Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 128 of 163
Found at i:41068155 original size:113 final size:113
Alignment explanation
Indices: 41067978--41068330 Score: 442
Period size: 113 Copynumber: 3.1 Consensus size: 113
41067968 ATAATAAGCA
* * *
41067978 TTAGCTGCG-TTTCATGAAAAGCGCCGCAAAAAACCTAAGGCCAACAACGCCGTTTTCTGAG-TT
1 TTAGCGGCGTTTTC-TGAAAAGCGTCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTT
*
41068041 TTGGGCCTTTAGCGGCATTTTTTAAAAAGCGCCGCTAATGTTCGGGGGAC-
65 TTGGGCCTTTAGCGGCATTTTTTAAAAAGCGCCGCTAATGCTC--GGGACT
* *
41068091 TTAGTGGCGTTTTCTGAAAAGCGTCGCAAAAAACCTAAGGCCAACGACGACGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTCTGAAAAGCGTCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
* * * ****
41068156 TGGGTCTGTAGCGGCATTTTTTCAAAAGCGCCGCTAATGCTCTTTCCT
66 TGGGCCTTTAGCGGCATTTTTTAAAAAGCGCCGCTAATGCTCGGGACT
* * * *
41068204 TTAGCGGCGTTTTCTAAAAAGCGTTGCAAAATACCTAAGGCCAACGGCGCCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTCTGAAAAGCGTCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
* * * * *
41068269 TGGGCCTTTAGCGGCGTTTTCTGAAAAGGCGCCGCTAATGCTCCGGCCT
66 TGGGCCTTTAGCGGCATTTT-TTAAAAAGCGCCGCTAATGCTCGGGACT
*
41068318 TTAGCGGCATTTT
1 TTAGCGGCGTTTT
41068331 TGAGGAAGCG
Statistics
Matches: 207, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
112 1 0.00
113 127 0.61
114 79 0.38
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (113 bp):
TTAGCGGCGTTTTCTGAAAAGCGTCGCAAAAAACCTAAGGCCAACGACGCCGTTTTCTGAGTTTT
TGGGCCTTTAGCGGCATTTTTTAAAAAGCGCCGCTAATGCTCGGGACT
Found at i:41069201 original size:7 final size:7
Alignment explanation
Indices: 41069191--41069328 Score: 114
Period size: 7 Copynumber: 19.6 Consensus size: 7
41069181 TGGTTTTTGA
41069191 GTTTGGG
1 GTTTGGG
* *
41069198 GTTTAGT
1 GTTTGGG
*
41069205 TTTTGGG
1 GTTTGGG
*
41069212 GTTAGGG
1 GTTTGGG
*
41069219 GTTTAGG
1 GTTTGGG
41069226 GTTTGGG
1 GTTTGGG
41069233 GTTTGGG
1 GTTTGGG
* **
41069240 ATTTTAG
1 GTTTGGG
* * *
41069247 TTTTTGA
1 GTTTGGG
41069254 GTTTGGG
1 GTTTGGG
* *
41069261 GTTTAGT
1 GTTTGGG
41069268 GTTTGGG
1 GTTTGGG
*
41069275 GTTAGGG
1 GTTTGGG
*
41069282 GTTTTGG
1 GTTTGGG
*
41069289 GTTTGGA
1 GTTTGGG
*
41069296 TTTTGGG
1 GTTTGGG
41069303 AGTTTGGG
1 -GTTTGGG
41069311 GTTTGGG
1 GTTTGGG
41069318 GTTTGGG
1 GTTTGGG
41069325 GTTT
1 GTTT
41069329 AAGGATAATT
Statistics
Matches: 99, Mismatches: 31, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
7 93 0.94
8 6 0.06
ACGTcount: A:0.07, C:0.00, G:0.45, T:0.48
Consensus pattern (7 bp):
GTTTGGG
Found at i:41069256 original size:63 final size:64
Alignment explanation
Indices: 41069170--41069303 Score: 216
Period size: 63 Copynumber: 2.1 Consensus size: 64
41069160 AATATTACGA
* * *
41069170 TTTGGGATTTTTGGTTTTTGAGTTTGGGGTTTAGTTTTTGGGGTTAGGGGTTTAGGGTTTGGGG
1 TTTGGGATTTTTAGTTTTTGAGTTTGGGGTTTAGTGTTTGGGGTTAGGGGTTTAGGGTTTGGAG
* *
41069234 TTTGGGA-TTTTAGTTTTTGAGTTTGGGGTTTAGTGTTTGGGGTTAGGGGTTTTGGGTTTGGAT
1 TTTGGGATTTTTAGTTTTTGAGTTTGGGGTTTAGTGTTTGGGGTTAGGGGTTTAGGGTTTGGAG
41069297 TTTGGGA
1 TTTGGGA
41069304 GTTTGGGGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 58 0.89
64 7 0.11
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (64 bp):
TTTGGGATTTTTAGTTTTTGAGTTTGGGGTTTAGTGTTTGGGGTTAGGGGTTTAGGGTTTGGAG
Found at i:41069311 original size:29 final size:28
Alignment explanation
Indices: 41069254--41069323 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
41069244 TAGTTTTTGA
*
41069254 GTTTGGGGTTTAG-TGTTTGGGGTTAGGG
1 GTTTGGGGTTTGGAT-TTTGGGGTTAGGG
* *
41069282 GTTTTGGGTTTGGATTTTGGGAGTTTGGG
1 GTTTGGGGTTTGGATTTTGGG-GTTAGGG
41069311 GTTTGGGGTTTGG
1 GTTTGGGGTTTGG
41069324 GGTTTAAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 17 0.47
29 19 0.53
ACGTcount: A:0.06, C:0.00, G:0.49, T:0.46
Consensus pattern (28 bp):
GTTTGGGGTTTGGATTTTGGGGTTAGGG
Found at i:41069593 original size:26 final size:26
Alignment explanation
Indices: 41069557--41069607 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
41069547 TTAAGGATGG
41069557 TTTAATGTTAAATTGAATTCATGAAC
1 TTTAATGTTAAATTGAATTCATGAAC
* *
41069583 TTTAGTGTTAAATTGTATTCATGAA
1 TTTAATGTTAAATTGAATTCATGAA
41069608 AACGACGCCG
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:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (26 bp):
TTTAATGTTAAATTGAATTCATGAAC
Found at i:41070358 original size:19 final size:19
Alignment explanation
Indices: 41070336--41070379 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
41070326 CTCTCATCTC
*
41070336 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* *
41070355 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
41070374 CCCCAA
1 CCCCAA
41070380 CGTAGTCCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.43, G:0.02, T:0.23
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:41070929 original size:22 final size:21
Alignment explanation
Indices: 41070886--41070929 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
41070876 CCTTCTGTAA
* *
41070886 TGGAAAAAAAAATGGTTGAGT
1 TGGAAAAAAAAATGATTAAGT
*
41070907 TGGAAAAAGAAAATTATTAAGT
1 TGGAAAAA-AAAATGATTAAGT
41070929 T
1 T
41070930 ATCATTAGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (21 bp):
TGGAAAAAAAAATGATTAAGT
Found at i:41072488 original size:18 final size:16
Alignment explanation
Indices: 41072456--41072645 Score: 84
Period size: 16 Copynumber: 11.6 Consensus size: 16
41072446 TAACTTAAAT
* * *
41072456 AACTCACATAATACAC
1 AACTTACATAAAATAC
41072472 AACTTACATAAAATAC
1 AACTTACATAAAATAC
41072488 AACTTACATAAAA-A-
1 AACTTACATAAAATAC
* ***
41072502 AGTCTATGACATAGCTTAC
1 A-ACT-T-ACATAAAATAC
* **
41072521 ATA-ATACATAACTTAC
1 A-ACTTACATAAAATAC
* *
41072537 ATAGCTTACATAAAAAAT
1 A-A-CTTACATAAAATAC
41072555 AACTTACATAAAATAC
1 AACTTACATAAAATAC
***
41072571 AACTTACATAGCTTAC
1 AACTTACATAAAATAC
* **
41072587 ATA-ATACATAACTTAC
1 A-ACTTACATAAAATAC
*
41072603 ATAGCTTACATAATAA-AT
1 A-A-CTTACATAA-AATAC
41072621 AACTTACATAAAATAC
1 AACTTACATAAAATAC
41072637 AACTTACAT
1 AACTTACAT
41072646 GGCTTACATA
Statistics
Matches: 134, Mismatches: 28, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
14 1 0.01
15 5 0.04
16 99 0.74
17 9 0.07
18 19 0.14
19 1 0.01
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (16 bp):
AACTTACATAAAATAC
Found at i:41072543 original size:25 final size:25
Alignment explanation
Indices: 41072510--41072564 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
41072500 AAAGTCTATG
* *
41072510 ACATAGCTTACATAATACATAACTT
1 ACATAGCTTACATAAAAAATAACTT
41072535 ACATAGCTTACATAAAAAATAACTT
1 ACATAGCTTACATAAAAAATAACTT
41072560 ACATA
1 ACATA
41072565 AAATACAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (25 bp):
ACATAGCTTACATAAAAAATAACTT
Found at i:41072571 original size:25 final size:25
Alignment explanation
Indices: 41072518--41072571 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
41072508 TGACATAGCT
* * ***
41072518 TACATAATACATAACTTACATAGCT
1 TACATAAAAAATAACTTACATAAAA
41072543 TACATAAAAAATAACTTACATAAAA
1 TACATAAAAAATAACTTACATAAAA
41072568 TACA
1 TACA
41072572 ACTTACATAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.28
Consensus pattern (25 bp):
TACATAAAAAATAACTTACATAAAA
Found at i:41072575 original size:41 final size:41
Alignment explanation
Indices: 41072516--41072605 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
41072506 TATGACATAG
* *
41072516 CTTACATAATACATAACTTACATAGCTTACATAAAAAATAA
1 CTTACATAAAACACAACTTACATAGCTTACATAAAAAATAA
* * *
41072557 CTTACATAAAATACAACTTACATAGCTTACATAATACATAA
1 CTTACATAAAACACAACTTACATAGCTTACATAAAAAATAA
41072598 CTTACATA
1 CTTACATA
41072606 GCTTACATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (41 bp):
CTTACATAAAACACAACTTACATAGCTTACATAAAAAATAA
Found at i:41072585 original size:25 final size:24
Alignment explanation
Indices: 41072557--41072630 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 24
41072547 TAAAAAATAA
*
41072557 CTTACATAAAATACAACTTACATAG
1 CTTACATAAAA-ATAACTTACATAG
*
41072582 CTTACATAATACATAACTTACATAG
1 CTTACATAA-AAATAACTTACATAG
41072607 CTTACATAATAAATAACTTACATA
1 CTTACATAA-AAATAACTTACATA
41072631 AAATACAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 44 0.98
26 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (24 bp):
CTTACATAAAAATAACTTACATAG
Found at i:41072599 original size:66 final size:66
Alignment explanation
Indices: 41072474--41072697 Score: 308
Period size: 66 Copynumber: 3.4 Consensus size: 66
41072464 TAATACACAA
* * *
41072474 CTTACATAAAATACAACTTACATAAAA-A-AGTCTATGACATAGCTTACATAATACATAACTTAC
1 CTTACATAAAAAATAACTTACATAAAATACA-ACT-T-ACATAGCTTACATAATACATAACTTAC
41072537 ATAG
63 ATAG
41072541 CTTACATAAAAAATAACTTACATAAAATACAACTTACATAGCTTACATAATACATAACTTACATA
1 CTTACATAAAAAATAACTTACATAAAATACAACTTACATAGCTTACATAATACATAACTTACATA
41072606 G
66 G
* * * *
41072607 CTTACATAATAAATAACTTACATAAAATACAACTTACATGGCTTACATAACACGTAACTTACATA
1 CTTACATAAAAAATAACTTACATAAAATACAACTTACATAGCTTACATAATACATAACTTACATA
*
41072672 A
66 G
* * *
41072673 CTTATATAATACATAACTTACATAA
1 CTTACATAAAAAATAACTTACATAA
41072698 TTTCGGAGCT
Statistics
Matches: 145, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
66 115 0.79
67 26 0.18
68 3 0.02
69 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.29
Consensus pattern (66 bp):
CTTACATAAAAAATAACTTACATAAAATACAACTTACATAGCTTACATAATACATAACTTACATA
G
Found at i:41072627 original size:41 final size:41
Alignment explanation
Indices: 41072582--41072698 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
41072572 ACTTACATAG
*
41072582 CTTACATAATACATAACTTACATAGCTTACATAATAAATAA
1 CTTACATAATATATAACTTACATAGCTTACATAATAAATAA
* * * * **
41072623 CTTACATAAAATACAACTTACATGGCTTACATAACACGTAA
1 CTTACATAATATATAACTTACATAGCTTACATAATAAATAA
*
41072664 CTTACATAACTTATATAA--TACATAACTTACATAAT
1 CTTACATAA--TATATAACTTACATAGCTTACATAAT
41072699 TTCGGAGCTG
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
41 57 0.92
43 5 0.08
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (41 bp):
CTTACATAATATATAACTTACATAGCTTACATAATAAATAA
Found at i:41072637 original size:25 final size:25
Alignment explanation
Indices: 41072584--41072637 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
41072574 TTACATAGCT
* ***
41072584 TACATAATACATAACTTACATAGCT
1 TACATAATAAATAACTTACATAAAA
41072609 TACATAATAAATAACTTACATAAAA
1 TACATAATAAATAACTTACATAAAA
41072634 TACA
1 TACA
41072638 ACTTACATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.30
Consensus pattern (25 bp):
TACATAATAAATAACTTACATAAAA
Found at i:41072665 original size:25 final size:25
Alignment explanation
Indices: 41072591--41072697 Score: 92
Period size: 25 Copynumber: 4.3 Consensus size: 25
41072581 GCTTACATAA
*
41072591 TACATAACTTACATAGCTTACATAA--
1 TACATAACTTACATAAC--ACATAACT
* * * *
41072616 TAAATAACTTACATAAAATACAACT
1 TACATAACTTACATAACACATAACT
** *
41072641 TACATGGCTTACATAACACGTAACT
1 TACATAACTTACATAACACATAACT
* *
41072666 TACATAACTTATATAATACATAACT
1 TACATAACTTACATAACACATAACT
41072691 TACATAA
1 TACATAA
41072698 TTTCGGAGCT
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
23 4 0.06
25 59 0.94
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.31
Consensus pattern (25 bp):
TACATAACTTACATAACACATAACT
Found at i:41075841 original size:13 final size:13
Alignment explanation
Indices: 41075798--41075834 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
41075788 TTACTAAAAT
*
41075798 TTACTTTAATATA
1 TTACTTAAATATA
*
41075811 TTACTTGAATATA
1 TTACTTAAATATA
41075824 TTACTTAAATA
1 TTACTTAAATA
41075835 ATTTACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:41077206 original size:43 final size:43
Alignment explanation
Indices: 41077082--41077207 Score: 148
Period size: 43 Copynumber: 2.9 Consensus size: 43
41077072 GTTTGCGAAG
*
41077082 AAAGCGCCGCTAAAGAACATGATCTTTAGCAGCG-TTTTTAGT
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTTACT
* *
41077124 AAAGCGCCGCTAACTACAGAACATGATCTTTAGCGGCGTTTGTTTCCT
1 AAAGCGCCGCT-A--A-AGAACATGATCTTTAGCAGCGTTT-TTTACT
* *
41077172 -AAGCGCCGCTAAAGAACATAACCTTTAGCAGCGTTT
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTT
41077208 AATTTTGTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
42 11 0.15
43 22 0.31
44 1 0.01
45 1 0.01
46 21 0.29
47 12 0.17
48 4 0.06
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTTACT
Found at i:41087520 original size:1 final size:1
Alignment explanation
Indices: 41087516--41087544 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
41087506 TTCAAAAAGC
41087516 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41087545 CACTAATAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41090310 original size:3 final size:3
Alignment explanation
Indices: 41090304--41090333 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41090294 GCTTCTTCTT
41090304 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
41090334 GTCTGTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:41095963 original size:3 final size:3
Alignment explanation
Indices: 41095957--41096057 Score: 202
Period size: 3 Copynumber: 33.7 Consensus size: 3
41095947 TTGTTGTACA
41095957 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41096005 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41096053 ATT AT
1 ATT AT
41096058 AAAACAACTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41102589 original size:108 final size:110
Alignment explanation
Indices: 41102397--41102663 Score: 272
Period size: 108 Copynumber: 2.4 Consensus size: 110
41102387 TTTACAGAAG
* ** * * ** *
41102397 ATGTCATGGGTTTCTCCCTCATGGACTTATACATATCTTCATGTCGTGATCTTTCAGTCTGATTT
1 ATGTCATGGGTCTCAACCACATGGACTTACACATATCTTCATGTCGTGATCTGACAGTCTAATTT
*
41102462 ACATTTCACCGAAAGCATCACCATGAATATTATCATTATCATATT
66 ACATTTCACCGAAAGCATCACCATGAATATTATCATAATCATATT
41102507 ATGTCATGGGTCTCAACCACATGGACTTACACAT-TC-TCATGTCGTGATCTGACAGT-TCAATT
1 ATGTCATGGGTCTCAACCACATGGACTTACACATATCTTCATGTCGTGATCTGACAGTCT-AATT
* * * * * * *
41102569 TTCATTTCACTG-GAGACATCACCATGAGTGTTTTCGTAATCATATT
65 TACATTTCACCGAAAG-CATCACCATGAATATTATCATAATCATATT
** * * * * * *
41102615 ATACCATGGGTCTCAGCTACATAGACTTCCACATATCTTCTTATCGTGA
1 ATGTCATGGGTCTCAACCACATGGACTTACACATATCTTCATGTCGTGA
41102664 CTTGCCAGTC
Statistics
Matches: 129, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
107 3 0.02
108 84 0.65
109 4 0.03
110 38 0.29
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (110 bp):
ATGTCATGGGTCTCAACCACATGGACTTACACATATCTTCATGTCGTGATCTGACAGTCTAATTT
ACATTTCACCGAAAGCATCACCATGAATATTATCATAATCATATT
Found at i:41104475 original size:25 final size:25
Alignment explanation
Indices: 41104427--41104579 Score: 91
Period size: 25 Copynumber: 6.2 Consensus size: 25
41104417 CTTATGAGTG
* ** *
41104427 TCCCGATATTTGGCTTTCACGAGCT
1 TCCCGATAATTGGCTCACATGAGCT
*
41104452 TCCCGATAATTAGCTCACATGAGCT
1 TCCCGATAATTGGCTCACATGAGCT
* *
41104477 TCCCGATTAA-TGGCTCTCCTGAGCT
1 TCCCGA-TAATTGGCTCACATGAGCT
* * *
41104502 TTCCGAT-ATTGGATCGCATGAGCT
1 TCCCGATAATTGGCTCACATGAGCT
* * * **
41104526 TCTCGATTA-CGGCTCTTATGAGCT
1 TCCCGATAATTGGCTCACATGAGCT
* *
41104550 T-CCTATTACA-TGGCTCACATGAGAT
1 TCCCGA-TA-ATTGGCTCACATGAGCT
41104575 TCCCG
1 TCCCG
41104580 TTATATGGCT
Statistics
Matches: 96, Mismatches: 26, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
23 3 0.03
24 31 0.32
25 57 0.59
26 5 0.05
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (25 bp):
TCCCGATAATTGGCTCACATGAGCT
Found at i:41104532 original size:24 final size:24
Alignment explanation
Indices: 41104469--41104532 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
41104459 AATTAGCTCA
* * *
41104469 CATGAGCTTCCCGATTAATGGCTCT
1 CATGAGCTTCTCGA-TAATGGATCG
* *
41104494 CCTGAGCTT-TCCGATATTGGATCG
1 CATGAGCTTCT-CGATAATGGATCG
41104518 CATGAGCTTCTCGAT
1 CATGAGCTTCTCGAT
41104533 TACGGCTCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 19 0.61
25 12 0.39
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.33
Consensus pattern (24 bp):
CATGAGCTTCTCGATAATGGATCG
Found at i:41104571 original size:49 final size:49
Alignment explanation
Indices: 41104438--41104579 Score: 126
Period size: 49 Copynumber: 2.9 Consensus size: 49
41104428 CCCGATATTT
* * * * *
41104438 GGCTTTCACGAGCTTCCCGATAATTAGCTCACATGAGCTTCCCGATTAAT
1 GGCTCTCATGAGCTTTCCGATAA-TGGCTCACATGAGCTTCCCGATTAAC
* * * * *
41104488 GGCTCTCCTGAGCTTTCCGATATTGGATCGCATGAGCTTCTCGATT-AC
1 GGCTCTCATGAGCTTTCCGATAATGGCTCACATGAGCTTCCCGATTAAC
* * *
41104536 GGCTCTTATGAGC-TTCCTATTACATGGCTCACATGAGATTCCCG
1 GGCTCTCATGAGCTTTCCGA-TA-ATGGCTCACATGAGCTTCCCG
41104580 TTATATGGCT
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
47 5 0.07
48 14 0.19
49 35 0.49
50 18 0.25
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (49 bp):
GGCTCTCATGAGCTTTCCGATAATGGCTCACATGAGCTTCCCGATTAAC
Found at i:41108656 original size:14 final size:15
Alignment explanation
Indices: 41108637--41108666 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41108627 TTATGAGTCC
41108637 AAAACAAAAAA-AAA
1 AAAACAAAAAAGAAA
41108651 AAAACAAAAAAGAAA
1 AAAACAAAAAAGAAA
41108666 A
1 A
41108667 GACACAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAAGAAA
Found at i:41113286 original size:2 final size:2
Alignment explanation
Indices: 41113279--41113306 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41113269 ATGCAAATTC
41113279 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
41113307 TGCAGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41116590 original size:42 final size:42
Alignment explanation
Indices: 41116530--41116611 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
41116520 AAATAGAGAG
* *
41116530 TTACACGGCTTGGACACACGAT-CGTGTCCTTACCTGTGTGAC
1 TTACACGGCCTGGACACACG-TCCGTGTCCTTACCCGTGTGAC
* *
41116572 TTACACGGCCTGGGCACACGTCCGTGTGCTTACCCGTGTG
1 TTACACGGCCTGGACACACGTCCGTGTCCTTACCCGTGTG
41116612 GCTCTAAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (42 bp):
TTACACGGCCTGGACACACGTCCGTGTCCTTACCCGTGTGAC
Found at i:41117272 original size:22 final size:23
Alignment explanation
Indices: 41117247--41117289 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
41117237 AATCGATTGC
*
41117247 AGGAA-AAAAGAAAAATAAAAGA
1 AGGAAGAAAAGAAAAAAAAAAGA
*
41117269 AGGAAGAACAGAAAAAAAAAA
1 AGGAAGAAAAGAAAAAAAAAA
41117290 CAAGAACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (23 bp):
AGGAAGAAAAGAAAAAAAAAAGA
Found at i:41118017 original size:32 final size:33
Alignment explanation
Indices: 41117958--41118023 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
41117948 GTTGTCGTGC
41117958 TGCAACATGCATGCAACAAAAAAAAAACAGACT
1 TGCAACATGCATGCAACAAAAAAAAAACAGACT
41117991 TGCAACATGCATGCAAC-AAAAAAAAACAGACT
1 TGCAACATGCATGCAACAAAAAAAAAACAGACT
41118023 T
1 T
41118024 AGCTGCATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.48
33 17 0.52
ACGTcount: A:0.53, C:0.21, G:0.12, T:0.14
Consensus pattern (33 bp):
TGCAACATGCATGCAACAAAAAAAAAACAGACT
Found at i:41118032 original size:29 final size:32
Alignment explanation
Indices: 41117960--41118023 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
41117950 TGTCGTGCTG
41117960 CAACATGCATGCAACAAAAAAAAAACAGACTT
1 CAACATGCATGCAACAAAAAAAAAACAGACTT
41117992 GCAACATGCATGCAAC-AAAAAAAAACAGACTT
1 -CAACATGCATGCAACAAAAAAAAAACAGACTT
41118024 AGCTGCATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.55, C:0.22, G:0.11, T:0.12
Consensus pattern (32 bp):
CAACATGCATGCAACAAAAAAAAAACAGACTT
Found at i:41120768 original size:3 final size:3
Alignment explanation
Indices: 41120762--41120787 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41120752 GAACAACAAC
41120762 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
41120788 AACAAATCAA
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:41120993 original size:22 final size:21
Alignment explanation
Indices: 41120947--41120995 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
41120937 AAATTATAAA
*
41120947 ATATAAAAATATATATATGTAC
1 ATATAAAAATATATACATG-AC
41120969 ATATAAGAAATAGTATACATG-C
1 ATATAA-AAATA-TATACATGAC
41120991 ATATA
1 ATATA
41120996 TATAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 12 0.50
23 5 0.21
24 7 0.29
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (21 bp):
ATATAAAAATATATACATGAC
Found at i:41120996 original size:24 final size:22
Alignment explanation
Indices: 41120947--41120997 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
41120937 AAATTATAAA
* *
41120947 ATATAAAAATATATATATGTAC
1 ATATAAAAATATATACATGCAC
*
41120969 ATATAAGAAATAGTATACATGCAT
1 ATATAA-AAATA-TATACATGCAC
41120993 ATATA
1 ATATA
41120998 TAACAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.25
23 5 0.21
24 13 0.54
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (22 bp):
ATATAAAAATATATACATGCAC
Found at i:41121540 original size:23 final size:22
Alignment explanation
Indices: 41121497--41121554 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
41121487 AAATGGTATC
* *
41121497 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
41121518 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
41121541 TGCATATCATATCT
1 TACAAATCATATCT
41121555 ATGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:41121570 original size:21 final size:21
Alignment explanation
Indices: 41121533--41121587 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
41121523 AATCATATCT
41121533 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
41121552 TCTATGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
41121573 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
41121588 CCTTGAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.31
21 22 0.69
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:41128507 original size:27 final size:26
Alignment explanation
Indices: 41128440--41128524 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 26
41128430 TACATAGTAT
41128440 TGGTGCCTATCTGGAAGGCG-C--TGG
1 TGGTGCCTATCTGG-AGGCGCCAATGG
* *
41128464 TGGTGCTTATTTGGGAGGCGCCAATGG
1 TGGTGCCTATCT-GGAGGCGCCAATGG
41128491 TGGTGCCTATCTAGGAGGCGCCAATGG
1 TGGTGCCTATCT-GGAGGCGCCAATGG
41128518 TGGTGCC
1 TGGTGCC
41128525 ATATTGAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.29
25 3 0.06
27 34 0.65
ACGTcount: A:0.14, C:0.20, G:0.40, T:0.26
Consensus pattern (26 bp):
TGGTGCCTATCTGGAGGCGCCAATGG
Found at i:41128647 original size:18 final size:20
Alignment explanation
Indices: 41128605--41128651 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
41128595 GAAACGGAAG
41128605 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
41128625 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
41128643 AAAGAAGAA
1 AAAGAAGAA
41128652 AAAAATTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:41128654 original size:22 final size:23
Alignment explanation
Indices: 41128601--41128654 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
41128591 TACAGAAACG
*
41128601 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
41128625 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
41128646 GAAGAAAAA
1 GAAGAAAAA
41128655 AATTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:41129220 original size:3 final size:3
Alignment explanation
Indices: 41129214--41129257 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
41129204 TTTTTTTTCT
*
41129214 TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TCC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
41129258 CCTTTCTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:41129234 original size:14 final size:14
Alignment explanation
Indices: 41129210--41129258 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
41129200 CCTTTTTTTT
41129210 TTCTT-TCTTCTTC
1 TTCTTCTCTTCTTC
41129223 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
41129237 TTCTTCTCCTTC-TC
1 TTCTTCT-CTTCTTC
41129251 TTCTTCTC
1 TTCTTCTC
41129259 CTTTCTCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.18
14 24 0.71
15 4 0.12
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:41129239 original size:20 final size:20
Alignment explanation
Indices: 41129214--41129257 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
41129204 TTTTTTTTCT
*
41129214 TTCTTCTTCTTCTTCTCTTC
1 TTCTTCTTCTCCTTCTCTTC
41129234 TTCTTCTTCTCCTTCTCTTC
1 TTCTTCTTCTCCTTCTCTTC
41129254 TTCT
1 TTCT
41129258 CCTTTCTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
TTCTTCTTCTCCTTCTCTTC
Found at i:41129259 original size:14 final size:15
Alignment explanation
Indices: 41129216--41129261 Score: 78
Period size: 14 Copynumber: 3.2 Consensus size: 15
41129206 TTTTTTCTTT
41129216 CTTCTTCTTCTTCT-
1 CTTCTTCTTCTTCTC
41129230 CTTCTTCTTCTTCTC
1 CTTCTTCTTCTTCTC
41129245 CTTC-TCTTCTTCTC
1 CTTCTTCTTCTTCTC
41129259 CTT
1 CTT
41129262 TCTCTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 27 0.87
15 4 0.13
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
CTTCTTCTTCTTCTC
Found at i:41129269 original size:14 final size:13
Alignment explanation
Indices: 41129220--41129269 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 13
41129210 TTCTTTCTTC
*
41129220 TTCTTCTTCTCTT
1 TTCTTCTTCTCCT
41129233 CTTCTTCTTCTCCT
1 -TTCTTCTTCTCCT
41129247 TCTCTTCTTCTCCT
1 T-TCTTCTTCTCCT
41129261 TTCTCTCTT
1 TTCT-TCTT
41129270 TTTTTTCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 4 0.12
14 29 0.88
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTTCTTCTCCT
Found at i:41129425 original size:27 final size:27
Alignment explanation
Indices: 41129394--41129459 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
41129384 GCAGAGGGCA
41129394 CCATTGGCGCCTCTCCATGAGGCTCCT
1 CCATTGGCGCCTCTCCATGAGGCTCCT
*
41129421 TCATTGGCGCCTCTCCATGAGGCTCCT
1 CCATTGGCGCCTCTCCATGAGGCTCCT
41129448 CCATTGGCGCCT
1 CCATTGGCGCCT
41129460 ACTAGACAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.11, C:0.39, G:0.23, T:0.27
Consensus pattern (27 bp):
CCATTGGCGCCTCTCCATGAGGCTCCT
Found at i:41137814 original size:29 final size:28
Alignment explanation
Indices: 41137782--41137865 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 28
41137772 TTTAAATGTG
* *
41137782 AAAATTAAATTATATATTTTTAAGATAAT
1 AAAATTAAATTTTATATTTTTAAAAT-AT
*
41137811 AAAAATATAATTTTAT-TATTTTAAAATAT
1 AAAATTA-AATTTTATAT-TTTTAAAATAT
*
41137840 TAAATTAAATTTTTATTATTTTTAAA
1 AAAATTAAA-TTTTA-TATTTTTAAA
41137866 GAAGTTAACT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
28 2 0.04
29 19 0.42
30 23 0.51
31 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
AAAATTAAATTTTATATTTTTAAAATAT
Found at i:41137863 original size:30 final size:30
Alignment explanation
Indices: 41137782--41137865 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 30
41137772 TTTAAATGTG
* *
41137782 AAAATTAAATTATA-TATTTTTAAGATAAT
1 AAAATTAAATTTTATTATTTTTAAAATAAT
*
41137811 AAAAATATAATTTTATTA-TTTTAAAAT-AT
1 AAAATTA-AATTTTATTATTTTTAAAATAAT
*
41137840 TAAATTAAATTTTTATTATTTTTAAA
1 AAAATTAAA-TTTTATTATTTTTAAA
41137866 GAAGTTAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.04
29 21 0.46
30 21 0.46
31 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
AAAATTAAATTTTATTATTTTTAAAATAAT
Found at i:41141094 original size:23 final size:24
Alignment explanation
Indices: 41141053--41141101 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
41141043 TATTTATTTT
*
41141053 TATTATTAAATAATTTAATAATAA
1 TATTATTAAATAATTTAATAACAA
41141077 TATTATTAAA-AATTTAATAACAA
1 TATTATTAAATAATTTAATAACAA
41141100 TA
1 TA
41141102 ACAATAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TATTATTAAATAATTTAATAACAA
Found at i:41141278 original size:16 final size:16
Alignment explanation
Indices: 41141257--41141287 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41141247 TGATTTACTA
41141257 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
41141273 ATTACAACTCTATTC
1 ATTACAACTCTATTC
41141288 AATTCTAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:41144913 original size:109 final size:109
Alignment explanation
Indices: 41144716--41144936 Score: 318
Period size: 109 Copynumber: 2.0 Consensus size: 109
41144706 TTTTTAATAT
* ** *
41144716 ATACAATTTATTATCTACACCAGTTGCATAATTAGTTTCAAACCATACGGGACATTGTTTATTAT
1 ATACAATCTATTATCTACACCAGTTGCATAATTAGTTTCAAACCATACCAGACATTGCTTATTAT
* * *
41144781 ATGTTACTTTTAAACAAACATTTGTGTTTTACGTTTTCACACGC
66 ATATTACTTTTAAACAAACATTTGTGTTTTAAGTTTTCACAAGC
** * *
41144825 ATACAATCTATTATCTACATTAGTTGCATAATTAGTTTCAAACCATACCAGTCATTGCTTATTGT
1 ATACAATCTATTATCTACACCAGTTGCATAATTAGTTTCAAACCATACCAGACATTGCTTATTAT
*
41144890 ATATTATTTTTAAACAAGA-ATTTGTGTTTTAAGTTTTCACAAGC
66 ATATTACTTTTAAACAA-ACATTTGTGTTTTAAGTTTTCACAAGC
41144934 ATA
1 ATA
41144937 TGCGTGTGAT
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
109 98 0.99
110 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (109 bp):
ATACAATCTATTATCTACACCAGTTGCATAATTAGTTTCAAACCATACCAGACATTGCTTATTAT
ATATTACTTTTAAACAAACATTTGTGTTTTAAGTTTTCACAAGC
Found at i:41146995 original size:28 final size:28
Alignment explanation
Indices: 41146936--41147010 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
41146926 AATTTTGGGT
* *
41146936 AAAATTATAAAATTTGTAAAGTAG-GAGA
1 AAAATTATAAAATTTGAAAAATAGAG-GA
*
41146964 AAAATTGTAAAATTTGAAAAATAGAGGCA
1 AAAATTATAAAATTTGAAAAATAGAGG-A
* *
41146993 AAAA-TATAATATCTGAAA
1 AAAATTATAAAATTTGAAA
41147011 GATAAGGGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 33 0.85
29 6 0.15
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.27
Consensus pattern (28 bp):
AAAATTATAAAATTTGAAAAATAGAGGA
Found at i:41153306 original size:43 final size:42
Alignment explanation
Indices: 41153102--41153322 Score: 273
Period size: 43 Copynumber: 5.2 Consensus size: 42
41153092 AGGTTAAGTT
** * *
41153102 TTTAGCGGCGTTT-TTTGAGAAGCGCCGCTAAAGGTTTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTTGGTC
* **** *
41153143 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTATAAACCATGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTA-AAGGTTTGGTC
* *
41153186 TATAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-TTGGTC
* *
41153229 TATAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTTGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTT-TGGTC
41153272 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-TTGGTC
41153315 TTTAGCGG
1 TTTAGCGG
41153323 GACGTTCTTT
Statistics
Matches: 154, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
41 13 0.08
42 16 0.10
43 124 0.81
44 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTTGGTC
Found at i:41153415 original size:22 final size:22
Alignment explanation
Indices: 41153387--41153429 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
41153377 TAGCGGCACT
*
41153387 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
41153409 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
41153430 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:41155838 original size:38 final size:40
Alignment explanation
Indices: 41155780--41155861 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 40
41155770 TTACAGGTTA
* * *
41155780 TAATGAGATCTAGCATTTGTTATAGATTTTTGGGT-TATT
1 TAATGAGATCTAGCACTTGTTACAGATTCTTGGGTATATT
*
41155819 TAATGAGATCTAGC-CTTGTTGCAGATTCTTGGGTAATATT
1 TAATGAGATCTAGCACTTGTTACAGATTCTTGGGT-ATATT
41155859 TAA
1 TAA
41155862 CATAGGTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 16 0.43
39 14 0.38
40 7 0.19
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.44
Consensus pattern (40 bp):
TAATGAGATCTAGCACTTGTTACAGATTCTTGGGTATATT
Found at i:41161822 original size:23 final size:24
Alignment explanation
Indices: 41161799--41161846 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
41161789 ACACACCAAT
41161799 ATCACAGCAAAGCTGCCAGTAATAGA
1 ATCACAGCAAAGCTGCCAGTAAT--A
* *
41161825 ATCGCAGCGAAGCTGCCAGTAA
1 ATCACAGCAAAGCTGCCAGTAA
41161847 CAGTATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (24 bp):
ATCACAGCAAAGCTGCCAGTAATA
Found at i:41162091 original size:27 final size:27
Alignment explanation
Indices: 41162061--41162272 Score: 268
Period size: 27 Copynumber: 7.9 Consensus size: 27
41162051 TTTATTTTAT
*
41162061 GGGGGTATTTCAGTCATTTTACCATTC
1 GGGGGTATTTCAGTCATTTTACCCTTC
*
41162088 GGGGGTATTTTTA-TCATTTTACCC-TC
1 GGGGGTA-TTTCAGTCATTTTACCCTTC
*
41162114 TGGGGGTATTTCGGTCATTTTACCCTTC
1 -GGGGGTATTTCAGTCATTTTACCCTTC
*
41162142 AGGGGTATTTC-GATCATTTTACCCTTC
1 GGGGGTATTTCAG-TCATTTTACCCTTC
* *
41162169 GGGGGTATTCCAGTCATTTTATCCTTC
1 GGGGGTATTTCAGTCATTTTACCCTTC
* *
41162196 GAGGGTATTTCAATCATTTTACCCTTC
1 GGGGGTATTTCAGTCATTTTACCCTTC
* * *
41162223 GAGGATATTTCAATCATTTTACCCTTC
1 GGGGGTATTTCAGTCATTTTACCCTTC
*
41162250 GAGGGTATTTCAGTCATTTTACC
1 GGGGGTATTTCAGTCATTTTACC
41162273 ACGAATCGTA
Statistics
Matches: 164, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
26 6 0.04
27 151 0.92
28 7 0.04
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (27 bp):
GGGGGTATTTCAGTCATTTTACCCTTC
Found at i:41164318 original size:32 final size:32
Alignment explanation
Indices: 41164267--41164331 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
41164257 AAAATTTGAA
* *
41164267 TTTTATTGAAATTTTCCA-CCAACT-TTGATTT
1 TTTTATTAAAATTTACCACCCAA-TATTGATTT
41164298 TTTTAATTAAAATTTACCACCCAATATTGATTT
1 TTTT-ATTAAAATTTACCACCCAATATTGATTT
41164331 T
1 T
41164332 GATGATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 4 0.14
32 13 0.45
33 12 0.41
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (32 bp):
TTTTATTAAAATTTACCACCCAATATTGATTT
Found at i:41168402 original size:25 final size:25
Alignment explanation
Indices: 41168367--41168415 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
41168357 TTTAAGAAGT
*
41168367 GCACTAACAACTTAATCATCTAGAC
1 GCACTAACAACTTAACCATCTAGAC
*
41168392 GCACTAGCAACTTAACCATCTAGA
1 GCACTAACAACTTAACCATCTAGA
41168416 GTAAGTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (25 bp):
GCACTAACAACTTAACCATCTAGAC
Found at i:41169959 original size:25 final size:25
Alignment explanation
Indices: 41169918--41169984 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
41169908 GCACTCTCTC
*
41169918 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATGTAACGGGAAGCTCATGT
* * *
41169943 GAGTCATGTAATGGGAATCTCATGT
1 GAGCCATGTAACGGGAAGCTCATGT
41169968 GAGCCATGTAACGGGAA
1 GAGCCATGTAACGGGAA
41169985 CGGGAAGCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.22
Consensus pattern (25 bp):
GAGCCATGTAACGGGAAGCTCATGT
Found at i:41179375 original size:23 final size:24
Alignment explanation
Indices: 41179339--41179383 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
41179329 ATTTATTGAG
*
41179339 TAATTAAAAATGTAACCATAAAAA
1 TAATTAAAAATGTAACAATAAAAA
41179363 TAATT-AAAATGTAACAATAAA
1 TAATTAAAAATGTAACAATAAA
41179384 TTGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (24 bp):
TAATTAAAAATGTAACAATAAAAA
Found at i:41179673 original size:2 final size:2
Alignment explanation
Indices: 41179660--41179691 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
41179650 GAAAATATTA
*
41179660 AT AT AC 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
41179692 GAGAGAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41184409 original size:42 final size:41
Alignment explanation
Indices: 41184321--41184437 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 41
41184311 GCGTTTACAG
*
41184321 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCATTAA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCATTAA
* * * **
41184362 AAAAAAGACGCCGTTAAAGATCATGTTCTTTAGTAGCGGTTTC
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCAGC-ATTAA
* * *
41184405 AAAAAATCACCACTAAAGATCATGTTCTTTAGC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGC
41184438 GGCGCTTTCA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 6 0.10
42 49 0.78
43 8 0.13
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (41 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCATTAA
Found at i:41184822 original size:21 final size:20
Alignment explanation
Indices: 41184768--41184835 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
41184758 GCTTCTCTCG
*
41184768 CTGCTTCTCTCACTGCAGCCT
1 CTGCTTC-CTCGCTGCAGCCT
*
41184789 TTGCATT-CTCGCTGCAGCCT
1 CTGC-TTCCTCGCTGCAGCCT
*
41184809 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTT-CCTCGCTGCAGCCT
41184830 CTGCTT
1 CTGCTT
41184836 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.05
20 15 0.38
21 21 0.52
22 2 0.05
ACGTcount: A:0.06, C:0.43, G:0.18, T:0.34
Consensus pattern (20 bp):
CTGCTTCCTCGCTGCAGCCT
Found at i:41184987 original size:99 final size:99
Alignment explanation
Indices: 41184798--41184978 Score: 299
Period size: 99 Copynumber: 1.8 Consensus size: 99
41184788 TTTGCATTCT
*
41184798 CGCTGCAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATT
1 CGCTGCAGCCTCTGCTTCCCTCGCTGCCCCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATT
* *** *
41184863 TCTTTTGAACCTCTGCTTCTCTCGCTGCTTCTCG
66 TCCTTTGAACCTCAAATTCGCTCGCTGCTTCTCG
*
41184897 CGCTGCAGCCTCTGCTTCCCTCGTTGCCCCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATT
1 CGCTGCAGCCTCTGCTTCCCTCGCTGCCCCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATT
41184962 TCCTTTGAACCTCAAAT
66 TCCTTTGAACCTCAAAT
41184979 GTGGTCGCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 76 1.00
ACGTcount: A:0.12, C:0.33, G:0.18, T:0.38
Consensus pattern (99 bp):
CGCTGCAGCCTCTGCTTCCCTCGCTGCCCCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATT
TCCTTTGAACCTCAAATTCGCTCGCTGCTTCTCG
Found at i:41221341 original size:117 final size:112
Alignment explanation
Indices: 41221058--41221351 Score: 414
Period size: 117 Copynumber: 2.6 Consensus size: 112
41221048 TTTTTTTTCA
41221058 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTATTTTTTTC
1 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTATTTTTTTC
* ******
41221123 ATATTTTTTATCTGATTCTGACATGAAAAAAAATAATTTTTTTTTCG
66 ATATTTTTTATCTGATTCTGACACGAAAAAAAATAATAAAAAATTCG
*
41221170 TGTACTGTGTACTGGGTGCCGACCATTGACAGGCCAGCACCCAAAAAAAATTTTTTTATTTATTT
1 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC----AAAATTTTTTT-TTTATTT
*
41221235 TTTT-GTATTTTTTTATCTGATTCTGACACGAAATAAAAATAA-AAAAAATTCG
61 TTTTCATA-TTTTTTATCTGATTCTGACACGAAA-AAAAATAATAAAAAATTCG
41221287 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTGT-TTTTTTT
1 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT-TATTTTTTT
41221351 C
65 C
41221352 TTTTTCGTAT
Statistics
Matches: 163, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
112 50 0.31
113 12 0.07
116 13 0.08
117 80 0.49
118 8 0.05
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (112 bp):
TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTATTTTTTTC
ATATTTTTTATCTGATTCTGACACGAAAAAAAATAATAAAAAATTCG
Found at i:41221940 original size:30 final size:31
Alignment explanation
Indices: 41221860--41221951 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 31
41221850 TATTTAATTA
*
41221860 ATTTTTAAAATTTAAAAATTATTATATATAAT
1 ATTTTTAAAATTTAAAAATAATTATATAT-AT
** * *
41221892 ATTTTTAATTTTTTAAAATAAATTCTATAT-T
1 ATTTTTAAAATTTAAAAAT-AATTATATATAT
*
41221923 -TTTTTAAAATTTAAAAATTAATTAAATAT
1 ATTTTTAAAATTTAAAAA-TAATTATATAT
41221952 TGACGTGATA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
30 22 0.46
31 2 0.04
32 16 0.33
33 8 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
ATTTTTAAAATTTAAAAATAATTATATATAT
Found at i:41227398 original size:17 final size:18
Alignment explanation
Indices: 41227365--41227410 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
41227355 TCATATCGAT
41227365 TTAA-AAATTTATATGTA
1 TTAATAAATTTATATGTA
41227382 -TAATAAATATTAT-TGTA
1 TTAATAAAT-TTATATGTA
*
41227399 TTAATATATTTA
1 TTAATAAATTTA
41227411 ATAGTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 11 0.44
18 11 0.44
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TTAATAAATTTATATGTA
Found at i:41235468 original size:25 final size:24
Alignment explanation
Indices: 41235439--41235520 Score: 77
Period size: 25 Copynumber: 3.6 Consensus size: 24
41235429 TTATTTTGTG
41235439 GCAAATGATGAATTAACGGTAAAAT
1 GCAAATGATGAATT-ACGGTAAAAT
* *
41235464 GCAAAGGATGAATT---G---ATT
1 GCAAATGATGAATTACGGTAAAAT
41235482 GCAAATGATGAATTGACGGTAAAAT
1 GCAAATGATGAATT-ACGGTAAAAT
*
41235507 GAAAATGATGAATT
1 GCAAATGATGAATT
41235521 GGCAGTATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
18 15 0.33
21 1 0.02
22 1 0.02
25 28 0.62
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (24 bp):
GCAAATGATGAATTACGGTAAAAT
Found at i:41235486 original size:18 final size:18
Alignment explanation
Indices: 41235463--41235497 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41235453 AACGGTAAAA
41235463 TGCAAAGGATGAATTGAT
1 TGCAAAGGATGAATTGAT
*
41235481 TGCAAATGATGAATTGA
1 TGCAAAGGATGAATTGA
41235498 CGGTAAAATG
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:0.40, C:0.06, G:0.26, T:0.29
Consensus pattern (18 bp):
TGCAAAGGATGAATTGAT
Found at i:41235501 original size:43 final size:43
Alignment explanation
Indices: 41235439--41235521 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
41235429 TTATTTTGTG
*
41235439 GCAAATGATGAATTAACGGTAAAATGCAAAGGATGAATTGATT
1 GCAAATGATGAATTAACGGTAAAATGAAAAGGATGAATTGATT
* *
41235482 GCAAATGATGAATTGACGGTAAAATGAAAATGATGAATTG
1 GCAAATGATGAATTAACGGTAAAATGAAAAGGATGAATTG
41235522 GCAGTATATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.25
Consensus pattern (43 bp):
GCAAATGATGAATTAACGGTAAAATGAAAAGGATGAATTGATT
Found at i:41235545 original size:24 final size:25
Alignment explanation
Indices: 41235481--41235546 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
41235471 ATGAATTGAT
*
41235481 TGCAAATGATGAATTGACGGTAAAA
1 TGCAAATGATGAATTGACAGTAAAA
* * *
41235506 TGAAAATGATGAATTGGCAGT-ATA
1 TGCAAATGATGAATTGACAGTAAAA
*
41235530 TGCAAAGGATGAATTGA
1 TGCAAATGATGAATTGA
41235547 TGATAAAAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 16 0.47
25 18 0.53
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (25 bp):
TGCAAATGATGAATTGACAGTAAAA
Found at i:41236658 original size:59 final size:60
Alignment explanation
Indices: 41236575--41236696 Score: 237
Period size: 59 Copynumber: 2.0 Consensus size: 60
41236565 GTCAGTATGC
41236575 TCACACTATAACACCCCGATCCGTGTCCGTCGCTGGATTAGAGTTACGAGGCATTACCGA
1 TCACACTATAACACCCCGATCCGTGTCCGTCGCTGGATTAGAGTTACGAGGCATTACCGA
41236635 TCACACTATAAC-CCCCGATCCGTGTCCGTCGCTGGATTAGAGTTACGAGGCATTACCGA
1 TCACACTATAACACCCCGATCCGTGTCCGTCGCTGGATTAGAGTTACGAGGCATTACCGA
41236694 TCA
1 TCA
41236697 AAACCTGACT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 50 0.81
60 12 0.19
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (60 bp):
TCACACTATAACACCCCGATCCGTGTCCGTCGCTGGATTAGAGTTACGAGGCATTACCGA
Found at i:41237023 original size:23 final size:22
Alignment explanation
Indices: 41236990--41237158 Score: 85
Period size: 23 Copynumber: 7.3 Consensus size: 22
41236980 AGAAATTGAG
41236990 CAGCATGTATATACCAATTTGGA
1 CAGCAT-TATATACCAATTTGGA
* *
41237013 CAGCACTTATACACAAAATTT-GA
1 CAGCA-TTATATAC-CAATTTGGA
* *
41237036 CAGCATGTATATACAAAATTGGA
1 CAGCAT-TATATACCAATTTGGA
* *
41237059 CAGCATT-TATTCACCAAAATTGGG
1 CAGCATTATA-T-ACC-AATTTGGA
* *
41237083 CAGCATATATGTAGCAATTTGGA
1 CAGCAT-TATATACCAATTTGGA
* *
41237106 CAACACTTATACATA-AAATTT-GA
1 CAGCA-TTAT--ATACCAATTTGGA
* *
41237129 CAGCATGTATATACAAAATTGGA
1 CAGCAT-TATATACCAATTTGGA
*
41237152 CAACATT
1 CAGCATT
41237159 TATTCACCAA
Statistics
Matches: 115, Mismatches: 16, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
21 5 0.04
22 15 0.13
23 63 0.55
24 27 0.23
25 4 0.03
26 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (22 bp):
CAGCATTATATACCAATTTGGA
Found at i:41237048 original size:46 final size:47
Alignment explanation
Indices: 41236959--41237172 Score: 229
Period size: 46 Copynumber: 4.6 Consensus size: 47
41236949 ATCTACCCTG
* * *
41236959 TTTGGACAGCTCTTATACATCAGAAA-TTGAGCAGCATGTATATACCAA
1 TTTGGACAGCACTTATACACCA-AAATTTGA-CAGCATGTATATACAAA
41237007 TTTGGACAGCACTTATACA-CAAAATTTGACAGCATGTATATACAAA
1 TTTGGACAGCACTTATACACCAAAATTTGACAGCATGTATATACAAA
* * * * * * *
41237053 ATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGC-AA
1 TTTGGACAGCACTTATACACCAAAATTTGACAGCATGTATATA-CAAA
* *
41237100 TTTGGACAACACTTATACA-TAAAATTTGACAGCATGTATATACAAA
1 TTTGGACAGCACTTATACACCAAAATTTGACAGCATGTATATACAAA
* * * *
41237146 ATTGGACAACATTTATTCACCAAAATT
1 TTTGGACAGCACTTATACACCAAAATT
41237173 NNNNNNNNNN
Statistics
Matches: 139, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
45 1 0.01
46 71 0.51
47 48 0.35
48 19 0.14
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (47 bp):
TTTGGACAGCACTTATACACCAAAATTTGACAGCATGTATATACAAA
Found at i:41237101 original size:93 final size:93
Alignment explanation
Indices: 41236960--41237172 Score: 320
Period size: 93 Copynumber: 2.3 Consensus size: 93
41236950 TCTACCCTGT
* * * *
41236960 TTGGACAGC-TCTTATACATCAGAAATTGAGCAGCATGTATATACCAATTTGGACAGCACTTATA
1 TTGGACAGCAT-TTATTCACCA-AAATTGAGCAGCATATATATACCAATTTGGACAACACTTATA
41237024 CACAAAATTTGACAGCATGTATATACAAAA
64 CACAAAATTTGACAGCATGTATATACAAAA
* * *
41237054 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATGTAGCAATTTGGACAACACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGAGCAGCATATATATACCAATTTGGACAACACTTATACA
*
41237119 TAAAATTTGACAGCATGTATATACAAAA
66 CAAAATTTGACAGCATGTATATACAAAA
*
41237147 TTGGACAACATTTATTCACCAAAATT
1 TTGGACAGCATTTATTCACCAAAATT
41237173 NNNNNNNNNN
Statistics
Matches: 109, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
93 91 0.83
94 17 0.16
95 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (93 bp):
TTGGACAGCATTTATTCACCAAAATTGAGCAGCATATATATACCAATTTGGACAACACTTATACA
CAAAATTTGACAGCATGTATATACAAAA
Found at i:41241725 original size:22 final size:22
Alignment explanation
Indices: 41241700--41241741 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41241690 TCAAAAGAGA
* *
41241700 CATAATTATTCTACTAATATCT
1 CATAACTATTCAACTAATATCT
*
41241722 CATAACTATTCAAGTAATAT
1 CATAACTATTCAACTAATAT
41241742 TACTTGTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (22 bp):
CATAACTATTCAACTAATATCT
Found at i:41242530 original size:21 final size:23
Alignment explanation
Indices: 41242486--41242529 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41242476 AAAATATTAA
**
41242486 ATATATTTTTTAATTAACATTTT
1 ATATATTTCATAATTAACATTTT
41242509 ATATATTTCATAATTAA-ATTT
1 ATATATTTCATAATTAACATTT
41242530 AAATTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATATTTCATAATTAACATTTT
Found at i:41246994 original size:43 final size:42
Alignment explanation
Indices: 41246902--41247006 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
41246892 GAGATTTTCG
* ** *
41246902 TGTAAGACCATGTCTGGGACATTGGCGTCGTATATGATTACG
1 TGTAAGACCATGTCTGGGACAGTGGAATCGTATATGATTACA
* * *
41246944 TGTAAGACCCTGTCTGGGACAGTGGAATCGTTGTTTGATTACA
1 TGTAAGACCATGTCTGGGACAGTGGAATCG-TATATGATTACA
* *
41246987 TGTAAGACCACGTTTGGGAC
1 TGTAAGACCATGTCTGGGAC
41247007 GTTGGCATTG
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
42 26 0.50
43 26 0.50
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACAGTGGAATCGTATATGATTACA
Found at i:41268291 original size:46 final size:46
Alignment explanation
Indices: 41268224--41268362 Score: 192
Period size: 46 Copynumber: 3.0 Consensus size: 46
41268214 CATGGCAAAG
* *
41268224 TGTGAAACGTA-TGTATGGTATTTCAGTGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGT-TATGGTATTTCAGTAAAGAAAACCATATTGAGT
*
41268270 TGTGAAAAGTAGTTATGGTATTTC-GATAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGTTATGGTATTTCAG-TAAAGAAAACCATATTGAGT
* * *
41268316 TGTGAAGAGTAGGTATGGTGTTTCAGTAAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGTTATGGTATTTCAGTAAAGAAAACCATATTGAGT
41268362 T
1 T
41268363 ATAGCAATGT
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
45 1 0.01
46 80 0.96
47 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (46 bp):
TGTGAAAAGTAGTTATGGTATTTCAGTAAAGAAAACCATATTGAGT
Found at i:41285132 original size:18 final size:18
Alignment explanation
Indices: 41285103--41285148 Score: 83
Period size: 18 Copynumber: 2.5 Consensus size: 18
41285093 TTCAAAATCA
41285103 AACAACGGCATGAATTTAG
1 AACAA-GGCATGAATTTAG
41285122 AACAAGGCATGAATTTAG
1 AACAAGGCATGAATTTAG
41285140 AACAAGGCA
1 AACAAGGCA
41285149 ACGACCGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (18 bp):
AACAAGGCATGAATTTAG
Found at i:41291520 original size:11 final size:11
Alignment explanation
Indices: 41291504--41291529 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41291494 TCAAAGCTGA
41291504 TACTAATAATT
1 TACTAATAATT
41291515 TACTAATAATT
1 TACTAATAATT
41291526 TACT
1 TACT
41291530 GCCCAACCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (11 bp):
TACTAATAATT
Found at i:41292770 original size:13 final size:13
Alignment explanation
Indices: 41292754--41292780 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41292744 TTTAAACTAA
41292754 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
41292767 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
41292780 A
1 A
41292781 ATGAAGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:41294471 original size:19 final size:20
Alignment explanation
Indices: 41294444--41294481 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
41294434 GTAGACATGA
41294444 ATCTATGATTTG-AGTTAAT
1 ATCTATGATTTGAAGTTAAT
*
41294463 ATCTCTGATTTGAAGTTAA
1 ATCTATGATTTGAAGTTAA
41294482 ATGCTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (20 bp):
ATCTATGATTTGAAGTTAAT
Found at i:41296540 original size:48 final size:49
Alignment explanation
Indices: 41296352--41296556 Score: 245
Period size: 48 Copynumber: 4.2 Consensus size: 49
41296342 TTTTTTTTTG
* * *
41296352 CTTTTCGTAAGCTTCCCCCATGCAT-TTGGAGCAGGGCCATTATTACTA
1 CTTTTCGTAAGCCTCCCCCATGCATCTGGGAGCAAGGCCATTATTACTA
* * * **
41296400 CTTTTCATAAGCCTCCCCCATGCGTTTAAGAGCAAGGCCATTATTACTA
1 CTTTTCGTAAGCCTCCCCCATGCATCTGGGAGCAAGGCCATTATTACTA
* * *
41296449 CTTTTTGTAAGCCTCCCTCAATGCATCTGGGA-CTAGGGCCATTATTACTA
1 CTTTTCGTAAGCCTCCC-CCATGCATCTGGGAGC-AAGGCCATTATTACTA
* *
41296499 CTTTTCGTAAGCCT-CTCCATGCATCTGGGAGCAAGGCCATTATTATTA
1 CTTTTCGTAAGCCTCCCCCATGCATCTGGGAGCAAGGCCATTATTACTA
*
41296547 CTTTTAGTAA
1 CTTTTCGTAA
41296557 ATTCTTCCCA
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
48 58 0.44
49 38 0.29
50 37 0.28
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (49 bp):
CTTTTCGTAAGCCTCCCCCATGCATCTGGGAGCAAGGCCATTATTACTA
Found at i:41296810 original size:200 final size:199
Alignment explanation
Indices: 41296450--41296812 Score: 507
Period size: 200 Copynumber: 1.8 Consensus size: 199
41296440 TTATTACTAC
* * * *
41296450 TTTTTGTAAGCCTCCCTCAATGCATCTGGGACTAGGGCCATTATTACTACTTTTCGTAAGCCTCT
1 TTTTTGTAAGCCTCCCCCAACGCATCTGGGACTAGGGCCATTATTACTACTTTCCATAAGCCTCT
* * * *
41296515 CCATGCATCTGGGAGCAAGGCCATTATTATTACTTTTAGTAAATTCTTCCCATGCGTCTAGGAGT
66 CCATGAATCTGAGAGCAAGGCCATTATTATTACTTTTAGTAAATTCTTCCCATACGTCTAGGAGC
*
41296580 AGAGTTATAATTTTTACTTTCTATAAGCCTCCCCTATGCGTTTGGAAGTAGGGTTATAATTTTTT
131 AGAGTTATAATTTTTACTTTCCATAAGCCTCCCCTATGCGTTTGGAAGTAGGGTTATAATTTTTT
41296645 TTAA
196 TTAA
* * *
41296649 TTTTTGTAAGCCTCCCCCTACGCGTCTGGGAGTAGGGCCATTATTACTACTTTCCATAAGCCTCC
1 TTTTTGTAAGCCTCCCCCAACGCATCTGGGACTAGGGCCATTATTACTACTTTCCATAAGCCT-C
* * * * *
41296714 TTCATGAATCTGAGAGCAGGGCCATTATT-TCTACTTTTCGTAAGTTC-TCTCCATATGTCTAGG
65 TCCATGAATCTGAGAGCAAGGCCATTATTAT-TACTTTTAGTAAATTCTTC-CCATACGTCTAGG
*
41296777 AGCA-ATGTTATAATTTTTACTTTCCGTAAGCCTCCC
128 AGCAGA-GTTATAATTTTTACTTTCCATAAGCCTCCC
41296813 TCATGCATCT
Statistics
Matches: 142, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
199 60 0.42
200 82 0.58
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (199 bp):
TTTTTGTAAGCCTCCCCCAACGCATCTGGGACTAGGGCCATTATTACTACTTTCCATAAGCCTCT
CCATGAATCTGAGAGCAAGGCCATTATTATTACTTTTAGTAAATTCTTCCCATACGTCTAGGAGC
AGAGTTATAATTTTTACTTTCCATAAGCCTCCCCTATGCGTTTGGAAGTAGGGTTATAATTTTTT
TTAA
Found at i:41298482 original size:6 final size:6
Alignment explanation
Indices: 41298473--41298510 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
41298463 CTATATAGGT
41298473 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT
41298511 GATTATCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:41303626 original size:9 final size:9
Alignment explanation
Indices: 41303612--41303696 Score: 118
Period size: 9 Copynumber: 9.4 Consensus size: 9
41303602 TTTGGTTAAA
41303612 AATTAACCG
1 AATTAACCG
41303621 AATTAACCG
1 AATTAACCG
*
41303630 AATTACCCG
1 AATTAACCG
*
41303639 AATTAACTG
1 AATTAACCG
41303648 AATTAACC-
1 AATTAACCG
*
41303656 AGATTACCCG
1 A-ATTAACCG
*
41303666 AATTACCCG
1 AATTAACCG
41303675 AATTAACCG
1 AATTAACCG
41303684 AATTAACCG
1 AATTAACCG
41303693 AATT
1 AATT
41303697 GAATCACTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
8 1 0.01
9 66 0.97
10 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:41303822 original size:18 final size:18
Alignment explanation
Indices: 41303799--41303852 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
41303789 AATTTTTATG
41303799 ATTGGGTTAGGTTGGGTA
1 ATTGGGTTAGGTTGGGTA
* *
41303817 ATTGGGTTGGGTTGGATA
1 ATTGGGTTAGGTTGGGTA
* *
41303835 CTTGGGTTTGGATTGGGT
1 ATTGGGTTAGG-TTGGGT
41303853 TTAGGTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.13, C:0.02, G:0.44, T:0.41
Consensus pattern (18 bp):
ATTGGGTTAGGTTGGGTA
Found at i:41312989 original size:125 final size:125
Alignment explanation
Indices: 41312767--41313020 Score: 420
Period size: 125 Copynumber: 2.0 Consensus size: 125
41312757 AACTTTGATG
*
41312767 ACTACTATTAACAATAGGATCAACTCCTCTATAAGAAGTCTTCAAAGTGTCGTTCTTTGAATAGC
1 ACTACTATTAACAATAGAATCAACTCCTCTATAAGAAGTCTTCAAAGTGTCGTTCTTTGAATAGC
* **
41312832 CAACTTAAACTGTCAACAATTGAAGGTATTATTCATGTATTGGAGTTTTATCCTCACTCT
66 CAACTTAAACGGTCAACAATTGAAGGTATTATTCATGTATTAAAGTTTTATCCTCACTCT
* * * * *
41312892 ACTACTATTAACAATAGAATCAACTCTTCTGTAAGAAGTCTTTAAAGTGTTGTTTTTTGAATAGC
1 ACTACTATTAACAATAGAATCAACTCCTCTATAAGAAGTCTTCAAAGTGTCGTTCTTTGAATAGC
41312957 CAACTTAAACGGTCAACAATTGAAGGTATTATTCATGTATTAAAGTTTTATCCTCACTCT
66 CAACTTAAACGGTCAACAATTGAAGGTATTATTCATGTATTAAAGTTTTATCCTCACTCT
41313017 -CTAC
1 ACTAC
41313021 GAAAAACTGT
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
124 4 0.03
125 116 0.97
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (125 bp):
ACTACTATTAACAATAGAATCAACTCCTCTATAAGAAGTCTTCAAAGTGTCGTTCTTTGAATAGC
CAACTTAAACGGTCAACAATTGAAGGTATTATTCATGTATTAAAGTTTTATCCTCACTCT
Found at i:41314578 original size:21 final size:20
Alignment explanation
Indices: 41314548--41314587 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
41314538 AATGTTTATA
*
41314548 ATTTTTTTTATTAATTTGAT
1 ATTTTTTTTATTAAATTGAT
41314568 ATTTATTTTTATTAAATTGA
1 ATTT-TTTTTATTAAATTGA
41314588 ATCATTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
ATTTTTTTTATTAAATTGAT
Found at i:41315158 original size:59 final size:57
Alignment explanation
Indices: 41315028--41315165 Score: 143
Period size: 59 Copynumber: 2.3 Consensus size: 57
41315018 TTTCTTTTTC
* *
41315028 TTTTTTGTCACTCAATTATGAAAAGTTACAAAATGGTGAACTAACTATTATTATATTT
1 TTTTTTGTCAC-CAATTATGAAAAGTTACAAAATAGTGAACTAACTATTATTATATCT
* * * *
41315086 TTATTTTGGTCACCAATTATGAAGAGTTACAAAATAGT-CACTCAACTATTCAATTCTGTCT
1 TT-TTTT-GTCACCAATTATGAAAAGTTACAAAATAGTGAACT-AACTATT--ATTATATCT
*
41315147 TTTTTTATCACCCAATTAT
1 TTTTTTGTCA-CCAATTAT
41315166 TTGGGATTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
58 5 0.07
59 37 0.55
60 17 0.25
61 8 0.12
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (57 bp):
TTTTTTGTCACCAATTATGAAAAGTTACAAAATAGTGAACTAACTATTATTATATCT
Found at i:41330259 original size:25 final size:25
Alignment explanation
Indices: 41330231--41330278 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
41330221 CAATTCATGG
41330231 GATCAAAACTGAATGTTCTGATACA
1 GATCAAAACTGAATGTTCTGATACA
41330256 GATCAAAACTGAATGTTCTGATA
1 GATCAAAACTGAATGTTCTGATA
41330279 GGTTGTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (25 bp):
GATCAAAACTGAATGTTCTGATACA
Found at i:41334931 original size:8 final size:8
Alignment explanation
Indices: 41334918--41334993 Score: 50
Period size: 8 Copynumber: 9.1 Consensus size: 8
41334908 TCAAAATTTT
41334918 ATTATAAA
1 ATTATAAA
41334926 ATTATAAA
1 ATTATAAA
41334934 A-TATATAA
1 ATTATA-AA
41334942 A-TAT-AA
1 ATTATAAA
*
41334948 ATTTTAAA
1 ATTATAAA
*
41334956 AGTTAAAATA
1 A-TTATAA-A
41334966 ATATATAAA
1 AT-TATAAA
*
41334975 AGTTAAAAA
1 A-TTATAAA
41334984 TATTATAAA
1 -ATTATAAA
41334993 A
1 A
41334994 AACATTTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
6 3 0.06
7 6 0.11
8 19 0.35
9 18 0.33
10 8 0.15
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (8 bp):
ATTATAAA
Found at i:41334985 original size:20 final size:17
Alignment explanation
Indices: 41334917--41334993 Score: 58
Period size: 18 Copynumber: 4.6 Consensus size: 17
41334907 TTCAAAATTT
*
41334917 TATTATAAAATTATAAAA
1 TATTATAAAAGT-TAAAA
41334935 TA-TAT-AAA--TATAAA
1 TATTATAAAAGTTA-AAA
41334949 T-TT-TAAAAGTTAAAA
1 TATTATAAAAGTTAAAA
41334964 TAATATATAAAAGTTAAAAA
1 T-AT-TATAAAAGTT-AAAA
41334984 TATTATAAAA
1 TATTATAAAA
41334994 AACATTTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
13 3 0.06
14 8 0.16
15 4 0.08
16 5 0.10
17 4 0.08
18 10 0.20
19 10 0.20
20 5 0.10
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TATTATAAAAGTTAAAA
Found at i:41334995 original size:20 final size:19
Alignment explanation
Indices: 41334953--41334995 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
41334943 TATAAATTTT
*
41334953 AAAAGTTAAAATAATATAT
1 AAAAGTTAAAATAATATAA
*
41334972 AAAAGTTAAAAATATTATAA
1 AAAAGTT-AAAATAATATAA
41334992 AAAA
1 AAAA
41334996 CATTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAAGTTAAAATAATATAA
Found at i:41340522 original size:46 final size:46
Alignment explanation
Indices: 41340453--41340542 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
41340443 AGCCTCTCCA
* * *
41340453 TTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTT
1 TTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCTT
*
41340499 TTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTC
1 TTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTC
41340543 CCACCTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47
Consensus pattern (46 bp):
TTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCTT
Found at i:41349069 original size:24 final size:24
Alignment explanation
Indices: 41349042--41349098 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
41349032 AAACCTAATT
41349042 CTAATCAAA-GTCAAATATATTATG
1 CTAAT-AAATGTCAAATATATTATG
* *
41349066 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATATATTATG
*
41349090 CTCATAAAT
1 CTAATAAAT
41349099 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATG
Found at i:41349104 original size:24 final size:24
Alignment explanation
Indices: 41349054--41349105 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
41349044 AATCAAAGTC
* **
41349054 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
41349078 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
41349102 AAAT
1 AAAT
41349106 CTTCTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:41349455 original size:38 final size:38
Alignment explanation
Indices: 41349406--41349481 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
41349396 AATGATACTG
41349406 AACATCAATGTGTTTTGATCTCTCATGAAACATTTGAT
1 AACATCAATGTGTTTTGATCTCTCATGAAACATTTGAT
*
41349444 AACATCAATGTGTTTTGTTCTCTCATGAAACATTTGAT
1 AACATCAATGTGTTTTGATCTCTCATGAAACATTTGAT
41349482 CTTTTGTAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (38 bp):
AACATCAATGTGTTTTGATCTCTCATGAAACATTTGAT
Found at i:41353516 original size:24 final size:24
Alignment explanation
Indices: 41353501--41353552 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41353491 AATCAAAGTC
41353501 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
41353525 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
41353549 AAAT
1 AAAT
41353553 CTTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:41355393 original size:91 final size:91
Alignment explanation
Indices: 41355228--41355393 Score: 226
Period size: 91 Copynumber: 1.8 Consensus size: 91
41355218 TGGTACTTTT
* * * *
41355228 GGTACTTGAATTTTCAAAATGCATCAAAAAGGCCCACAAACCTTTTCAAAAAAAAGCAATTAAAT
1 GGTACTTGAACTTTCAAAATGCATCAAAAAGACCCACAAACCTTTTCAAAAAAAAGCAATGAAAC
41355293 CCCTACTTTTTTTTTACACTCAGTTG
66 CCCTACTTTTTTTTTACACTCAGTTG
* * * * *
41355319 GGTACTTGAACTTTCAAAATGTATCAAAAAGACCCTCAAACTTTTTTCAAAAAAAA-TAATGAAG
1 GGTACTTGAACTTTCAAAATGCATCAAAAAGACCCACAAAC-CTTTTCAAAAAAAAGCAATGAAA
*
41355383 CCCCTGCTTTT
65 CCCCTACTTTT
41355394 ATTAAAAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
91 51 0.80
92 13 0.20
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.31
Consensus pattern (91 bp):
GGTACTTGAACTTTCAAAATGCATCAAAAAGACCCACAAACCTTTTCAAAAAAAAGCAATGAAAC
CCCTACTTTTTTTTTACACTCAGTTG
Found at i:41356129 original size:37 final size:38
Alignment explanation
Indices: 41356060--41356131 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
41356050 GGGGTCGTTA
* **
41356060 ATTTTTTAATGATATTTATAAAATTTTATAATTTTTTT
1 ATTTTTTAACGATATTTATAAAAAATTATAATTTTTTT
* *
41356098 ATTTTTT-ACGATTTTTATAAAAAATTCTAATTTT
1 ATTTTTTAACGATATTTATAAAAAATTATAATTTT
41356132 AATAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 22 0.76
38 7 0.24
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (38 bp):
ATTTTTTAACGATATTTATAAAAAATTATAATTTTTTT
Found at i:41356147 original size:45 final size:43
Alignment explanation
Indices: 41356093--41356226 Score: 108
Period size: 44 Copynumber: 3.0 Consensus size: 43
41356083 TTTTATAATT
*
41356093 TTTTTATTTTTTACGATTTTTATAAAAAATTCTAATTTTAATAAA
1 TTTTAATTTTTTA-G-TTTTTATAAAAAATTCTAATTTTAATAAA
* * * * **
41356138 TTTTAA-TTTTTATGTTTCTATTAAAATTTAATAATTTTTCTAAA
1 TTTTAATTTTTTA-GTTTTTATAAAAAATT-CTAATTTTAATAAA
* * *
41356182 ATTTATTTTTTTATTTTTTATAAAAAAAATTCTAATTTTTAATAA
1 TTTTAATTTTTTAGTTTTTAT--AAAAAATTCTAA-TTTTAATAA
41356227 GAGCAGGGGC
Statistics
Matches: 67, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
43 12 0.18
44 28 0.42
45 14 0.21
46 13 0.19
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (43 bp):
TTTTAATTTTTTAGTTTTTATAAAAAATTCTAATTTTAATAAA
Found at i:41356420 original size:90 final size:89
Alignment explanation
Indices: 41356231--41356430 Score: 249
Period size: 90 Copynumber: 2.2 Consensus size: 89
41356221 TAATAAGAGC
* *
41356231 AGGGGCTTAATTGCTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGTATTTTGAAAGTTCAAGTA
1 AGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
*
41356296 CCCAATTGAGTGAAAAAAAAGAGT
66 CCCAATTGAGTGAAAAAAAAAAGT
* * * * * * **
41356320 AAGAGTTTAATTGCATTTTTTGAAGAAGTTTGAGGGTCTTTTTTATGCATTTTTAAAGTTCCGGT
1 AGGGGCTTAATTGC-TTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGT
* *
41356385 GCTCAATTGAGTGTAAAAAAAAAAG-
65 ACCCAATTGAGTG-AAAAAAAAAAGT
41356410 AGGGGCTTAATTGCTCTTTTT
1 AGGGGCTTAATTGCT-TTTTT
41356431 TTTTTAAGTT
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
89 12 0.13
90 70 0.76
91 10 0.11
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (89 bp):
AGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
CCCAATTGAGTGAAAAAAAAAAGT
Found at i:41363006 original size:42 final size:42
Alignment explanation
Indices: 41362944--41363041 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
41362934 TAAATCCCGA
*
41362944 TTAGAAAAATTGTTTTGACTGAGTTGATGTCCCAAATGCTCGG
1 TTAGAAAAATT-ATTTGACTGAGTTGATGTCCCAAATGCTCGG
*
41362987 TTAGAAAACTTATTTGACTGAGTTGATGTCCCAAATGCTCGG
1 TTAGAAAAATTATTTGACTGAGTTGATGTCCCAAATGCTCGG
41363029 TTAGAAAAATTAT
1 TTAGAAAAATTAT
41363042 AAAAATGCCC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 42 0.81
43 10 0.19
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (42 bp):
TTAGAAAAATTATTTGACTGAGTTGATGTCCCAAATGCTCGG
Found at i:41366017 original size:22 final size:22
Alignment explanation
Indices: 41365971--41366011 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
41365961 AAAAAATTCT
*
41365971 AAAAACTCATAAAATTATTTTA
1 AAAAACTCATAAAACTATTTTA
41365993 AAAAACT-A-AAAACTATTTT
1 AAAAACTCATAAAACTATTTT
41366012 TGAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAACTCATAAAACTATTTTA
Found at i:41378646 original size:42 final size:42
Alignment explanation
Indices: 41378597--41378742 Score: 152
Period size: 42 Copynumber: 3.5 Consensus size: 42
41378587 GAGTTTCAGA
*
41378597 TTAACCCTTCTGGGTTTCAGTTCAGCTCTTTTGAGCTTCAAT
1 TTAACCCTTATGGGTTTCAGTTCAGCTCTTTTGAGCTTCAAT
* * * * *
41378639 TTAACCCTAATTGGTTTCCGTTTAGCTCTTTTAAGCTTCAGA-
1 TTAACCCTTATGGGTTTCAGTTCAGCTCTTTTGAGCTTCA-AT
* * **
41378681 TTAACCCTTATGGGTTTCCGTTCAGCT-TCTATGAGCTTCCGT
1 TTAACCCTTATGGGTTTCAGTTCAGCTCT-TTTGAGCTTCAAT
*
41378723 TTAACCCTTACTGGTTTTCA
1 TTAACCCTTA-TGGGTTTCA
41378743 TTTAGCACTT
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.01
42 76 0.89
43 8 0.09
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (42 bp):
TTAACCCTTATGGGTTTCAGTTCAGCTCTTTTGAGCTTCAAT
Found at i:41378738 original size:84 final size:84
Alignment explanation
Indices: 41378591--41378748 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 84
41378581 TCATATGAGT
* * *
41378591 TTCAGATTAACCCTTCTGGGTTTCAGTTCAGCTCTTTTGAGCTTCAATTTAACCCTAATTGGTTT
1 TTCAGATTAACCCTTATGGGTTTCAGTTCAGCTCTTATGAGCTTCAATTTAACCCTAACTGGTTT
*
41378656 CCGTTTAGCTCTTTTAAGC
66 CCATTTAGCTCTTTTAAGC
* ** *
41378675 TTCAGATTAACCCTTATGGGTTTCCGTTCAGCT-TCTATGAGCTTCCGTTTAACCCTTACTGGTT
1 TTCAGATTAACCCTTATGGGTTTCAGTTCAGCTCT-TATGAGCTTCAATTTAACCCTAACTGGTT
*
41378739 TTCATTTAGC
65 TCCATTTAGC
41378749 ACTTATGTGC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
83 1 0.02
84 63 0.98
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.42
Consensus pattern (84 bp):
TTCAGATTAACCCTTATGGGTTTCAGTTCAGCTCTTATGAGCTTCAATTTAACCCTAACTGGTTT
CCATTTAGCTCTTTTAAGC
Found at i:41380425 original size:45 final size:45
Alignment explanation
Indices: 41380376--41380482 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
41380366 TGTCATGATA
* *
41380376 TTACTTACTTCCTTCATGATGCCACT-GCAT-TTTTCAGCTATGGTC
1 TTACTTACTTCCATCATAATGCCA-TAGCATCTTTT-AGCTATGGTC
** * *
41380421 TTACTTGTTTTCATCATAATGCCATAGCATCTTTTGGCTATGGTC
1 TTACTTACTTCCATCATAATGCCATAGCATCTTTTAGCTATGGTC
**
41380466 TTACTCGCTTCCATCAT
1 TTACTTACTTCCATCAT
41380483 GTTTAAGATA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
44 1 0.02
45 46 0.90
46 4 0.08
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.43
Consensus pattern (45 bp):
TTACTTACTTCCATCATAATGCCATAGCATCTTTTAGCTATGGTC
Found at i:41381284 original size:34 final size:34
Alignment explanation
Indices: 41381241--41381309 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
41381231 TCAAACTTGG
41381241 AGGCCATGGAGGTTCAGTATGATAAGGAAGATCT
1 AGGCCATGGAGGTTCAGTATGATAAGGAAGATCT
41381275 AGGCCATGGAGGTTCAGTATGATAAGGAAGATCT
1 AGGCCATGGAGGTTCAGTATGATAAGGAAGATCT
41381309 A
1 A
41381310 ATGTTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.23
Consensus pattern (34 bp):
AGGCCATGGAGGTTCAGTATGATAAGGAAGATCT
Found at i:41390289 original size:28 final size:29
Alignment explanation
Indices: 41390238--41390292 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
41390228 TTGACTGATT
* *
41390238 AAAAAATTATTAAAATTATTTTAAAATGA
1 AAAAAATTATAAAAATTATGTTAAAATGA
41390267 AAAAAATTATAAAAATTA-GTTAAAAT
1 AAAAAATTATAAAAATTATGTTAAAAT
41390293 TTTTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAAAATTATAAAAATTATGTTAAAATGA
Found at i:41390330 original size:10 final size:10
Alignment explanation
Indices: 41390317--41390349 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
41390307 TAAAGAATAT
41390317 AAAAGTTTTA
1 AAAAGTTTTA
41390327 AAAAGTTTTA
1 AAAAGTTTTA
41390337 AAATA-TTTTA
1 AAA-AGTTTTA
41390347 AAA
1 AAA
41390350 TATTTAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 21 0.95
11 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (10 bp):
AAAAGTTTTA
Found at i:41390356 original size:9 final size:10
Alignment explanation
Indices: 41390322--41390354 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
41390312 AATATAAAAG
41390322 TTTTAAAA-A
1 TTTTAAAATA
41390331 GTTTTAAAATA
1 -TTTTAAAATA
41390342 TTTTAAAATA
1 TTTTAAAATA
41390352 TTT
1 TTT
41390355 AAGTTTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 21 0.95
11 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:41402452 original size:29 final size:27
Alignment explanation
Indices: 41402419--41402503 Score: 71
Period size: 29 Copynumber: 3.0 Consensus size: 27
41402409 AGTGCAGTAA
41402419 TAGAACAGAATAGCACCGAAGTGCAAT
1 TAGAACAGAATAGCACCGAAGTGCAAT
* * ** *
41402446 GTCAGAATAGAATAACACTAAAGTGTTTAAT
1 -T-AGAACAGAATAGCACCGAAGTG--CAAT
* *
41402477 TAGAACAGAGTGGCACCGAAGTGCAAT
1 TAGAACAGAATAGCACCGAAGTGCAAT
41402504 AGCAGAATAA
Statistics
Matches: 42, Mismatches: 12, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
27 3 0.07
28 1 0.02
29 34 0.81
30 1 0.02
31 3 0.07
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.20
Consensus pattern (27 bp):
TAGAACAGAATAGCACCGAAGTGCAAT
Found at i:41406386 original size:28 final size:28
Alignment explanation
Indices: 41406346--41406402 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
41406336 TGTAGAGAAG
41406346 ATAGAGAATTTTGAAGTAAAAGTAATAT
1 ATAGAGAATTTTGAAGTAAAAGTAATAT
*
41406374 ATAGAGAATTTTGAAGTAAAGGTAATAT
1 ATAGAGAATTTTGAAGTAAAAGTAATAT
41406402 A
1 A
41406403 CATTCCATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (28 bp):
ATAGAGAATTTTGAAGTAAAAGTAATAT
Found at i:41412292 original size:18 final size:18
Alignment explanation
Indices: 41412269--41412312 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
41412259 GTTCAAGGTG
41412269 TAATTAAATTAAAATT-TT
1 TAATTAAA-TAAAATTATT
*
41412287 TAATTAAATAAATTTATT
1 TAATTAAATAAAATTATT
41412305 TAATTAAA
1 TAATTAAA
41412313 AATCTATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTAAATAAAATTATT
Found at i:41419093 original size:22 final size:23
Alignment explanation
Indices: 41419060--41419102 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
41419050 AATTACATCT
* *
41419060 AAAAAATATTAATATTATCATGA
1 AAAAAATATTAAAAATATCATGA
41419083 AAAAAAT-TTAAAAATATCAT
1 AAAAAATATTAAAAATATCAT
41419103 TCTATTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAATATTAAAAATATCATGA
Found at i:41423171 original size:16 final size:15
Alignment explanation
Indices: 41423146--41423176 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
41423136 AAAGAAACAG
41423146 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
41423161 AAAAGAAAAAAAAGAA
1 AAAA-AAAAAAAAGAA
41423177 TAGGAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:41432907 original size:2 final size:2
Alignment explanation
Indices: 41432900--41432936 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41432890 GAACCTAGAG
41432900 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41432937 TGTTTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:41468752 original size:14 final size:15
Alignment explanation
Indices: 41468720--41468753 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41468710 ATGTCCCAAG
41468720 TTTCATTATTTTACT
1 TTTCATTATTTTACT
41468735 TTTCATTATTTT-CT
1 TTTCATTATTTTACT
41468749 TTTCA
1 TTTCA
41468754 ACGAACTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTCATTATTTTACT
Done.