTTTGAAGAAGGAGATTTAAATTAGCTCCTGAGACCCCAGCAAGATTGCTT
* * * *
4130602 GCTGATAATGGAGATCCGTCGCCCTCCACAAGATATTTAACATGCTTCTCCTAAC
66 GCTGACAATGGAGATCCATAGCCCTCCACAAGACATTTAACATGCTTCTCCTAAC
* *
4130657 ACATCCCACCACCATTTTGAAGAAGGAGATTTAAATTGGCTCCTGATACCCCAGCAAGATTGCTT
1 ACATCCCACCACCATTTTGAAGAAGGAGATTTAAATTAGCTCCTGAGACCCCAGCAAGATTGCTT
* * *
4130722 GCTGACGATGGAGATCCATAGCTCTCCACGAGACATTTAACATGCTTC
66 GCTGACAATGGAGATCCATAGCCCTCCACAAGACATTTAACATGCTTC
4130770 ACATTTACAG
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (120 bp):
ACATCCCACCACCATTTTGAAGAAGGAGATTTAAATTAGCTCCTGAGACCCCAGCAAGATTGCTT
GCTGACAATGGAGATCCATAGCCCTCCACAAGACATTTAACATGCTTCTCCTAAC
Found at i:4131828 original size:41 final size:41
Alignment explanation
Indices: 4131771--4131848 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
4131761 CTGAAAGCAG
*
4131771 AGTGATAGAAGATGGTTCTTTGAAAGAAAGAATAAAAGTTA
1 AGTGATACAAGATGGTTCTTTGAAAGAAAGAATAAAAGTTA
*
4131812 AGTGATACAAGTTGGTTCTTTGAAAGAAAGAATAAAA
1 AGTGATACAAGATGGTTCTTTGAAAGAAAGAATAAAA
4131849 AGTATCTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (41 bp):
AGTGATACAAGATGGTTCTTTGAAAGAAAGAATAAAAGTTA
Found at i:4136963 original size:40 final size:41
Alignment explanation
Indices: 4136880--4136963 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 41
4136870 CTGTTATCTA
* * *
4136880 CATGCTTTCTAAAGAAAATTCACCATTTTTTTTTTTGTGAG
1 CATGCTTTCTAAAGAAAATTCACCATGTTTTTTGTTGTCAG
* *
4136921 CATGCTTTTTAAAGAAAATTTACCA-GTTTTTTGTTGTCAG
1 CATGCTTTCTAAAGAAAATTCACCATGTTTTTTGTTGTCAG
4136961 CAT
1 CAT
4136964 CCTGGTCCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
40 15 0.39
41 23 0.61
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (41 bp):
CATGCTTTCTAAAGAAAATTCACCATGTTTTTTGTTGTCAG
Found at i:4142211 original size:2 final size:2
Alignment explanation
Indices: 4142199--4142243 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4142189 GTTACAATTG
*
4142199 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4142241 AT A
1 AT A
4142244 ATACGAAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4145981 original size:18 final size:18
Alignment explanation
Indices: 4145958--4145995 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4145948 CTAAAACTTA
4145958 TTTTAT-TGTTATAATATT
1 TTTTATATGTTAT-ATATT
*
4145976 TTTTATATTTTATATATT
1 TTTTATATGTTATATATT
4145994 TT
1 TT
4145996 ATAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTATATGTTATATATT
Found at i:4146238 original size:29 final size:29
Alignment explanation
Indices: 4146198--4146256 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
4146188 GTTTAAATAA
4146198 AAATTTTAATTTATTTAATTGAATAA-ATT
1 AAATTTTAATTTATTT-ATTGAATAATATT
*
4146227 AAATTATT-ATTTATTTGTTGAATAATATT
1 AAATT-TTAATTTATTTATTGAATAATATT
4146256 A
1 A
4146257 TAAAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 17 0.63
30 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
AAATTTTAATTTATTTATTGAATAATATT
Found at i:4150211 original size:18 final size:19
Alignment explanation
Indices: 4150188--4150233 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
4150178 AAATAATTAT
4150188 AATATAATATA-ATTAAAA
1 AATATAATATATATTAAAA
*
4150206 AATATAAATATATTTTAAAA
1 AATAT-AATATATATTAAAA
*
4150226 TATATAAT
1 AATATAAT
4150234 TACAATACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 9 0.38
20 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATAATATATATTAAAA
Found at i:4152328 original size:3 final size:3
Alignment explanation
Indices: 4152320--4152344 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4152310 ATTTATTTAT
4152320 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
4152345 AATTGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4152609 original size:20 final size:20
Alignment explanation
Indices: 4152584--4152633 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
4152574 ATATATATAA
*
4152584 TTTTTTTAAGAATAATCAAT
1 TTTTTTTAAAAATAATCAAT
* *
4152604 TTTTTTTAAAAATGATTAAT
1 TTTTTTTAAAAATAATCAAT
4152624 TTTTTTTAAA
1 TTTTTTTAAA
4152634 TAATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTTTAAAAATAATCAAT
Found at i:4153317 original size:4 final size:4
Alignment explanation
Indices: 4153308--4153339 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
4153298 TTGAAAGTGG
4153308 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
4153340 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:4153631 original size:14 final size:14
Alignment explanation
Indices: 4153582--4153631 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
4153572 TTTATAAGTA
4153582 TTTAT-TAA-TATT
1 TTTATATAATTATT
*
4153594 TTTA-ATAATTATA
1 TTTATATAATTATT
*
4153607 TTTATTTAATTATT
1 TTTATATAATTATT
*
4153621 TTTATAAAATT
1 TTTATATAATT
4153632 TTAAAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 7 0.23
13 7 0.23
14 16 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATATAATTATT
Found at i:4154127 original size:26 final size:25
Alignment explanation
Indices: 4154069--4154127 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 25
4154059 TATAATATAA
*
4154069 AAATATATAAAATATAATAATTTTT
1 AAATATATAAAACATAATAATTTTT
*
4154094 ATTTAATATATTAATACATAATAATTTTT
1 A---AATATA-TAAAACATAATAATTTTT
4154123 AAATA
1 AAATA
4154128 AAAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
25 1 0.04
26 4 0.14
28 6 0.21
29 17 0.61
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATATATAAAACATAATAATTTTT
Found at i:4154788 original size:23 final size:23
Alignment explanation
Indices: 4154744--4154788 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4154734 AATAAATGTA
*
4154744 TAAAATATTTTAATATAATTATT
1 TAAAATATTTTAAGATAATTATT
* *
4154767 TAAAATATTTTTAGATATTTAT
1 TAAAATATTTTAAGATAATTAT
4154789 ATTTTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TAAAATATTTTAAGATAATTATT
Found at i:4155277 original size:11 final size:11
Alignment explanation
Indices: 4155261--4155285 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4155251 TGATGCAGAG
4155261 ACAGCTAGCAC
1 ACAGCTAGCAC
4155272 ACAGCTAGCAC
1 ACAGCTAGCAC
4155283 ACA
1 ACA
4155286 TATGAGCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.36, G:0.16, T:0.08
Consensus pattern (11 bp):
ACAGCTAGCAC
Found at i:4155598 original size:25 final size:28
Alignment explanation
Indices: 4155554--4155606 Score: 85
Period size: 25 Copynumber: 2.0 Consensus size: 28
4155544 CCAATAAAAA
4155554 TTATAATAAATACATAATATTTTTAATT
1 TTATAATAAATACATAATATTTTTAATT
4155582 TTATAA-AAATA-AT-ATATTTTTAATT
1 TTATAATAAATACATAATATTTTTAATT
4155607 AAAATCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.48
26 2 0.08
27 5 0.20
28 6 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATAATAAATACATAATATTTTTAATT
Found at i:4156702 original size:2 final size:2
Alignment explanation
Indices: 4156695--4156731 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4156685 CGCCTAAAGA
4156695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4156732 ATGTTGAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4158926 original size:22 final size:22
Alignment explanation
Indices: 4158901--4158942 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4158891 AAAATTATAA
*
4158901 ATTTTAAAATTTATTAAATATT
1 ATTTTAAAATTAATTAAATATT
*
4158923 ATTTTTAAATTAATTAAATA
1 ATTTTAAAATTAATTAAATA
4158943 AATAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTAAAATTAATTAAATATT
Found at i:4159742 original size:16 final size:16
Alignment explanation
Indices: 4159721--4159770 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
4159711 TTATATATTT
4159721 TTATTTTTTATTTATA
1 TTATTTTTTATTTATA
4159737 TTATTTTATT-TTTATAA
1 TTATTTT-TTATTTAT-A
* *
4159754 TAATTTTTTAATTATA
1 TTATTTTTTATTTATA
4159770 T
1 T
4159771 ATTAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTTTATTTATA
Found at i:4159762 original size:19 final size:19
Alignment explanation
Indices: 4159708--4159777 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 19
4159698 AAAAGAGTTG
4159708 ATATTATATATTTTTATTTTT
1 ATATTA-AT-TTTTTATTTTT
4159729 -TATTTATATTATTTTATTTTT
1 ATA-TTA-ATT-TTTTATTTTT
* * *
4159750 ATAATAATTTTTTAATTAT
1 ATATTAATTTTTTATTTTT
4159769 ATATTAATT
1 ATATTAATT
4159778 ATATTTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 16 0.38
20 6 0.14
21 18 0.43
22 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATTAATTTTTTATTTTT
Found at i:4160625 original size:37 final size:33
Alignment explanation
Indices: 4160573--4160639 Score: 80
Period size: 37 Copynumber: 1.9 Consensus size: 33
4160563 AATTTTATAA
4160573 AAATTAAAAAAATAAACATTTATTATTTTTATTTATG
1 AAATTAAAAAAAT-AA-ATTT-TTA-TTTTATTTATG
**
4160610 AAATTAAAACTATAAATTTTTATTTTATTT
1 AAATTAAAAAAATAAATTTTTATTTTATTT
4160640 TAGTTACACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 8 0.29
34 3 0.11
35 4 0.14
36 2 0.07
37 11 0.39
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (33 bp):
AAATTAAAAAAATAAATTTTTATTTTATTTATG
Found at i:4162829 original size:32 final size:31
Alignment explanation
Indices: 4162780--4162857 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 31
4162770 ATACGAAAGA
*
4162780 ATAATATAAATATAATATATTAAAA-TTTAT
1 ATAAAATAAATATAATATATTAAAATTTTAT
4162810 ATAAAATAAATTATTAATATATTAAAATTTTAT
1 ATAAAATAAA-TA-TAATATATTAAAATTTTAT
4162843 ATAAATATATAATAT
1 ATAAA-ATA-AATAT
4162858 TTTACATTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
30 9 0.21
31 2 0.05
32 13 0.31
33 11 0.26
34 5 0.12
35 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAAAATAAATATAATATATTAAAATTTTAT
Found at i:4163941 original size:17 final size:17
Alignment explanation
Indices: 4163915--4163955 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4163905 ACATGATTTG
4163915 TTCA-TTTTTTATCAAA
1 TTCATTTTTTTATCAAA
*
4163931 TTCATTTTTTTATTAAA
1 TTCATTTTTTTATCAAA
*
4163948 TTTATTTT
1 TTCATTTT
4163956 CAAAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCATTTTTTTATCAAA
Found at i:4163971 original size:30 final size:29
Alignment explanation
Indices: 4163918--4163984 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
4163908 TGATTTGTTC
*
4163918 ATTTTTTATC-AAATTCATTTTTTTATTAA
1 ATTTTTT-TCAAAATTCATATTTTTATTAA
* *
4163947 ATTTATTTTCAAAATTTATATTTTTATTTA
1 ATTT-TTTTCAAAATTCATATTTTTATTAA
4163977 ATTTTTTT
1 ATTTTTTT
4163985 AAATATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (29 bp):
ATTTTTTTCAAAATTCATATTTTTATTAA
Found at i:4164495 original size:29 final size:29
Alignment explanation
Indices: 4164433--4164509 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 29
4164423 TAATTAAATT
* *
4164433 TATTTATACATTAAATTATTTACTAAACA
1 TATTTATAAATTAAATTATTAACTAAACA
*
4164462 AATTTAATAAATTAAATTA-TAACATAAA-A
1 TATTT-ATAAATTAAATTATTAAC-TAAACA
* *
4164491 TATTTTTTAATTTAAATTA
1 TA-TTTATAAATTAAATTA
4164510 ATTTAATTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
TATTTATAAATTAAATTATTAACTAAACA
Found at i:4166445 original size:17 final size:17
Alignment explanation
Indices: 4166423--4166455 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4166413 TAGTCTGATT
4166423 TTATTTCAAAT-TATTAG
1 TTATTT-AAATATATTAG
4166440 TTATTTAAATATATTA
1 TTATTTAAATATATTA
4166456 ATATATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
TTATTTAAATATATTAG
Found at i:4173256 original size:9 final size:8
Alignment explanation
Indices: 4173237--4173273 Score: 51
Period size: 7 Copynumber: 4.8 Consensus size: 8
4173227 AAAGTTCAAT
4173237 GCCCCCCC
1 GCCCCCCC
4173245 GCCCCTCCC
1 GCCCC-CCC
4173254 GCCCCCCC
1 GCCCCCCC
4173262 -CCCCCCC
1 GCCCCCCC
4173269 -CCCCC
1 GCCCCC
4173274 TTCCCTCCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 12 0.43
8 8 0.29
9 8 0.29
ACGTcount: A:0.00, C:0.89, G:0.08, T:0.03
Consensus pattern (8 bp):
GCCCCCCC
Found at i:4174129 original size:19 final size:19
Alignment explanation
Indices: 4174086--4174129 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4174076 TTTATAAAAT
* *
4174086 AAAAATTATTTTTTTCTTA
1 AAAAATTAATTTTTTCTGA
**
4174105 CTAAATTAATTTTTTCTGA
1 AAAAATTAATTTTTTCTGA
4174124 AAAAAT
1 AAAAAT
4174130 AAAATTATAA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (19 bp):
AAAAATTAATTTTTTCTGA
Found at i:4174834 original size:11 final size:11
Alignment explanation
Indices: 4174818--4174898 Score: 62
Period size: 11 Copynumber: 7.5 Consensus size: 11
4174808 TTATTTAAAA
4174818 TATATAATATT
1 TATATAATATT
4174829 TATATAATATT
1 TATATAATATT
4174840 TATA-AAT-TT
1 TATATAATATT
*
4174849 TTTATAAT-TT
1 TATATAATATT
*
4174859 TATA-ATTATAT
1 TATATAATAT-T
* *
4174870 TATATTTATTTT
1 TATA-TAATATT
*
4174882 TAATATTATATT
1 T-ATATAATATT
4174894 TATAT
1 TATAT
4174899 TTTTTTATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
9 7 0.12
10 12 0.21
11 24 0.42
12 9 0.16
13 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATAATATT
Found at i:4174870 original size:31 final size:30
Alignment explanation
Indices: 4174820--4174900 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
4174810 ATTTAAAATA
*
4174820 TATAATATTTAT-ATAATATTTATAAATTT-TT
1 TATAAT-TTTATAATTATATTTAT--ATTTATT
4174851 TATAATTTTATAATTATA-TTATATTTATT
1 TATAATTTTATAATTATATTTATATTTATT
* * *
4174880 TTTAATATTATATTTATATTT
1 TATAATTTTATAATTATATTT
4174901 TTTTATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.09
29 17 0.40
30 11 0.26
31 11 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TATAATTTTATAATTATATTTATATTTATT
Found at i:4174872 original size:19 final size:20
Alignment explanation
Indices: 4174820--4174873 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
4174810 ATTTAAAATA
4174820 TATAATATTTA-TATAATATT
1 TATAA-ATTTATTATAATATT
*
4174840 TATAAATTTTTTATAAT-TT
1 TATAAATTTATTATAATATT
4174859 TAT-AATTATATTATA
1 TATAAATT-TATTATA
4174874 TTTATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 4 0.13
19 15 0.50
20 11 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATAAATTTATTATAATATT
Found at i:4174876 original size:18 final size:17
Alignment explanation
Indices: 4174828--4174911 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
4174818 TATATAATAT
*
4174828 TTATATAATATTTATAAA
1 TTATATTATATTTAT-AA
*
4174846 TT-TTTTATAATTTTATAA
1 TTATATTAT-A-TTTATAA
**
4174864 TTATATTATATTTATTT
1 TTATATTATATTTATAA
4174881 TTAATATTATATTTAT-A
1 TT-ATATTATATTTATAA
* *
4174898 TTTTTTTATATTTA
1 TTATATTATATTTA
4174912 AAATAATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
16 10 0.19
17 13 0.24
18 21 0.39
19 10 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATATTATATTTATAA
Found at i:4174878 original size:6 final size:6
Alignment explanation
Indices: 4174857--4174911 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
4174847 TTTTTATAAT
* *
4174857 TTTATA ATTATA -TTATA TTTATT TTTA-A TATTATA TTTATA TTT-T-
1 TTTATA TTTATA TTTATA TTTATA TTTATA T-TTATA TTTATA TTTATA
4174902 TTTATA TTTA
1 TTTATA TTTA
4174912 AAATAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
4 3 0.07
5 8 0.20
6 28 0.68
7 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:4174896 original size:29 final size:28
Alignment explanation
Indices: 4174848--4174912 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
4174838 TTTATAAATT
*
4174848 TTTTATAATTTTATAATTATATTATATTTA
1 TTTT-TAATATTATAATTATATT-TATTTA
* *
4174878 TTTTTAATATTATATTTATATTTTTTTA
1 TTTTTAATATTATAATTATATTTATTTA
*
4174906 TATTTAA
1 TTTTTAA
4174913 AATAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 11 0.35
29 16 0.52
30 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTTAATATTATAATTATATTTATTTA
Found at i:4174956 original size:97 final size:96
Alignment explanation
Indices: 4174795--4174971 Score: 211
Period size: 97 Copynumber: 1.8 Consensus size: 96
4174785 TTTTTGTACT
* * * *
4174795 TTTATATTTTTTATTATTTAAAATATATAATATTTATATAATATTTATAAATTTTTTATAATTTT
1 TTTATATTTTTTATTATTTAAAATATATAAAAATTATATAATATTAATAAATTTTTTAAAATTTT
4174860 ATA-ATTATATTATATTTATTTTTAATATTATA
66 ATATATT-TA-TATATTTATTTTTAATATTATA
* *
4174892 TTTATATTTTTT-TATATTTAAAATA-ATAAAAATTAT-TACATGTTAAT-TATTTATTTAAATA
1 TTTATATTTTTTAT-TATTTAAAATATATAAAAATTATATA-ATATTAATAAATTT-TTTAAA-A
4174953 TTTTATATATTTATATATT
62 TTTTATATATTTATATATT
4174972 CTTATTATTG
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
95 6 0.09
96 27 0.39
97 33 0.48
98 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (96 bp):
TTTATATTTTTTATTATTTAAAATATATAAAAATTATATAATATTAATAAATTTTTTAAAATTTT
ATATATTTATATATTTATTTTTAATATTATA
Found at i:4174963 original size:17 final size:17
Alignment explanation
Indices: 4174942--4174980 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4174932 TGTTAATTAT
4174942 TTATTTAAATATT-TTA
1 TTATTTAAATATTCTTA
*
4174958 TATATTTATATATTCTTA
1 T-TATTTAAATATTCTTA
4174976 TTATT
1 TTATT
4174981 GTAGACACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.75
18 4 0.20
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTTAAATATTCTTA
Found at i:4175251 original size:13 final size:13
Alignment explanation
Indices: 4175233--4175257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4175223 CATAAAGTGT
4175233 TGTATCGATACAA
1 TGTATCGATACAA
4175246 TGTATCGATACA
1 TGTATCGATACA
4175258 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4175255 original size:33 final size:33
Alignment explanation
Indices: 4175213--4175279 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4175203 TTCAACGATT
4175213 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
4175246 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
4175279 T
1 T
4175280 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:4175338 original size:13 final size:13
Alignment explanation
Indices: 4175320--4175344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4175310 ATCACTTAAA
4175320 TGTATCGATACAT
1 TGTATCGATACAT
4175333 TGTATCGATACA
1 TGTATCGATACA
4175345 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4175475 original size:52 final size:52
Alignment explanation
Indices: 4175333--4175481 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 52
4175323 ATCGATACAT
** **
4175333 TGTATCGATACACTGA-TCTTTGTATCGATACATGCAGAAAAATTTGCCCAGA
1 TGTATCGATACACT-ATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* **
4175385 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
4175437 TGTATCGATACACTATTCAATGTATCGATACATACAGGCAAATTT
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
4175482 TCATATTTCG
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 1 0.01
52 84 0.99
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:4178552 original size:21 final size:22
Alignment explanation
Indices: 4178534--4178581 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
4178524 GACAATTATG
4178534 TTTATATAA-TTTTTTATTATAT
1 TTTA-ATAACTTTTTTATTATAT
4178556 TTTAATAACTTTTTT-TT-TA-
1 TTTAATAACTTTTTTATTATAT
4178575 TTTAATA
1 TTTAATA
4178582 TTCATATCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.28
20 2 0.08
21 6 0.24
22 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTAATAACTTTTTTATTATAT
Found at i:4178863 original size:11 final size:11
Alignment explanation
Indices: 4178847--4178911 Score: 55
Period size: 11 Copynumber: 6.1 Consensus size: 11
4178837 AACATATTTA
4178847 TATATTTATAT
1 TATATTTATAT
*
4178858 TATATTCATAT
1 TATATTTATAT
*
4178869 TATTTTTTATAT
1 TA-TATTTATAT
*
4178881 AATATTT-TAT
1 TATATTTATAT
4178891 T-T-TTTATAT
1 TATATTTATAT
* *
4178900 TTTATTCATAT
1 TATATTTATAT
4178911 T
1 T
4178912 TTATCTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
8 3 0.07
9 5 0.12
10 4 0.09
11 23 0.53
12 8 0.19
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTTATAT
Found at i:4179135 original size:20 final size:20
Alignment explanation
Indices: 4179110--4179148 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4179100 TTTTATTGTT
*
4179110 TAAAATATTATAAATTTATA
1 TAAAATATTAAAAATTTATA
*
4179130 TAAAATTTTAAAAATTTAT
1 TAAAATATTAAAAATTTAT
4179149 TTTATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAATATTAAAAATTTATA
Found at i:4179375 original size:27 final size:27
Alignment explanation
Indices: 4179345--4179417 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 27
4179335 TTTTAATAAA
*
4179345 TAAATAATTATTTAA-TA-TAATTTAATT
1 TAAAT-ATTATATAATTATTAATTTAA-T
4179372 TAAAT-TTATATAATTATTAATTTAAT
1 TAAATATTATATAATTATTAATTTAAT
4179398 TAAATATT-TATAGA-TATTAA
1 TAAATATTATATA-ATTATTAA
4179418 AAATTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 7 0.17
26 18 0.44
27 16 0.39
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TAAATATTATATAATTATTAATTTAAT
Found at i:4179394 original size:22 final size:21
Alignment explanation
Indices: 4179354--4179404 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
4179344 ATAAATAATT
4179354 ATTTAATATAATTTAATTTAA
1 ATTTAATATAATTTAATTTAA
4179375 ATTT-ATATAATTATTAATTT-A
1 ATTTAATATAA-T-TTAATTTAA
*
4179396 ATTAAATAT
1 ATTTAATAT
4179405 TTATAGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATATAATTTAATTTAA
Found at i:4180918 original size:36 final size:37
Alignment explanation
Indices: 4180872--4180953 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 37
4180862 ATTTTATTTT
4180872 TAAATGTAATTATAAAAATATCAATATAAA-AAAA-TTAA
1 TAAAT-TAATTATAAAAA-ATCAA-ATAAATAAAATTTAA
* *
4180910 -AAATTAATTTTAAAAAATTAAATAAATAAAATTTAA
1 TAAATTAATTATAAAAAATCAAATAAATAAAATTTAA
4180946 TAAATTAA
1 TAAATTAA
4180954 AAATCTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
34 5 0.13
35 8 0.21
36 15 0.38
37 11 0.28
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (37 bp):
TAAATTAATTATAAAAAATCAAATAAATAAAATTTAA
Found at i:4180936 original size:23 final size:22
Alignment explanation
Indices: 4180900--4180956 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
4180890 TATCAATATA
* *
4180900 AAAAAATT-AAAAATTAATTTT
1 AAAAAATTAAAAAATAAAATTT
4180921 AAAAAATTAAATAAATAAAATTT
1 AAAAAATTAAA-AAATAAAATTT
*
4180944 AATAAATTAAAAA
1 AAAAAATTAAAAA
4180957 TCTTATAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.26
22 4 0.13
23 19 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAAATTAAAAAATAAAATTT
Found at i:4180940 original size:14 final size:15
Alignment explanation
Indices: 4180923--4180955 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4180913 TTAATTTTAA
4180923 AAAATTAAATAAA-T
1 AAAATTAAATAAATT
*
4180937 AAAATTTAATAAATT
1 AAAATTAAATAAATT
4180952 AAAA
1 AAAA
4180956 ATCTTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATTAAATAAATT
Found at i:4180997 original size:28 final size:27
Alignment explanation
Indices: 4180934--4181004 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
4180924 AAATTAAATA
*
4180934 AATAAAATTTA-ATAAATTAAAAATCT
1 AATAAAATTTATATAAATGAAAAATCT
*
4180960 TATAACAATTTATATAAATGAAAAGTATC-
1 AATAA-AATTTATATAAATGAAAA--ATCT
*
4180989 AATAAAATTGATATAA
1 AATAAAATTTATATAA
4181005 TCAAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 4 0.11
27 6 0.16
28 20 0.54
29 4 0.11
30 3 0.08
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (27 bp):
AATAAAATTTATATAAATGAAAAATCT
Found at i:4181280 original size:14 final size:15
Alignment explanation
Indices: 4181223--4181283 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 15
4181213 TAAAATTTTA
*
4181223 AATTTATTAAATATT
1 AATTTTTTAAATATT
4181238 -A-TTTTTATAATA--
1 AATTTTTTA-AATATT
*
4181250 AATTAATTTAAATATT
1 AATT-TTTTAAATATT
4181266 AATTTTTTAAA-ATT
1 AATTTTTTAAATATT
4181280 AATT
1 AATT
4181284 AAATTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
13 6 0.16
14 17 0.46
15 10 0.27
16 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTTTTAAATATT
Found at i:4181284 original size:30 final size:28
Alignment explanation
Indices: 4181221--4181285 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
4181211 AGTAAAATTT
* *
4181221 TAAATTTA-TTAAATATTATTTTTATAA
1 TAAATTAATTTAAATATTATTTTTAAAA
4181248 TAAATTAATTTAAATATTAATTTTTTAAAA
1 TAAATTAATTTAAATATT-A-TTTTTAAAA
*
4181278 TTAATTAA
1 TAAATTAA
4181286 ATTATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 7 0.22
28 9 0.28
29 1 0.03
30 15 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TAAATTAATTTAAATATTATTTTTAAAA
Found at i:4181291 original size:26 final size:24
Alignment explanation
Indices: 4181218--4181287 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 24
4181208 TCGAGTAAAA
*
4181218 TTTT-AAATTTATTAAATATTATT
1 TTTTAAAATTAATTAAATATTATT
4181241 TTTATAATAAATTAATTTAAATATTAATT
1 TTT-T-A-AAATTAA-TTAAATATT-ATT
4181270 TTTTAAAATTAATTAAAT
1 TTTTAAAATTAATTAAAT
4181288 TATTTAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
23 3 0.08
24 1 0.03
25 6 0.15
26 7 0.17
27 7 0.17
28 10 0.25
29 6 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTAAAATTAATTAAATATTATT
Found at i:4182911 original size:3 final size:3
Alignment explanation
Indices: 4182905--4182949 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
4182895 GGTGAGTGAG
4182905 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4182950 GTTTCAAGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4183150 original size:17 final size:17
Alignment explanation
Indices: 4183124--4183156 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4183114 GAAAAAATGA
*
4183124 TTTTATAAATTTTTAAT
1 TTTTAAAAATTTTTAAT
4183141 TTTTAAAAATTTTTAA
1 TTTTAAAAATTTTTAA
4183157 AATAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAAATTTTTAAT
Found at i:4187958 original size:2 final size:2
Alignment explanation
Indices: 4187951--4187984 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4187941 AAGCACTGGT
4187951 GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4187985 TGAGGCAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4188239 original size:2 final size:2
Alignment explanation
Indices: 4188232--4188322 Score: 76
Period size: 2 Copynumber: 44.5 Consensus size: 2
4188222 CTCGACGCAA
* * * *
4188232 CT CT CT CT CC CT -T TT CT CT CT CT CT CT CT CT CT GCA GT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT CT CT
* * * *
4188274 TT ACAG CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CA CT
1 CT -C-T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4188318 CT CT C
1 CT CT C
4188323 AAGAAAGTCA
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
1 1 0.01
2 67 0.96
3 2 0.03
ACGTcount: A:0.04, C:0.45, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:4188784 original size:2 final size:2
Alignment explanation
Indices: 4188772--4188801 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4188762 CTAGTTGACT
4188772 TC TC TC T- 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 TC TC T
4188802 GATAATGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:4189738 original size:2 final size:2
Alignment explanation
Indices: 4189731--4189762 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4189721 TTGGACGCAA
*
4189731 CT CT CT CT CT CT CT CT CT CT CT CT CT CG CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4189763 TTGACTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:4192955 original size:16 final size:17
Alignment explanation
Indices: 4192934--4192969 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
4192924 AAAATTTATA
4192934 TAGAAGTGTTT-TATTT
1 TAGAAGTGTTTATATTT
*
4192950 TAGAAGTTTTTATATTT
1 TAGAAGTGTTTATATTT
4192967 TAG
1 TAG
4192970 TGACCTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (17 bp):
TAGAAGTGTTTATATTT
Found at i:4193384 original size:14 final size:14
Alignment explanation
Indices: 4193367--4193415 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 14
4193357 ACTTTATAAA
4193367 TATAATTAAAAAAT
1 TATAATTAAAAAAT
4193381 TAT-ATCATAAAAAAT
1 TATAAT--TAAAAAAT
*
4193396 T-TATTTAAAAAAT
1 TATAATTAAAAAAT
4193409 TATAATT
1 TATAATT
4193416 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 11 0.38
14 8 0.28
15 10 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TATAATTAAAAAAT
Found at i:4193416 original size:15 final size:14
Alignment explanation
Indices: 4193367--4193417 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
4193357 ACTTTATAAA
*
4193367 TATAATTAAAAAAT
1 TATATTTAAAAAAT
*
4193381 TATATCATAAAAAAT
1 TATAT-TTAAAAAAT
4193396 T-TATTTAAAAAAT
1 TATATTTAAAAAAT
4193409 TATAATTTA
1 TAT-ATTTA
4193418 TTTTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 9 0.29
14 8 0.26
15 14 0.45
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TATATTTAAAAAAT
Found at i:4198337 original size:23 final size:22
Alignment explanation
Indices: 4198311--4198367 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
4198301 AAAGAAATTT
*
4198311 TAAAATATTGATATTTAATGAAA
1 TAAAATATTGATAATTAA-GAAA
*
4198334 TAAAATATAATTATAATTAAGAAA
1 TAAAATAT--TGATAATTAAGAAA
4198358 TAATAATATT
1 TAA-AATATT
4198368 AAGAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 9 0.31
24 7 0.24
25 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (22 bp):
TAAAATATTGATAATTAAGAAA
Found at i:4198647 original size:15 final size:16
Alignment explanation
Indices: 4198627--4198657 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4198617 TTTTGAATAA
4198627 TTTTAA-TTATTTTAT
1 TTTTAATTTATTTTAT
4198642 TTTTAATTTATTTTAT
1 TTTTAATTTATTTTAT
4198658 CAAATAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAATTTATTTTAT
Found at i:4199006 original size:22 final size:23
Alignment explanation
Indices: 4198968--4199023 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
4198958 AGGTAAACAT
* *
4198968 ATAAATGAATATGTTCATAAATA
1 ATAAATAAATATATTCATAAATA
* *
4198991 ATTAA-AAATATATTCATGAATA
1 ATAAATAAATATATTCATAAATA
4199013 ATAAATAAATA
1 ATAAATAAATA
4199024 ATTAGGGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (23 bp):
ATAAATAAATATATTCATAAATA
Found at i:4199228 original size:2 final size:2
Alignment explanation
Indices: 4199223--4199265 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4199213 CTTCAAAGTT
4199223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4199265 T
1 T
4199266 CTCTTGAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.