Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 126 of 168
Found at i:36638269 original size:68 final size:69
Alignment explanation
Indices: 36638190--36638327 Score: 233
Period size: 69 Copynumber: 2.0 Consensus size: 69
36638180 ACATATTATG
* * *
36638190 AAATTGGAAACGCTTTCTCCCTCATG-AATCTGAGCACAGCTTTCAAGGTTAGAACATTCATTCC
1 AAATTGGAAACGCTTTCTACCTCATGCAACCTGAGCACAGCTTTCAAGGGTAGAACATTCATTCC
36638254 TAAA
66 TAAA
*
36638258 AAATTGGAAACGCTTTCTACCTCATGCAACCTGAGCACAGCTTTCAGGGGTAGAACATTCATTCC
1 AAATTGGAAACGCTTTCTACCTCATGCAACCTGAGCACAGCTTTCAAGGGTAGAACATTCATTCC
36638323 TAAA
66 TAAA
36638327 A
1 A
36638328 TGATAAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 25 0.38
69 40 0.62
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (69 bp):
AAATTGGAAACGCTTTCTACCTCATGCAACCTGAGCACAGCTTTCAAGGGTAGAACATTCATTCC
TAAA
Found at i:36641724 original size:24 final size:24
Alignment explanation
Indices: 36641696--36641744 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
36641686 AAACAAGAAG
36641696 ATACAGGGAAGAAAATGGTGTCAA
1 ATACAGGGAAGAAAATGGTGTCAA
36641720 ATACAGGGAAGAAAATGGTGTCAA
1 ATACAGGGAAGAAAATGGTGTCAA
36641744 A
1 A
36641745 GGAGTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.29, T:0.16
Consensus pattern (24 bp):
ATACAGGGAAGAAAATGGTGTCAA
Found at i:36642952 original size:3 final size:3
Alignment explanation
Indices: 36642944--36642973 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
36642934 AGATTTTACT
36642944 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
36642974 AACATATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:36648580 original size:130 final size:130
Alignment explanation
Indices: 36648347--36648606 Score: 511
Period size: 130 Copynumber: 2.0 Consensus size: 130
36648337 CTGCCAAATA
36648347 AAATTAATAGAAATTAGGGTTTTTTCTTTCTAAATATCACCCTTTAGTAAATGTTTCGGGAAATG
1 AAATTAATAGAAATTAGGGTTTTTTCTTTCTAAATATCACCCTTTAGTAAATGTTTCGGGAAATG
36648412 GAAAAATAGCACTATGAAGCATGCTATATTAAAAAAAAGGTTATTTTTTTAAATTTTAGTTGGCT
66 GAAAAATAGCACTATGAAGCATGCTATATTAAAAAAAAGGTTATTTTTTTAAATTTTAGTTGGCT
*
36648477 AAATTACTAGAAATTAGGGTTTTTTCTTTCTAAATATCACCCTTTAGTAAATGTTTCGGGAAATG
1 AAATTAATAGAAATTAGGGTTTTTTCTTTCTAAATATCACCCTTTAGTAAATGTTTCGGGAAATG
36648542 GAAAAATAGCACTATGAAGCATGCTATATTAAAAAAAAGGTTATTTTTTTAAATTTTAGTTGGCT
66 GAAAAATAGCACTATGAAGCATGCTATATTAAAAAAAAGGTTATTTTTTTAAATTTTAGTTGGCT
36648607 TTTTCAATAA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 129 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (130 bp):
AAATTAATAGAAATTAGGGTTTTTTCTTTCTAAATATCACCCTTTAGTAAATGTTTCGGGAAATG
GAAAAATAGCACTATGAAGCATGCTATATTAAAAAAAAGGTTATTTTTTTAAATTTTAGTTGGCT
Found at i:36649846 original size:16 final size:16
Alignment explanation
Indices: 36649825--36649857 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
36649815 TTCGCTGTAT
36649825 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
36649841 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
36649857 T
1 T
36649858 AGCAATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:36649902 original size:45 final size:44
Alignment explanation
Indices: 36649837--36649933 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
36649827 GAATAGAGGC
36649837 GTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* * *
36649882 GTAATGGAATAGAGGTGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
*
36649926 GGAATGGA
1 GTAATGGA
36649934 GGTGTAATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.51
45 22 0.47
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:36650131 original size:17 final size:18
Alignment explanation
Indices: 36650090--36650124 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36650080 TTATTATTAA
*
36650090 ATATATTTTAATTAAAAT
1 ATATAATTTAATTAAAAT
36650108 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
36650125 TTTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:36650266 original size:16 final size:16
Alignment explanation
Indices: 36650245--36650283 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
36650235 ATTTAATAAA
36650245 ATTCTTAATAATCAAT
1 ATTCTTAATAATCAAT
36650261 ATTCTTAATAATCAAT
1 ATTCTTAATAATCAAT
36650277 ATTCTTA
1 ATTCTTA
36650284 TAACAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTCTTAATAATCAAT
Found at i:36651792 original size:13 final size:13
Alignment explanation
Indices: 36651774--36651798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36651764 GCCTTAACAA
36651774 GAGCAGCACTCAT
1 GAGCAGCACTCAT
36651787 GAGCAGCACTCA
1 GAGCAGCACTCA
36651799 AAATAGATTT
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:0.32, G:0.24, T:0.12
Consensus pattern (13 bp):
GAGCAGCACTCAT
Found at i:36663674 original size:21 final size:21
Alignment explanation
Indices: 36663648--36663687 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36663638 TGCTTCTTTG
*
36663648 AATCGATTCTTTGTTGTTTTA
1 AATCGATTCTTTATTGTTTTA
*
36663669 AATCGATTGTTTATTGTTT
1 AATCGATTCTTTATTGTTT
36663688 GAATAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.57
Consensus pattern (21 bp):
AATCGATTCTTTATTGTTTTA
Found at i:36665594 original size:20 final size:22
Alignment explanation
Indices: 36665565--36665620 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
36665555 TTTCACAAAC
36665565 AAATTCTCTCAATTTCCTTCAA
1 AAATTCTCTCAATTTCCTTCAA
**
36665587 AAATTCTCTCAATTTCCTTTTA
1 AAATTCTCTCAATTTCCTTCAA
36665609 AAATTCTCTCAA
1 AAATTCTCTCAA
36665621 ACTCTCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTCTCTCAATTTCCTTCAA
Found at i:36665628 original size:30 final size:30
Alignment explanation
Indices: 36665592--36665650 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
36665582 TTCAAAAATT
* ** *
36665592 CTCTCAATTTCCTTTTAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
36665622 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
36665651 TTTCCTTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.32, G:0.00, T:0.37
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:36665661 original size:21 final size:22
Alignment explanation
Indices: 36665622--36665663 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
36665612 TTCTCTCAAA
36665622 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
36665644 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
36665664 ATCTCCAAAT
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:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:36665729 original size:27 final size:27
Alignment explanation
Indices: 36665698--36665759 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
36665688 TTTTTCCATT
36665698 AAATTTCATTTTTTTAAGAA-AATTTTA
1 AAATTTCATTTTTTTAA-AATAATTTTA
* *
36665725 CAATTTTTTATTTTTTTAAAATAATTTTA
1 -AA-ATTTCATTTTTTTAAAATAATTTTA
36665754 AAATTT
1 AAATTT
36665760 TTAATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 3 0.10
28 6 0.21
29 20 0.69
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (27 bp):
AAATTTCATTTTTTTAAAATAATTTTA
Found at i:36665743 original size:29 final size:29
Alignment explanation
Indices: 36665705--36665761 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
36665695 ATTAAATTTC
*
36665705 ATTTTTTTAAGAA-AATTTTACAATTTTTT
1 ATTTTTTTAA-AATAATTTTAAAATTTTTT
36665734 ATTTTTTTAAAATAATTTTAAAATTTTT
1 ATTTTTTTAAAATAATTTTAAAATTTTT
36665762 AATATTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTTTTAAAATAATTTTAAAATTTTTT
Found at i:36665769 original size:28 final size:29
Alignment explanation
Indices: 36665709--36665769 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
36665699 AATTTCATTT
* * *
36665709 TTTTAAGAAAATTTTACAATTTTTTATTT
1 TTTTAAGAAAATTTTACAAATTTTTAATA
36665738 TTTTAA-AATAATTTTA-AAATTTTTAATA
1 TTTTAAGAA-AATTTTACAAATTTTTAATA
36665766 TTTT
1 TTTT
36665770 CAACCATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTAAGAAAATTTTACAAATTTTTAATA
Found at i:36665769 original size:29 final size:29
Alignment explanation
Indices: 36665708--36665769 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
36665698 AAATTTCATT
* * *
36665708 TTTTTAAGAAAATTTTACAATTTTTTATT
1 TTTTTAAGAAAATTTTAAAATTTTTAATA
36665737 TTTTTAA-AATAATTTTAAAATTTTTAATA
1 TTTTTAAGAA-AATTTTAAAATTTTTAATA
36665766 TTTT
1 TTTT
36665770 CAACCATGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAAATTTTTAATA
Found at i:36665896 original size:14 final size:15
Alignment explanation
Indices: 36665867--36665900 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
36665857 ATATTTTATA
36665867 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
36665882 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
36665896 TTTTA
1 TTTTA
36665901 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:36668093 original size:23 final size:23
Alignment explanation
Indices: 36668067--36668174 Score: 113
Period size: 23 Copynumber: 4.9 Consensus size: 23
36668057 AAAACCCTAA
*
36668067 CCTAACTTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
36668090 CCTAACCTAATTGAATT--AAA-
1 CCTAACCTAATTTAATTAAAAAC
36668110 ---AACCTAATTTAATTAAAAAC
1 CCTAACCTAATTTAATTAAAAAC
*
36668130 CCTAACCTAACTTAATGT-AAAAC
1 CCTAACCTAATTTAAT-TAAAAAC
*
36668153 CCTAACCTAACTTAACTTAAAA
1 CCTAACCTAATTTAA-TTAAAA
36668175 CCTAACTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
17 13 0.18
19 3 0.04
21 3 0.04
23 48 0.67
24 5 0.07
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (23 bp):
CCTAACCTAATTTAATTAAAAAC
Found at i:36668115 original size:17 final size:17
Alignment explanation
Indices: 36668093--36668130 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
36668083 TAAAAACCCT
36668093 AACCTAATTGAATTAAA
1 AACCTAATTGAATTAAA
*
36668110 AACCTAATTTAATTAAA
1 AACCTAATTGAATTAAA
36668127 AACC
1 AACC
36668131 CTAACCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (17 bp):
AACCTAATTGAATTAAA
Found at i:36668129 original size:40 final size:41
Alignment explanation
Indices: 36668074--36668157 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 41
36668064 TAACCTAACT
36668074 TAATTTAATTAAAAACCCTAACCTAA-TTGAAT-TAAAAACC
1 TAATTTAATTAAAAACCCTAACCTAACTT-AATGTAAAAACC
*
36668114 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCC
1 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAAACC
36668155 TAA
1 TAA
36668158 CCTAACTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 29 0.71
41 12 0.29
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (41 bp):
TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAAACC
Found at i:36671618 original size:125 final size:124
Alignment explanation
Indices: 36671396--36671676 Score: 404
Period size: 125 Copynumber: 2.3 Consensus size: 124
36671386 CCACGAGGGC
36671396 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * **
36671461 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTGCCCAATATAGCATCCTTGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTGCCCAA-ATAGCATCCTAGTAGAA
* * *
36671521 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAATTATTTCTTACATGACC-ACTGTAGC
1 GCGATTTGACACTATTTGCTCAG-AAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGC
* *
36671585 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
65 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTGCCCAAATAGCATCCTAGTAGAA
** *
36671645 GCGATTTCCCACTATTTGAC-CAGATACGTCAA
1 GCGATTTGACACTATTTG-CTCAGAAACGTCAA
36671677 CTCGAAATTT
Statistics
Matches: 140, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
123 8 0.06
124 32 0.23
125 69 0.49
126 31 0.22
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (124 bp):
GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTGCCCAAATAGCATCCTAGTAGAA
Found at i:36680010 original size:29 final size:29
Alignment explanation
Indices: 36679954--36680010 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
36679944 ATTTTCAAAA
** * *
36679954 TATTTTTAAAATACTTTTTTTATTTTTTT
1 TATTTTTAAAATAAATTTTTGATATTTTT
*
36679983 TATTTTTAAAATAAATTTTTGGTATTTT
1 TATTTTTAAAATAAATTTTTGATATTTT
36680011 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (29 bp):
TATTTTTAAAATAAATTTTTGATATTTTT
Found at i:36682712 original size:17 final size:17
Alignment explanation
Indices: 36682654--36682734 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
36682644 TTATATCTAC
36682654 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
36682671 TAAATTTAACATT-TTATAT
1 T--ATTT-ATATTATTAAAT
36682690 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
36682707 TGTTTAGTCA-TATTGAA-
1 TATTTA-T-ATTATTAAAT
36682724 TATTTATATTA
1 TATTTATATTA
36682735 AAATTGAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
15 1 0.02
16 7 0.14
17 20 0.40
18 7 0.14
19 11 0.22
20 4 0.08
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:36683436 original size:26 final size:26
Alignment explanation
Indices: 36683376--36683438 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
36683366 TTTACTCTAG
* * *
36683376 TAAAATTATGACGATTTTACCCCTAA
1 TAAAATTTTGATGATTTTACCCCCAA
36683402 TAAAATTTTGATGATTTTACCCCCAA
1 TAAAATTTTGATGATTTTACCCCCAA
*
36683428 TAAAGTTTTGA
1 TAAAATTTTGA
36683439 GAAAATTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (26 bp):
TAAAATTTTGATGATTTTACCCCCAA
Found at i:36684598 original size:47 final size:47
Alignment explanation
Indices: 36684544--36684638 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
36684534 TGATAGCGTC
36684544 AACTGTCGGTTCGGTCAAGGTTACGCAAAATGTATCCCAATGGTTAG
1 AACTGTCGGTTCGGTCAAGGTTACGCAAAATGTATCCCAATGGTTAG
*
36684591 AACTGTCGGTTCGGTCAAGGTTGCGCAAAATGTATCCCAATGGTTAG
1 AACTGTCGGTTCGGTCAAGGTTACGCAAAATGTATCCCAATGGTTAG
36684638 A
1 A
36684639 TCGGACTAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (47 bp):
AACTGTCGGTTCGGTCAAGGTTACGCAAAATGTATCCCAATGGTTAG
Found at i:36696233 original size:13 final size:13
Alignment explanation
Indices: 36696215--36696244 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
36696205 ATTTTTTTAA
*
36696215 TATAAAATATTTC
1 TATAAAATATTAC
36696228 TATAAAATATTAC
1 TATAAAATATTAC
36696241 TATA
1 TATA
36696245 GTGGAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
TATAAAATATTAC
Found at i:36700230 original size:15 final size:16
Alignment explanation
Indices: 36700204--36700237 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
36700194 TGAAAGGTAT
36700204 TAATTAGATTAATTAG
1 TAATTAGATTAATTAG
*
36700220 TAATT-GATTAATTGG
1 TAATTAGATTAATTAG
36700235 TAA
1 TAA
36700238 AATCTCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
TAATTAGATTAATTAG
Found at i:36700745 original size:87 final size:87
Alignment explanation
Indices: 36700599--36700854 Score: 399
Period size: 87 Copynumber: 2.9 Consensus size: 87
36700589 CGAGGCATGG
* * *
36700599 TCAAGTTGTTGGCATCGTTGCCAAGGAGGTTTAGGTGCTAATTTGATTTAGTAGTAAATTGTGTA
1 TCAAGTTGTTGGCGTCGTTGCTAGGGAGGTTTAGGTGCTAATTTGATTTAGTAGTAAATTGTGTA
*
36700664 GGATAGTTAAGATAAGTCACGA
66 GGCTAGTTAAGATAAGTCACGA
*
36700686 TCAAGTTGTTGGCGTCGTTGCTAGGGTGGTTTAGGTGCTAATTTGATTTAGTAGTAAATTGTGTA
1 TCAAGTTGTTGGCGTCGTTGCTAGGGAGGTTTAGGTGCTAATTTGATTTAGTAGTAAATTGTGTA
*
36700751 GGCTAGTTAAGATAAGTCACGG
66 GGCTAGTTAAGATAAGTCACGA
* *
36700773 TCAAGTTGTTGGCGTCGTTG-TCAGGGAGGTTTATGTGCTAATTTGATTTAATAGTAAATTGTGC
1 TCAAGTTGTTGGCGTCGTTGCT-AGGGAGGTTTAGGTGCTAATTTGATTTAGTAGTAAATTGTG-
*
36700837 T-GGCTAGTTAGGATAAGT
64 TAGGCTAGTTAAGATAAGT
36700855 AGTGAATTCG
Statistics
Matches: 157, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
86 1 0.01
87 155 0.99
88 1 0.01
ACGTcount: A:0.25, C:0.09, G:0.29, T:0.37
Consensus pattern (87 bp):
TCAAGTTGTTGGCGTCGTTGCTAGGGAGGTTTAGGTGCTAATTTGATTTAGTAGTAAATTGTGTA
GGCTAGTTAAGATAAGTCACGA
Found at i:36700895 original size:4 final size:4
Alignment explanation
Indices: 36700886--36700910 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
36700876 TACGTCACTT
36700886 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
36700911 AGTTTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:36703272 original size:3 final size:3
Alignment explanation
Indices: 36703264--36703288 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36703254 AGTTAGATTC
36703264 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
36703289 TGATAGAAGA
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):
TAT
Found at i:36709293 original size:24 final size:24
Alignment explanation
Indices: 36709233--36709293 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
36709223 GTACATGTAT
*
36709233 GCTCATACGAGCGATAAACGGTAA
1 GCTCATACGAGCTATAAACGGTAA
* *
36709257 GCTC-TGCCAAGCTA-AAATCGGTAA
1 GCTCAT-ACGAGCTATAAA-CGGTAA
36709281 GCTCATACGAGCT
1 GCTCATACGAGCT
36709294 GTGGTGTGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
23 4 0.14
24 24 0.83
25 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.20
Consensus pattern (24 bp):
GCTCATACGAGCTATAAACGGTAA
Found at i:36710191 original size:19 final size:18
Alignment explanation
Indices: 36710140--36710192 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
36710130 TCAGATCGAT
*
36710140 AATTCATCAAACATTTAAC
1 AATT-ATCAATCATTTAAC
* *
36710159 AAATATCATTTCATTTCAAC
1 AATTATCA-ATCATTT-AAC
36710179 AATTATCAATCATT
1 AATTATCAATCATT
36710193 CATAAGCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 4 0.15
19 13 0.48
20 10 0.37
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTATCAATCATTTAAC
Found at i:36714334 original size:13 final size:13
Alignment explanation
Indices: 36714316--36714345 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
36714306 AGCCCAAACT
*
36714316 CAATTACTCAACC
1 CAATTACCCAACC
36714329 CAATTACCCAACC
1 CAATTACCCAACC
36714342 CAAT
1 CAAT
36714346 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:36714497 original size:9 final size:9
Alignment explanation
Indices: 36714485--36714561 Score: 75
Period size: 9 Copynumber: 8.4 Consensus size: 9
36714475 AAAATAAAAA
36714485 AATTCGGGT
1 AATTCGGGT
*
36714494 AATTAGGGT
1 AATTCGGGT
*
36714503 ATTTTTC-GGT
1 A--ATTCGGGT
*
36714513 AATTCGGTT
1 AATTCGGGT
*
36714522 AATTCGGTT
1 AATTCGGGT
*
36714531 AATTCAGGT
1 AATTCGGGT
*
36714540 AATTCAGGT
1 AATTCGGGT
36714549 AATTCGGGT
1 AATTCGGGT
36714558 AATT
1 AATT
36714562 TTTAACCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
8 3 0.05
9 48 0.84
10 4 0.07
11 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:36716673 original size:11 final size:11
Alignment explanation
Indices: 36716659--36716723 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
36716649 ATTTTTTTAA
36716659 TTTTAAAATAT
1 TTTTAAAATAT
36716670 TTTTAAAATAT
1 TTTTAAAATAT
* *
36716681 TTTT-TATTAT
1 TTTTAAAATAT
36716691 TTTT---A-A-
1 TTTTAAAATAT
36716697 TTTTAAAATAT
1 TTTTAAAATAT
36716708 TTTTAAAATACT
1 TTTTAAAATA-T
36716720 TTTT
1 TTTT
36716724 TAATTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
6 4 0.09
7 1 0.02
9 1 0.02
10 9 0.20
11 25 0.56
12 5 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:36716694 original size:38 final size:39
Alignment explanation
Indices: 36716642--36716733 Score: 147
Period size: 38 Copynumber: 2.4 Consensus size: 39
36716632 ATATATTTAT
36716642 TTTTTTAATT-TTTTTAATTTTAAAATATTTTTAAAATA-
1 TTTTTT-ATTATTTTTAATTTTAAAATATTTTTAAAATAC
36716680 TTTTTTATTATTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTATTATTTTTAATTTTAAAATATTTTTAAAATAC
36716719 TTTTTTA--ATTTTTAA
1 TTTTTTATTATTTTTAA
36716734 AATAAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
37 11 0.21
38 34 0.65
39 7 0.13
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (39 bp):
TTTTTTATTATTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:36716743 original size:20 final size:20
Alignment explanation
Indices: 36716706--36716744 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
36716696 ATTTTAAAAT
**
36716706 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
36716726 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
36716745 GGTATTTATT
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:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:36716751 original size:22 final size:20
Alignment explanation
Indices: 36716705--36716762 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
36716695 AATTTTAAAA
*
36716705 TATTTTTAAAAT-ACTTTTT
1 TATTTTTAAAATAAATTTTT
36716724 TAATTTTTAAAATAAATTTTT
1 T-ATTTTTAAAATAAATTTTT
36716745 GGTATTTATTAAAA-AAAT
1 --TATTT-TTAAAATAAAT
36716763 GGGTCGGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 6 0.18
22 8 0.24
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTTAAAATAAATTTTT
Found at i:36723440 original size:18 final size:19
Alignment explanation
Indices: 36723405--36723443 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
36723395 ATATGTATGA
36723405 TTAAATCAAAATTAAAAAT
1 TTAAATCAAAATTAAAAAT
*
36723424 TTAAATCATAA-TAAAAAT
1 TTAAATCAAAATTAAAAAT
36723442 TT
1 TT
36723444 CATGTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAATCAAAATTAAAAAT
Found at i:36730622 original size:28 final size:29
Alignment explanation
Indices: 36730581--36730643 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
36730571 ATTTGATAAA
* *
36730581 AAAAATATCTACTT-CCTCCTAAAGTTTG
1 AAAAATACCCACTTACCTCCTAAAGTTTG
*
36730609 AAAAATACCCACTTATCTCCTAAAGTTTG
1 AAAAATACCCACTTACCTCCTAAAGTTTG
36730638 ATAAAA
1 A-AAAA
36730644 ATACATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 12 0.40
29 14 0.47
30 4 0.13
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAAATACCCACTTACCTCCTAAAGTTTG
Found at i:36733687 original size:16 final size:16
Alignment explanation
Indices: 36733654--36733685 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
36733644 CCGCCGCTAC
36733654 AAACATTTATAATTTT
1 AAACATTTATAATTTT
36733670 AAACACTTTATAATTT
1 AAACA-TTTATAATTT
36733686 AACATTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
AAACATTTATAATTTT
Found at i:36734291 original size:13 final size:12
Alignment explanation
Indices: 36734273--36734302 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
36734263 TTTAGTCATA
36734273 TAATAAATTATAT
1 TAATAAATTAT-T
36734286 TAATAAATTATT
1 TAATAAATTATT
36734298 TAATA
1 TAATA
36734303 TTTCAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATAAATTATT
Found at i:36734676 original size:21 final size:21
Alignment explanation
Indices: 36734652--36734693 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36734642 TTAATATATG
*
36734652 TAAAAATATATATATAAAATA
1 TAAAAATATAGATATAAAATA
**
36734673 TAAATTTATAGATATAAAATA
1 TAAAAATATAGATATAAAATA
36734694 AACTCAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAATATAGATATAAAATA
Found at i:36734867 original size:14 final size:14
Alignment explanation
Indices: 36734841--36734880 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
36734831 AAAATATTAA
36734841 ATTTTCA-AAAATT
1 ATTTTCAGAAAATT
36734854 ATTTTCAGAAAATT
1 ATTTTCAGAAAATT
36734868 ATTTTCAGTAAAA
1 ATTTTCAG-AAAA
36734881 CAAGCATACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 7 0.28
14 14 0.56
15 4 0.16
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (14 bp):
ATTTTCAGAAAATT
Found at i:36735283 original size:2 final size:2
Alignment explanation
Indices: 36735276--36735313 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
36735266 ACAATAATTG
36735276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36735314 GCAGAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36736066 original size:13 final size:13
Alignment explanation
Indices: 36736048--36736073 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36736038 TTTATACATT
36736048 AAAATTTTAATTC
1 AAAATTTTAATTC
36736061 AAAATTTTAATTC
1 AAAATTTTAATTC
36736074 GACTCTACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATTTTAATTC
Found at i:36737406 original size:19 final size:21
Alignment explanation
Indices: 36737384--36737431 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
36737374 TAATATATAA
*
36737384 AAATAATTTTA-ATT-ATATT
1 AAATAATTTAATATTAATATT
36737403 AAATAATTTAATATTAATATT
1 AAATAATTTAATATTAATATT
*
36737424 ATATAATT
1 AAATAATT
36737432 ATCATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
20 3 0.12
21 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATAATTTAATATTAATATT
Found at i:36740922 original size:11 final size:11
Alignment explanation
Indices: 36740888--36740922 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
36740878 TCACAATATT
36740888 ATAAAAGAAAAA
1 ATAAAA-AAAAA
*
36740900 ATAATAAAAAA
1 ATAAAAAAAAA
36740911 ATAAAAAAAAA
1 ATAAAAAAAAA
36740922 A
1 A
36740923 AGGAGGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (11 bp):
ATAAAAAAAAA
Found at i:36751754 original size:12 final size:13
Alignment explanation
Indices: 36751739--36751800 Score: 60
Period size: 12 Copynumber: 5.1 Consensus size: 13
36751729 TACAATATTA
36751739 ATTAAATT-TAAT
1 ATTAAATTCTAAT
*
36751751 ATTAACTTCT-A-
1 ATTAAATTCTAAT
* *
36751762 ATTAATTTCTATT
1 ATTAAATTCTAAT
36751775 ATTAAATT-TAAT
1 ATTAAATTCTAAT
*
36751787 ATTAACTTCTAAT
1 ATTAAATTCTAAT
36751800 A
1 A
36751801 AACTTTTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
11 9 0.22
12 18 0.45
13 13 0.32
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAAATTCTAAT
Found at i:36751782 original size:36 final size:36
Alignment explanation
Indices: 36751734--36751816 Score: 123
Period size: 36 Copynumber: 2.3 Consensus size: 36
36751724 TAAATTACAA
*
36751734 TATTAATTAAATTTAATATTAACTTCTAATTAA-TTT
1 TATT-ATTAAATTTAATATTAACTTCTAATAAACTTT
36751770 CTATTATTAAATTTAATATTAACTTCTAATAAACTTT
1 -TATTATTAAATTTAATATTAACTTCTAATAAACTTT
*
36751807 TATAATTAAA
1 TATTATTAAA
36751817 CCATTTGGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 36 0.84
37 7 0.16
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.49
Consensus pattern (36 bp):
TATTATTAAATTTAATATTAACTTCTAATAAACTTT
Found at i:36751786 original size:23 final size:22
Alignment explanation
Indices: 36751727--36751786 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
36751717 TACTGTATAA
36751727 ATTACAATATTAATTAAATTTAAT
1 ATTA-AAT-TTAATTAAATTTAAT
* * *
36751751 ATTAACTTCTAATTAATTTCTATT
1 ATTAAATT-TAATTAAATT-TAAT
36751775 ATTAAATTTAAT
1 ATTAAATTTAAT
36751787 ATTAACTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.03
23 15 0.50
24 14 0.47
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAAATTTAATTAAATTTAAT
Found at i:36755271 original size:16 final size:16
Alignment explanation
Indices: 36755250--36755281 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
36755240 AGTCGGTTAC
36755250 GCACGAGGAAGGATTA
1 GCACGAGGAAGGATTA
36755266 GCACGAGGAAGGATTA
1 GCACGAGGAAGGATTA
36755282 CGGTCACATG
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:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (16 bp):
GCACGAGGAAGGATTA
Found at i:36756079 original size:24 final size:24
Alignment explanation
Indices: 36756044--36756107 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
36756034 AGCGAATTAG
*
36756044 ATTA-AAATATATGTATATATATAA
1 ATTATAAA-ATATGTATACATATAA
* * **
36756068 ATTATAAAATATATGTACATATGT
1 ATTATAAAATATGTATACATATAA
36756092 ATTATAAAA-ATGTATA
1 ATTATAAAATATGTATA
36756108 GATGTATGCG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 5 0.16
24 24 0.75
25 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (24 bp):
ATTATAAAATATGTATACATATAA
Found at i:36756234 original size:2 final size:2
Alignment explanation
Indices: 36756229--36756271 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
36756219 TTAAAAAAAA
36756229 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36756271 A
1 A
36756272 CACGTGCATG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36757838 original size:17 final size:17
Alignment explanation
Indices: 36757816--36757855 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
36757806 ACAAATTATT
36757816 TTTGGGCTT-GTTGGGTA
1 TTTGGGCTTGGTT-GGTA
36757833 TTTGGGCTTGGTTGGTA
1 TTTGGGCTTGGTTGGTA
36757850 TTTGGG
1 TTTGGG
36757856 TTAGGCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.05, C:0.05, G:0.42, T:0.47
Consensus pattern (17 bp):
TTTGGGCTTGGTTGGTA
Found at i:36759980 original size:20 final size:20
Alignment explanation
Indices: 36759955--36760006 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
36759945 TATGGATCAC
*
36759955 TCCATTTACTTTCTTACCAT
1 TCCATTTACTTACTTACCAT
*
36759975 TCCATTTACTTACTTTCCAT
1 TCCATTTACTTACTTACCAT
*
36759995 TTCATTTACTTA
1 TCCATTTACTTA
36760007 GCATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (20 bp):
TCCATTTACTTACTTACCAT
Found at i:36760834 original size:36 final size:36
Alignment explanation
Indices: 36760753--36760844 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 36
36760743 ATCAGTCCAA
* * *
36760753 CCAAAACACACCAGATGCTCACATGAGCCAATGCCT
1 CCAAAACACACCAGATGCTCACACGAACCAATCCCT
* *
36760789 -TAAAGACACACTAGATGCTCACACGAACCAATCCCT
1 CCAAA-ACACACCAGATGCTCACACGAACCAATCCCT
36760825 CCAAAACACACCA-ATGCTCA
1 CCAAAACACACCAGATGCTCA
36760845 TAAGAGCTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
35 10 0.21
36 34 0.72
37 3 0.06
ACGTcount: A:0.39, C:0.36, G:0.11, T:0.14
Consensus pattern (36 bp):
CCAAAACACACCAGATGCTCACACGAACCAATCCCT
Found at i:36760908 original size:35 final size:35
Alignment explanation
Indices: 36760820--36760908 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
36760810 CACGAACCAA
*
36760820 TCCCTCCAAAACACACCAATGCTCATAAGAGCTAG
1 TCCCTCCGAAACACACCAATGCTCATAAGAGCTAG
** *
36760855 TCCAACTGAAACACACCAATGCTCCA-AAGAGCTAG
1 TCCCTCCGAAACACACCAATGCT-CATAAGAGCTAG
* *
36760890 TCCCTCCGAGACATACCAA
1 TCCCTCCGAAACACACCAA
36760909 ACAGAGAGTA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 42 0.95
36 2 0.05
ACGTcount: A:0.37, C:0.35, G:0.12, T:0.16
Consensus pattern (35 bp):
TCCCTCCGAAACACACCAATGCTCATAAGAGCTAG
Found at i:36770647 original size:29 final size:29
Alignment explanation
Indices: 36770605--36770661 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
36770595 TTATGGAAGA
* * *
36770605 GGTGGAGAACTTGTTCGTTGAGAGTTCGC
1 GGTGAAGAACTTGTTCATTGAGAATTCGC
36770634 GGTGAAGAACTTGTTCATTGAGAATTCG
1 GGTGAAGAACTTGTTCATTGAGAATTCG
36770662 TGTCAAGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.33, T:0.32
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCATTGAGAATTCGC
Found at i:36771817 original size:2 final size:2
Alignment explanation
Indices: 36771812--36771854 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
36771802 AGAATTAGAA
36771812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36771854 A
1 A
36771855 CAAATTTAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36772373 original size:31 final size:31
Alignment explanation
Indices: 36772338--36772397 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
36772328 AGCCACTAAA
* *
36772338 GTTTTAAATAATTTTTATTTTGGTCACTCAT
1 GTTTTAAATAATTTCTATTTTAGTCACTCAT
* *
36772369 GTTTTATATCATTTCTATTTTAGTCACTC
1 GTTTTAAATAATTTCTATTTTAGTCACTC
36772398 TCTATTCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.55
Consensus pattern (31 bp):
GTTTTAAATAATTTCTATTTTAGTCACTCAT
Found at i:36773412 original size:31 final size:31
Alignment explanation
Indices: 36773376--36773434 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
36773366 ACTTAATAGA
* *
36773376 GAGTGACCAAAATAGAAACGATCTAAAACGT
1 GAGTGACAAAAATAAAAACGATCTAAAACGT
**
36773407 GAGTGACAAAAATAAAAATTATCTAAAA
1 GAGTGACAAAAATAAAAACGATCTAAAA
36773435 TGTTAGTAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (31 bp):
GAGTGACAAAAATAAAAACGATCTAAAACGT
Found at i:36774706 original size:17 final size:17
Alignment explanation
Indices: 36774684--36774720 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
36774674 CAGAAAAATG
*
36774684 GGCTCACATGCCCATGT
1 GGCTCACACGCCCATGT
36774701 GGCTCACACGCCCATGT
1 GGCTCACACGCCCATGT
36774718 GGC
1 GGC
36774721 CCACTCGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.38, G:0.27, T:0.19
Consensus pattern (17 bp):
GGCTCACACGCCCATGT
Found at i:36781869 original size:212 final size:212
Alignment explanation
Indices: 36781502--36781928 Score: 845
Period size: 212 Copynumber: 2.0 Consensus size: 212
36781492 ATTCATAAGG
36781502 GATAAGTGCATAAGGGATTCAACAAGGATTAAACAAAGCCCAACTATCTATTTTGATATTAACAA
1 GATAAGTGCATAAGGGATTCAACAAGGATTAAACAAAGCCCAACTATCTATTTTGATATTAACAA
*
36781567 ACTCCTTAAGTTAGGAGTAGTTAATAAATAATGGCAAATTCAGAGGCAACACCACAACTTCAATG
66 ACTCCTTAAGTTAGGAGTAGTTAATAAATAATGGCAAATTCAGAGGCAACACCACAACTTAAATG
36781632 CTTTTCTGGGTCATTTTATTTGTCAACCTATTTATGTTTTTAATTGTTTCAAGTGTAAAGTCTAA
131 CTTTTCTGGGTCATTTTATTTGTCAACCTATTTATGTTTTTAATTGTTTCAAGTGTAAAGTCTAA
36781697 AAACGTACCAGTTGTGA
196 AAACGTACCAGTTGTGA
36781714 GATAAGTGCATAAGGGATTCAACAAGGATTAAACAAAGCCCAACTATCTATTTTGATATTAACAA
1 GATAAGTGCATAAGGGATTCAACAAGGATTAAACAAAGCCCAACTATCTATTTTGATATTAACAA
36781779 ACTCCTTAAGTTAGGAGTAGTTAATAAATAATGGCAAATTCAGAGGCAACACCACAACTTAAATG
66 ACTCCTTAAGTTAGGAGTAGTTAATAAATAATGGCAAATTCAGAGGCAACACCACAACTTAAATG
36781844 CTTTTCTGGGTCATTTTATTTGTCAACCTATTTATGTTTTTAATTGTTTCAAGTGTAAAGTCTAA
131 CTTTTCTGGGTCATTTTATTTGTCAACCTATTTATGTTTTTAATTGTTTCAAGTGTAAAGTCTAA
36781909 AAACGTACCAGTTGTGA
196 AAACGTACCAGTTGTGA
36781926 GAT
1 GAT
36781929 CGTTGCCACC
Statistics
Matches: 214, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 214 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (212 bp):
GATAAGTGCATAAGGGATTCAACAAGGATTAAACAAAGCCCAACTATCTATTTTGATATTAACAA
ACTCCTTAAGTTAGGAGTAGTTAATAAATAATGGCAAATTCAGAGGCAACACCACAACTTAAATG
CTTTTCTGGGTCATTTTATTTGTCAACCTATTTATGTTTTTAATTGTTTCAAGTGTAAAGTCTAA
AAACGTACCAGTTGTGA
Found at i:36782192 original size:22 final size:22
Alignment explanation
Indices: 36782127--36782193 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
36782117 TTTATTGTTC
*
36782127 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
36782149 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
36782171 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
36782193 A
1 A
36782194 TGACTCTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:36791640 original size:22 final size:21
Alignment explanation
Indices: 36791605--36791645 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
36791595 TCTCATCATT
*
36791605 TTTACCCATGATAACTTTGGC
1 TTTACCCATAATAACTTTGGC
*
36791626 TTTACCCCATAATAATTTTG
1 TTTA-CCCATAATAACTTTG
36791646 TCTTGTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (21 bp):
TTTACCCATAATAACTTTGGC
Found at i:36793160 original size:40 final size:40
Alignment explanation
Indices: 36793110--36793239 Score: 210
Period size: 40 Copynumber: 3.2 Consensus size: 40
36793100 TTTAAAAATT
36793110 TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
36793150 TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
* *
36793190 TTTAAAAAAAATT--AAAAAGTATGTAAAAAATATTTTAAAA
1 -TT-AAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
36793230 TTAAAAAAAT
1 TTAAAAAAAT
36793240 AAATATATTT
Statistics
Matches: 86, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
38 8 0.09
39 2 0.02
40 65 0.76
41 2 0.02
42 9 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (40 bp):
TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:36793230 original size:10 final size:11
Alignment explanation
Indices: 36793097--36793189 Score: 65
Period size: 11 Copynumber: 8.9 Consensus size: 11
36793087 GGCCCATTTT
36793097 TATTTT-AAAA
1 TATTTTAAAAA
36793107 -ATTTTAAAAA
1 TATTTTAAAAA
* **
36793117 AATTAAAAAAA
1 TATTTTAAAAA
36793128 GTATTTTAAAAA
1 -TATTTTAAAAA
36793140 TATTTT--AAA
1 TATTTTAAAAA
36793149 -A--TTAAAAA
1 TATTTTAAAAA
* **
36793157 AATTAAAAAAA
1 TATTTTAAAAA
36793168 GTATTTTAAAAA
1 -TATTTTAAAAA
36793180 TATTTTAAAA
1 TATTTTAAAA
36793190 TTTAAAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
6 2 0.03
8 4 0.06
9 9 0.14
10 4 0.06
11 29 0.45
12 16 0.25
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:36794267 original size:29 final size:29
Alignment explanation
Indices: 36794182--36794269 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
36794172 GATTAAATCA
* *
36794182 AAATTAAAGTTTCAAATATACATTTAAACC
1 AAATTAAAGTTT-AAATATACAATTACACC
* * * *
36794212 ACAATTAGAGTTTTACATGTATAATTACACC
1 A-AATTAAAG-TTTAAATATACAATTACACC
*
36794243 AAATTAAAGTTTATATATACAATTACA
1 AAATTAAAGTTTAAATATACAATTACA
36794270 TATTAAATCA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
29 15 0.33
30 8 0.17
31 20 0.43
32 3 0.07
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (29 bp):
AAATTAAAGTTTAAATATACAATTACACC
Found at i:36800980 original size:17 final size:17
Alignment explanation
Indices: 36800958--36800993 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
36800948 TAGATGTGAT
36800958 AAAAACATTCTTGAAAA
1 AAAAACATTCTTGAAAA
* *
36800975 AAAAACATTTTTTAAAA
1 AAAAACATTCTTGAAAA
36800992 AA
1 AA
36800994 CGCTTTCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAAACATTCTTGAAAA
Found at i:36801102 original size:22 final size:22
Alignment explanation
Indices: 36801051--36801143 Score: 75
Period size: 22 Copynumber: 4.3 Consensus size: 22
36801041 CATTTGTTTA
* * *
36801051 TTATTATTATTTAAT-ATTGTT
1 TTATTTTTAATTAATAATTATT
* * *
36801072 TTAAGTTTTAATTAATAAATATG
1 TT-ATTTTTAATTAATAATTATT
* *
36801095 TTATTTTTAAGTT-AT-TTTGTT
1 TTATTTTTAA-TTAATAATTATT
36801116 TTATTTTTAATTAATAATTATT
1 TTATTTTTAATTAATAATTATT
36801138 TTATTT
1 TTATTT
36801144 ATATAAATAA
Statistics
Matches: 54, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
20 2 0.04
21 16 0.30
22 29 0.54
23 7 0.13
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.63
Consensus pattern (22 bp):
TTATTTTTAATTAATAATTATT
Found at i:36809384 original size:43 final size:43
Alignment explanation
Indices: 36809334--36809453 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 43
36809324 GGTCATGTTC
*
36809334 TTTAGCGGCGCTTTTTCCAAAAATGCCG-TAATAGATT-CTGACT
1 TTTAGCGGCGCTTTTTCCAAAAACGCCGCTAAT-GATTGC-GACT
* * *
36809377 TTTAGCGGCGC-TTTTCTCACAAACGCCGCTAGTGTTTGGCGACT
1 TTTAGCGGCGCTTTTTC-CAAAAACGCCGCTAATGATT-GCGACT
* *
36809421 TTTAGCGGCGCTTTTTCGAAAAACGCCACTAAT
1 TTTAGCGGCGCTTTTTCCAAAAACGCCGCTAAT
36809454 TTTAGAATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
42 5 0.08
43 23 0.36
44 30 0.47
45 6 0.09
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTTCCAAAAACGCCGCTAATGATTGCGACT
Found at i:36812307 original size:111 final size:110
Alignment explanation
Indices: 36812105--36812387 Score: 417
Period size: 111 Copynumber: 2.6 Consensus size: 110
36812095 AAGGAAAATG
* * *
36812105 TTTTAAAATAAGGCAATATTTCGCGTTTGGGAAACTCGAGAAAACATGCCCTAAGGTGCTGGGTG
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
* * * * *
36812170 TTGATTTTTCTCGTCCAACCATATGGCTTAATATCCTTTTAAAAC
66 TTGATTTTCCTCGTCAAACCAAATGGCTTAATATCCTTCTAAAAA
36812215 TTTTAAGAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
1 TTTTAA-AATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
*
36812280 GTTGATTTTCCTCGTTAAACCAAATGGCTTAATATCCTTCTAAAAA
65 GTTGATTTTCCTCGTCAAACCAAATGGCTTAATATCCTTCTAAAAA
* * * * *
36812326 TTTCAAAATAAGGCAATGTTTTGCATTT-GGAAATTCGAG-GAACGTGCCCTAAGGTGTTGGGT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
36812388 TTCGGTTTCT
Statistics
Matches: 158, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
108 20 0.13
109 11 0.07
110 27 0.17
111 100 0.63
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (110 bp):
TTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
TTGATTTTCCTCGTCAAACCAAATGGCTTAATATCCTTCTAAAAA
Found at i:36821830 original size:21 final size:21
Alignment explanation
Indices: 36821806--36821936 Score: 122
Period size: 21 Copynumber: 6.3 Consensus size: 21
36821796 GTGTTTTACT
* *
36821806 TTCTGTTTAGCTCTTTTGAGC
1 TTCTGTTCAGCTCTTATGAGC
* *
36821827 TTCTGTTCAGTTCTTATAAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
36821848 TTCTGTTCAACTTTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
36821869 TTATGTTCAGCTCTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
36821890 TTCTGTTTAGCTCTCATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
36821911 TTCTATTAAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTATGAGC
36821930 TTCTGTT
1 TTCTGTT
36821937 GGCGTATCTG
Statistics
Matches: 89, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
19 10 0.11
20 1 0.01
21 78 0.88
ACGTcount: A:0.16, C:0.18, G:0.17, T:0.49
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:36822183 original size:10 final size:8
Alignment explanation
Indices: 36822168--36822194 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
36822158 TGATGGCATA
36822168 TGATATAT
1 TGATATAT
36822176 TGATATAT
1 TGATATAT
36822184 TGATATAT
1 TGATATAT
36822192 TGA
1 TGA
36822195 AATGGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (8 bp):
TGATATAT
Found at i:36823903 original size:10 final size:10
Alignment explanation
Indices: 36823888--36823975 Score: 60
Period size: 10 Copynumber: 8.9 Consensus size: 10
36823878 AATTTATGAA
36823888 TTTAATAATT
1 TTTAATAATT
* *
36823898 TTTAATTACT
1 TTTAATAATT
*
36823908 TTTAA-GA-T
1 TTTAATAATT
36823916 TTT-ATATATT
1 TTTAATA-ATT
36823926 TTT-ATAAATT
1 TTTAAT-AATT
36823936 TTTAATAATT
1 TTTAATAATT
*
36823946 TTTACA-ACTT
1 TTTA-ATAATT
*
36823956 TTTAAAAATT
1 TTTAATAATT
36823966 TTATAATAAT
1 TT-TAATAAT
36823976 ATAAGAACTT
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
7 1 0.02
8 4 0.06
9 3 0.05
10 45 0.71
11 10 0.16
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (10 bp):
TTTAATAATT
Found at i:36831821 original size:13 final size:12
Alignment explanation
Indices: 36831772--36831822 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
36831762 TTGCTATTGT
*
36831772 AATTTTTTAATAA
1 AATTTTTTTAT-A
36831785 AATTTAATTTTA-A
1 AATTT--TTTTATA
36831798 AATTTTTTTATA
1 AATTTTTTTATA
36831810 AATTTTGTTTATA
1 AATTTT-TTTATA
36831823 GTTTTTATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 5 0.15
12 7 0.21
13 17 0.52
15 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
AATTTTTTTATA
Found at i:36836673 original size:138 final size:136
Alignment explanation
Indices: 36836289--36836674 Score: 442
Period size: 141 Copynumber: 2.8 Consensus size: 136
36836279 GATAAAATCG
* * * *
36836289 CAATTATTTAACCATCTAACTAAAGGAGCTAATATATT-AAAAAT-ATT---AATTAAAAA-TTT
1 CAATTATCTAACCATCTAACCAAA-GAACTAATATATTAAAAAATAATTAAAAATTAAAAAGCTT
* * * *
36836348 GAAGCAACATGAAATAAAAAATATACAAATGGGAGTAGTAGAAGAATCGAACTCGAAACTCAAGG
65 GAAGCAACATGAAAT-AAAAA-ATACAAATGTGAGTAGAAGAGGAATCAAACTCGAAACTCAAGG
36836413 ATGTAATTA
128 ATGTAATTA
* * * * *
36836422 CAATTATCTAACCATCTAACGAAAAAACTATAAATACTAAAAAATATTAATTAAAATTTTAAAAA
1 CAATTATCTAACCATCTAACCAAAGAACTA-ATATA-TTAAAAA-A-TAATTAAAA-ATTAAAAA
* * *
36836487 GCTTGAAGCAACATGAAATAAAAAATACAAATATGAGTAAAAGAGGAATCAAACTCGAGACTCAA
61 GCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAGGAATCAAACTCGAAACTCAA
*
36836552 GGATGTGATTA
126 GGATGTAATTA
*
36836563 CAATTATCTAACCATCTAACCAAAGAACTAATATGTTAAAACAATAATTAAAAACTTAAAAAGCT
1 CAATTATCTAACCATCTAACCAAAGAACTAATATATTAAAA-AATAATTAAAAA-TTAAAAAGCT
* * * *
36836628 TAAAGCAACATGAAATTAAAAATACAAATGTGAGTAGGAGGGGAATC
64 TGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAGGAATC
36836675 GAACCCAAGA
Statistics
Matches: 212, Mismatches: 28, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
132 4 0.02
133 26 0.12
134 1 0.00
135 4 0.02
136 1 0.00
137 1 0.00
138 63 0.30
139 6 0.03
140 4 0.02
141 73 0.34
142 12 0.06
143 17 0.08
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (136 bp):
CAATTATCTAACCATCTAACCAAAGAACTAATATATTAAAAAATAATTAAAAATTAAAAAGCTTG
AAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAGGAATCAAACTCGAAACTCAAGGATG
TAATTA
Found at i:36836692 original size:138 final size:136
Alignment explanation
Indices: 36836289--36836693 Score: 430
Period size: 138 Copynumber: 2.9 Consensus size: 136
36836279 GATAAAATCG
* * * *
36836289 CAATTATTTAACCATCTAACTAAAGGAGCTAATATATT-AAAAAT-ATT---AATTAAAAA-TTT
1 CAATTATCTAACCATCTAACCAAA-GAACTAATATATTAAAAAATAATTAAAAATTAAAAAGCTT
* * * *
36836348 GAAGCAACATGAAATAAAAAATATACAAATGGGAGTAGTAGAAGAATCGAACTCGAA-ACTCAAG
65 GAAGCAACATGAAAT-AAAAA-ATACAAATGTGAGTAGAAGAGGAATCGAAC-CCAAGACTCAAG
36836412 GATGTAATTA
127 GATGTAATTA
* * * * *
36836422 CAATTATCTAACCATCTAACGAAAAAACTATAAATACTAAAAAATATTAATTAAAATTTTAAAAA
1 CAATTATCTAACCATCTAACCAAAGAACTA-ATATA-TTAAAAA-A-TAATTAAAA-ATTAAAAA
* * * * *
36836487 GCTTGAAGCAACATGAAATAAAAAATACAAATATGAGTAAAAGAGGAATCAAACTCGAGACTCAA
61 GCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAGGAATCGAACCCAAGACTCAA
*
36836552 GGATGTGATTA
126 GGATGTAATTA
*
36836563 CAATTATCTAACCATCTAACCAAAGAACTAATATGTTAAAACAATAATTAAAAACTTAAAAAGCT
1 CAATTATCTAACCATCTAACCAAAGAACTAATATATTAAAA-AATAATTAAAAA-TTAAAAAGCT
* * * *
36836628 TAAAGCAACATGAAATTAAAAATACAAATGTGAGTAGGAGGGGAATCGAACCCAAGACAT-AAGG
64 TGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAGGAATCGAACCCAAGAC-TCAAGG
36836692 AT
128 AT
36836694 AAAATACTAA
Statistics
Matches: 224, Mismatches: 33, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
132 4 0.02
133 26 0.12
134 1 0.00
135 4 0.02
136 1 0.00
137 1 0.00
138 77 0.34
139 7 0.03
140 5 0.02
141 69 0.31
142 12 0.05
143 17 0.08
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (136 bp):
CAATTATCTAACCATCTAACCAAAGAACTAATATATTAAAAAATAATTAAAAATTAAAAAGCTTG
AAGCAACATGAAATAAAAAATACAAATGTGAGTAGAAGAGGAATCGAACCCAAGACTCAAGGATG
TAATTA
Found at i:36837296 original size:31 final size:31
Alignment explanation
Indices: 36837256--36837324 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
36837246 TTTGGGTTAG
*
36837256 GACTGAAATTTCA-AAATTCAAAAAGTACAAA
1 GACT-AAAATTCACAAATTCAAAAAGTACAAA
* * *
36837287 GACTAAAATTGACTAGTTCAAAAAGTACAAA
1 GACTAAAATTCACAAATTCAAAAAGTACAAA
36837318 GACTAAA
1 GACTAAA
36837325 TTTGTTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.54, C:0.13, G:0.12, T:0.22
Consensus pattern (31 bp):
GACTAAAATTCACAAATTCAAAAAGTACAAA
Found at i:36852710 original size:3 final size:3
Alignment explanation
Indices: 36852672--36852697 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36852662 TTCATAACAA
36852672 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
36852698 ACAACAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:36857639 original size:22 final size:22
Alignment explanation
Indices: 36857611--36857653 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
36857601 ATTTCGCCTT
* *
36857611 CAATTTGGTACTTAAGGTTTTC
1 CAATTTGATACTCAAGGTTTTC
36857633 CAATTTGATACTCAAGGTTTT
1 CAATTTGATACTCAAGGTTTT
36857654 TTCCTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (22 bp):
CAATTTGATACTCAAGGTTTTC
Found at i:36859925 original size:27 final size:26
Alignment explanation
Indices: 36859895--36859959 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 26
36859885 GCTTCATTTG
* *
36859895 TTTTTCAAAAATATTTTTTATTTTTTA
1 TTTTT-AAAAATATTTTTCATTTTCTA
36859922 TTTTTATAAAATATTTTTCATTTTCTA
1 TTTTTA-AAAATATTTTTCATTTTCTA
36859949 TTTTTAAAAAT
1 TTTTTAAAAAT
36859960 TTTAAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTTAAAAATATTTTTCATTTTCTA
Found at i:36861067 original size:21 final size:21
Alignment explanation
Indices: 36861041--36861085 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
36861031 ACAAGGAAAC
36861041 CATCATCCATCTGAAATGATG
1 CATCATCCATCTGAAATGATG
36861062 CATCATCCATCTGAAATGATG
1 CATCATCCATCTGAAATGATG
36861083 CAT
1 CAT
36861086 AGTGAGCAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (21 bp):
CATCATCCATCTGAAATGATG
Found at i:36883389 original size:169 final size:171
Alignment explanation
Indices: 36883107--36883432 Score: 487
Period size: 169 Copynumber: 1.9 Consensus size: 171
36883097 GGGGGAGGGC
* *
36883107 TCTCGTCATGGTATACCCTTTGAGGGTGTCAAGTTGACAATATTTCTTCATCATTTAAGTTAGTG
1 TCTCGTCATGGTATACCCCTTAAGGGTGTCAAGTTGACAATATTTCTT-ATCATTTAAGTTAGTG
* * *
36883172 ATGTGACTTGATGTGATGGAAATACGAGGCATGTGAGTATTGGATATCAGTTGTCTTACT-AGAT
65 ATGTGACTTGATGTGATGGAAATACGAGGCATATGAGTATTGGATATCAATTATCTTACTAAG-T
**
36883236 GATAATTGCAAGTTGACAAATTAGTTTAAGGGAGGAGGAGGAT
129 GATAATTGCAACCTGACAAATTAGTTTAAGGGAGGAGGAGGAT
* *
36883279 TCTCGTCATGGTATACCCCTTAAGGGTGTTAGGTTGACAATATTTC-T-TCATTTAAGTTAGTGA
1 TCTCGTCATGGTATACCCCTTAAGGGTGTCAAGTTGACAATATTTCTTATCATTTAAGTTAGTGA
** * *
36883342 TGTGACTTGATGTGATGGAGGTACGGGGCATATGAGTGTTGGATATCAATTATCTTACTAAGTGA
66 TGTGACTTGATGTGATGGAAATACGAGGCATATGAGTATTGGATATCAATTATCTTACTAAGTGA
*
36883407 TAATTGCAACCTGATAAATTAGTTTA
131 TAATTGCAACCTGACAAATTAGTTTA
36883433 GTTTGACATA
Statistics
Matches: 139, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
169 94 0.68
170 2 0.01
171 1 0.01
172 42 0.30
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.36
Consensus pattern (171 bp):
TCTCGTCATGGTATACCCCTTAAGGGTGTCAAGTTGACAATATTTCTTATCATTTAAGTTAGTGA
TGTGACTTGATGTGATGGAAATACGAGGCATATGAGTATTGGATATCAATTATCTTACTAAGTGA
TAATTGCAACCTGACAAATTAGTTTAAGGGAGGAGGAGGAT
Found at i:36885498 original size:101 final size:101
Alignment explanation
Indices: 36885323--36885513 Score: 364
Period size: 101 Copynumber: 1.9 Consensus size: 101
36885313 GGTGGTAGCT
36885323 TTGTTTTCTTTTCAATCTCTTCATGCACCTTGTTTGAGTTTTGAGAATGTAACCTGTAAAATTGT
1 TTGTTTTCTTTTCAATCTCTTCATGCACCTTGTTTGAGTTTTGAGAATGTAACCTGTAAAATTGT
36885388 TATGTCCTCATTGTTAGTAAATTGAAGAATGTAACC
66 TATGTCCTCATTGTTAGTAAATTGAAGAATGTAACC
* *
36885424 TTGTTTTCTTTTCAATCTCTTTATGCACCTTGTTTGGGTTTTGAGAATGTAACCTGTAAAATTGT
1 TTGTTTTCTTTTCAATCTCTTCATGCACCTTGTTTGAGTTTTGAGAATGTAACCTGTAAAATTGT
36885489 TATGTCCTCATTGTTAGTAAATTGA
66 TATGTCCTCATTGTTAGTAAATTGA
36885514 TTAATGCCTG
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 88 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (101 bp):
TTGTTTTCTTTTCAATCTCTTCATGCACCTTGTTTGAGTTTTGAGAATGTAACCTGTAAAATTGT
TATGTCCTCATTGTTAGTAAATTGAAGAATGTAACC
Found at i:36891543 original size:21 final size:23
Alignment explanation
Indices: 36891501--36891543 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
36891491 TAATTAATCA
*
36891501 TAAATAGAAGCAAATCTCTTTTC
1 TAAATAGAAGCAAATATCTTTTC
*
36891524 TAAA-AGAAG-AAATATGTTTT
1 TAAATAGAAGCAAATATCTTTT
36891544 AAAAAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (23 bp):
TAAATAGAAGCAAATATCTTTTC
Found at i:36891617 original size:22 final size:20
Alignment explanation
Indices: 36891580--36891619 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
36891570 AAGAGCAGTA
*
36891580 CAAAAAAGGATAAATCAAAT
1 CAAAAAAGAATAAATCAAAT
36891600 CAAAAAAGAAATAGAATCAA
1 CAAAAAAG-AATA-AATCAA
36891620 CAATTTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.68, C:0.10, G:0.10, T:0.12
Consensus pattern (20 bp):
CAAAAAAGAATAAATCAAAT
Found at i:36894749 original size:18 final size:19
Alignment explanation
Indices: 36894711--36894751 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
36894701 ATCAAAACTC
36894711 GTTTCTCCAAAGTTTTAAA
1 GTTTCTCCAAAGTTTTAAA
*
36894730 GTTTCTCCAAA-TTTTCAA
1 GTTTCTCCAAAGTTTTAAA
36894748 GTTT
1 GTTT
36894752 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (19 bp):
GTTTCTCCAAAGTTTTAAA
Found at i:36895001 original size:15 final size:15
Alignment explanation
Indices: 36894981--36895037 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
36894971 ATTCAATATT
36894981 AATATTTTAATAATA
1 AATATTTTAATAATA
*
36894996 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
36895015 AATATATTAATAATA
1 AATATTTTAATAATA
36895030 AATATTTT
1 AATATTTT
36895038 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:36897020 original size:45 final size:45
Alignment explanation
Indices: 36896951--36897053 Score: 161
Period size: 45 Copynumber: 2.3 Consensus size: 45
36896941 TAGTACCTAA
* *
36896951 GTACTCTATTCAAAGTTTACCAATGTAAACTACTTGGATTACTTGT
1 GTAC-CTATTCAAAGCTTACCAATGTAAACTACTTAGATTACTTGT
* *
36896997 GTACCTATTCAAAGCTTGCCAATGTAAATTACTTAGATTACTTGT
1 GTACCTATTCAAAGCTTACCAATGTAAACTACTTAGATTACTTGT
36897042 GTACCTATTCAA
1 GTACCTATTCAA
36897054 TGTCCCAACA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 49 0.92
46 4 0.08
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (45 bp):
GTACCTATTCAAAGCTTACCAATGTAAACTACTTAGATTACTTGT
Found at i:36898408 original size:57 final size:57
Alignment explanation
Indices: 36898318--36898494 Score: 223
Period size: 57 Copynumber: 3.1 Consensus size: 57
36898308 GAATTAGTGA
*
36898318 AAAATGGAGAAATGGGAAATCATTTGGAAATGATTAT-GTCTTTCTCCAAAATGAAAATG
1 AAAATGGAGAAAT-GGAAA-CATTTGAAAATGATTATGGT-TTTCTCCAAAATGAAAATG
* *
36898377 AAAATGGAGAAATAGAAACATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAATA
1 AAAATGGAGAAATGGAAACATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAATG
* ** * **
36898434 AAAATAGAGAAATGGAATTATTT-AGAAATGAATATGGTTTTCTATAAAATGAAAATG
1 AAAATGGAGAAATGGAAACATTTGA-AAATGATTATGGTTTTCTCCAAAATGAAAATG
36898491 AAAA
1 AAAA
36898495 ATAAATTTAT
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
56 1 0.01
57 85 0.81
58 6 0.06
59 13 0.12
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.29
Consensus pattern (57 bp):
AAAATGGAGAAATGGAAACATTTGAAAATGATTATGGTTTTCTCCAAAATGAAAATG
Found at i:36900351 original size:17 final size:17
Alignment explanation
Indices: 36900329--36900369 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
36900319 GAAATAAAAC
36900329 AAAATATATTTTCATCA
1 AAAATATATTTTCATCA
36900346 AAAATATATTTTCATCA
1 AAAATATATTTTCATCA
36900363 AAAATAT
1 AAAATAT
36900370 CAAATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATATTTTCATCA
Found at i:36903627 original size:43 final size:43
Alignment explanation
Indices: 36903566--36903648 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
36903556 AGTTGGAAGA
36903566 CAACTCCTTTAGTGTTCCACTTTCATGTGTTGTAGTAGCCTTC
1 CAACTCCTTTAGTGTTCCACTTTCATGTGTTGTAGTAGCCTTC
36903609 CAACTCCTTTAGTGTTCCACTTTCATGTGTTGTAGTAGCC
1 CAACTCCTTTAGTGTTCCACTTTCATGTGTTGTAGTAGCC
36903649 ATCATGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (43 bp):
CAACTCCTTTAGTGTTCCACTTTCATGTGTTGTAGTAGCCTTC
Found at i:36920004 original size:40 final size:39
Alignment explanation
Indices: 36919946--36920029 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 39
36919936 AATTTATTTT
*
36919946 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATAAAAAAAAGTATTTTAAAAATATTTTAAAATTA
*
36919985 AAAAATAATAAAAAAGTATTTTAAAATTATTTTAAAATTA
1 AAAAATAA-AAAAAAGTATTTTAAAAATATTTTAAAATTA
36920025 AAAAA
1 AAAAA
36920030 ATTTTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
39 7 0.17
40 35 0.83
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (39 bp):
AAAAATAAAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:36920039 original size:40 final size:39
Alignment explanation
Indices: 36919946--36920040 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 39
36919936 AATTTATTTT
*
36919946 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTA
* *
36919985 AAAAATAATAAAAAAGTATTTTAAAATTATTTTAAAATTAA
1 AAAAAT-TTAAAAAAGTATTTTAAAAATATTTTAAAATT-A
36920026 AAAAATTTTAAAAAA
1 AAAAA-TTTAAAAAA
36920041 TAAATATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 6 0.12
40 29 0.59
41 13 0.27
42 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (39 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:36920563 original size:19 final size:19
Alignment explanation
Indices: 36920520--36920564 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
36920510 TAATTTTTTT
36920520 AAAAAATTATTAAAAATGC
1 AAAAAATTATTAAAAATGC
* *
36920539 ACAAAATT-TTATAAAATGG
1 AAAAAATTATTA-AAAATGC
36920558 AAAAAAT
1 AAAAAAT
36920565 CCAATTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (19 bp):
AAAAAATTATTAAAAATGC
Found at i:36920687 original size:15 final size:15
Alignment explanation
Indices: 36920650--36920689 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
36920640 CCCTTTTCCC
36920650 TTTTCTTT-TTTTTA
1 TTTTCTTTCTTTTTA
36920664 TTTAT-TTTCTTTTTA
1 TTT-TCTTTCTTTTTA
36920679 TTTTCTTTCTT
1 TTTTCTTTCTT
36920690 CACATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTCTTTTTA
Found at i:36920748 original size:27 final size:26
Alignment explanation
Indices: 36920718--36920770 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
36920708 TCTAGTTATA
*
36920718 CTTT-TTTCCATTTTCATTTTCATTTTC
1 CTTTCTTTCC-TTTT-ATTTTAATTTTC
36920745 CTTTCGTTTCCTTTTATTTTAATTTT
1 CTTTC-TTTCCTTTTATTTTAATTTT
36920771 TTTCCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 14 0.61
28 4 0.17
29 5 0.22
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (26 bp):
CTTTCTTTCCTTTTATTTTAATTTTC
Found at i:36923656 original size:21 final size:22
Alignment explanation
Indices: 36923632--36923673 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
36923622 TTTAAAATTT
36923632 TAATTAAT-ATTTTTTTAAAAA
1 TAATTAATAATTTTTTTAAAAA
*
36923653 TAATTATTCAATTTTTTTAAA
1 TAATTAAT-AATTTTTTTAAA
36923674 GGTTGATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTAATAATTTTTTTAAAAA
Found at i:36923718 original size:6 final size:7
Alignment explanation
Indices: 36923691--36923717 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
36923681 GGATTTATCT
36923691 TAAAAAA
1 TAAAAAA
36923698 TAAAAAA
1 TAAAAAA
36923705 TAAAAAA
1 TAAAAAA
36923712 TAAAAA
1 TAAAAA
36923718 TGACCAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:36928289 original size:22 final size:21
Alignment explanation
Indices: 36928264--36928313 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
36928254 TTATCATTTC
* *
36928264 AATAAAAAATATTTTATATTAA
1 AATAAAAAATATATAAT-TTAA
*
36928286 AATAATAAAGTATATAATTTAA
1 AATAA-AAAATATATAATTTAA
36928308 AATAAA
1 AATAAA
36928314 TTTTATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 14 0.58
23 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AATAAAAAATATATAATTTAA
Found at i:36931346 original size:30 final size:30
Alignment explanation
Indices: 36931294--36931411 Score: 195
Period size: 29 Copynumber: 4.0 Consensus size: 30
36931284 TACTTTTTAA
36931294 TTTTTTAATTTTAAAATA-TTTTAAAATAT
1 TTTTTTAATTTTAAAATATTTTTAAAATAT
36931323 TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATA-T
*
36931354 TTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTAAAATATTTTTAAAATAT
*
36931384 TTTTTTAATTTTTAAA-ATTTTTAAAATA
1 TTTTTTAATTTTAAAATATTTTTAAAATA
36931412 AAAATGGCCC
Statistics
Matches: 85, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
29 30 0.35
30 25 0.29
31 30 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAT
Found at i:36931360 original size:31 final size:31
Alignment explanation
Indices: 36931294--36931411 Score: 199
Period size: 31 Copynumber: 3.9 Consensus size: 31
36931284 TACTTTTTAA
36931294 TTTTTTAATTTTAAAATA-TTTTAAAATA-T
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
36931323 TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
36931354 TTTTTTAATTTTAAAATATTTTTAAAATAC-
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
*
36931384 TTTTTTAATTTTTAAA-ATTTTTAAAATA
1 TTTTTTAATTTTAAAATATTTTTAAAATA
36931412 AAAATGGCCC
Statistics
Matches: 86, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
29 30 0.35
30 25 0.29
31 31 0.36
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:36931404 original size:8 final size:9
Alignment explanation
Indices: 36931302--36931410 Score: 56
Period size: 9 Copynumber: 11.0 Consensus size: 9
36931292 AATTTTTTAA
36931302 TTTTAAAAT
1 TTTTAAAAT
36931311 ATTTTAAAATAT
1 -TTTT-AAA-AT
**
36931323 TTTTTTAAT
1 TTTTAAAAT
*
36931332 TTTAAAATAT
1 TTTTAAA-AT
36931342 TTTTAAAATACT
1 TTTT-AAA-A-T
**
36931354 TTTTTTAAT
1 TTTTAAAAT
*
36931363 TTTAAAATAT
1 TTTTAAA-AT
36931373 TTTTAAAAT
1 TTTTAAAAT
**
36931382 ACTTTTTTAAT
1 --TTTTAAAAT
36931393 TTTTAAAAT
1 TTTTAAAAT
36931402 TTTTAAAAT
1 TTTTAAAAT
36931411 AAAAATGGCC
Statistics
Matches: 75, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
9 29 0.39
10 19 0.25
11 20 0.27
12 7 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:36931785 original size:62 final size:62
Alignment explanation
Indices: 36931703--36931826 Score: 185
Period size: 62 Copynumber: 2.0 Consensus size: 62
36931693 GCATGGTATT
* * * * * **
36931703 ACTTGATCTCATTTATAATCTTTCTTGATGTAGCGCTTTCGTTTTATGAATTTGTGCTTCAA
1 ACTTGATCTCACTTACAATCTTTCTTGATGAAGCGCTCTCGCTTTATGAATTTAAGCTTCAA
36931765 ACTTGATCTCACTTACAATCTTTCTTGATGAAGCGCTCTCGCTTTATGAATTTAAGCTTCAA
1 ACTTGATCTCACTTACAATCTTTCTTGATGAAGCGCTCTCGCTTTATGAATTTAAGCTTCAA
36931827 GAGGCCTCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (62 bp):
ACTTGATCTCACTTACAATCTTTCTTGATGAAGCGCTCTCGCTTTATGAATTTAAGCTTCAA
Found at i:36932717 original size:16 final size:15
Alignment explanation
Indices: 36932681--36932716 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
36932671 CAAAATCAAG
36932681 ATTTTTACAACATCC
1 ATTTTTACAACATCC
* *
36932696 ATTTTTACAATATTC
1 ATTTTTACAACATCC
36932711 ATTTTT
1 ATTTTT
36932717 TTCTTTATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTTACAACATCC
Found at i:36933005 original size:18 final size:18
Alignment explanation
Indices: 36932982--36933017 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36932972 TGATAAATAA
* *
36932982 ATAATTATAATTCATTTT
1 ATAATTAAAATTAATTTT
36933000 ATAATTAAAATTAATTTT
1 ATAATTAAAATTAATTTT
36933018 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAATTAAAATTAATTTT
Found at i:36933436 original size:34 final size:35
Alignment explanation
Indices: 36933392--36933458 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
36933382 CAGTAAAATA
36933392 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
36933426 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
36933459 CTGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:36933517 original size:32 final size:31
Alignment explanation
Indices: 36933439--36933523 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
36933429 TCTGTAAAAT
* *
36933439 GATTTACTGGAAAATATTTTCTGGTGTTTGGTA
1 GATTT-CT-GAAAATATTTTCTGCTGTTTGGCA
* * *
36933472 AATCTGTGTAAAATATTTTCTGCTGTTTGGCA
1 GATTTCTG-AAAATATTTTCTGCTGTTTGGCA
36933504 GATTTCCTGAAAATATTTTC
1 GATTT-CTGAAAATATTTTC
36933524 CGGAAAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
31 1 0.02
32 36 0.86
33 5 0.12
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (31 bp):
GATTTCTGAAAATATTTTCTGCTGTTTGGCA
Found at i:36936260 original size:25 final size:27
Alignment explanation
Indices: 36936205--36936272 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
36936195 AAGCTTTGAG
36936205 GAATGGAAAATGTCTGCTGCTTAGAAGA
1 GAATGGAAAATGTCT-CTGCTTAGAAGA
36936233 GAATGGAAAATGT-T-TGCTTAG-AGAA
1 GAATGGAAAATGTCTCTGCTTAGAAG-A
36936258 GAATGGAAAATGTCT
1 GAATGGAAAATGTCT
36936273 TATCAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
24 2 0.05
25 21 0.55
26 1 0.03
27 1 0.03
28 13 0.34
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.26
Consensus pattern (27 bp):
GAATGGAAAATGTCTCTGCTTAGAAGA
Found at i:36936555 original size:52 final size:52
Alignment explanation
Indices: 36936493--36936596 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
36936483 AAATTTTGTG
* * *
36936493 TTTCTAAAAAATAAGTAATTTAGTATTTATCAATTTGGAGGGTGAGTATATA
1 TTTCTAAAAAATAAGCAATTTAGCATTTATCAATTTCGAGGGTGAGTATATA
36936545 TTTCTAAAAAATAAGCAATTTAGCATTTATCAATTTCGAGGGTGAGTATATA
1 TTTCTAAAAAATAAGCAATTTAGCATTTATCAATTTCGAGGGTGAGTATATA
36936597 AAGGCAATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (52 bp):
TTTCTAAAAAATAAGCAATTTAGCATTTATCAATTTCGAGGGTGAGTATATA
Found at i:36940431 original size:21 final size:21
Alignment explanation
Indices: 36940407--36940449 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
36940397 AAAGTAATTT
36940407 AGTACAATACATTTCTCATCA
1 AGTACAATACATTTCTCATCA
*
36940428 AGTACAATACCTTTCTCATCA
1 AGTACAATACATTTCTCATCA
36940449 A
1 A
36940450 CAACCAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.33
Consensus pattern (21 bp):
AGTACAATACATTTCTCATCA
Found at i:36947363 original size:42 final size:38
Alignment explanation
Indices: 36947265--36947352 Score: 176
Period size: 38 Copynumber: 2.3 Consensus size: 38
36947255 CTAGTCTACA
36947265 TATGTGGTGTGTAGGGATGGATGGGTCTTTCAAGGTCC
1 TATGTGGTGTGTAGGGATGGATGGGTCTTTCAAGGTCC
36947303 TATGTGGTGTGTAGGGATGGATGGGTCTTTCAAGGTCC
1 TATGTGGTGTGTAGGGATGGATGGGTCTTTCAAGGTCC
36947341 TATGTGGTGTGT
1 TATGTGGTGTGT
36947353 TTGGTTGGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.15, C:0.09, G:0.40, T:0.36
Consensus pattern (38 bp):
TATGTGGTGTGTAGGGATGGATGGGTCTTTCAAGGTCC
Found at i:36951918 original size:25 final size:25
Alignment explanation
Indices: 36951869--36951919 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
36951859 AGAAATATAG
* *
36951869 TTTTCTCTTCCATTTTCATCCCTTA
1 TTTTCTCCTCCATTTTCATACCTTA
* *
36951894 TTTTCTCCTCCTTTTTCATAGCTTA
1 TTTTCTCCTCCATTTTCATACCTTA
36951919 T
1 T
36951920 AACTATAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.29, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTCTCCTCCATTTTCATACCTTA
Found at i:36958091 original size:25 final size:25
Alignment explanation
Indices: 36958063--36958133 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 25
36958053 TATAACTAGA
*
36958063 AGCTTACAAAGAGC-CTATAACGGGT
1 AGCTTACAAAGAGCAAT-TAACGGGT
*
36958088 AGC-TCCAAAGAGCAATTAACGGGT
1 AGCTTACAAAGAGCAATTAACGGGT
*
36958112 AGC-TCCGAAA-AGCAATTAACGG
1 AGCTTAC-AAAGAGCAATTAACGG
36958134 AAAGCACCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
24 35 0.83
25 7 0.17
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (25 bp):
AGCTTACAAAGAGCAATTAACGGGT
Found at i:36958107 original size:24 final size:24
Alignment explanation
Indices: 36958080--36958133 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
36958070 AAAGAGCCTA
36958080 TAACGGGTAGCTCC-AAAGAGCAAT
1 TAACGGGTAGCTCCGAAA-AGCAAT
36958104 TAACGGGTAGCTCCGAAAAGCAAT
1 TAACGGGTAGCTCCGAAAAGCAAT
36958128 TAACGG
1 TAACGG
36958134 AAAGCACCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (24 bp):
TAACGGGTAGCTCCGAAAAGCAAT
Found at i:36958863 original size:2 final size:2
Alignment explanation
Indices: 36958856--36958887 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36958846 AGATATTTTC
36958856 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
36958888 CAATAGCAGC
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:36969183 original size:16 final size:16
Alignment explanation
Indices: 36969146--36969187 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
36969136 TTAATCATAT
*
36969146 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
36969162 TT-AAATATATTATAA
1 TTAAAATATATTATAA
36969177 TTAAAATATAT
1 TTAAAATATAT
36969188 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Done.