Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 138 of 240
Found at i:42984859 original size:54 final size:54
Alignment explanation
Indices: 42984722--42984869 Score: 154
Period size: 54 Copynumber: 2.7 Consensus size: 54
42984712 CAGGTTGCGG
* * * * * * *
42984722 CTATTTGATAGGCGTTACTAGTTGAGCCTATCTCAGAGGTGCGACTAGTTGAGC
1 CTATCTGACAGGCGTGAGTAGTTGAGCCTATCTCAAAGGCGCGACTAGTTCAGC
* * * * *
42984776 CTATCTCACAGGCGCG-GCTAGTTCAGCCTATCTCACAGGCGCGGCTAGTTCAGC
1 CTATCTGACAGGCGTGAG-TAGTTGAGCCTATCTCAAAGGCGCGACTAGTTCAGC
* *
42984830 CTATCTGACAGGCGTGAGTAGTTGTGCCTAACTCAAAGGC
1 CTATCTGACAGGCGTGAGTAGTTGAGCCTATCTCAAAGGC
42984870 ACGAATGGTG
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
54 74 0.99
55 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.26
Consensus pattern (54 bp):
CTATCTGACAGGCGTGAGTAGTTGAGCCTATCTCAAAGGCGCGACTAGTTCAGC
Found at i:42988392 original size:33 final size:33
Alignment explanation
Indices: 42988355--42988418 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
42988345 ATACGGGTCG
* *
42988355 GAAGGGGCAGAGTGCTAAGGTGGATACGAGCCA
1 GAAGGAGCAGAGTACTAAGGTGGATACGAGCCA
** *
42988388 GAAGGAGTGGAGTACTGAGGTGGATACGAGC
1 GAAGGAGCAGAGTACTAAGGTGGATACGAGC
42988419 TAGGATGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.44, T:0.14
Consensus pattern (33 bp):
GAAGGAGCAGAGTACTAAGGTGGATACGAGCCA
Found at i:42988432 original size:33 final size:33
Alignment explanation
Indices: 42988372--42988443 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
42988362 CAGAGTGCTA
*
42988372 AGGTGGATACGAGCCAGAAGGAGTGGAGTACTG
1 AGGTGGATACGAGCCAGAAGGACTGGAGTACTG
* * *
42988405 AGGTGGATACGAGCTAGGATGACTGGAGTACTG
1 AGGTGGATACGAGCCAGAAGGACTGGAGTACTG
42988438 AGGTGG
1 AGGTGG
42988444 TAGTGGGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.11, G:0.43, T:0.18
Consensus pattern (33 bp):
AGGTGGATACGAGCCAGAAGGACTGGAGTACTG
Found at i:42992476 original size:22 final size:20
Alignment explanation
Indices: 42992451--42992491 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
42992441 TTTAATCAAC
*
42992451 ATTTTAATAAATCAATAAAAAA
1 ATTTAAATAAAT-AA-AAAAAA
42992473 ATTTAAATAAATAAAAAAA
1 ATTTAAATAAATAAAAAAA
42992492 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
ATTTAAATAAATAAAAAAAA
Found at i:42992485 original size:18 final size:18
Alignment explanation
Indices: 42992458--42992492 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42992448 AACATTTTAA
*
42992458 TAAATCAATAAAAAAATT
1 TAAATAAATAAAAAAATT
42992476 TAAATAAATAAAAAAAT
1 TAAATAAATAAAAAAAT
42992493 AAAATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATAAATAAAAAAATT
Found at i:42992502 original size:18 final size:18
Alignment explanation
Indices: 42992459--42992500 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
42992449 ACATTTTAAT
* *
42992459 AAATCAATAAAAAAATTT
1 AAATAAATAAAAAAATTA
42992477 AAATAAATAAAAAAA-TA
1 AAATAAATAAAAAAATTA
42992494 AAATAAA
1 AAATAAA
42992501 ATTACATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATAAATAAAAAAATTA
Found at i:42992707 original size:60 final size:60
Alignment explanation
Indices: 42992634--42992752 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
42992624 ATACTAAACT
* * *
42992634 AAACACAACAATTTATAACTTAATCATAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCATAAATTACTAACAAATTAATTTTAAAATAATTAC
*
42992694 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAATCATAAATTACTAACAAATTAATTTTAAAATAATTA
42992753 TAAAAAGCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCATAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:42992824 original size:7 final size:7
Alignment explanation
Indices: 42992814--42992839 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42992804 ACTAAACATA
42992814 AATAATT
1 AATAATT
42992821 AATAATT
1 AATAATT
42992828 AATAATT
1 AATAATT
42992835 AATAA
1 AATAA
42992840 CAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Found at i:42992930 original size:8 final size:8
Alignment explanation
Indices: 42992913--42992993 Score: 57
Period size: 8 Copynumber: 10.4 Consensus size: 8
42992903 AATACATTAC
42992913 CTTT-TTT
1 CTTTCTTT
42992920 CTTTCTTT
1 CTTTCTTT
42992928 CTTTCTTT
1 CTTTCTTT
42992936 C-TTC-TT
1 CTTTCTTT
42992942 C-TTCTCTT
1 CTTTCT-TT
42992950 C-TTC-TT
1 CTTTCTTT
*
42992956 CTTTTTTT
1 CTTTCTTT
42992964 CTTCTCCTTT
1 CTT-T-CTTT
*
42992974 CTCTCTTTT
1 CTTTC-TTT
*
42992983 CTTTCTGT
1 CTTTCTTT
42992991 CTT
1 CTT
42992994 CCGGTGGTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
6 9 0.15
7 9 0.15
8 29 0.48
9 9 0.15
10 5 0.08
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.70
Consensus pattern (8 bp):
CTTTCTTT
Found at i:42992940 original size:11 final size:11
Alignment explanation
Indices: 42992913--42992993 Score: 58
Period size: 11 Copynumber: 6.9 Consensus size: 11
42992903 AATACATTAC
*
42992913 CTTTTTTCTTT
1 CTTTCTTCTTT
42992924 CTTTCTTTCTTT
1 CTTTC-TTCTTT
42992936 C-TTCTTCTTCT
1 CTTTCTTCTT-T
42992947 CTTCTTCTTCTTT
1 C-T-TTCTTCTTT
* *
42992960 TTTTCTTC-TC
1 CTTTCTTCTTT
42992970 CTTTCTCTCTTTT
1 CTTTCT-TC-TTT
42992983 CTTTCTGTCTT
1 CTTTCT-TCTT
42992994 CCGGTGGTGA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
10 11 0.20
11 17 0.30
12 10 0.18
13 10 0.18
14 8 0.14
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.70
Consensus pattern (11 bp):
CTTTCTTCTTT
Found at i:42992951 original size:14 final size:13
Alignment explanation
Indices: 42992918--42992994 Score: 74
Period size: 13 Copynumber: 6.0 Consensus size: 13
42992908 ATTACCTTTT
42992918 TTCTTTC-T-TTC
1 TTCTTTCTTCTTC
42992929 TTTCTTTCTTCTTC
1 -TTCTTTCTTCTTC
42992943 TTCTCTTCTTCTTC
1 TTCT-TTCTTCTTC
42992957 TT-TTT-TTCTTC
1 TTCTTTCTTCTTC
*
42992968 TCCTTTCTCTCTT-
1 TTCTTTCT-TCTTC
42992981 TTCTTTCTGTCTTC
1 TTCTTTCT-TCTTC
42992995 CGGTGGTGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
11 7 0.13
12 12 0.22
13 18 0.33
14 18 0.33
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (13 bp):
TTCTTTCTTCTTC
Found at i:42993045 original size:20 final size:20
Alignment explanation
Indices: 42993020--42993063 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
42993010 TTTTTCTTCC
* *
42993020 CATTGAAGGGACAGCAGCAG
1 CATTGAAGGGACAACAACAG
42993040 CATTGAAGGGACAACAACAG
1 CATTGAAGGGACAACAACAG
42993060 CATT
1 CATT
42993064 AATGGTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (20 bp):
CATTGAAGGGACAACAACAG
Found at i:42995244 original size:40 final size:40
Alignment explanation
Indices: 42995059--42995244 Score: 211
Period size: 40 Copynumber: 4.7 Consensus size: 40
42995049 GCTCCTCGTT
* * *
42995059 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
* * *
42995099 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
42995139 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTACT-TCGCA
* * *
42995179 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-ACTTCGCA
42995220 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42995245 CATCATTCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
39 4 0.03
40 105 0.85
41 14 0.11
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
Found at i:43004752 original size:40 final size:40
Alignment explanation
Indices: 43004567--43004752 Score: 220
Period size: 40 Copynumber: 4.7 Consensus size: 40
43004557 GCTCCTCGTT
* * *
43004567 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
* *
43004607 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
43004647 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTACT-TCGCA
* * *
43004687 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-ACTTCGCA
43004728 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43004753 CATCATTCAA
Statistics
Matches: 126, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
39 4 0.03
40 107 0.85
41 14 0.11
42 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
Found at i:43006677 original size:23 final size:23
Alignment explanation
Indices: 43006641--43006688 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
43006631 TTTGGCGGTA
*
43006641 TCAAAGCTTAGGTTATTTAACAC
1 TCAAACCTTAGGTTATTTAACAC
*
43006664 TCAAACCTTTGGTTATTTAACAC
1 TCAAACCTTAGGTTATTTAACAC
43006687 TC
1 TC
43006689 GGACCGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (23 bp):
TCAAACCTTAGGTTATTTAACAC
Found at i:43022123 original size:16 final size:16
Alignment explanation
Indices: 43022102--43022133 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43022092 CCTTTCATGC
43022102 CCCAAAATTCTTAGTT
1 CCCAAAATTCTTAGTT
43022118 CCCAAAATTCTTAGTT
1 CCCAAAATTCTTAGTT
43022134 TTAGTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (16 bp):
CCCAAAATTCTTAGTT
Found at i:43022461 original size:28 final size:28
Alignment explanation
Indices: 43022421--43022481 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
43022411 CCTTTTTGGC
*
43022421 TTCTTGTTCCTTAGGTTGCCATTTCAAT
1 TTCTTGTTCCTTAGGCTGCCATTTCAAT
* * *
43022449 TTCTTGTTCCTTATGCTGTCGTTTCAAT
1 TTCTTGTTCCTTAGGCTGCCATTTCAAT
43022477 TTCTT
1 TTCTT
43022482 TCCTTTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.11, C:0.21, G:0.13, T:0.54
Consensus pattern (28 bp):
TTCTTGTTCCTTAGGCTGCCATTTCAAT
Found at i:43032850 original size:5 final size:6
Alignment explanation
Indices: 43032840--43032895 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
43032830 TTAGTTTAGC
* *
43032840 ATTTTT ATTTTA ATTTTA ATTTTA TGTTTTTA A-TTTA ATTTTTA CATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA --ATTTTA ATTTTA A-TTTTA -ATTTTA
43032891 ATTTT
1 ATTTT
43032896 TCTTTTGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
5 5 0.12
6 22 0.52
7 9 0.21
8 6 0.14
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (6 bp):
ATTTTA
Found at i:43032890 original size:14 final size:13
Alignment explanation
Indices: 43032840--43032896 Score: 66
Period size: 14 Copynumber: 4.5 Consensus size: 13
43032830 TTAGTTTAGC
43032840 ATTTTT-ATTTTA
1 ATTTTTAATTTTA
43032852 A-TTTTAATTTTA
1 ATTTTTAATTTTA
*
43032864 TGTTTTTAA-TTTA
1 -ATTTTTAATTTTA
43032877 ATTTTTACATTTTA
1 ATTTTTA-ATTTTA
43032891 ATTTTT
1 ATTTTT
43032897 CTTTTGTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 4 0.11
12 13 0.34
13 5 0.13
14 16 0.42
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (13 bp):
ATTTTTAATTTTA
Found at i:43035671 original size:17 final size:17
Alignment explanation
Indices: 43035649--43035691 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
43035639 CACGGCCTAG
*
43035649 CCACATGGTCATGTGGT
1 CCACATGGTCATGTGGC
* **
43035666 CCACATAGTTGTGTGGC
1 CCACATGGTCATGTGGC
43035683 CCACATGGT
1 CCACATGGT
43035692 TTGACTCATG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (17 bp):
CCACATGGTCATGTGGC
Found at i:43035873 original size:16 final size:16
Alignment explanation
Indices: 43035849--43035893 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
43035839 ATTTCTTACT
*
43035849 TTTACTTTTACTTTTA
1 TTTATTTTTACTTTTA
43035865 TTTATTTTTACTTTTTA
1 TTTATTTTTAC-TTTTA
*
43035882 TTT-TTTTGACTT
1 TTTATTTTTACTT
43035894 ATATGTTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 2 0.08
16 16 0.62
17 8 0.31
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTATTTTTACTTTTA
Found at i:43039132 original size:75 final size:75
Alignment explanation
Indices: 43038981--43039144 Score: 206
Period size: 75 Copynumber: 2.2 Consensus size: 75
43038971 ACTTAGATTT
* * * * *
43038981 CCCGACAACGATGACCTACCACCTTAGATTGCAAGGCAAAGATGGTTTATCGAATGAAATTTGTC
1 CCCGACAATGATGACCTACCACCTAAGATTGCAA-GCAAAGATGGTTTATCGAATCAAATCTATC
*
43039046 ATCCTGAGTTG
65 ATCCCGAGTTG
* *
43039057 CCCGAAAATGATGACCTACCA-CTAAGGATTGCCAA-CAATGATGGTTTATCGAATCAAATCTAT
1 CCCGACAATGATGACCTACCACCTAA-GATTG-CAAGCAAAGATGGTTTATCGAATCAAATCTAT
*
43039120 CATCCCGGGTTG
64 CATCCCGAGTTG
43039132 CCCGACAATGATG
1 CCCGACAATGATG
43039145 GTTCACAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
75 49 0.64
76 24 0.32
77 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (75 bp):
CCCGACAATGATGACCTACCACCTAAGATTGCAAGCAAAGATGGTTTATCGAATCAAATCTATCA
TCCCGAGTTG
Found at i:43039690 original size:14 final size:14
Alignment explanation
Indices: 43039602--43039693 Score: 103
Period size: 14 Copynumber: 6.4 Consensus size: 14
43039592 ATACACTATA
43039602 AGCTCGCACATTAGGT
1 AGCTCGCACA--AGGT
*
43039618 AGCTCGTACAAGAGT
1 AGCTCGCACAAG-GT
* *
43039633 AACTCGCACAAGGA
1 AGCTCGCACAAGGT
43039647 AGCTCGCACAAGGT
1 AGCTCGCACAAGGT
*
43039661 AGTTCGCACAAGGT
1 AGCTCGCACAAGGT
* *
43039675 AGCTCACACAAAGT
1 AGCTCGCACAAGGT
43039689 AGCTC
1 AGCTC
43039694 CAACAATGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
14 44 0.68
15 12 0.18
16 9 0.14
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (14 bp):
AGCTCGCACAAGGT
Found at i:43040267 original size:27 final size:29
Alignment explanation
Indices: 43040222--43040285 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 29
43040212 ACCTTTTCCC
* *
43040222 CTTTTTTCTCTCTATTTTTTATTGTCTTT
1 CTTTTTTCTCTCTACTTTTGATTGTCTTT
* *
43040251 CTTTTTTCTCT-T-CTTTTGCTTTTCTTT
1 CTTTTTTCTCTCTACTTTTGATTGTCTTT
43040278 CATTTTTT
1 C-TTTTTT
43040286 TCCTTTCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 12 0.40
28 7 0.23
29 11 0.37
ACGTcount: A:0.05, C:0.19, G:0.03, T:0.73
Consensus pattern (29 bp):
CTTTTTTCTCTCTACTTTTGATTGTCTTT
Found at i:43040291 original size:19 final size:19
Alignment explanation
Indices: 43040251--43040309 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 19
43040241 TATTGTCTTT
* * *
43040251 CTTTT-TTCTCTTCTTTTG
1 CTTTTCTTCTATTTTTTTC
43040269 CTTTTCTT-TCATTTTTTTC
1 CTTTTCTTCT-ATTTTTTTC
43040288 C-TTTCTTCTATTTTTCTTC
1 CTTTTCTTCTATTTTT-TTC
43040307 CTT
1 CTT
43040310 GATCTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 18 0.55
19 14 0.42
20 1 0.03
ACGTcount: A:0.03, C:0.24, G:0.02, T:0.71
Consensus pattern (19 bp):
CTTTTCTTCTATTTTTTTC
Found at i:43040353 original size:22 final size:21
Alignment explanation
Indices: 43040328--43040371 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
43040318 TTTTCCTTTT
*
43040328 TGCTTCCAATTTTCAGCAACCA
1 TGCTGCCAATTTTCAGC-ACCA
*
43040350 TGCTGCCAATTTTTAGCACCA
1 TGCTGCCAATTTTCAGCACCA
43040371 T
1 T
43040372 AATCTCTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (21 bp):
TGCTGCCAATTTTCAGCACCA
Found at i:43044979 original size:119 final size:120
Alignment explanation
Indices: 43044797--43045019 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
43044787 TCCTCGTTCA
*
43044797 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
43044862 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * **
43044917 AATGCCTTCGGG-CTTGGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
43044979 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
43045020 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 65 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:43045019 original size:40 final size:40
Alignment explanation
Indices: 43044795--43045019 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
43044785 GCTCCTCGTT
* *
43044795 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
43044835 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
43044875 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
43044915 CCAATGCCTTCGGG-CTTGGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
43044954 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
43044995 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43045020 CATCATTCAA
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 118 0.73
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:43053019 original size:119 final size:120
Alignment explanation
Indices: 43052837--43053059 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 120
43052827 TCCTCGTTCA
*
43052837 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
43052902 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * **
43052957 AATGCCTTCGGG-CTTGGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * * *
43053019 ATATGGTCACTTAGCACAAAGCCTTTGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
43053060 CATCATTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.05
119 64 0.73
120 20 0.23
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:43053059 original size:40 final size:40
Alignment explanation
Indices: 43052835--43053059 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
43052825 GCTCCTCGTT
* *
43052835 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
43052875 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
43052915 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
43052955 CCAATGCCTTCGGG-CTTGGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
43052994 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
*
43053035 CAAA-GCCTTTGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43053060 CATCATTCAA
Statistics
Matches: 161, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 117 0.73
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:43065165 original size:28 final size:28
Alignment explanation
Indices: 43065095--43065157 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
43065085 AACAGTACAG
* * *
43065095 TGTGGGCCTTAGCTCAATACAGCAATAA
1 TGTGAGCCTTAGCCCAATACAGCAACAA
*
43065123 TGTGAGCCTTAGCCCAATACAGTAACAA
1 TGTGAGCCTTAGCCCAATACAGCAACAA
43065151 TGT-AGCC
1 TGTGAGCC
43065158 CTTTGCCCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (28 bp):
TGTGAGCCTTAGCCCAATACAGCAACAA
Found at i:43065346 original size:26 final size:26
Alignment explanation
Indices: 43065324--43065388 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
43065314 AGTAAAGCTA
43065324 CCAGTAACAGTATCGCAACAAAGTTG
1 CCAGTAACAGTATCGCAACAAAGTTG
* * * *
43065350 CTAGCAACAGTATCGCAGCAATGTTG
1 CCAGTAACAGTATCGCAACAAAGTTG
43065376 CCAGTAACAGTAT
1 CCAGTAACAGTAT
43065389 ACTTCCTCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (26 bp):
CCAGTAACAGTATCGCAACAAAGTTG
Found at i:43065555 original size:27 final size:26
Alignment explanation
Indices: 43065533--43065729 Score: 104
Period size: 27 Copynumber: 7.4 Consensus size: 26
43065523 AGGGGTATAA
43065533 TAGTCATTTTACCTTATGAGGGTATT
1 TAGTCATTTTACCTTATGAGGGTATT
* *
43065559 TCGGTCATTTCACCCTT-TGA-GGTATTT
1 T-AGTCATTTTA-CCTTATGAGGGTA-TT
*
43065586 TAGTCATTTTACCCTATGA-GGTAATT
1 TAGTCATTTTACCTTATGAGGGT-ATT
* *
43065612 TGGTCATTTCT-CC-CATCGAGGGTATT
1 TAGTCATTT-TACCTTAT-GAGGGTATT
* * * *
43065638 TCGGTTATTTCACCCTT-TGGGGGTATT
1 T-AGTCATTTTA-CCTTATGAGGGTATT
* *
43065665 TCAGTCATTTTACCCTGT-AGGAGTATT
1 T-AGTCATTTTACCTTATGAGG-GTATT
*
43065692 TCAGTCATTTTACC-TATCGGGGGTATT
1 T-AGTCATTTTACCTTAT-GAGGGTATT
*
43065719 TCAATCATTTT
1 T-AGTCATTTT
43065730 CCCATAAATC
Statistics
Matches: 136, Mismatches: 19, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
25 5 0.04
26 44 0.32
27 78 0.57
28 9 0.07
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.43
Consensus pattern (26 bp):
TAGTCATTTTACCTTATGAGGGTATT
Found at i:43065590 original size:53 final size:54
Alignment explanation
Indices: 43065534--43065720 Score: 179
Period size: 53 Copynumber: 3.5 Consensus size: 54
43065524 GGGGTATAAT
*
43065534 AGTCATTTTACCTTATGAGGGTATTTCGGTCATTTCACCCTTTGA-GGTATTTT
1 AGTCATTTTACCTTATGAGGGTATTTCGGTCATTTCACCCTTTGAGGGTATTTC
* * * *
43065587 AGTCATTTTACCCTATGA-GGTAATTT-GGTCATTTCTCCCATCGAGGGTATTTC
1 AGTCATTTTACCTTATGAGGGT-ATTTCGGTCATTTCACCCTTTGAGGGTATTTC
* * * * * * *
43065640 GGTTATTTCACCCTT-TGGGGGTATTTCAGTCATTTTACCCTGT-AGGAGTATTTC
1 AGTCATTTTA-CCTTATGAGGGTATTTCGGTCATTTCACCCTTTGAGG-GTATTTC
*
43065694 AGTCATTTTACC-TATCGGGGGTATTTC
1 AGTCATTTTACCTTAT-GAGGGTATTTC
43065721 AATCATTTTC
Statistics
Matches: 107, Mismatches: 19, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
52 19 0.18
53 47 0.44
54 41 0.38
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (54 bp):
AGTCATTTTACCTTATGAGGGTATTTCGGTCATTTCACCCTTTGAGGGTATTTC
Found at i:43065591 original size:26 final size:26
Alignment explanation
Indices: 43065534--43065701 Score: 126
Period size: 27 Copynumber: 6.3 Consensus size: 26
43065524 GGGGTATAAT
*
43065534 AGTCATTTTA-CCTTATGAGGGTATTTC
1 AGTCATTTCACCCTT-TGA-GGTATTTC
* *
43065561 GGTCATTTCACCCTTTGAGGTATTTT
1 AGTCATTTCACCCTTTGAGGTATTTC
* *
43065587 AGTCATTTTACCCTATGAGGTAATTT-
1 AGTCATTTCACCCTTTGAGGT-ATTTC
* * * *
43065613 GGTCATTTCTCCCATCGAGGGTATTTC
1 AGTCATTTCACCCTTTGA-GGTATTTC
* * *
43065640 GGTTATTTCACCCTTTGGGGGTATTTC
1 AGTCATTTCACCCTTT-GAGGTATTTC
* *
43065667 AGTCATTTTACCCTGT-AGGAGTATTTC
1 AGTCATTTCACCCTTTGA-G-GTATTTC
43065694 AGTCATTT
1 AGTCATTT
43065702 TACCTATCGG
Statistics
Matches: 112, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
26 42 0.38
27 65 0.58
28 5 0.04
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.43
Consensus pattern (26 bp):
AGTCATTTCACCCTTTGAGGTATTTC
Found at i:43070077 original size:21 final size:20
Alignment explanation
Indices: 43070045--43070086 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
43070035 TTTAACTAAA
43070045 TTAATTCGCTAACACCAAATT
1 TTAATTCGCTAAC-CCAAATT
*
43070066 TTAATTTC-CTAACCTAAATT
1 TTAA-TTCGCTAACCCAAATT
43070086 T
1 T
43070087 ATTAATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 9 0.47
22 3 0.16
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.40
Consensus pattern (20 bp):
TTAATTCGCTAACCCAAATT
Found at i:43070111 original size:19 final size:19
Alignment explanation
Indices: 43070083--43070128 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
43070073 CCTAACCTAA
43070083 ATTT-ATTAATTCT-AATTT
1 ATTTAATTAATTCTGAA-TT
*
43070101 TTTTAATTAATTCTGAATT
1 ATTTAATTAATTCTGAATT
43070120 ATTTAATTA
1 ATTTAATTA
43070129 TCTAACCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.79
20 2 0.08
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTAATTAATTCTGAATT
Found at i:43072851 original size:76 final size:76
Alignment explanation
Indices: 43072692--43072859 Score: 219
Period size: 76 Copynumber: 2.2 Consensus size: 76
43072682 CCGAATTTCC
* * * * * *
43072692 AGACAACGATGGTTTATCGAATCAAATCTTTCATCCTGGGTTGCCCAGAAATGATAGCCTACCAC
1 AGACAATGATGGTTCATCGAATCAAATATGTCATCCTGGGTTGCCAAGAAATGATAACCTACCAC
**
43072757 ATCGAATTGCT
66 ATCGAATCACT
* *
43072768 CGACAATGATGGTTCATCGAATCAAATATGTCATCCTGGGTTGCCAAGCAATGATAACCTACCAC
1 AGACAATGATGGTTCATCGAATCAAATATGTCATCCTGGGTTGCCAAGAAATGATAACCTACCAC
* *
43072833 CTCGGATCACT
66 ATCGAATCACT
*
43072844 AGGCAATGATGGTTCA
1 AGACAATGATGGTTCA
43072860 CAAAATAATA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (76 bp):
AGACAATGATGGTTCATCGAATCAAATATGTCATCCTGGGTTGCCAAGAAATGATAACCTACCAC
ATCGAATCACT
Found at i:43076950 original size:15 final size:16
Alignment explanation
Indices: 43076926--43076964 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
43076916 TCATTCAATG
*
43076926 AATATCTTTTT-CATA
1 AATATTTTTTTACATA
43076941 AATATTTTTTTACATA
1 AATATTTTTTTACATA
*
43076957 AAGATTTT
1 AATATTTT
43076965 AGTTTTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (16 bp):
AATATTTTTTTACATA
Found at i:43077546 original size:19 final size:19
Alignment explanation
Indices: 43077505--43077545 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
43077495 TTTTGAGCAA
*
43077505 TTTAATTTTTTTATCTTCT
1 TTTAATTTCTTTATCTTCT
*
43077524 TTTAACTTTCTTTATTTTCT
1 TTTAA-TTTCTTTATCTTCT
43077544 TT
1 TT
43077546 ATTTTTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTAATTTCTTTATCTTCT
Found at i:43079592 original size:21 final size:21
Alignment explanation
Indices: 43079566--43079619 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
43079556 CAGCGGTGGA
*
43079566 GGTGAGATTAGTTACTGTAGC
1 GGTGAGATTAGATACTGTAGC
*
43079587 GGTGAGATTGGATACTGTAGC
1 GGTGAGATTAGATACTGTAGC
*
43079608 AGTGAGATTAGA
1 GGTGAGATTAGA
43079620 AACAATGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.35, T:0.30
Consensus pattern (21 bp):
GGTGAGATTAGATACTGTAGC
Found at i:43083740 original size:18 final size:18
Alignment explanation
Indices: 43083698--43083740 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
43083688 GCCCATTCCG
*
43083698 AAGTATATATATATACAT
1 AAGTATGTATATATACAT
43083716 ATA-TATGTATATATACAT
1 A-AGTATGTATATATACAT
43083734 AAGTATG
1 AAGTATG
43083741 CCCATTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (18 bp):
AAGTATGTATATATACAT
Found at i:43084248 original size:28 final size:28
Alignment explanation
Indices: 43084210--43084335 Score: 200
Period size: 28 Copynumber: 4.5 Consensus size: 28
43084200 TAAATTGTAC
*
43084210 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
43084238 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
43084266 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
43084294 AACACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
43084321 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43084336 GACTTAATAT
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
27 23 0.25
28 70 0.75
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATAT
Found at i:43091892 original size:18 final size:18
Alignment explanation
Indices: 43091850--43091892 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
43091840 GCCCATTCCG
*
43091850 AAGTATATATATATACAT
1 AAGTATGTATATATACAT
43091868 ATA-TATGTATATATACAT
1 A-AGTATGTATATATACAT
43091886 AAGTATG
1 AAGTATG
43091893 CCCATTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (18 bp):
AAGTATGTATATATACAT
Found at i:43092500 original size:27 final size:28
Alignment explanation
Indices: 43092362--43092487 Score: 209
Period size: 28 Copynumber: 4.5 Consensus size: 28
43092352 TAAATTGTAC
*
43092362 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
43092390 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
43092418 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
43092446 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATAT
*
43092473 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43092488 GACTTAATAT
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 24 0.25
28 71 0.75
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATAT
Found at i:43096622 original size:14 final size:15
Alignment explanation
Indices: 43096603--43096635 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
43096593 AAGGTTAAAG
43096603 AAAAA-CACTTTTCA
1 AAAAACCACTTTTCA
*
43096617 AAAAACCATTTTTCA
1 AAAAACCACTTTTCA
43096632 AAAA
1 AAAA
43096636 TAAACTAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAACCACTTTTCA
Found at i:43109567 original size:13 final size:13
Alignment explanation
Indices: 43109551--43109575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43109541 AAATTTTTAA
43109551 CTTTTCAAAAGTG
1 CTTTTCAAAAGTG
43109564 CTTTTCAAAAGT
1 CTTTTCAAAAGT
43109576 ACTTCTGAAA
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:0.12, T:0.40
Consensus pattern (13 bp):
CTTTTCAAAAGTG
Found at i:43110072 original size:13 final size:13
Alignment explanation
Indices: 43110056--43110119 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
43110046 TTTAAACCAA
*
43110056 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
43110069 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
43110082 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
43110095 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
43110108 ACTTTTCAAAAG
1 ACTTTTCAAAAG
43110120 TAATGAAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
12 4 0.09
13 36 0.82
14 4 0.09
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:43111998 original size:9 final size:9
Alignment explanation
Indices: 43111984--43112066 Score: 103
Period size: 9 Copynumber: 9.2 Consensus size: 9
43111974 AGTGGATCAT
*
43111984 ATGATGCTG
1 ATGATGATG
*
43111993 ATGATGCTG
1 ATGATGATG
43112002 ATGATGATG
1 ATGATGATG
43112011 ATGATGATG
1 ATGATGATG
43112020 ATGATGATG
1 ATGATGATG
* **
43112029 AGGATGCGG
1 ATGATGATG
*
43112038 ATGAGGATG
1 ATGATGATG
43112047 ATGATGATG
1 ATGATGATG
*
43112056 ATAATGATG
1 ATGATGATG
43112065 AT
1 AT
43112067 ACCAATAATG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 64 1.00
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (9 bp):
ATGATGATG
Found at i:43112003 original size:6 final size:6
Alignment explanation
Indices: 43111984--43112066 Score: 103
Period size: 6 Copynumber: 13.8 Consensus size: 6
43111974 AGTGGATCAT
* * *
43111984 ATGATG CTGATG ATGCTG ATGATG ATGATG ATGATG ATGATG ATGAGG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
** * *
43112032 ATGCGG ATGAGG ATGATG ATGATG ATAATG ATGAT
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGAT
43112067 ACCAATAATG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (6 bp):
ATGATG
Found at i:43112845 original size:52 final size:53
Alignment explanation
Indices: 43112739--43112849 Score: 197
Period size: 52 Copynumber: 2.1 Consensus size: 53
43112729 GGAAACTGAA
43112739 AAATTTCTCACCTTTCGCATTTAGTATGAATCTAACATGTTTAAGCTGCAATT
1 AAATTTCTCACCTTTCGCATTTAGTATGAATCTAACATGTTTAAGCTGCAATT
* *
43112792 AAATTTCTCACCTTTTGTATTTAGTATG-ATCTAACATGTTTAAGCTGCAATT
1 AAATTTCTCACCTTTCGCATTTAGTATGAATCTAACATGTTTAAGCTGCAATT
43112844 AAATTT
1 AAATTT
43112850 GTAGTTTGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.54
53 26 0.46
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (53 bp):
AAATTTCTCACCTTTCGCATTTAGTATGAATCTAACATGTTTAAGCTGCAATT
Found at i:43125746 original size:27 final size:27
Alignment explanation
Indices: 43125715--43125802 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 27
43125705 CACGACTTTT
*
43125715 ATTTCTTAGATCACCACAAAGGCTTCC
1 ATTTCTTAGATTACCACAAAGGCTTCC
* * * *
43125742 ATTTCTTAAATTTCCACAAAAGCTTTC
1 ATTTCTTAGATTACCACAAAGGCTTCC
* * **
43125769 ATTTCTTGGATTGCCACAAAGATTTCC
1 ATTTCTTAGATTACCACAAAGGCTTCC
43125796 ATTTCTT
1 ATTTCTT
43125803 TTTGCATGTT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (27 bp):
ATTTCTTAGATTACCACAAAGGCTTCC
Found at i:43129040 original size:25 final size:25
Alignment explanation
Indices: 43128981--43129069 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
43128971 ATTCATGTAT
* * * *
43128981 GCTCATATGAGCTGTA-AATGGTAA
1 GCTCATGTGAGCTGAATAACGGAAA
* *
43129005 GCTCCTCTGAGCTGAATAACGGAAA
1 GCTCATGTGAGCTGAATAACGGAAA
*
43129030 GCTCATGTGAGTTGAATAAC-GAGAA
1 GCTCATGTGAGCTGAATAACGGA-AA
*
43129055 GCTCATGCGAGCTGA
1 GCTCATGTGAGCTGA
43129070 GTATCAGGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
24 15 0.28
25 38 0.72
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (25 bp):
GCTCATGTGAGCTGAATAACGGAAA
Found at i:43134108 original size:47 final size:47
Alignment explanation
Indices: 43134045--43134545 Score: 710
Period size: 47 Copynumber: 10.6 Consensus size: 47
43134035 CCCTTCGGGA
* * *
43134045 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
43134092 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43134139 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
43134186 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
43134233 CTTATCACACATACT-CA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATA-TACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
43134280 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
43134327 CTTATCAC--ACATACACATGCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
43134372 CTTATCACATATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43134423 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
43134470 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
43134519 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
43134546 TATTCAAATA
Statistics
Matches: 419, Mismatches: 23, Indels: 24
0.90 0.05 0.05
Matches are distributed among these distances:
45 40 0.10
46 2 0.00
47 289 0.69
49 46 0.11
51 42 0.10
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:43136056 original size:56 final size:56
Alignment explanation
Indices: 43135989--43136108 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
43135979 TATTAGTTTA
43135989 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
43136045 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
43136101 TTGCCCAT
1 TTGCCCAT
43136109 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:43138696 original size:49 final size:47
Alignment explanation
Indices: 43138636--43139082 Score: 672
Period size: 47 Copynumber: 9.6 Consensus size: 47
43138626 GATAATTGTG
* * *
43138636 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGGTGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
43138683 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
43138730 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
43138779 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCTGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
43138828 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
43138875 ATGTGAAAGTGTATATA--TG-T---GCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
43138916 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
43138963 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
43139010 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
43139057 ATGTGGAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
43139083 TCCCGAAGGG
Statistics
Matches: 370, Mismatches: 22, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
41 38 0.10
43 2 0.01
44 2 0.01
45 2 0.01
47 232 0.63
49 94 0.25
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:43138910 original size:88 final size:88
Alignment explanation
Indices: 43138807--43139077 Score: 389
Period size: 88 Copynumber: 3.0 Consensus size: 88
43138797 ATGTGATAAG
*
43138807 GCCTAATGGCTGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
1 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
43138872 TGAATGTGAAAGTGTATATATGT
66 TGAATGTGAAAGTGTATATATGT
*
43138895 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGA
1 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
43138960 TGAATGTGAAAGTGTATATATGTGAT
66 TGAATGTGAAAGTGTATATA--TG-T
* * * * * *
43138986 GAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACG
1 ---GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
* * *
43139051 TGATGGATGTGGAAGTGTATAAATGT
63 TGATGAATGTGAAAGTGTATATATGT
43139077 G
1 G
43139078 ATAAGTCCCG
Statistics
Matches: 165, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
88 84 0.51
90 2 0.01
91 2 0.01
92 2 0.01
94 75 0.45
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.29
Consensus pattern (88 bp):
GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
TGAATGTGAAAGTGTATATATGT
Found at i:43146127 original size:55 final size:52
Alignment explanation
Indices: 43145994--43146129 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 52
43145984 CTCATGTCGG
* * * *
43145994 TGCCCATGCCATGTACCAGACATGGTCTTACGGGGGACCTCTCATCTCGATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGAGACCTCTCATCTCAATA
* * * *
43146046 --CTAACGCCATGTCCCAGACATAGTCTTACGTGAGACCTCTCATAACTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGAGACCTCTCAT--CTCAAT-A
43146099 TGCCAATGCCATGTCCCAGACATGGTCTTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC
43146130 ATAGGGTCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
50 36 0.53
52 5 0.07
53 1 0.01
55 26 0.38
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGGGAGACCTCTCATCTCAATA
Found at i:43152057 original size:26 final size:27
Alignment explanation
Indices: 43152027--43152082 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
43152017 ATGAAAATTA
43152027 TACAAATCACATAAATA-T-AATTCAAT
1 TACAAA-CACATAAATACTCAATTCAAT
* *
43152053 TAC-AACATATAAATACTCAATTTAAT
1 TACAAACACATAAATACTCAATTCAAT
43152079 TACA
1 TACA
43152083 CAAACTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 9 0.36
25 3 0.12
26 13 0.52
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (27 bp):
TACAAACACATAAATACTCAATTCAAT
Found at i:43153930 original size:29 final size:29
Alignment explanation
Indices: 43153889--43154231 Score: 126
Period size: 29 Copynumber: 11.8 Consensus size: 29
43153879 CGATGGTCAT
* * *
43153889 AACCGTCCTTTTTCATATTCGATCGTCGA
1 AACCATCCCTTTTCATATTCGATAGTCGA
* * *
43153918 AACCATCCCTTTTCGTAGTT-GATGGTCGT
1 AACCATCCCTTTTCATA-TTCGATAGTCGA
* * * *
43153947 CATCATCCCTTTTCAT-TATCAATAGCCG-
1 AACCATCCCTTTTCATAT-TCGATAGTCGA
* * * *
43153975 AACCTATCCCTTTTCACATTTGATGGTCGT
1 AACC-ATCCCTTTTCATATTCGATAGTCGA
* ** *
43154005 CACCATCCCTTTTTGT-TGTCGATTGTC-A
1 AACCATCCCTTTTCATAT-TCGATAGTCGA
* * * *
43154033 TCACCGTCCCATTTCATAATCGATAG-CTGA
1 -AACCATCCCTTTTCATATTCGATAGTC-GA
* * * * * *
43154063 AGCTATCCCTTTTCACATTTGATGGTCGT
1 AACCATCCCTTTTCATATTCGATAGTCGA
* * * *
43154092 CACCATCCCTTTTCGT-TGTCGATGGTCGT
1 AACCATCCCTTTTCATAT-TCGATAGTCGA
* * * * *
43154121 CACCATCGCATTTCATAATCGATAGCCGA
1 AACCATCCCTTTTCATATTCGATAGTCGA
* * * * *
43154150 AGCTATTCCTTTTCATATTTGATAGCCGA
1 AACCATCCCTTTTCATATTCGATAGTCGA
* * *
43154179 AGCTATCCCTTTTCATATTCGATA-ACTGA
1 AACCATCCCTTTTCATATTCGATAGTC-GA
* * *
43154208 AGCTATCCCTTTTCATATTTGATA
1 AACCATCCCTTTTCATATTCGATA
43154232 ACCAAAGCTA
Statistics
Matches: 233, Mismatches: 66, Indels: 30
0.71 0.20 0.09
Matches are distributed among these distances:
27 1 0.00
28 7 0.03
29 217 0.93
30 8 0.03
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.38
Consensus pattern (29 bp):
AACCATCCCTTTTCATATTCGATAGTCGA
Found at i:43154048 original size:87 final size:87
Alignment explanation
Indices: 43153919--43154172 Score: 373
Period size: 87 Copynumber: 2.9 Consensus size: 87
43153909 GATCGTCGAA
* * * * * * *
43153919 ACCATCCCTTTTCGTAGTTGATGGTCGTCATCATCCCTTTTCATTATCAATAGCCGAACCTATCC
1 ACCATCCCTTTTCGTTGTCGATGGTCGTCACCATCCCATTTCATAATCGATAGCCGAAGCTATCC
43153984 CTTTTCACATTTGATGGTCGTC
66 CTTTTCACATTTGATGGTCGTC
* * * * *
43154006 ACCATCCCTTTTTGTTGTCGATTGTCATCACCGTCCCATTTCATAATCGATAGCTGAAGCTATCC
1 ACCATCCCTTTTCGTTGTCGATGGTCGTCACCATCCCATTTCATAATCGATAGCCGAAGCTATCC
43154071 CTTTTCACATTTGATGGTCGTC
66 CTTTTCACATTTGATGGTCGTC
* *
43154093 ACCATCCCTTTTCGTTGTCGATGGTCGTCACCATCGCATTTCATAATCGATAGCCGAAGCTATTC
1 ACCATCCCTTTTCGTTGTCGATGGTCGTCACCATCCCATTTCATAATCGATAGCCGAAGCTATCC
*
43154158 CTTTTCATATTTGAT
66 CTTTTCACATTTGAT
43154173 AGCCGAAGCT
Statistics
Matches: 147, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 147 1.00
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (87 bp):
ACCATCCCTTTTCGTTGTCGATGGTCGTCACCATCCCATTTCATAATCGATAGCCGAAGCTATCC
CTTTTCACATTTGATGGTCGTC
Found at i:43154201 original size:58 final size:58
Alignment explanation
Indices: 43154131--43154252 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 58
43154121 CACCATCGCA
* * * *
43154131 TTTCATAATCGATAGCCGAAGCTATTCCTTTTCATATTTGATAGCCGAAGCTATCCCT
1 TTTCATAATCGATAACCGAAGCTATCCCTTTTCATATTTGATAACCAAAGCTATCCCT
* *
43154189 TTTCATATTCGATAACTGAAGCTATCCCTTTTCATATTTGATAACCAAAGCTATCCCT
1 TTTCATAATCGATAACCGAAGCTATCCCTTTTCATATTTGATAACCAAAGCTATCCCT
43154247 TTTCAT
1 TTTCAT
43154253 TGGTCGATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.39
Consensus pattern (58 bp):
TTTCATAATCGATAACCGAAGCTATCCCTTTTCATATTTGATAACCAAAGCTATCCCT
Found at i:43154232 original size:29 final size:29
Alignment explanation
Indices: 43154131--43154252 Score: 172
Period size: 29 Copynumber: 4.2 Consensus size: 29
43154121 CACCATCGCA
* * * *
43154131 TTTCATAATCGATAGCCGAAGCTATTCCT
1 TTTCATATTTGATAACCGAAGCTATCCCT
*
43154160 TTTCATATTTGATAGCCGAAGCTATCCCT
1 TTTCATATTTGATAACCGAAGCTATCCCT
* *
43154189 TTTCATATTCGATAACTGAAGCTATCCCT
1 TTTCATATTTGATAACCGAAGCTATCCCT
*
43154218 TTTCATATTTGATAACCAAAGCTATCCCT
1 TTTCATATTTGATAACCGAAGCTATCCCT
43154247 TTTCAT
1 TTTCAT
43154253 TGGTCGATGA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.39
Consensus pattern (29 bp):
TTTCATATTTGATAACCGAAGCTATCCCT
Found at i:43156600 original size:30 final size:30
Alignment explanation
Indices: 43156564--43156656 Score: 145
Period size: 29 Copynumber: 3.2 Consensus size: 30
43156554 GAAATTTTAT
43156564 TCGATGGTCATCACCATCCCTTTTCATTAA
1 TCGATGGTCATCACCATCCCTTTTCATTAA
*
43156594 TCGATGGTCATCACCATCCCTTTTCA-TAG
1 TCGATGGTCATCACCATCCCTTTTCATTAA
* *
43156623 TTGATGGTCATCACCATTCCTTTTCATT-A
1 TCGATGGTCATCACCATCCCTTTTCATTAA
43156652 TCGAT
1 TCGAT
43156657 AGCCAAAGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
29 30 0.53
30 27 0.47
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.39
Consensus pattern (30 bp):
TCGATGGTCATCACCATCCCTTTTCATTAA
Found at i:43156673 original size:29 final size:30
Alignment explanation
Indices: 43156641--43156823 Score: 148
Period size: 29 Copynumber: 6.3 Consensus size: 30
43156631 CATCACCATT
*
43156641 CCTTTTCATTA-TCGATAGCCAAAGTTATC
1 CCTTTTCATTATTCGATAGCCAAAGCTATC
* *
43156670 CCTTTTCA-TATTTGATAGCCGAAGCTATC
1 CCTTTTCATTATTCGATAGCCAAAGCTATC
* *** * *
43156699 CCTTTTCA-TATTCGATGGTCGTCA-CTGTA
1 CCTTTTCATTATTCGATAG-CCAAAGCTATC
* * * **
43156728 CCATTTCA-TAATCGATATCCGGAGCTA-C
1 CCTTTTCATTATTCGATAGCCAAAGCTATC
43156756 CCTTTTCA-TATTCGATAGCCAAAGCTATC
1 CCTTTTCATTATTCGATAGCCAAAGCTATC
* **
43156785 CCTTTTC-TTATTTGATAGCTGAAGCTATC
1 CCTTTTCATTATTCGATAGCCAAAGCTATC
43156814 CCTTTTCATT
1 CCTTTTCATT
43156824 GGTCGATGAT
Statistics
Matches: 121, Mismatches: 27, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
28 26 0.21
29 91 0.75
30 4 0.03
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (30 bp):
CCTTTTCATTATTCGATAGCCAAAGCTATC
Found at i:43156716 original size:87 final size:85
Alignment explanation
Indices: 43156609--43156796 Score: 232
Period size: 87 Copynumber: 2.2 Consensus size: 85
43156599 GGTCATCACC
* * * *
43156609 ATCCCTTTTCATAGTTGATGGTCATCACCATTCCTTTTCATTATCGATAGCCAAAGTTATCCCTT
1 ATCCCTTTTCATA-TTGATGGTCATCACCATACCATTTCATAATCGATAGCCAAAGCTA-CCCTT
* *
43156674 TTCATATTTGATAGCCGAAGCT
64 TTCATATTCGATAGCCAAAGCT
* ** * **
43156696 ATCCCTTTTCATATTCGATGGTCGTCACTGTACCATTTCATAATCGATATCCGGAGCTACCCTTT
1 ATCCCTTTTCATATT-GATGGTCATCACCATACCATTTCATAATCGATAGCCAAAGCTACCCTTT
43156761 TCATATTCGATAGCCAAAGCT
65 TCATATTCGATAGCCAAAGCT
*
43156782 ATCCCTTTTCTTATT
1 ATCCCTTTTCATATT
43156797 TGATAGCTGA
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
86 41 0.47
87 46 0.53
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (85 bp):
ATCCCTTTTCATATTGATGGTCATCACCATACCATTTCATAATCGATAGCCAAAGCTACCCTTTT
CATATTCGATAGCCAAAGCT
Found at i:43156821 original size:86 final size:87
Alignment explanation
Indices: 43156609--43156822 Score: 202
Period size: 86 Copynumber: 2.5 Consensus size: 87
43156599 GGTCATCACC
* * * * * * *
43156609 ATCCCTTTTCATAGTT-GATGGTCATCACCATTCCTTTTCATTATCGATAGCCAAAGTTATCCCT
1 ATCCCTTTTCATA-TTCGATGCTCGTAACTATACCTTTTCATAATCGATAGCCAAAGCTATCCCT
* *
43156673 TTTCATATTTGATAGCCGAAGCT
65 TTTCATATTCGATAGCCAAAGCT
* * * * * **
43156696 ATCCCTTTTCATATTCGATGGTCGTCACTGTACCATTTCATAATCGATATCCGGAGCTA-CCCTT
1 ATCCCTTTTCATATTCGATGCTCGTAACTATACCTTTTCATAATCGATAGCCAAAGCTATCCCTT
43156760 TTCATATTCGATAGCCAAAGCT
66 TTCATATTCGATAGCCAAAGCT
* * *
43156782 ATCCCTTTTCTTATTTGATAGCT-G-AAGCTATCCCTTTTCAT
1 ATCCCTTTTCATATTCGAT-GCTCGTAA-CTATACCTTTTCAT
43156823 TGGTCGATGA
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
85 1 0.01
86 56 0.53
87 48 0.46
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (87 bp):
ATCCCTTTTCATATTCGATGCTCGTAACTATACCTTTTCATAATCGATAGCCAAAGCTATCCCTT
TTCATATTCGATAGCCAAAGCT
Found at i:43167589 original size:16 final size:17
Alignment explanation
Indices: 43167568--43167600 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43167558 TTGAGCAAGT
*
43167568 ATAATG-TATTTGGTTA
1 ATAATGTTATTTAGTTA
43167584 ATAATGTTATTTAGTTA
1 ATAATGTTATTTAGTTA
43167601 TGACATGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (17 bp):
ATAATGTTATTTAGTTA
Found at i:43176616 original size:26 final size:26
Alignment explanation
Indices: 43176585--43176639 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
43176575 AACACACCAA
43176585 TATTGCAGCAAAGTTACCAGTAATAG
1 TATTGCAGCAAAGTTACCAGTAATAG
43176611 TATTGCAGCAAAGTTACCAGTAATAG
1 TATTGCAGCAAAGTTACCAGTAATAG
43176637 TAT
1 TAT
43176640 ATGTGGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (26 bp):
TATTGCAGCAAAGTTACCAGTAATAG
Found at i:43176852 original size:27 final size:26
Alignment explanation
Indices: 43176829--43176972 Score: 117
Period size: 27 Copynumber: 5.3 Consensus size: 26
43176819 AAAGGTATAA
43176829 TAGTCATTTTACCCTACGGGGGTATTT
1 TAGTCATTTTACCCTACGGGGGTA-TT
* *
43176856 TGGTCATTTTACCTTACGGGGGTATT
1 TAGTCATTTTACCCTACGGGGGTATT
* **
43176882 TCGCTCATTTTACCCTATAGGGGTACTT
1 TAG-TCATTTTACCCTACGGGGGTA-TT
** * * *
43176910 CGGTCATTTTACCCTATGAGAGTATT
1 TAGTCATTTTACCCTACGGGGGTATT
** *
43176936 CCGGTCATTTTACCCTATGGGGGTATT
1 -TAGTCATTTTACCCTACGGGGGTATT
*
43176963 TCAATCATTT
1 T-AGTCATTT
43176973 ATTGACCTCT
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
26 6 0.06
27 88 0.91
28 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (26 bp):
TAGTCATTTTACCCTACGGGGGTATT
Found at i:43176972 original size:54 final size:54
Alignment explanation
Indices: 43176831--43176964 Score: 178
Period size: 54 Copynumber: 2.5 Consensus size: 54
43176821 AGGTATAATA
* * * * * *
43176831 GTCATTTTACCCTACGGGGGTATTTTGGTCATTTTACCTTACGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACGAGAGTATTCCG
* * * *
43176885 CTCATTTTACCCTATAGGGGTACTTCGGTCATTTTACCCTATGAGAGTATTCCG
1 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACGAGAGTATTCCG
43176939 GTCATTTTACCCTATGGGGGTATTTC
1 GTCATTTTACCCTATGGGGGTATTTC
43176965 AATCATTTAT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (54 bp):
GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTACGAGAGTATTCCG
Found at i:43178976 original size:20 final size:18
Alignment explanation
Indices: 43178951--43178997 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
43178941 AAACAATTAT
*
43178951 AAAAAACTAAAGAATATATA
1 AAAAAACTAAA-AA-ATAGA
43178971 AAAAAACTTAAAAAATAGA
1 AAAAAAC-TAAAAAATAGA
43178990 AAAAAACT
1 AAAAAACT
43178998 CTAAACCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 9 0.36
21 4 0.16
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.17
Consensus pattern (18 bp):
AAAAAACTAAAAAATAGA
Found at i:43178982 original size:21 final size:19
Alignment explanation
Indices: 43178951--43179002 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
43178941 AAACAATTAT
*
43178951 AAAAAAC-TAAAGAATATATA
1 AAAAAACTTAAA-AA-ATAGA
43178971 AAAAAACTTAAAAAATAGA
1 AAAAAACTTAAAAAATAGA
43178990 AAAAAACTCTAAA
1 AAAAAACT-TAAA
43179003 CCCTAAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.41
20 13 0.45
21 4 0.14
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.17
Consensus pattern (19 bp):
AAAAAACTTAAAAAATAGA
Found at i:43199255 original size:40 final size:40
Alignment explanation
Indices: 43199211--43199290 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
43199201 ACACGTTCAG
* *
43199211 GGGTACTAAAGTACAAAAAGGGGCATGTATGTGCAAACAT
1 GGGTACCAAAGTACAAAAAGGGGCACGTATGTGCAAACAT
* **
43199251 GGGTACCGAAGTACAATCAGGGGCACGTATGTGCAAACAT
1 GGGTACCAAAGTACAAAAAGGGGCACGTATGTGCAAACAT
43199291 TCAATAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (40 bp):
GGGTACCAAAGTACAAAAAGGGGCACGTATGTGCAAACAT
Found at i:43201220 original size:28 final size:28
Alignment explanation
Indices: 43201176--43201265 Score: 137
Period size: 28 Copynumber: 3.2 Consensus size: 28
43201166 TATACAGTAT
* *
43201176 CAGT-ACAGTGTGGGCCTTAGCCCATTA
1 CAGTAACAGTGTGAGCCTTAGCCCAATA
43201203 CAGTAACAGTGTGAGCCTTAGCCCAATA
1 CAGTAACAGTGTGAGCCTTAGCCCAATA
* *
43201231 TAGTAACAATGTGAGCCTTAGCCCAATA
1 CAGTAACAGTGTGAGCCTTAGCCCAATA
43201259 CAGTAAC
1 CAGTAAC
43201266 CAGTACAATG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 4 0.07
28 53 0.93
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (28 bp):
CAGTAACAGTGTGAGCCTTAGCCCAATA
Found at i:43201395 original size:26 final size:26
Alignment explanation
Indices: 43201366--43201416 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
43201356 CCAACACACC
* *
43201366 AATATCGCAGCAAAGCTGCCAGTAAT
1 AATAACGCAACAAAGCTGCCAGTAAT
43201392 AATAACGCAACAAAGCTGCCAGTAA
1 AATAACGCAACAAAGCTGCCAGTAA
43201417 CAGTATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (26 bp):
AATAACGCAACAAAGCTGCCAGTAAT
Found at i:43201634 original size:27 final size:27
Alignment explanation
Indices: 43201589--43201810 Score: 236
Period size: 27 Copynumber: 8.2 Consensus size: 27
43201579 CATAACGGTC
*
43201589 ATTTTACCCCTTC-AGGGGTATTTTAGTC
1 ATTTTA-CCCTTCGA-GGGTATTTTAGTA
*
43201617 ATTTTACCCTTCGAGGGTATTTCAGTA
1 ATTTTACCCTTCGAGGGTATTTTAGTA
** *
43201644 ATTTTACCCTTTAAGGGTATTTCAGTA
1 ATTTTACCCTTCGAGGGTATTTTAGTA
* *
43201671 A-TTTACCCTTCGAGGGAATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTTAGTA
* *
43201697 ATTTTACTCTTCGAGTGTATTTT-GTTA
1 ATTTTACCCTTCGAGGGTATTTTAG-TA
*
43201724 ATTTTACCCTTCGAGGGTA-TTTCGATA
1 ATTTTACCCTTCGAGGGTATTTTAG-TA
* *
43201751 ATTTTACCCTTTGAGTGTATTTTAGTA
1 ATTTTACCCTTCGAGGGTATTTTAGTA
* * * *
43201778 ATTTTACCATTCGAGGGCATTTCAGAA
1 ATTTTACCCTTCGAGGGTATTTTAGTA
43201805 ATTTTA
1 ATTTTA
43201811 TCCTATAGGA
Statistics
Matches: 165, Mismatches: 24, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
26 25 0.15
27 129 0.78
28 11 0.07
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTTAGTA
Found at i:43201825 original size:107 final size:107
Alignment explanation
Indices: 43201617--43201815 Score: 276
Period size: 107 Copynumber: 1.9 Consensus size: 107
43201607 TATTTTAGTC
*
43201617 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTTAAGGGTATTTCAGTAATTTACCCTTC
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTTAAGGGTATTTCAGTAATTTACCATTC
** * * *
43201682 GAGGGAATTTTGGTAATTTTACTCTTCGAGTGTATTTTGTTA
66 GAGGGAATTTCAGAAATTTTACTCCTAGAGTGTATTTTGTTA
* * *
43201724 ATTTTACCCTTCGAGGGTATTTC-GATAATTTTACCCTTTGAGTGTATTTTAGTAATTTTACCAT
1 ATTTTACCCTTCGAGGGTATTTCAG-TAATTTTACCCTTTAAGGGTATTTCAGTAA-TTTACCAT
*
43201788 TCGAGGGCATTTCAGAAATTTTA-TCCTA
64 TCGAGGGAATTTCAGAAATTTTACTCCTA
43201816 TAGGATATTT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 1 0.01
107 53 0.66
108 26 0.32
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.44
Consensus pattern (107 bp):
ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTTAAGGGTATTTCAGTAATTTACCATTC
GAGGGAATTTCAGAAATTTTACTCCTAGAGTGTATTTTGTTA
Found at i:43201861 original size:27 final size:27
Alignment explanation
Indices: 43201821--43201920 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
43201811 TCCTATAGGA
* *
43201821 TATTTCGATCATTCTACGTTATGGGGG
1 TATTTCGGTCATTCTACCTTATGGGGG
* * *
43201848 TATTTCGGTTATTCTACCCTATAGGGG
1 TATTTCGGTCATTCTACCTTATGGGGG
*
43201875 TATTTCGGTCATTCTACCTTATGAGGG
1 TATTTCGGTCATTCTACCTTATGGGGG
* *
43201902 TATTTTGGTCATTTTACCT
1 TATTTCGGTCATTCTACCT
43201921 AATTTAGGGT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (27 bp):
TATTTCGGTCATTCTACCTTATGGGGG
Found at i:43208088 original size:12 final size:12
Alignment explanation
Indices: 43208071--43208097 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43208061 TACACGCCCA
43208071 TGTGCTAGGCCG
1 TGTGCTAGGCCG
43208083 TGTGCTAGGCCG
1 TGTGCTAGGCCG
43208095 TGT
1 TGT
43208098 AATAGCCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.22, G:0.41, T:0.30
Consensus pattern (12 bp):
TGTGCTAGGCCG
Found at i:43208274 original size:29 final size:29
Alignment explanation
Indices: 43208231--43208293 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
43208221 TTACAAGCCA
* * *
43208231 CTCACACTATTTGATTCAATACGAAGTGT
1 CTCACACAATCTGATTCAATACGAAATGT
*
43208260 TTCACACAATCTGATTCAATACGAAATGT
1 CTCACACAATCTGATTCAATACGAAATGT
43208289 CTCAC
1 CTCAC
43208294 CTTTCTGACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (29 bp):
CTCACACAATCTGATTCAATACGAAATGT
Found at i:43209742 original size:12 final size:12
Alignment explanation
Indices: 43209707--43209742 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
43209697 GAAAAATTTA
*
43209707 ATAATAATATAA
1 ATAATAATATAT
*
43209719 ATGATAATATAT
1 ATAATAATATAT
43209731 ATAATAATATAT
1 ATAATAATATAT
43209743 TTAAAGTCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:43210539 original size:20 final size:20
Alignment explanation
Indices: 43210502--43210541 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43210492 GCTGCGCCTC
*
43210502 TCCTTTTCTTTTTCCTTTTT
1 TCCTTTTCTTTCTCCTTTTT
43210522 TCCTTTTC-TTCTCTCTTTTT
1 TCCTTTTCTTTCTC-CTTTTT
43210542 CTCTCATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TCCTTTTCTTTCTCCTTTTT
Found at i:43215579 original size:12 final size:12
Alignment explanation
Indices: 43215544--43215579 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
43215534 GAAAAATTTA
*
43215544 ATAATAATATAA
1 ATAATAATATAT
*
43215556 ATGATAATATAT
1 ATAATAATATAT
43215568 ATAATAATATAT
1 ATAATAATATAT
43215580 TTAAAGTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:43220245 original size:30 final size:30
Alignment explanation
Indices: 43220209--43220407 Score: 138
Period size: 30 Copynumber: 6.7 Consensus size: 30
43220199 AATCGAAGTT
* *
43220209 ATCCC-TTTCATAGTTCGATAGCCAAAGCT
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCC
* * * * **
43220238 ATCCCCTTTCATAATTTGATGGTCCTCA-CC
1 ATCCCTTTTCATAGTTCGATAG-CCGAAGCC
* * * * *
43220268 ATCCTTTTTCATAATTTGATAGTCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCC
* *
43220298 ATCCATTTTCATAGATCGATAGCCGAAGCC
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCC
* ** *
43220328 ATCCCTTTTCATAGTTCGATGGTTGTCA-CC
1 ATCCCTTTTCATAGTTCGATAGCCG-AAGCC
*
43220358 ATCCCTTTTCAT--TATCGATAGCCGAAGCT
1 ATCCCTTTTCATAGT-TCGATAGCCGAAGCC
**
43220387 ATCCCTTTTCATTCTTCGATA
1 ATCCCTTTTCATAGTTCGATA
43220408 ATCGACATTA
Statistics
Matches: 132, Mismatches: 30, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
28 2 0.02
29 27 0.20
30 98 0.74
31 5 0.04
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.37
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATAGCCGAAGCC
Found at i:43220332 original size:90 final size:88
Alignment explanation
Indices: 43220201--43220398 Score: 243
Period size: 90 Copynumber: 2.2 Consensus size: 88
43220191 AATTCCATAA
* * * * *
43220201 TCGAAGTTATCCCTTTCATAGTTCGATAGCCAAAGCTATCCCCTTTCATAATTTGATGGTCCTCA
1 TCGAAGCTATCCTTTTCATAGATCGATAGCCAAAGCCATCCCCTTTCATAATTCGATGGTCCTCA
* *
43220266 CCATCCTTTTTCATAATTTGATAG
66 CCATCCCTTTTCATAA-TCGATAG
* * * **
43220290 TCGAAGCTATCCATTTTCATAGATCGATAGCCGAAGCCATCCCTTTTCATAGTTCGATGGTTGTC
1 TCGAAGCTATCC-TTTTCATAGATCGATAGCCAAAGCCATCCCCTTTCATAATTCGATGGTCCTC
*
43220355 ACCATCCCTTTTCATTATCGATAG
65 ACCATCCCTTTTCATAATCGATAG
*
43220379 CCGAAGCTATCCCTTTTCAT
1 TCGAAGCTAT-CCTTTTCAT
43220399 TCTTCGATAA
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
89 33 0.35
90 60 0.65
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (88 bp):
TCGAAGCTATCCTTTTCATAGATCGATAGCCAAAGCCATCCCCTTTCATAATTCGATGGTCCTCA
CCATCCCTTTTCATAATCGATAG
Found at i:43222336 original size:18 final size:19
Alignment explanation
Indices: 43222313--43222350 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
43222303 AGGTTTTGTA
*
43222313 TTTAAACCAA-AACCATTT
1 TTTAAAACAACAACCATTT
*
43222331 TTTAAAACAACAACTATTT
1 TTTAAAACAACAACCATTT
43222350 T
1 T
43222351 GAATTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTAAAACAACAACCATTT
Found at i:43229523 original size:41 final size:41
Alignment explanation
Indices: 43229467--43229589 Score: 133
Period size: 41 Copynumber: 3.0 Consensus size: 41
43229457 ATAATCACAT
* *
43229467 ATCGATGCTAGTGTCCCAGACAGGGTCTTACACGA-AACAA
1 ATCGATGCCAATGTCCCAGACAGGGTCTTACACGAGAACAA
* *
43229507 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAGTACAA
1 AT-CGATGCCAATGTCCCAGACAGGGTCTTACACG-AGAACAA
* * * *
43229550 GTCGATGACAACGTCCCAGAC-GTGGTCTTACACGATAACA
1 ATCGATGCCAATGTCCCAGACAG-GGTCTTACACGAGAACA
43229590 TATATCAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
40 2 0.03
41 33 0.48
42 29 0.42
43 5 0.07
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGATGCCAATGTCCCAGACAGGGTCTTACACGAGAACAA
Found at i:43229569 original size:42 final size:41
Alignment explanation
Indices: 43229479--43229589 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 41
43229469 CGATGCTAGT
* * *
43229479 GTCCCAGACAGGGTCTTACACGAAACAAATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGAAACAAATACGATGACAAC
* *
43229520 GTCCCAGACATGGTCTTACACGTAGTACAAGT-CGATGACAAC
1 GTCCCAGACATGGTCTTACACG-A-AACAAATACGATGACAAC
*
43229562 GTCCCAGACGTGGTCTTACACGATAACA
1 GTCCCAGACATGGTCTTACACGA-AACA
43229590 TATATCAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 25 0.42
42 30 0.50
43 5 0.08
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (41 bp):
GTCCCAGACATGGTCTTACACGAAACAAATACGATGACAAC
Found at i:43233947 original size:49 final size:49
Alignment explanation
Indices: 43233890--43233983 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
43233880 TACCATGCAA
* * *
43233890 TGCTAAACTTGTTCTTCCACTATCTACACTCTTATTACTATTTATACAT
1 TGCTAAACTTATTCTTCCACTATCTACACTCTAATCACTATTTATACAT
43233939 TGCTAAACTTATTCTTCCACTATCTACACTCTAATCACTATTTAT
1 TGCTAAACTTATTCTTCCACTATCTACACTCTAATCACTATTTAT
43233984 CCCTTCTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.44
Consensus pattern (49 bp):
TGCTAAACTTATTCTTCCACTATCTACACTCTAATCACTATTTATACAT
Found at i:43234475 original size:13 final size:13
Alignment explanation
Indices: 43234439--43234467 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43234429 TGGGTCACAA
43234439 GCCCATGTGTGTT
1 GCCCATGTGTGTT
43234452 GCCCATGTGTGTT
1 GCCCATGTGTGTT
43234465 GCC
1 GCC
43234468 TCTGTGTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.28, G:0.31, T:0.34
Consensus pattern (13 bp):
GCCCATGTGTGTT
Found at i:43236519 original size:8 final size:8
Alignment explanation
Indices: 43236500--43236557 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
43236490 TGCGTGATTC
43236500 TTCTTCTTT
1 TTCTT-TTT
43236509 TTCTTTTT
1 TTCTTTTT
*
43236517 TTCTTTCT
1 TTCTTTTT
*
43236525 TTCTTTCT
1 TTCTTTTT
43236533 TTCTTTCTT
1 TTCTTT-TT
* *
43236542 TTAATTTCT
1 TT-CTTTTT
43236551 TTCTTTT
1 TTCTTTT
43236558 GTTTGCACGC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
8 27 0.66
9 11 0.27
10 3 0.07
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (8 bp):
TTCTTTTT
Found at i:43236525 original size:4 final size:4
Alignment explanation
Indices: 43236508--43236556 Score: 62
Period size: 4 Copynumber: 11.8 Consensus size: 4
43236498 TCTTCTTCTT
* *
43236508 TTTC TTTT TTTC TTTC TTTC TTTC TTTC TTTC TTTTAA TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC TTTC TTT
43236557 TGTTTGCACG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 33 0.85
5 6 0.15
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:43239776 original size:27 final size:25
Alignment explanation
Indices: 43239745--43240049 Score: 158
Period size: 27 Copynumber: 11.4 Consensus size: 25
43239735 TAACAATCAT
43239745 TTTACACTATGAGGGTATTTTGGTCA
1 TTTAC-CTATGAGGGTATTTTGGTCA
43239771 TATTACCCTATG-GGG-ATCTTTCGGTCA
1 T-TTA-CCTATGAGGGTAT-TTT-GGTCA
*
43239798 TTCTATCTTATGAGGGTATTTTGGTCA
1 TT-TA-CCTATGAGGGTATTTTGGTCA
* *
43239825 TTCTATCTTATGAGGGTATTTCGGTCA
1 TT-TA-CCTATGAGGGTATTTTGGTCA
* * * *
43239852 TATTACTCTACGGGGGGTATTTCGATCA
1 T-TTAC-CTA-TGAGGGTATTTTGGTCA
43239880 TTCTAACCTATGAGGGTATTTTGGTCA
1 TT-T-ACCTATGAGGGTATTTTGGTCA
** *
43239907 TTTTACCCTATG-GGGTATTTCAGTTA
1 -TTTA-CCTATGAGGGTATTTTGGTCA
*
43239933 TTCTATCTTATG-GGGTATTTCT-GTCA
1 TT-TA-CCTATGAGGGTATTT-TGGTCA
43239959 TTTTACCTTATCG-GGGTATTTTGGTCA
1 -TTTACC-TAT-GAGGGTATTTTGGTCA
* *
43239986 TTTTACCCTATG-GGTGTATTTCGGTTA
1 -TTTA-CCTATGAGG-GTATTTTGGTCA
* *
43240013 TTTTACCTTAT-AGGGGTATTTCGATCA
1 -TTTACC-TATGA-GGGTATTTTGGTCA
43240040 TTTTACCTAT
1 -TTTACCTAT
43240050 TTTACGGTCT
Statistics
Matches: 231, Mismatches: 23, Indels: 50
0.76 0.08 0.16
Matches are distributed among these distances:
25 5 0.02
26 53 0.23
27 136 0.59
28 33 0.14
29 4 0.02
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (25 bp):
TTTACCTATGAGGGTATTTTGGTCA
Found at i:43239847 original size:54 final size:53
Alignment explanation
Indices: 43239741--43240033 Score: 265
Period size: 54 Copynumber: 5.5 Consensus size: 53
43239731 GCCATAACAA
*
43239741 TCATTTTACAC-TATGAGGGTATTTTGGTCATAT-TACCCTATGGGGATCTTTCGG
1 TCATTTTAC-CTTATGAGGGTATTTTGGTCAT-TCTACCCTATGGGG-TATTTCGG
* * * *
43239795 TCATTCTATCTTATGAGGGTATTTTGGTCATTCTATCTTATGAGGGTATTTCGG
1 TCATTTTACCTTATGAGGGTATTTTGGTCATTCTACCCTATG-GGGTATTTCGG
* * * * * * *
43239849 TCATATTA-CTCTACGGGGGGTATTTCGATCATTCTAACCTATGAGGGTATTTTGG
1 TCATTTTACCT-TA-TGAGGGTATTTTGGTCATTCTACCCTATG-GGGTATTTCGG
* ** * * * *
43239904 TCATTTTACCCTATG-GGGTATTTCAGTTATTCTATCTTATGGGGTATTTCTG
1 TCATTTTACCTTATGAGGGTATTTTGGTCATTCTACCCTATGGGGTATTTCGG
*
43239956 TCATTTTACCTTATCG-GGGTATTTTGGTCATTTTACCCTATGGGTGTATTTCGG
1 TCATTTTACCTTAT-GAGGGTATTTTGGTCATTCTACCCTATGGG-GTATTTCGG
*
43240010 TTATTTTACCTTAT-AGGGGTATTT
1 TCATTTTACCTTATGA-GGGTATTT
43240034 CGATCATTTT
Statistics
Matches: 196, Mismatches: 33, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
52 22 0.11
53 48 0.24
54 79 0.40
55 46 0.23
56 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.45
Consensus pattern (53 bp):
TCATTTTACCTTATGAGGGTATTTTGGTCATTCTACCCTATGGGGTATTTCGG
Found at i:43239881 original size:55 final size:53
Alignment explanation
Indices: 43239811--43240041 Score: 207
Period size: 53 Copynumber: 4.3 Consensus size: 53
43239801 TATCTTATGA
* * * *
43239811 GGGTATTTTGGTCATTCTATCTTATGAGGGTATTTCGGTCATATTACTCTACGGG
1 GGGTATTTCGATCATTCTATCTTATGAGGGTATTTCGGTCATTTTACCCTA--GG
* * * *
43239866 GGGTATTTCGATCATTCTAACCTATGAGGGTATTTTGGTCATTTTACCCTATG
1 GGGTATTTCGATCATTCTATCTTATGAGGGTATTTCGGTCATTTTACCCTAGG
* * * *
43239919 GGGTATTTC-AGTTATTCTATCTTATG-GGGTATTTCTGTCATTTTACCTTATCG
1 GGGTATTTCGA-TCATTCTATCTTATGAGGGTATTTCGGTCATTTTACCCTA-GG
* * * * * * * *
43239972 GGGTATTTTGGTCATTTTACCCTATG-GGTGTATTTCGGTTATTTTACCTTATAG
1 GGGTATTTCGATCATTCTATCTTATGAGG-GTATTTCGGTCATTTTACCCTA-GG
43240026 GGGTATTTCGATCATT
1 GGGTATTTCGATCATT
43240042 TTACCTATTT
Statistics
Matches: 146, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
52 22 0.15
53 44 0.30
54 36 0.25
55 44 0.30
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (53 bp):
GGGTATTTCGATCATTCTATCTTATGAGGGTATTTCGGTCATTTTACCCTAGG
Found at i:43243136 original size:27 final size:27
Alignment explanation
Indices: 43243059--43243268 Score: 237
Period size: 27 Copynumber: 7.8 Consensus size: 27
43243049 GCAATTATGG
* *
43243059 GGGGTATGTTGGTCATTTTACCCTAT-
1 GGGGTATTTTGATCATTTTACCCTATA
* * * * *
43243085 GGGCTATTTCGGTCATTCTATCCTATA
1 GGGGTATTTTGATCATTTTACCCTATA
*
43243112 GGGGTATTTTGATAATTTTACCCTA-A
1 GGGGTATTTTGATCATTTTACCCTATA
43243138 GGCGGTATTTTGATCATTTTACCCTAT-
1 GG-GGTATTTTGATCATTTTACCCTATA
*
43243165 GAGGGTATTTTGATCATTTTACCCTATG
1 G-GGGTATTTTGATCATTTTACCCTATA
* * *
43243193 GGGGTATTTCGATTATTTTACCCTATG
1 GGGGTATTTTGATCATTTTACCCTATA
* *
43243220 GGGGTATTTCGGTCATTTTACCCTATA
1 GGGGTATTTTGATCATTTTACCCTATA
* *
43243247 AGGGTATTTTGACCATTTTACC
1 GGGGTATTTTGATCATTTTACC
43243269 TATTTTAGGG
Statistics
Matches: 158, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
26 24 0.15
27 132 0.84
28 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGGTATTTTGATCATTTTACCCTATA
Found at i:43243211 original size:81 final size:81
Alignment explanation
Indices: 43243061--43243268 Score: 274
Period size: 81 Copynumber: 2.6 Consensus size: 81
43243051 AATTATGGGG
* * * * * * *
43243061 GGTATGTTGGTCATTTTACCCTATG-GGCTATTTCGGTCATTCTATCCTATAGGGGTATTTTGAT
1 GGTATTTTGGTCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATAGGGGTATTTCGAT
43243125 AATTTTACCCTAAGGC
66 AATTTTACCCTAAGGC
* *
43243141 GGTATTTTGATCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTTCGAT
1 GGTATTTTGGTCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATAGGGGTATTTCGAT
* * *
43243206 TATTTTACCCTATGGG
66 AATTTTACCCTAAGGC
* * *
43243222 GGTATTTCGGTCATTTTACCCTATAAGGGTATTTTGACCATTTTACC
1 GGTATTTTGGTCATTTTACCCTATGAGGGTATTTTGATCATTTTACC
43243269 TATTTTAGGG
Statistics
Matches: 111, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 23 0.21
81 88 0.79
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (81 bp):
GGTATTTTGGTCATTTTACCCTATGAGGGTATTTTGATCATTTTACCCTATAGGGGTATTTCGAT
AATTTTACCCTAAGGC
Found at i:43246662 original size:10 final size:10
Alignment explanation
Indices: 43246647--43246675 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
43246637 TCTAAATCCT
43246647 GACTCAACTC
1 GACTCAACTC
43246657 GACTCAACTC
1 GACTCAACTC
43246667 GACTCAACT
1 GACTCAACT
43246676 ATGGCATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.38, G:0.10, T:0.21
Consensus pattern (10 bp):
GACTCAACTC
Found at i:43247574 original size:17 final size:17
Alignment explanation
Indices: 43247531--43247574 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
43247521 CAATGTGTGT
*
43247531 TGCCCGTGTGTGACACA
1 TGCCCGTGTGCGACACA
* *
43247548 TCCCCATGTGCGACACA
1 TGCCCGTGTGCGACACA
43247565 TGCCCGTGTG
1 TGCCCGTGTG
43247575 GCCAGGCTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.16, C:0.34, G:0.27, T:0.23
Consensus pattern (17 bp):
TGCCCGTGTGCGACACA
Found at i:43249260 original size:28 final size:29
Alignment explanation
Indices: 43249178--43249253 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 29
43249168 CAATAGTAGT
*
43249178 GTGTGGGCCATAGCCCAATACAGTAACAAA
1 GTGTGGGCCTTAGCCCAATACAGTAAC-AA
*
43249208 ATGTGGGCCTTAGCCCAATACAGTAAC-A
1 GTGTGGGCCTTAGCCCAATACAGTAACAA
43249236 GTGTGGGCCTTAGCCCAA
1 GTGTGGGCCTTAGCCCAA
43249254 AATAGTATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 18 0.42
30 25 0.58
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (29 bp):
GTGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:43250646 original size:27 final size:27
Alignment explanation
Indices: 43250606--43250962 Score: 357
Period size: 27 Copynumber: 13.3 Consensus size: 27
43250596 GGCTTGGGCC
43250606 GTAAAATTACTGAAATACCCTCGATGG
1 GTAAAATTACTGAAATACCCTCGATGG
* *
43250633 GTAAAATTATTGAAATACCCTCGATAG
1 GTAAAATTACTGAAATACCCTCGATGG
* * * *
43250660 GTAAAATTACCGAAATATCCACGATAG
1 GTAAAATTACTGAAATACCCTCGATGG
* *
43250687 ATAAAACTACTGAAATACCCTCGATGG
1 GTAAAATTACTGAAATACCCTCGATGG
* * *
43250714 GTAAAATTATTGAAATACCTTCGATAG
1 GTAAAATTACTGAAATACCCTCGATGG
* *
43250741 GTAAAATTACTGAAATACCTTTGAT-G
1 GTAAAATTACTGAAATACCCTCGATGG
** *
43250767 GTAAAATTACCAAAATACCCTCGATAG
1 GTAAAATTACTGAAATACCCTCGATGG
* * *
43250794 GCAAAATTATTGAAATACCCTCAATGG
1 GTAAAATTACTGAAATACCCTCGATGG
43250821 GTAAAATTA-TCGAAATACCCTCGATGG
1 GTAAAATTACT-GAAATACCCTCGATGG
* * * *
43250848 GTAAAATTTCTAAAATACCCCCAATGG
1 GTAAAATTACTGAAATACCCTCGATGG
**
43250875 GTAAAATTAC-GAAAATACCC-CTGAAAG
1 GTAAAATTACTG-AAATACCCTC-GATGG
* * *
43250902 GTAAAA-TAATCAAAATACCCTTGATGG
1 GTAAAATTACT-GAAATACCCTCGATGG
* *
43250929 GTAAAATTACCGAAATA-CCTCTATAGG
1 GTAAAATTACTGAAATACCCTCGAT-GG
43250956 GTAAAAT
1 GTAAAAT
43250963 GACCGTTCTA
Statistics
Matches: 270, Mismatches: 50, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
26 31 0.11
27 236 0.87
28 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (27 bp):
GTAAAATTACTGAAATACCCTCGATGG
Found at i:43251099 original size:26 final size:26
Alignment explanation
Indices: 43251070--43251122 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
43251060 GCATCTCTTT
*
43251070 TGCGTTACTGTTACTGGCAGATTTGC
1 TGCGTTACTATTACTGGCAGATTTGC
* *
43251096 TGCGTTATTATTACTGGCAGCTTTGC
1 TGCGTTACTATTACTGGCAGATTTGC
43251122 T
1 T
43251123 ACGATATTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.42
Consensus pattern (26 bp):
TGCGTTACTATTACTGGCAGATTTGC
Found at i:43251130 original size:26 final size:26
Alignment explanation
Indices: 43251080--43251130 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
43251070 TGCGTTACTG
* *
43251080 TTACTGGCAGATTTGCTGCGTTATTA
1 TTACTGGCAGATTTGCTACGATATTA
*
43251106 TTACTGGCAGCTTTGCTACGATATT
1 TTACTGGCAGATTTGCTACGATATT
43251131 GGTGTGTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (26 bp):
TTACTGGCAGATTTGCTACGATATTA
Found at i:43253204 original size:34 final size:35
Alignment explanation
Indices: 43253153--43253237 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
43253143 GTTTCAAAGG
43253153 TATT-AAAGTGTGGTTG-TTTCACATATTACAATGA
1 TATTCAAA-TGTGGTTGTTTTCACATATTACAATGA
* * * *
43253187 TATTCAAATGTGGTTGTTTTTACATGTTATAATGT
1 TATTCAAATGTGGTTGTTTTCACATATTACAATGA
* *
43253222 TGTCCAAATGTGGTTG
1 TATTCAAATGTGGTTG
43253238 CTTTGCATGT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
34 12 0.28
35 31 0.72
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (35 bp):
TATTCAAATGTGGTTGTTTTCACATATTACAATGA
Found at i:43253254 original size:34 final size:35
Alignment explanation
Indices: 43253191--43253261 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
43253181 CAATGATATT
* *
43253191 CAAATGTGGTTGTTTTTACATGTTATAATGTTGTC
1 CAAATGTGGTTGTCTTTACATGTTATAATGCTGTC
*
43253226 CAAATGTGGTTG-CTTTGCATG-TATTAATGCTGTC
1 CAAATGTGGTTGTCTTTACATGTTA-TAATGCTGTC
43253260 CA
1 CA
43253262 TTTTTTGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 2 0.06
34 18 0.56
35 12 0.38
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (35 bp):
CAAATGTGGTTGTCTTTACATGTTATAATGCTGTC
Found at i:43253361 original size:69 final size:69
Alignment explanation
Indices: 43253251--43253379 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 69
43253241 TGCATGTATT
* * **
43253251 AATGCTGTCCATTTTTTGTACAAATCTATGATGTCTGAATGTTGT-TAATGCTGTCCAAATTAGT
1 AATGCTGTCCATTTTTGGTACAAATCAATGATGTCCAAATGTT-TCTAATGCTGTCCAAATTAGT
43253315 GCGTA
65 GCGTA
* * * *
43253320 AATGCTGTCCATTTTTGGTACAAGTCAATGCTGTCCAAATGTTTCTACTGTTGTCCAAAT
1 AATGCTGTCCATTTTTGGTACAAATCAATGATGTCCAAATGTTTCTAATGCTGTCCAAAT
43253380 ATTTGTGAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 1 0.02
69 50 0.98
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (69 bp):
AATGCTGTCCATTTTTGGTACAAATCAATGATGTCCAAATGTTTCTAATGCTGTCCAAATTAGTG
CGTA
Found at i:43258256 original size:6 final size:6
Alignment explanation
Indices: 43258245--43258270 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43258235 AGACTGAACA
43258245 GAAAGT GAAAGT GAAAGT GAAAGT GA
1 GAAAGT GAAAGT GAAAGT GAAAGT GA
43258271 TAGTCTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAAGT
Found at i:43259952 original size:40 final size:40
Alignment explanation
Indices: 43259908--43260039 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
43259898 TGTTTAGCTT
* * *
43259908 TTAGTGTACGATTCGAGATAGCTTCGACTATTTATGGCAC
1 TTAGTGTGCGATTCGAGATAGCTTCGGCTATATATGGCAC
* *
43259948 TTAGTGTGCGATT-GGGAATAGCTTCGGCTATATATGACAC
1 TTAGTGTGCGATTCGAG-ATAGCTTCGGCTATATATGGCAC
** * * *
43259988 TTAGTGTGCGAGACTAAGATAGCTTCGGCTATGTAAGGCAC
1 TTAGTGTGCGATTC-GAGATAGCTTCGGCTATATATGGCAC
43260029 TTAGTGTGCGA
1 TTAGTGTGCGA
43260040 GATTATAATA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.03
40 43 0.56
41 31 0.40
42 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (40 bp):
TTAGTGTGCGATTCGAGATAGCTTCGGCTATATATGGCAC
Found at i:43260019 original size:41 final size:41
Alignment explanation
Indices: 43259923--43260059 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
43259913 GTACGATTCG
* * *
43259923 AGATAGCTTCGACTATTTATGGCACTTAGTGTGC--GATTG
1 AGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATTA
* * *
43259962 GGAATAGCTTCGGCTATATATGACACTTAGTGTGCGAGACTA
1 AG-ATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATTA
* *
43260004 AGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGAGATTA
1 AGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATTA
43260045 TA-ATAGCTTCGGCTA
1 -AGATAGCTTCGGCTA
43260060 AGCGATGGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 29 0.35
41 48 0.58
42 5 0.06
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (41 bp):
AGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATTA
Found at i:43260802 original size:34 final size:35
Alignment explanation
Indices: 43260742--43260808 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
43260732 TGATATCCAA
* *
43260742 ATGTGGTTGTTTTTACATGTTATAATGTTGTCCGG
1 ATGTGGTTGTCTTTACATGTTATAATGCTGTCCGG
*
43260777 ATGTGGTTG-CTTTGCATG-TATTAATGCTGTCC
1 ATGTGGTTGTCTTTACATGTTA-TAATGCTGTCC
43260809 ATTTTGAGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 2 0.07
34 17 0.61
35 9 0.32
ACGTcount: A:0.16, C:0.12, G:0.25, T:0.46
Consensus pattern (35 bp):
ATGTGGTTGTCTTTACATGTTATAATGCTGTCCGG
Found at i:43270030 original size:24 final size:24
Alignment explanation
Indices: 43269997--43270087 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
43269987 TTGTCACCCC
43269997 CAGCTCGTGAGAGCATACTGATTA
1 CAGCTCGTGAGAGCATACTGATTA
*
43270021 CAGCTTGTGAGAGCATACCT-ATTA
1 CAGCTCGTGAGAGCATA-CTGATTA
* *
43270045 TAGCTCGTGAGAGTATA-TAGATTTA
1 CAGCTCGTGAGAGCATACT-GA-TTA
* *
43270070 CAGCTCGGGTGAGCATAC
1 CAGCTCGTGAGAGCATAC
43270088 ATGTTCAGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
22 1 0.02
24 35 0.65
25 18 0.33
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (24 bp):
CAGCTCGTGAGAGCATACTGATTA
Found at i:43271183 original size:15 final size:15
Alignment explanation
Indices: 43271165--43271215 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
43271155 TCTATCGTGT
43271165 GTGACACATGGCCAG
1 GTGACACATGGCCAG
*
43271180 GTG--ACATGGCCGTG
1 GTGACACATGGCC-AG
43271194 TGTGACACATGGCCAG
1 -GTGACACATGGCCAG
43271210 GTGACA
1 GTGACA
43271216 TGGCCGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 8 0.27
14 1 0.03
15 12 0.40
16 1 0.03
17 8 0.27
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (15 bp):
GTGACACATGGCCAG
Found at i:43271188 original size:13 final size:13
Alignment explanation
Indices: 43271170--43271220 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
43271160 CGTGTGTGAC
43271170 ACATGGCCAGGTG
1 ACATGGCCAGGTG
*
43271183 ACATGGCCGTGTGTG
1 ACATGGCC-AG-GTG
43271198 ACACATGGCCAGGTG
1 --ACATGGCCAGGTG
43271213 ACATGGCC
1 ACATGGCC
43271221 GTGTGTCCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 16 0.50
14 1 0.03
15 6 0.19
16 1 0.03
17 8 0.25
ACGTcount: A:0.22, C:0.25, G:0.35, T:0.18
Consensus pattern (13 bp):
ACATGGCCAGGTG
Found at i:43271196 original size:30 final size:30
Alignment explanation
Indices: 43271160--43271226 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
43271150 GTGTCTCTAT
43271160 CGTGTGTGACACATGGCCAGGTGACATGGC
1 CGTGTGTGACACATGGCCAGGTGACATGGC
43271190 CGTGTGTGACACATGGCCAGGTGACATGGC
1 CGTGTGTGACACATGGCCAGGTGACATGGC
43271220 CGTGTGT
1 CGTGTGT
43271227 CCCCTATAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.18, C:0.22, G:0.37, T:0.22
Consensus pattern (30 bp):
CGTGTGTGACACATGGCCAGGTGACATGGC
Found at i:43272662 original size:20 final size:20
Alignment explanation
Indices: 43272613--43272667 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
43272603 CATAATAAAA
*
43272613 GTACCAAAGTACAAACAGGG
1 GTACCAAAGTACAATCAGGG
* ** *
43272633 GCACGTAAGTGCAATCAGGG
1 GTACCAAAGTACAATCAGGG
43272653 GTACCAAAGTACAAT
1 GTACCAAAGTACAAT
43272668 AATTTTCTAT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (20 bp):
GTACCAAAGTACAATCAGGG
Found at i:43272867 original size:17 final size:16
Alignment explanation
Indices: 43272836--43272869 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
43272826 TATCCAAGTT
*
43272836 TTAATCAATATATTAA
1 TTAATCAATAAATTAA
43272852 TTAATACAATAAATTAA
1 TTAAT-CAATAAATTAA
43272869 T
1 T
43272870 CTCATACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAATCAATAAATTAA
Found at i:43283073 original size:26 final size:26
Alignment explanation
Indices: 43283044--43283102 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
43283034 AGCAAAGCTG
* *
43283044 CCAGTAATAGTGATGCAACAAAGTTA
1 CCAGTAATAGTAATACAACAAAGTTA
*
43283070 CCAGTAATAGTAATACAACAAAGTTT
1 CCAGTAATAGTAATACAACAAAGTTA
43283096 CCAGTAA
1 CCAGTAA
43283103 CAATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (26 bp):
CCAGTAATAGTAATACAACAAAGTTA
Found at i:43283304 original size:27 final size:27
Alignment explanation
Indices: 43283273--43283331 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
43283263 CAACTCCTAG
43283273 GGGTATAACAGTCATTGTACCCTATGA
1 GGGTATAACAGTCATTGTACCCTATGA
** * *
43283300 GGGTATTTCAGTCATTTTACCCTTTGA
1 GGGTATAACAGTCATTGTACCCTATGA
43283327 GGGTA
1 GGGTA
43283332 ATTTAGTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (27 bp):
GGGTATAACAGTCATTGTACCCTATGA
Found at i:43283339 original size:27 final size:27
Alignment explanation
Indices: 43283282--43283558 Score: 190
Period size: 27 Copynumber: 10.3 Consensus size: 27
43283272 GGGGTATAAC
*
43283282 AGTCATTGTACCCTAT-GAGGGT-ATTT
1 AGTCATTTTACCCT-TCGAGGGTAATTT
*
43283308 CAGTCATTTTACCCTTTGAGGGTAATTT
1 -AGTCATTTTACCCTTCGAGGGTAATTT
* * * *
43283336 AGTCATTTTACCTTTTGGGGGTAATTC
1 AGTCATTTTACCCTTCGAGGGTAATTT
* * * *
43283363 AATCATTCTACCCTTCGAGTGTAATTC
1 AGTCATTTTACCCTTCGAGGGTAATTT
* * * *
43283390 GGTCACTTTACCCTTCGGGGGTAATTC
1 AGTCATTTTACCCTTCGAGGGTAATTT
* * *
43283417 AGTCACTTTACCCTCCGGGGGTAA-TT
1 AGTCATTTTACCCTTCGAGGGTAATTT
*
43283443 CGATCATTTTACCCTTCG-GGGTAATTT
1 AG-TCATTTTACCCTTCGAGGGTAATTT
* * *
43283470 GGTCATTTTACCGTTC-AGGGATAATTC
1 AGTCATTTTACCCTTCGAGGG-TAATTT
* * * * *
43283497 GGTCATTTT-CGTCTACGGGGGTAATTC
1 AGTCATTTTAC-CCTTCGAGGGTAATTT
* *
43283524 GGTCATTTTACCTTTC-AGGAGTAATTT
1 AGTCATTTTACCCTTCGAGG-GTAATTT
*
43283551 GGTCATTT
1 AGTCATTT
43283559 GCCCGTTATT
Statistics
Matches: 206, Mismatches: 34, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
26 28 0.14
27 170 0.83
28 8 0.04
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (27 bp):
AGTCATTTTACCCTTCGAGGGTAATTT
Done.