Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 25 of 198
Found at i:7293703 original size:12 final size:11
Alignment explanation
Indices: 7293686--7293838 Score: 56
Period size: 12 Copynumber: 14.1 Consensus size: 11
7293676 TACACAACAC
7293686 ATAACTTACAT
1 ATAACTTACAT
7293697 AATAACTTAC--
1 -ATAACTTACAT
* *
7293707 ATAAGTTATAT
1 ATAACTTACAT
*
7293718 ATAAACTTATAT
1 AT-AACTTACAT
7293730 ATAACTTACAT
1 ATAACTTACAT
* *
7293741 ACATAACTTAAACC
1 --ATAACTTACA-T
* * *
7293755 AAAATTTATAT
1 ATAACTTACAT
7293766 ATAAACTTAC--
1 AT-AACTTACAT
*
7293776 ACAAC--AC--
1 ATAACTTACAT
*
7293783 ATAATTTACAT
1 ATAACTTACAT
7293794 AATAACTTAC--
1 -ATAACTTACAT
*
7293804 ATAACTTATAT
1 ATAACTTACAT
*
7293815 ATAAACTTATAT
1 AT-AACTTACAT
7293827 ATAACTTACAT
1 ATAACTTACAT
7293838 A
1 A
7293839 CATAACTTAA
Statistics
Matches: 107, Mismatches: 19, Indels: 31
0.68 0.12 0.20
Matches are distributed among these distances:
7 5 0.05
9 20 0.19
10 1 0.01
11 22 0.21
12 50 0.47
13 9 0.08
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (11 bp):
ATAACTTACAT
Found at i:7293710 original size:21 final size:21
Alignment explanation
Indices: 7293684--7293750 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
7293674 CTTACACAAC
7293684 ACATAACTTACATAATAACTT
1 ACATAACTTACATAATAACTT
* *
7293705 ACATAAGTTATAT-ATAAACTTAT
1 ACATAACTTACATAAT-AAC-T-T
*
7293728 ATATAACTTACATACATAACTT
1 ACATAACTTACATA-ATAACTT
7293750 A
1 A
7293751 AACCAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
20 2 0.06
21 14 0.39
22 3 0.08
23 12 0.33
24 3 0.08
25 2 0.06
ACGTcount: A:0.48, C:0.15, G:0.01, T:0.36
Consensus pattern (21 bp):
ACATAACTTACATAATAACTT
Found at i:7293764 original size:36 final size:35
Alignment explanation
Indices: 7293724--7293873 Score: 117
Period size: 36 Copynumber: 4.5 Consensus size: 35
7293714 ATATATAAAC
7293724 TTATATATAACTTACATACATAACTTAAACCAAAAT
1 TTATATATAACTTACATACATAACTTAAA-CAAAAT
*
7293760 TTATATATAAACTTAC--AC--AAC----ACATAAT
1 TTATATAT-AACTTACATACATAACTTAAACAAAAT
* * * *
7293788 TTACATAATAAC-T---TACATAACTTATATATAAAC
1 TTATAT-ATAACTTACATACATAACTTAAACA-AAAT
7293821 TTATATATAACTTACATACATAACTTAAATCAAAAT
1 TTATATATAACTTACATACATAACTTAAA-CAAAAT
7293857 TTATATATAAACTTACA
1 TTATATAT-AACTTACA
7293874 CAACACACAA
Statistics
Matches: 89, Mismatches: 9, Indels: 31
0.69 0.07 0.24
Matches are distributed among these distances:
26 2 0.02
27 1 0.01
28 16 0.18
29 3 0.03
32 7 0.08
33 11 0.12
35 2 0.02
36 31 0.35
37 16 0.18
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.35
Consensus pattern (35 bp):
TTATATATAACTTACATACATAACTTAAACAAAAT
Found at i:7293766 original size:48 final size:44
Alignment explanation
Indices: 7293686--7293871 Score: 192
Period size: 48 Copynumber: 3.9 Consensus size: 44
7293676 TACACAACAC
* *
7293686 ATAACTTACATAATAACTTACATAAGTTATATATAAACTTATAT
1 ATAACTTACATAATAACTTACAAAATTTATATATAAACTTATAT
* *
7293730 ATAACTTACATACATAACTTAAACCAAAATTTATATATAAACTTACACAACAC
1 ATAACTTACATA-ATAACTT--A-CAAAATTTATATATAAACTT-----ATAT
* * *
7293783 ATAATTTACATAATAACTTACATAACTTATATATAAACTTATAT
1 ATAACTTACATAATAACTTACAAAATTTATATATAAACTTATAT
7293827 ATAACTTACATACATAACTTAAATCAAAATTTATATATAAACTTA
1 ATAACTTACATA-ATAACTT--A-CAAAATTTATATATAAACTTA
7293872 CACAACACAC
Statistics
Matches: 117, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
44 25 0.21
45 14 0.12
47 2 0.02
48 37 0.32
49 18 0.15
50 1 0.01
52 7 0.06
53 13 0.11
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (44 bp):
ATAACTTACATAATAACTTACAAAATTTATATATAAACTTATAT
Found at i:7293804 original size:97 final size:97
Alignment explanation
Indices: 7293659--7293905 Score: 419
Period size: 97 Copynumber: 2.6 Consensus size: 97
7293649 TAACATATAT
*
7293659 AAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAAGTTATATATAAAC
1 AAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTATATATAAAC
7293724 TTATATATAACTTACATACATAACTTAAACCA
66 TTATATATAACTTACATACATAACTTAAACCA
*
7293756 AAATTTATATATAAACTTACACAACACATAATTTACATAATAACTTACATAACTTATATATAAAC
1 AAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTATATATAAAC
*
7293821 TTATATATAACTTACATACATAACTTAAATCA
66 TTATATATAACTTACATACATAACTTAAACCA
* **
7293853 AAATTTATATATAAACTTACACAACACACAA-AAACA-AA-AACTTACATAACTTA
1 AAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTA
7293906 CATAATACAT
Statistics
Matches: 144, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
94 15 0.10
95 2 0.01
96 3 0.02
97 124 0.86
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (97 bp):
AAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTATATATAAAC
TTATATATAACTTACATACATAACTTAAACCA
Found at i:7293807 original size:21 final size:21
Alignment explanation
Indices: 7293781--7293847 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
7293771 CTTACACAAC
*
7293781 ACATAATTTACATAATAACTT
1 ACATAACTTACATAATAACTT
*
7293802 ACATAACTTATAT-ATAAACTTAT
1 ACATAACTTACATAAT-AAC-T-T
*
7293825 ATATAACTTACATACATAACTT
1 ACATAACTTACATA-ATAACTT
7293847 A
1 A
7293848 AATCAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
20 2 0.05
21 14 0.38
22 3 0.08
23 13 0.35
24 3 0.08
25 2 0.05
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (21 bp):
ACATAACTTACATAATAACTT
Found at i:7293905 original size:9 final size:9
Alignment explanation
Indices: 7293891--7294250 Score: 221
Period size: 9 Copynumber: 42.2 Consensus size: 9
7293881 CAAAAACAAA
7293891 AACTTACAT
1 AACTTACAT
7293900 AACTTACAT
1 AACTTACAT
7293909 AA--TACAT
1 AACTTACAT
7293916 AACTTACAT
1 AACTTACAT
* *
7293925 AACCTACTT
1 AACTTACAT
7293934 AA--TACAT
1 AACTTACAT
*
7293941 AACTTGCAT
1 AACTTACAT
*
7293950 AACCTACAT
1 AACTTACAT
*
7293959 AA--TACAC
1 AACTTACAT
*
7293966 AGCTTACAT
1 AACTTACAT
* *
7293975 --GTGTAAAT
1 AACT-TACAT
*
7293983 AA--TACAC
1 AACTTACAT
7293990 AACTTACAT
1 AACTTACAT
7293999 AACTTACAT
1 AACTTACAT
* *
7294008 ACCCTACAT
1 AACTTACAT
* *
7294017 AAATTAAAT
1 AACTTACAT
*
7294026 AAGTTACAT
1 AACTTACAT
7294035 AA-TAATACAT
1 AACT--TACAT
* *
7294045 ACCCTACAT
1 AACTTACAT
* *
7294054 AAATTAAAT
1 AACTTACAT
*
7294063 AAGTTACAT
1 AACTTACAT
7294072 AA-TATACA-
1 AACT-TACAT
* *
7294080 AA--AACAAA
1 AACTTAC-AT
7294088 AACTTACAT
1 AACTTACAT
7294097 AACTTACAT
1 AACTTACAT
*
7294106 AA--TACAC
1 AACTTACAT
7294113 AACTTACAT
1 AACTTACAT
*
7294122 AACTTATAT
1 AACTTACAT
*
7294131 AA--TACAC
1 AACTTACAT
7294138 AACTTACAT
1 AACTTACAT
7294147 AACTTACAT
1 AACTTACAT
7294156 AA--TACAT
1 AACTTACAT
*
7294163 AATTTACAT
1 AACTTACAT
7294172 AACTTACAT
1 AACTTACAT
*
7294181 AA--GACAT
1 AACTTACAT
7294188 AACTTACAT
1 AACTTACAT
* *
7294197 AAGTTTCAT
1 AACTTACAT
*
7294206 AA--TACAC
1 AACTTACAT
*
7294213 AACTTACAC
1 AACTTACAT
*
7294222 AACTTGCAT
1 AACTTACAT
7294231 AACTTACAT
1 AACTTACAT
7294240 AACTTACAT
1 AACTTACAT
7294249 AA
1 AA
7294251 TGTATAGTGC
Statistics
Matches: 273, Mismatches: 49, Indels: 58
0.72 0.13 0.15
Matches are distributed among these distances:
6 2 0.01
7 54 0.20
8 10 0.04
9 199 0.73
10 8 0.03
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.29
Consensus pattern (9 bp):
AACTTACAT
Found at i:7293919 original size:25 final size:24
Alignment explanation
Indices: 7293891--7294250 Score: 192
Period size: 25 Copynumber: 14.1 Consensus size: 24
7293881 CAAAAACAAA
7293891 AACTTACATAACTTACATAA-TACAT
1 AACTTACATAA--TACATAATTACAT
*
7293916 AACTTACATAACCTACTTAA-TACAT
1 AACTTACATAA--TACATAATTACAT
* *
7293941 AACTTGCATAACCTACATAA-TACAC
1 AACTTACATAA--TACATAATTACAT
* ** * *
7293966 AGCTTACATGTGTAAATAA-TACAC
1 AACTTACAT-AATACATAATTACAT
**
7293990 AACTTACATAACTTACATACCCTACAT
1 AACTTACATAA--TACATA-ATTACAT
* *
7294017 AAATTAAATAAGTTACATAATAATACAT
1 AACTTACATAA--TACATAAT--TACAT
* * *
7294045 ACCCTACATAAATTAAATAAGTTACAT
1 AACTTACAT-AA-TACATAA-TTACAT
* *
7294072 AA-TATACA-AAAACAAAAACTTACAT
1 AACT-TACATAATAC-ATAA-TTACAT
*
7294097 AACTTACATAATACACAACTTACAT
1 AACTTACATAATACATAA-TTACAT
* *
7294122 AACTTATATAATACACAACTTACAT
1 AACTTACATAATACATAA-TTACAT
7294147 AACTTACATAATACATAATTTACAT
1 AACTTACATAATACATAA-TTACAT
*
7294172 AACTTACATAAGACATAACTTACAT
1 AACTTACATAATACATAA-TTACAT
* * * *
7294197 AAGTTTCATAATACACAACTTACAC
1 AACTTACATAATACATAA-TTACAT
*
7294222 AACTTGCATAACTTACATAACTTACAT
1 AACTTACATAA--TACATAA-TTACAT
7294249 AA
1 AA
7294251 TGTATAGTGC
Statistics
Matches: 271, Mismatches: 49, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
24 20 0.07
25 182 0.67
26 5 0.02
27 44 0.16
28 17 0.06
29 3 0.01
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.29
Consensus pattern (24 bp):
AACTTACATAATACATAATTACAT
Found at i:7293951 original size:50 final size:49
Alignment explanation
Indices: 7293891--7294250 Score: 282
Period size: 50 Copynumber: 7.2 Consensus size: 49
7293881 CAAAAACAAA
*
7293891 AACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACAT
1 AACTTACATAACTTACATAATACATAACTTACATAACTTAC-TAATACAT
* * * * *** * * *
7293941 AACTTGCATAACCTACATAATACACAGCTTACATGTGTAAATAATACAC
1 AACTTACATAACTTACATAATACATAACTTACATAACTTACTAATACAT
* * * *
7293990 AACTTACATAACTTACATACCCTACATAAATTAAATAAGTTAC--ATA-AT
1 AACTTACATAACTTACATA--ATACATAACTTACATAACTTACTAATACAT
* * * * * * *
7294038 AA--TACATACCCTACATAAATTAAATAAGTTACATAA-TATACAAAAACAAA
1 AACTTACATAACTTACAT-AA-TACATAACTTACATAACT-TACTAATAC-AT
* * *
7294088 AACTTACATAACTTACATAATACACAACTTACATAACTTATATAATACAC
1 AACTTACATAACTTACATAATACATAACTTACATAACTTA-CTAATACAT
* *
7294138 AACTTACATAACTTACATAATACATAATTTACATAACTTACATAAGACAT
1 AACTTACATAACTTACATAATACATAACTTACATAACTTAC-TAATACAT
* * * * *
7294188 AACTTACATAAGTTTCATAATACACAACTTACACAACTTGCATAACTTACAT
1 AACTTACATAACTTACATAATACATAACTTACATAACTTAC-TAA--TACAT
7294240 AACTTACATAA
1 AACTTACATAA
7294251 TGTATAGTGC
Statistics
Matches: 242, Mismatches: 52, Indels: 30
0.75 0.16 0.09
Matches are distributed among these distances:
45 1 0.00
46 28 0.12
47 1 0.00
48 5 0.02
49 27 0.11
50 133 0.55
51 20 0.08
52 27 0.11
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.29
Consensus pattern (49 bp):
AACTTACATAACTTACATAATACATAACTTACATAACTTACTAATACAT
Found at i:7294047 original size:37 final size:36
Alignment explanation
Indices: 7293993--7294079 Score: 149
Period size: 37 Copynumber: 2.4 Consensus size: 36
7293983 AATACACAAC
7293993 TTACATAACT-TACATACCCTACATAAATTAAATAAG
1 TTACATAA-TATACATACCCTACATAAATTAAATAAG
7294029 TTACATAATAATACATACCCTACATAAATTAAATAAG
1 TTACATAAT-ATACATACCCTACATAAATTAAATAAG
7294066 TTACATAATATACA
1 TTACATAATATACA
7294080 AAAACAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
35 1 0.02
36 13 0.27
37 35 0.71
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.31
Consensus pattern (36 bp):
TTACATAATATACATACCCTACATAAATTAAATAAG
Found at i:7296605 original size:21 final size:21
Alignment explanation
Indices: 7296580--7296675 Score: 104
Period size: 21 Copynumber: 4.4 Consensus size: 21
7296570 CAACAACTTA
*
7296580 AAGCAGAGGCAGCAGCGAGGG
1 AAGCAGAGGCAGCAGCGAGAG
*
7296601 AAGCAGAGGCTA-CAGCAAGAG
1 AAGCAGAGGC-AGCAGCGAGAG
*
7296622 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
* *
7296643 AAGCAGTGAGAGAAGCAGCGATAG
1 AAGCA--GAG-GCAGCAGCGAGAG
7296667 AAGCAGAGG
1 AAGCAGAGG
7296676 TTCAAAAGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
21 41 0.65
22 4 0.06
23 3 0.05
24 15 0.24
ACGTcount: A:0.39, C:0.17, G:0.41, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:7296653 original size:12 final size:12
Alignment explanation
Indices: 7296633--7296672 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
7296623 AGCAGAGGCT
7296633 GCAGCGAGAGAA
1 GCAGCGAGAGAA
*
7296645 GCAGTGAGAGAA
1 GCAGCGAGAGAA
*
7296657 GCAGCGATAGAA
1 GCAGCGAGAGAA
7296669 GCAG
1 GCAG
7296673 AGGTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.40, T:0.05
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:7297168 original size:42 final size:41
Alignment explanation
Indices: 7297109--7297230 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 41
7297099 GTTTGTGAAA
*
7297109 TAAGCGTCGCTAAAGAACACTACTATTAGCGGCGTTTT-TGACC
1 TAAGCGCCGCTAAAGAACA-TACT-TTAGCGGCGTTTTCT-ACC
* * *
7297152 -AAGTGCCGCTATAGAACATTACTTTTAGCGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACA-TAC-TTTAGCGGCGTTTTCTACC
7297194 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
1 TAAGCGCCGCTAAAGAACAT-A-CTTTAGCGGCGTTT
7297231 ATTTCCTTAG
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
42 34 0.51
43 32 0.48
44 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (41 bp):
TAAGCGCCGCTAAAGAACATACTTTAGCGGCGTTTTCTACC
Found at i:7297212 original size:43 final size:42
Alignment explanation
Indices: 7297109--7297251 Score: 155
Period size: 43 Copynumber: 3.4 Consensus size: 42
7297099 GTTTGTGAAA
* * * *
7297109 TAAGCGTCGCTAAAGAACACTACTATTAGCGGCGTTTTTGACC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTT-TCC
* *
7297152 -AAGTGCCGCTATAGAACATTACTTTTAGCGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTT-TTCC
*
7297194 TAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTATTTCC
1 TAAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTT-TTTCC
* *
7297237 TTAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
7297252 TTAGCGACGT
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
42 35 0.41
43 49 0.58
44 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTCC
Found at i:7299191 original size:17 final size:18
Alignment explanation
Indices: 7299169--7299203 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
7299159 GCAGACAACC
7299169 TAAAAAG-AAATTTACTA
1 TAAAAAGAAAATTTACTA
7299186 TAAAAAGAAAATTTACTA
1 TAAAAAGAAAATTTACTA
7299204 ATAATTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (18 bp):
TAAAAAGAAAATTTACTA
Found at i:7301881 original size:2 final size:2
Alignment explanation
Indices: 7301868--7301897 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
7301858 TCAGAAAGGA
*
7301868 AT AT AA 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
7301898 TTTATTGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7302671 original size:7 final size:7
Alignment explanation
Indices: 7302659--7302684 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
7302649 TGAAAGCATC
7302659 CTCCCAA
1 CTCCCAA
7302666 CTCCCAA
1 CTCCCAA
7302673 CTCCCAA
1 CTCCCAA
7302680 CTCCC
1 CTCCC
7302685 TCCACCACAC
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:0.23, C:0.62, G:0.00, T:0.15
Consensus pattern (7 bp):
CTCCCAA
Found at i:7305988 original size:19 final size:19
Alignment explanation
Indices: 7305950--7305988 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
7305940 AAAACAATGA
*
7305950 AAGAATTTACCTAATTTAG
1 AAGAATTTACCTAATCTAG
7305969 AAGAATTTGACCTAA-CTAG
1 AAGAATTT-ACCTAATCTAG
7305988 A
1 A
7305989 TTCAAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (19 bp):
AAGAATTTACCTAATCTAG
Found at i:7307118 original size:58 final size:58
Alignment explanation
Indices: 7307041--7307161 Score: 163
Period size: 58 Copynumber: 2.1 Consensus size: 58
7307031 AAACTTCCTA
* * *
7307041 ACATATTTATTTTTAGAATTTTTAGAA-GATTTATTATACAACGAAAACAACACAAAAC
1 ACATATTTATTTTTAGAATTTTT-GAAGGACTAATTAAACAACGAAAACAACACAAAAC
* * * *
7307099 ACATTTTTATTTTTGGAATTTTTGAAGGACTAATTAAACAAGGGAAACAACACAAAAC
1 ACATATTTATTTTTAGAATTTTTGAAGGACTAATTAAACAACGAAAACAACACAAAAC
7307157 ACATA
1 ACATA
7307162 AAATTGATAG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
57 3 0.06
58 51 0.94
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.32
Consensus pattern (58 bp):
ACATATTTATTTTTAGAATTTTTGAAGGACTAATTAAACAACGAAAACAACACAAAAC
Found at i:7310961 original size:105 final size:105
Alignment explanation
Indices: 7310818--7311080 Score: 339
Period size: 105 Copynumber: 2.5 Consensus size: 105
7310808 AACATATGTT
* * * * *
7310818 AACGAACTATTTAGGAGTCGCAATCTTAAATCAACTAACTCAAATAAATTTAGGTTGCA-ATCTT
1 AACGAGCTATTTAGGAGTTGCAATCTTAAATCTACTAACTCAAAGAAACTTAGGTTG-AGATCTT
* * *
7310882 AAATTAGCTAACCTTTGTAATATCAGCTGTGAACGTAGGAC
65 AAATCAACCAACCTTTGTAATATCAGCTGTGAACGTAGGAC
* * *
7310923 AACGAGTTGTTTAGGAGTTGCAATCTTAAATCTGCTAACTCAAAGAAACTTAGGTTGAGATCTTA
1 AACGAGCTATTTAGGAGTTGCAATCTTAAATCTACTAACTCAAAGAAACTTAGGTTGAGATCTTA
* * *
7310988 AATCAACCAACCTTTGTAATATCGGCTGTGAATGTAGGTC
66 AATCAACCAACCTTTGTAATATCAGCTGTGAACGTAGGAC
** * * *
7311028 AGTGAGCTATTTAGGAGTTACGATATTAAATCTACTAACTCAAAGAAACTTAG
1 AACGAGCTATTTAGGAGTTGCAATCTTAAATCTACTAACTCAAAGAAACTTAG
7311081 TTATGAACGT
Statistics
Matches: 135, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
104 1 0.01
105 134 0.99
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (105 bp):
AACGAGCTATTTAGGAGTTGCAATCTTAAATCTACTAACTCAAAGAAACTTAGGTTGAGATCTTA
AATCAACCAACCTTTGTAATATCAGCTGTGAACGTAGGAC
Found at i:7321172 original size:11 final size:11
Alignment explanation
Indices: 7321158--7321193 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
7321148 ATATCCTAAC
7321158 AATAATAATAA
1 AATAATAATAA
*
7321169 AATAATAGTAA
1 AATAATAATAA
*
7321180 TATAATAATAA
1 AATAATAATAA
7321191 AAT
1 AAT
7321194 GACAACAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
AATAATAATAA
Found at i:7325202 original size:3 final size:3
Alignment explanation
Indices: 7325194--7325226 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
7325184 TGTTGGTAGA
7325194 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
7325227 TTAGTGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:7326541 original size:22 final size:22
Alignment explanation
Indices: 7326511--7326552 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
7326501 ATCTAATAAT
*
7326511 AAATGTTTT-ATAATATAAAATA
1 AAATATTTTAATAATA-AAAATA
7326533 AAATATTTTAATAATAAAAA
1 AAATATTTTAATAATAAAAA
7326553 CATGAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATATTTTAATAATAAAAATA
Found at i:7329087 original size:22 final size:21
Alignment explanation
Indices: 7329052--7329100 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
7329042 TAATTATTAT
* * *
7329052 AAAATATTTTAAATAAAAGATC
1 AAAATATGTCAAATAAAAG-TA
*
7329074 AAAATATGTCAAATTAAAGTA
1 AAAATATGTCAAATAAAAGTA
7329095 AAAATA
1 AAAATA
7329101 GGAAGTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (21 bp):
AAAATATGTCAAATAAAAGTA
Found at i:7330653 original size:14 final size:14
Alignment explanation
Indices: 7330636--7330663 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7330626 ATAAACAAAC
7330636 AAATAAATCAATAA
1 AAATAAATCAATAA
7330650 AAATAAATCAATAA
1 AAATAAATCAATAA
7330664 CATGCAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATCAATAA
Found at i:7330842 original size:27 final size:26
Alignment explanation
Indices: 7330786--7330844 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
7330776 AAAAGGGTAC
* *
7330786 AAAATATATACATGTACATATATAAA
1 AAAATATATACATATACATAGATAAA
*
7330812 AAAATTATATACATATATATAGATTATAA
1 AAAA-TATATACATATACATAGA-TA-AA
7330841 AAAA
1 AAAA
7330845 AGATAATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.15
27 15 0.56
28 2 0.07
29 6 0.22
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (26 bp):
AAAATATATACATATACATAGATAAA
Found at i:7330856 original size:31 final size:32
Alignment explanation
Indices: 7330804--7330863 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
7330794 TACATGTACA
*
7330804 TATATAAAAAAATTATATACATATATATAGAT
1 TATATAAAAAAATAATATACATATATATAGAT
7330836 TATA-AAAAAAGATAAT-TACATATATATA
1 TATATAAAAAA-ATAATATACATATATATA
7330864 TAAACAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (32 bp):
TATATAAAAAAATAATATACATATATATAGAT
Found at i:7331049 original size:17 final size:17
Alignment explanation
Indices: 7331029--7331072 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
7331019 AGGAAATAAA
7331029 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
7331046 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
7331063 -ATATGTATAT
1 AAAATGTATAT
7331073 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:7331055 original size:27 final size:27
Alignment explanation
Indices: 7331025--7331076 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
7331015 AGTTAGGAAA
*
7331025 TAAAAAAATGTATATGTATATAAAATG
1 TAAAAAAATATATATGTATATAAAATG
***
7331052 TAAATGTATATATATGTATATAAAA
1 TAAAAAAATATATATGTATATAAAA
7331077 GTTATGCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (27 bp):
TAAAAAAATATATATGTATATAAAATG
Found at i:7331201 original size:3 final size:3
Alignment explanation
Indices: 7331193--7331231 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
7331183 GTATATATAG
* *
7331193 TAA TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7331232 CTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:7331596 original size:21 final size:21
Alignment explanation
Indices: 7331547--7331644 Score: 121
Period size: 21 Copynumber: 4.7 Consensus size: 21
7331537 AAATTAAATC
*
7331547 TCTAAGATTACA-AAATCATA
1 TCTAAGATTGCATAAATCATA
7331567 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTGCATAAATCATA
*
7331591 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATAAATCATA
7331612 TCTAAGATTGCAT--ATCATA
1 TCTAAGATTGCATAAATCATA
*
7331631 TCTAAGATTACATA
1 TCTAAGATTGCATA
7331645 TCCTTGAAGA
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
19 18 0.26
21 33 0.47
23 11 0.16
24 8 0.11
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (21 bp):
TCTAAGATTGCATAAATCATA
Found at i:7332142 original size:44 final size:44
Alignment explanation
Indices: 7332089--7332201 Score: 156
Period size: 44 Copynumber: 2.6 Consensus size: 44
7332079 GATCTACTCT
* *
7332089 ACTGCAACTTCAGAGAGATAAGATCT-GTGGTTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGAT-TAGTGGCTTTAATCCGCTCC
* * *
7332133 ACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTAGTGGCTTTAATCCGCTCC
*
7332177 ACTGCAACTTTAGGGAGATAAGATT
1 ACTGCAACTTCAGGGAGATAAGATT
7332202 CGCCATCTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 1 0.02
44 60 0.98
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATTAGTGGCTTTAATCCGCTCC
Found at i:7332497 original size:50 final size:50
Alignment explanation
Indices: 7332394--7332511 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 50
7332384 TCCAAGCCTT
* *
7332394 AACGCCAAGAAGATAAGATTCGTCGTCGTGGCTTCAATCTGCTCCGTTAC
1 AACGCCAAGAAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCATTAC
* ** *
7332444 AACGCCAGAGAAG-TAAGATTCGCCGTTGTGGCTTCAATCTTTTCCATTGC
1 AACGCCA-AGAAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCATTAC
* **
7332494 AACGTCAAGGCGATAAGA
1 AACGCCAAGAAGATAAGA
7332512 CTGATGCCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 3 0.05
50 49 0.86
51 5 0.09
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (50 bp):
AACGCCAAGAAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCATTAC
Found at i:7332730 original size:44 final size:44
Alignment explanation
Indices: 7332675--7333522 Score: 219
Period size: 44 Copynumber: 19.3 Consensus size: 44
7332665 GCTGTTGGTG
*
7332675 CAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** * * ****
7332719 CAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
*
7332763 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * ** * * ****
7332807 CATGG-AGGCAAGGT-TGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CA-GGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
* *
7332851 CATGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * * ** ** * ****
7332895 TAGGGAGGCAAG-GCTGGTGTCTTCGATTTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
* * *
7332939 CAAGAAGGCAAGATTTGCTATTTTTAACCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** * * ****
7332983 CAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
* *
7333027 TAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** * * ****
7333071 TAGTG-AGGCAAG-GCTGATGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAG-GAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
*
7333115 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** * * * ****
7333159 TAGTG-AGGCAAG-GCTGGTGTCTTCGATCTACTTCGCTGTCGGTG
1 CAG-GAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
* *
7333203 CAGGAAGGCAAAATCTGCTATTTTTAACCTGCTCCGCTACAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** ** ** * * ****
7333247 TAGGGAGGCAAG-GCTGGTGTCATCGATTTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
*
7333291 CAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * ** * * ****
7333335 TAGGGAGGCAAG-GCTAG-TATCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCT-GCTATTTTTAACCTGCTCCGCTG-CAACC
* * *
7333379 CAAGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTGTAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
* * * * * ** * * ****
7333423 CAGGGAGGCAAGGT-TGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
* *
7333467 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGTTGTAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
*
7333511 CAGGGAGGCAAG
1 CAGGAAGGCAAG
7333523 GTTGGTGTCT
Statistics
Matches: 502, Mismatches: 276, Indels: 52
0.60 0.33 0.06
Matches are distributed among these distances:
43 149 0.30
44 203 0.40
45 150 0.30
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.28
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
Found at i:7332763 original size:88 final size:88
Alignment explanation
Indices: 7332653--7333570 Score: 1503
Period size: 88 Copynumber: 10.4 Consensus size: 88
7332643 GTTGGGGTCA
* * *
7332653 TCGATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
7332718 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
7332741 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
7332806 CCATGGAGGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
7332829 TCGATCTGCTTCGCTGTCGGTGCATGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
*
7332894 CTAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
7332917 TCGATTTGCTTCGCTGTCGGTGCAAGAAGGCAAGATTTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
7332982 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
7333005 TCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* * *
7333070 CTAGTGAGGCAAGGCTGATGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
7333093 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
7333158 CTAGTGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
7333181 TCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAAATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
7333246 CTAGGGAGGCAAGGCTGGTGTCA
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * *
7333269 TCGATTTGCTTCACTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* * *
7333334 CTAGGGAGGCAAGGCTAGTATCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * **
7333357 TCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTGTAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
*
7333422 CCAGGGAGGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* **
7333445 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGTTGTAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
*
7333510 CCAGGGAGGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
7333533 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCT
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCT
7333571 TTAATCTTCA
Statistics
Matches: 783, Mismatches: 47, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 783 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:7338643 original size:14 final size:14
Alignment explanation
Indices: 7338626--7338653 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7338616 ATAAACAAAC
7338626 AAATAAATCAATAA
1 AAATAAATCAATAA
7338640 AAATAAATCAATAA
1 AAATAAATCAATAA
7338654 CATGCAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATCAATAA
Found at i:7340228 original size:3 final size:3
Alignment explanation
Indices: 7340220--7340278 Score: 109
Period size: 3 Copynumber: 19.3 Consensus size: 3
7340210 ATGAAAATAG
7340220 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7340268 AAT ATAT AAT A
1 AAT A-AT AAT A
7340279 TGTGCATGTG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:7340349 original size:3 final size:3
Alignment explanation
Indices: 7340338--7340428 Score: 128
Period size: 3 Copynumber: 29.7 Consensus size: 3
7340328 ATTGTAAAAA
*
7340338 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
7340386 AAT AAT AGT GAT AAT AAT AAC AAT AAT AAT AACTT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AA
7340429 GAAAATCAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
3 75 0.96
5 3 0.04
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:7340767 original size:23 final size:24
Alignment explanation
Indices: 7340737--7340783 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
7340727 AAATTAAATC
7340737 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
*
7340760 TCTAAGATTGCATAAATCATATCT
1 TCTAAGATTACATAAATCATATCT
7340784 AAGATTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:7340781 original size:24 final size:24
Alignment explanation
Indices: 7340737--7340802 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 24
7340727 AAATTAAATC
*
7340737 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTGCATAAATCATATCT
7340760 TCTAAGATTGCATAAATCATA---
1 TCTAAGATTGCATAAATCATATCT
7340781 TCTAAGATTGCAT--ATCATATCT
1 TCTAAGATTGCATAAATCATATCT
7340803 AAGATTACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 6 0.16
21 13 0.34
23 11 0.29
24 8 0.21
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (24 bp):
TCTAAGATTGCATAAATCATATCT
Found at i:7340786 original size:21 final size:21
Alignment explanation
Indices: 7340737--7340813 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 21
7340727 AAATTAAATC
7340737 TCTAAGATTACA-AAATCATA
1 TCTAAGATTACATAAATCATA
*
7340757 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTACATAAATCATA
*
7340781 TCTAAGATTGCAT--ATCATA
1 TCTAAGATTACATAAATCATA
7340800 TCTAAGATTACATA
1 TCTAAGATTACATA
7340814 TCCTTGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
19 18 0.36
21 13 0.26
23 11 0.22
24 8 0.16
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (21 bp):
TCTAAGATTACATAAATCATA
Found at i:7362159 original size:3 final size:3
Alignment explanation
Indices: 7362151--7362175 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7362141 CGGCTGGAGT
7362151 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
7362176 GAGATAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:7370055 original size:24 final size:25
Alignment explanation
Indices: 7370009--7370056 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
7369999 TATATTAGGC
* *
7370009 ATTAAAATATTTTTAATAATATTAT
1 ATTAAAATATATTAAATAATATTAT
*
7370034 ATTAAAAT-TATTAAATATTATTA
1 ATTAAAATATATTAAATAATATTA
7370057 ATAATTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTAAAATATATTAAATAATATTAT
Found at i:7387678 original size:49 final size:50
Alignment explanation
Indices: 7387528--7387713 Score: 152
Period size: 49 Copynumber: 3.8 Consensus size: 50
7387518 AGCTCTTCCT
*** * * *
7387528 AGCCATATAACGGG-AGCTCATTTGAGCCATTTAA-CGGGAAGCTCATGTA
1 AGCCATATAACGGGAAGCTCAAGAGAGCCA-TTAATGGGGAAGCTCATATG
* **
7387577 AGCCA-ATATCGGGAAGCTCCAA-AGAGCCAATT-ATTAGGAAGCTCATATG
1 AGCCATATAACGGGAAGCT-CAAGAGAGCC-ATTAATGGGGAAGCTCATATG
*
7387626 AGCCATA-AACGGGAAGCTCAAGAGAGCCATTAATGGGGAAGCTCGTGA-G
1 AGCCATATAACGGGAAGCTCAAGAGAGCCATTAATGGGGAAGCTCAT-ATG
* * * *
7387675 AGCCATATAACGAGATGCTCATGAGAGCTAATTAATGGG
1 AGCCATATAACGGGAAGCTCAAGAGAGC-CATTAATGGG
7387714 ACGCTCTTGT
Statistics
Matches: 112, Mismatches: 15, Indels: 18
0.77 0.10 0.12
Matches are distributed among these distances:
48 14 0.12
49 67 0.60
50 22 0.20
51 9 0.08
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.20
Consensus pattern (50 bp):
AGCCATATAACGGGAAGCTCAAGAGAGCCATTAATGGGGAAGCTCATATG
Found at i:7387699 original size:25 final size:25
Alignment explanation
Indices: 7387528--7387702 Score: 134
Period size: 25 Copynumber: 7.1 Consensus size: 25
7387518 AGCTCTTCCT
**
7387528 AGCCATATAACGGG-AGCTCATTTG
1 AGCCATATAACGGGAAGCTCATGAG
*
7387552 AGCCATTTAACGGGAAGCTCATGTA-
1 AGCCATATAACGGGAAGCTCATG-AG
* *
7387577 AGCCA-ATATCGGGAAGCTCCA-AAG
1 AGCCATATAACGGGAAGCT-CATGAG
*
7387601 AGCCAATTATTA--GGAAGCTCAT-ATG
1 AGCC-A-TATAACGGGAAGCTCATGA-G
*
7387626 AGCCATA-AACGGGAAGCTCAAGAG
1 AGCCATATAACGGGAAGCTCATGAG
* *
7387650 AGCCAT-TAATGGGGAAGCTCGTGAG
1 AGCCATATAA-CGGGAAGCTCATGAG
* *
7387675 AGCCATATAACGAGATGCTCATGAG
1 AGCCATATAACGGGAAGCTCATGAG
7387700 AGC
1 AGC
7387703 TAATTAATGG
Statistics
Matches: 119, Mismatches: 17, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
22 1 0.01
23 3 0.03
24 50 0.42
25 60 0.50
26 3 0.03
27 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.19
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGAG
Found at i:7390857 original size:23 final size:23
Alignment explanation
Indices: 7390830--7390882 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
7390820 AGTGTTATTG
7390830 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
7390853 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
7390876 ATCAGTG
1 ATCAGTG
7390883 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:7393154 original size:2 final size:2
Alignment explanation
Indices: 7393141--7393190 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
7393131 GCCAATTTTA
*
7393141 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7393183 AT AT AT AT
1 AT AT AT AT
7393191 CAATAGCAGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7403210 original size:17 final size:19
Alignment explanation
Indices: 7403188--7403224 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
7403178 AAGCAAAAGA
7403188 ATTTC-ATATTA-TGAGAT
1 ATTTCAATATTAGTGAGAT
*
7403205 ATTTCAATTTTAGTGAGAT
1 ATTTCAATATTAGTGAGAT
7403224 A
1 A
7403225 GGGTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (19 bp):
ATTTCAATATTAGTGAGAT
Found at i:7404282 original size:6 final size:6
Alignment explanation
Indices: 7404271--7404299 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
7404261 CCCAAACTGG
7404271 ACTGAT ACTGAT ACTGAT ACTGAT ACTGA
1 ACTGAT ACTGAT ACTGAT ACTGAT ACTGA
7404300 AAAGGACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (6 bp):
ACTGAT
Found at i:7410165 original size:28 final size:28
Alignment explanation
Indices: 7410133--7410189 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
7410123 TAGCATCTCT
*
7410133 TAAATCATACCTTTCATATTTATGAATA
1 TAAATCATACATTTCATATTTATGAATA
*
7410161 TAAATCATACATTTCATGTTTATGAATA
1 TAAATCATACATTTCATATTTATGAATA
7410189 T
1 T
7410190 TCATACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (28 bp):
TAAATCATACATTTCATATTTATGAATA
Found at i:7410344 original size:33 final size:33
Alignment explanation
Indices: 7410307--7410384 Score: 77
Period size: 33 Copynumber: 2.4 Consensus size: 33
7410297 TGGCCCTGTC
** * * *
7410307 ATGGTCTTACATTCGTACTGCCATAACCCAGTT
1 ATGGTCTTACATTCAAAATACCATAACCCAGCT
* *
7410340 ATGGTTTTATCA-TCAAAATACCATAGCCCAGCT
1 ATGGTCTTA-CATTCAAAATACCATAACCCAGCT
7410373 ATGGTCTTACAT
1 ATGGTCTTACAT
7410385 ATAAACACTG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
32 2 0.06
33 31 0.89
34 2 0.06
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (33 bp):
ATGGTCTTACATTCAAAATACCATAACCCAGCT
Found at i:7410434 original size:101 final size:101
Alignment explanation
Indices: 7410325--7410520 Score: 311
Period size: 101 Copynumber: 1.9 Consensus size: 101
7410315 ACATTCGTAC
*
7410325 TGCCATAACCCAGTTATGGTTTTATCATCAAAATACCATAGCCCAGCTATGGTCTTACATATAAA
1 TGCCATAACCCAGTTATGGTCTTATCATCAAAATACCATAGCCCAGCTATGGTCTTACATATAAA
*
7410390 CACTGCCATGGTCGAACCATGGTCTTACGTCTATAG
66 CACTGCCATGGTCCAACCATGGTCTTACGTCTATAG
* * * * * * *
7410426 TGCCATAACCTAGTTATGGTCTTATCATTAGAATGCCATATCCTAGCTATGGTTTTACATATAAA
1 TGCCATAACCCAGTTATGGTCTTATCATCAAAATACCATAGCCCAGCTATGGTCTTACATATAAA
7410491 CACTGCCATGGTCCAACCATGGTCTTACGT
66 CACTGCCATGGTCCAACCATGGTCTTACGT
7410521 GTGAATGCAA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 86 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (101 bp):
TGCCATAACCCAGTTATGGTCTTATCATCAAAATACCATAGCCCAGCTATGGTCTTACATATAAA
CACTGCCATGGTCCAACCATGGTCTTACGTCTATAG
Found at i:7417856 original size:73 final size:72
Alignment explanation
Indices: 7417772--7417953 Score: 197
Period size: 73 Copynumber: 2.5 Consensus size: 72
7417762 TATTGTAACA
* * * *
7417772 ATTTAATTTTGTTACAATTACTTATGATTTTCGTGTAAAAAAATTGGTCACA-AACAAATTT-AA
1 ATTTAA-TTTGTCACAATTACTTACGATTTTAGTGTAAAAAAATTAG-C-CATAA-AAATTTGAA
*
7417835 TAACTGTGCCC
62 TAACTGTGACC
* * * *
7417846 ATTTAATTTGTCACAATTGCTTACGATTTTAGTGTACAAAACTTAGCCATAAAAATTTGAATAAT
1 ATTTAATTTGTCACAATTACTTACGATTTTAGTGTAAAAAAATTAGCCATAAAAATTTGAATAAC
7417911 TGTGACC
66 TGTGACC
* * *
7417918 ATTTAATTTCGACATAATTACTTACAATTTTAGTGT
1 ATTTAATTT-GTCACAATTACTTACGATTTTAGTGT
7417954 TCGACATTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
71 8 0.09
72 23 0.25
73 55 0.60
74 6 0.07
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (72 bp):
ATTTAATTTGTCACAATTACTTACGATTTTAGTGTAAAAAAATTAGCCATAAAAATTTGAATAAC
TGTGACC
Found at i:7422174 original size:17 final size:17
Alignment explanation
Indices: 7422152--7422191 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
7422142 AACTCCAACA
7422152 AGCTTCTGACCCAATCG
1 AGCTTCTGACCCAATCG
*
7422169 AGCTTCTGACTCAATCG
1 AGCTTCTGACCCAATCG
7422186 AGCTTC
1 AGCTTC
7422192 CGATAATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.28
Consensus pattern (17 bp):
AGCTTCTGACCCAATCG
Found at i:7423363 original size:101 final size:101
Alignment explanation
Indices: 7423124--7423363 Score: 338
Period size: 101 Copynumber: 2.4 Consensus size: 101
7423114 AATTCATCCT
* * * *
7423124 TTACATTCGTAGTGCCATAACTCATTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGAT
1 TTACGTTCATAGTGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGAT
*
7423189 CTTACATATAAACACTGCTATGGTCCAACCATGGTC
66 CTTACATATAAACACTGCTATAGTCCAACCATGGTC
* * * * *
7423225 TTACGTTCATAGTGCCACAACCCAGTTATGGTATTATCATCAGAATGCCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGAT
*
7423290 CTTACATATAAACACTG-TCATAGTCTAACCATGGTC
66 CTTACATATAAACACTGCT-ATAGTCCAACCATGGTC
** *
7423326 TTACGTTCATAGTGTTATAACCCAATTATGATCTTATC
1 TTACGTTCATAGTGCCATAACCCAATTATGGTCTTATC
7423364 CGTCAATTCA
Statistics
Matches: 122, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
100 1 0.01
101 121 0.99
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGAT
CTTACATATAAACACTGCTATAGTCCAACCATGGTC
Found at i:7424089 original size:13 final size:13
Alignment explanation
Indices: 7424071--7424096 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7424061 ATATTTTTAC
7424071 AAAATTTCCCTTT
1 AAAATTTCCCTTT
7424084 AAAATTTCCCTTT
1 AAAATTTCCCTTT
7424097 TATTCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATTTCCCTTT
Found at i:7429522 original size:17 final size:17
Alignment explanation
Indices: 7429502--7429536 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
7429492 TTAAAATTAT
7429502 TAAATA-TTAAAATAAAA
1 TAAATATTTAAAA-AAAA
7429519 TAAATATTTAAAAAAAA
1 TAAATATTTAAAAAAAA
7429536 T
1 T
7429537 TAAAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATATTTAAAAAAAA
Found at i:7429540 original size:18 final size:18
Alignment explanation
Indices: 7429500--7429540 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
7429490 GTTTAAAATT
7429500 ATTAAATATTAAAATAAA
1 ATTAAATATTAAAATAAA
7429518 A-TAAATATTTAAAA-AAA
1 ATTAAATA-TTAAAATAAA
7429535 ATTAAA
1 ATTAAA
7429541 ATATAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAAATATTAAAATAAA
Found at i:7431561 original size:14 final size:14
Alignment explanation
Indices: 7431542--7431569 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7431532 CAGATTATCA
7431542 CATATTTCATTTTT
1 CATATTTCATTTTT
7431556 CATATTTCATTTTT
1 CATATTTCATTTTT
7431570 TTTACTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (14 bp):
CATATTTCATTTTT
Found at i:7433009 original size:30 final size:29
Alignment explanation
Indices: 7432971--7433078 Score: 87
Period size: 29 Copynumber: 3.7 Consensus size: 29
7432961 TTAATTAATT
*
7432971 TTTTAAAATTTAAAAATTA-TAAAAACTA
1 TTTTAAAAATTAAAAATTACTAAAAACTA
* * *
7432999 TTTCTAAAAATTAAAAATCATTTAAAACTA
1 TTT-TAAAAATTAAAAATTACTAAAAACTA
* *
7433029 --TTAAAAATTATAAAAATTACAAATAAAATA
1 TTTTAAAAA-T-TAAAAATTACTAA-AAACTA
*
7433059 TTTTTAAATATTAAAAATTA
1 -TTTTAAAAATTAAAAATTA
7433079 ATTAAATGCT
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
27 6 0.10
28 5 0.08
29 23 0.37
30 13 0.21
31 9 0.14
32 1 0.02
33 6 0.10
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (29 bp):
TTTTAAAAATTAAAAATTACTAAAAACTA
Found at i:7433891 original size:28 final size:26
Alignment explanation
Indices: 7433860--7433914 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 26
7433850 AATACTTTAA
7433860 AATATATTAAAATTCATAATAAATA-AAT
1 AATATA-TAAAA-TC-TAATAAATACAAT
7433888 AATATATAAAATCTAATAAATACAAT
1 AATATATAAAATCTAATAAATACAAT
7433914 A
1 A
7433915 TTGGGCTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 9 0.35
26 6 0.23
27 5 0.19
28 6 0.23
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (26 bp):
AATATATAAAATCTAATAAATACAAT
Found at i:7434276 original size:21 final size:23
Alignment explanation
Indices: 7434243--7434285 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
7434233 TTTGTGCATG
7434243 TATCAATCTTCT-A-CCTTCACA
1 TATCAATCTTCTAAGCCTTCACA
7434264 TATCATATC-TCTAAGCCTTCAC
1 TATCA-ATCTTCTAAGCCTTCAC
7434286 TCTCTCACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.28, C:0.33, G:0.02, T:0.37
Consensus pattern (23 bp):
TATCAATCTTCTAAGCCTTCACA
Found at i:7434425 original size:14 final size:13
Alignment explanation
Indices: 7434406--7434439 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
7434396 AAAACCTTAA
7434406 CTTTTTTTGTTTTC
1 CTTTTTTT-TTTTC
7434420 CTTTTTTTTTTTC
1 CTTTTTTTTTTTC
*
7434433 ATTTTTT
1 CTTTTTT
7434440 GAAAGGTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (13 bp):
CTTTTTTTTTTTC
Found at i:7447229 original size:103 final size:103
Alignment explanation
Indices: 7447112--7447334 Score: 322
Period size: 103 Copynumber: 2.2 Consensus size: 103
7447102 AAGTATTTTT
* * * *
7447112 TTTATATAACTATTAACAGTAAATAGTTTATTTATCAAAATATCATTATCAACATTAAATATAAA
1 TTTATGTAAATATTAACAGTAAATAATTTATTTATCAAAATATCATTATCAACACTAAATATAAA
** *
7447177 ATTAAAATATACTATCTGTTTTTGTACTCTATATTAAA
66 ATTAAAATATACTATCCATTTTTATACTCTATATTAAA
* * *
7447215 TTTATGTAAATATTAACAGTAAATAATTTATTTATCAAAATATCATTATCGATACTACATATAAA
1 TTTATGTAAATATTAACAGTAAATAATTTATTTATCAAAATATCATTATCAACACTAAATATAAA
*
7447280 ATTAACATATACTATCCATTTTTATACTCTATATTAAA
66 ATTAAAATATACTATCCATTTTTATACTCTATATTAAA
*
7447318 TTT-TGTACAACATTAAC
1 TTTATGTA-AATATTAAC
7447335 TTACCAACCA
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 4 0.04
103 103 0.96
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (103 bp):
TTTATGTAAATATTAACAGTAAATAATTTATTTATCAAAATATCATTATCAACACTAAATATAAA
ATTAAAATATACTATCCATTTTTATACTCTATATTAAA
Found at i:7453086 original size:24 final size:24
Alignment explanation
Indices: 7453058--7453103 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
7453048 TCTTTCTAGA
**
7453058 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAACATTTATTAGTATAAT
7453082 ATATTTAACATTTATTAGTATA
1 ATATTTAACATTTATTAGTATA
7453104 GTTTATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (24 bp):
ATATTTAACATTTATTAGTATAAT
Found at i:7457798 original size:88 final size:85
Alignment explanation
Indices: 7457686--7457983 Score: 251
Period size: 88 Copynumber: 3.4 Consensus size: 85
7457676 TAGTGCTTCG
* * *
7457686 GTCCACTCCACTGCAACGTCAGGGAGATAGGATTTGTAACTTCAATCTGCTCTACTACAACTTCA
1 GTCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGT--CTTCAATCTGCTCTACTGCAACTTCA
*
7457751 GGGAGATAAGATTGATTTATTCG
64 GGGAGATAAGATTGATTT-TTCA
* * * ** * * * *
7457774 GTCTGCTCCACTGTAACTTCAGGGAGATAAGACCTG-CTACGATCTACTCTACTGCAACTTCAGA
1 GTCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTCTTCAATCTGCTCTACTGCAACTTCAGG
**
7457838 GAGATAAGATCCATCATTTT-A
66 GAGATAAGATTGAT--TTTTCA
* * * * * *
7457859 ATCCGCTCCACTGTAACTTCAGAGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCA
1 GTCCGCTCCACTGCAACTTCAGGGAGATAGGA-T-TTGTCTTCAATCTGCTCTACTGCAACTTCA
* *
7457924 AGGAGATAAGATTCGCCA-TCTTCA
64 GGGAGATAAGATT-G--ATTTTTCA
* * *
7457948 GTCTGCCCCACTGCAACTTTAGGGAGATAGGATTTG
1 GTCCGCTCCACTGCAACTTCAGGGAGATAGGATTTG
7457984 CAGTTTCACC
Statistics
Matches: 164, Mismatches: 37, Indels: 19
0.75 0.17 0.09
Matches are distributed among these distances:
85 63 0.38
86 2 0.01
87 7 0.04
88 64 0.39
89 27 0.16
91 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (85 bp):
GTCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTCTTCAATCTGCTCTACTGCAACTTCAGG
GAGATAAGATTGATTTTTCA
Found at i:7457881 original size:44 final size:44
Alignment explanation
Indices: 7457824--7457935 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 44
7457814 GATCTACTCT
*
7457824 ACTGCAACTTCAGAGAGATAAGATCCA-TCATTTTAATCCGCTCC
1 ACTGCAACTTCAGAGAGATAAGAT-CATTCACTTTAATCCGCTCC
* * * ** *
7457868 ACTGTAACTTCAGAGAGATAGGATTATTGGCTTTAATCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATCATTCACTTTAATCCGCTCC
7457912 ACTGCAACTTCA-AGGAGATAAGAT
1 ACTGCAACTTCAGA-GAGATAAGAT
7457936 TCGCCATCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 2 0.04
44 55 0.96
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAAGATCATTCACTTTAATCCGCTCC
Found at i:7473037 original size:27 final size:27
Alignment explanation
Indices: 7473007--7473079 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 27
7472997 TGTCTTGAAT
7473007 TTGTTAGATATTGATTATGTTTTAAGC
1 TTGTTAGATATTGATTATGTTTTAAGC
7473034 TTGTTAGATATTGAATTGATTATGTTTTAAGC
1 TTGTTAG--A-T--ATTGATTATGTTTTAAGC
*
7473066 TTGTTGGATATTGA
1 TTGTTAGATATTGA
7473080 AATGATTGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
27 12 0.30
29 2 0.05
30 2 0.05
32 24 0.60
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTTAAGC
Found at i:7473052 original size:32 final size:32
Alignment explanation
Indices: 7473016--7473086 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
7473006 TTTGTTAGAT
7473016 ATTGATTATGTTTTAAGCTTGTTAGATATTGA
1 ATTGATTATGTTTTAAGCTTGTTAGATATTGA
*
7473048 ATTGATTATGTTTTAAGCTTGTTGGATATTGA
1 ATTGATTATGTTTTAAGCTTGTTAGATATTGA
*
7473080 AATGATT
1 ATTGATT
7473087 GACAATGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.49
Consensus pattern (32 bp):
ATTGATTATGTTTTAAGCTTGTTAGATATTGA
Found at i:7479138 original size:23 final size:23
Alignment explanation
Indices: 7479109--7479253 Score: 200
Period size: 23 Copynumber: 6.3 Consensus size: 23
7479099 ATAAGTGCCA
7479109 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
7479132 CATTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
7479155 CACTGAAATGTAGGCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
7479178 CACTGATATGTAGCAGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
7479201 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
7479224 CACTGATATGTAGCCGCAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
7479247 CACTGAT
1 CACTGAT
7479254 CAATAACACT
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 104 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:7479753 original size:30 final size:30
Alignment explanation
Indices: 7479705--7479763 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
7479695 TCCTTGACTC
*
7479705 AAACTTTTTCAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * * *
7479735 AAACTTTTGCATATTTACACTTTTTCCCC
1 AAACTTTTGCAAAATTACAATTTTGCCCC
7479764 AAAGCTCGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.03, T:0.42
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:7481019 original size:18 final size:18
Alignment explanation
Indices: 7480996--7481037 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
7480986 TTCAAGGTGT
7480996 AATTAATTTAAAATT-TTC
1 AATTAA-TTAAAATTATTC
*
7481014 AATTAATTAAAATTATTT
1 AATTAATTAAAATTATTC
7481032 AATTAA
1 AATTAA
7481038 AAACTTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTAATTAAAATTATTC
Found at i:7482362 original size:32 final size:31
Alignment explanation
Indices: 7482312--7482372 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 31
7482302 AAAATCGAAA
* *
7482312 AATTTTTTGAATTTCGAGTTAA-TCGAATCG
1 AATTATTTGAATTTCGAGTCAACTCGAATCG
7482342 AATTATTTGAATAATTCGAGTCAACTCGAAT
1 AATTATTTGAAT--TTCGAGTCAACTCGAAT
7482373 AACTCGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
32 9 0.35
33 6 0.23
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (31 bp):
AATTATTTGAATTTCGAGTCAACTCGAATCG
Found at i:7482533 original size:11 final size:11
Alignment explanation
Indices: 7482514--7482575 Score: 62
Period size: 11 Copynumber: 6.0 Consensus size: 11
7482504 TCTCAACAAA
*
7482514 AATTACAAAAT
1 AATTTCAAAAT
7482525 AATTTCAAAAT
1 AATTTCAAAAT
*
7482536 AATTTTAAAA-
1 AATTTCAAAAT
7482546 AATTT-AAAAT
1 AATTTCAAAAT
7482556 AATTAT-AAAAT
1 AATT-TCAAAAT
7482567 --TTTCAAAAT
1 AATTTCAAAAT
7482576 TTATGTATTC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
8 1 0.02
9 11 0.24
10 9 0.20
11 25 0.54
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTTCAAAAT
Found at i:7482556 original size:20 final size:22
Alignment explanation
Indices: 7482514--7482575 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 22
7482504 TCTCAACAAA
*
7482514 AATTACAAAATAATTTCAAAAT
1 AATTATAAAATAATTTCAAAAT
*
7482536 AATTTTAAAA-AATTT-AAAAT
1 AATTATAAAATAATTTCAAAAT
7482556 AATTATAAAAT--TTTCAAAAT
1 AATTATAAAATAATTTCAAAAT
7482576 TTATGTATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 19 0.54
21 5 0.14
22 8 0.23
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTATAAAATAATTTCAAAAT
Found at i:7482620 original size:20 final size:20
Alignment explanation
Indices: 7482582--7482620 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7482572 AAATTTATGT
*
7482582 ATTCTTAAAAAATTCTAAAA
1 ATTCTTAAAAAATTATAAAA
7482602 ATTC-TAAAAAATATATAAA
1 ATTCTTAAAAAAT-TATAAA
7482621 GAAAGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTCTTAAAAAATTATAAAA
Found at i:7483245 original size:20 final size:21
Alignment explanation
Indices: 7483222--7483261 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
7483212 TAATCTAATC
* *
7483222 ATTTTTAATA-AAATTAATTT
1 ATTTTAAATACAAATAAATTT
7483242 ATTTTAAATACAAATAAATT
1 ATTTTAAATACAAATAAATT
7483262 AATATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTAAATACAAATAAATTT
Found at i:7483662 original size:15 final size:15
Alignment explanation
Indices: 7483638--7483667 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7483628 TACATATTTT
7483638 ATTAAATAATAAAAA
1 ATTAAATAATAAAAA
*
7483653 ATTAAGTAATAAAAA
1 ATTAAATAATAAAAA
7483668 TAATTAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
ATTAAATAATAAAAA
Found at i:7485556 original size:2 final size:2
Alignment explanation
Indices: 7485551--7485581 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7485541 TATATGCGTG
7485551 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7485582 ACAAACTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7486851 original size:13 final size:13
Alignment explanation
Indices: 7486833--7486863 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
7486823 CTTGGGTTAT
*
7486833 TTTGGGTTTGCTG
1 TTTGGGTTGGCTG
7486846 TTTGGGTTGGCTG
1 TTTGGGTTGGCTG
7486859 TTTGG
1 TTTGG
7486864 TGAGGCCCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.42, T:0.52
Consensus pattern (13 bp):
TTTGGGTTGGCTG
Found at i:7489059 original size:3 final size:3
Alignment explanation
Indices: 7489051--7489086 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
7489041 AGGTGTCGTC
7489051 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7489087 CTTTCTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:7493029 original size:51 final size:50
Alignment explanation
Indices: 7492947--7493051 Score: 165
Period size: 51 Copynumber: 2.1 Consensus size: 50
7492937 GTAGCTATAA
* * *
7492947 ATCATTTGTTTATATTAAGTGTCCATGTGTTGTATGTATCAAGATAGGGT
1 ATCATTTGTTTATATTAAGTGTCCATGTGTTGCACGTATAAAGATAGGGT
*
7492997 ATCATTTGTTTATATTTAAGTGTCCATTTGTTGCACGTATAAAGATAGGGT
1 ATCATTTGTTTATA-TTAAGTGTCCATGTGTTGCACGTATAAAGATAGGGT
7493048 ATCA
1 ATCA
7493052 AAACCAGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 14 0.28
51 36 0.72
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.43
Consensus pattern (50 bp):
ATCATTTGTTTATATTAAGTGTCCATGTGTTGCACGTATAAAGATAGGGT
Found at i:7500290 original size:11 final size:11
Alignment explanation
Indices: 7500272--7500301 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
7500262 TTTATATATT
7500272 TATTTTTTTTA
1 TATTTTTTTTA
*
7500283 TGTTTTTTTTA
1 TATTTTTTTTA
7500294 TATTTTTT
1 TATTTTTT
7500302 ACCTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (11 bp):
TATTTTTTTTA
Found at i:7500915 original size:21 final size:21
Alignment explanation
Indices: 7500891--7500946 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 21
7500881 TTTTCATAAT
7500891 TTTTTA-TTTTAAAAAATATA
1 TTTTTATTTTTAAAAAATATA
7500911 TTTTTATTTTTAAAAAATTTATA
1 TTTTTATTTTTAAAAAA--TATA
7500934 GTTTTTAATTTTT
1 -TTTTT-ATTTTT
7500947 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.19
21 10 0.32
23 4 0.13
24 5 0.16
25 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTATTTTTAAAAAATATA
Found at i:7504247 original size:21 final size:22
Alignment explanation
Indices: 7504205--7504259 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
7504195 GGCCTGGCCC
*
7504205 ATTTTTTAAATAAACACCAAAAA
1 ATTTTTTAAA-AAACACAAAAAA
*
7504228 ATTTTTTAAAAAATA-AAAAAA
1 ATTTTTTAAAAAACACAAAAAA
* *
7504249 GTATTTTAAAA
1 ATTTTTTAAAA
7504260 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 14 0.50
22 4 0.14
23 10 0.36
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (22 bp):
ATTTTTTAAAAAACACAAAAAA
Found at i:7504270 original size:11 final size:11
Alignment explanation
Indices: 7504244--7504313 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
7504234 TAAAAAATAA
7504244 AAAAAGTATTTT
1 AAAAA-TATTTT
7504256 -AAAATATTTT
1 AAAAATATTTT
7504266 AAAAATA----
1 AAAAATATTTT
* **
7504273 AAAAAAATTAA
1 AAAAATATTTT
7504284 AAAAAGTATTTT
1 AAAAA-TATTTT
7504296 AAAAATATTTT
1 AAAAATATTTT
7504307 AAAAATA
1 AAAAATA
7504314 AAAATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
7 6 0.12
10 6 0.12
11 28 0.58
12 8 0.17
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:7504285 original size:40 final size:40
Alignment explanation
Indices: 7504235--7504317 Score: 150
Period size: 41 Copynumber: 2.1 Consensus size: 40
7504225 AAAATTTTTT
7504235 AAAAAATAAAAAAAGTATTTT-AAAATATTTTAAAAATAA
1 AAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAATAA
7504274 AAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAATAA
1 AAAAAA-TAAAAAAAGTATTTTAAAAATATTTTAAAAATAA
7504315 AAA
1 AAA
7504318 TAAAAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 6 0.14
40 15 0.36
41 21 0.50
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (40 bp):
AAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAATAA
Found at i:7509360 original size:34 final size:34
Alignment explanation
Indices: 7509317--7509382 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
7509307 ACCTCCCCAC
7509317 TGGCCTTTCTTTTTCATTAGAGAATAAACTGTTT
1 TGGCCTTTCTTTTTCATTAGAGAATAAACTGTTT
*
7509351 TGGCCTTTCTTTTTCATTATAGAATAAACTGT
1 TGGCCTTTCTTTTTCATTAGAGAATAAACTGT
7509383 CTCTTGGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (34 bp):
TGGCCTTTCTTTTTCATTAGAGAATAAACTGTTT
Found at i:7516944 original size:19 final size:19
Alignment explanation
Indices: 7516920--7516966 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
7516910 TATACTTGTT
7516920 TATTTATTTTAATTAATCA
1 TATTTATTTTAATTAATCA
*
7516939 TATTTAATTTAATTAATCA
1 TATTTATTTTAATTAATCA
*
7516958 TAATTATTT
1 TATTTATTT
7516967 AACCTTAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTATTTTAATTAATCA
Found at i:7534479 original size:12 final size:12
Alignment explanation
Indices: 7534462--7534486 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7534452 GGTGTTCATT
7534462 CGGTTAACCGAC
1 CGGTTAACCGAC
7534474 CGGTTAACCGAC
1 CGGTTAACCGAC
7534486 C
1 C
7534487 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:7534683 original size:27 final size:27
Alignment explanation
Indices: 7534647--7534732 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
7534637 TTTGGTTAAA
*
7534647 AATTACCCGAATTACCCGAATTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
* *
7534674 AATTAACCGAATTAACCGAACTAACCG
1 AATTAACCGAATTACCCGAATTAACCG
* *
7534701 AATT-ACCGAAAAATACCCGAATTACCCG
1 AATTAACCG--AATTACCCGAATTAACCG
7534729 AATT
1 AATT
7534733 TTTTTATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 4 0.08
27 28 0.56
28 18 0.36
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTAACCG
Found at i:7534732 original size:9 final size:9
Alignment explanation
Indices: 7534647--7534710 Score: 94
Period size: 9 Copynumber: 7.2 Consensus size: 9
7534637 TTTGGTTAAA
*
7534647 AATTACCCG
1 AATTAACCG
*
7534656 AATTACCCG
1 AATTAACCG
7534665 AATTAACCG
1 AATTAACCG
7534674 AATTAACCG
1 AATTAACCG
7534683 AATTAACCG
1 AATTAACCG
*
7534692 AACTAACCG
1 AATTAACCG
7534701 AATT-ACCG
1 AATTAACCG
7534709 AA
1 AA
7534711 AAATACCCGA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
8 6 0.12
9 46 0.88
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (9 bp):
AATTAACCG
Found at i:7536570 original size:22 final size:21
Alignment explanation
Indices: 7536545--7536585 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
7536535 AATTACAAAA
7536545 AAAAAATACAAAAATATATTTT
1 AAAAAATACAAAAAT-TATTTT
*
7536567 AAAAATTACAAAAATTATT
1 AAAAAATACAAAAATTATT
7536586 AAAATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAATACAAAAATTATTTT
Found at i:7537022 original size:28 final size:27
Alignment explanation
Indices: 7536990--7537099 Score: 91
Period size: 28 Copynumber: 3.9 Consensus size: 27
7536980 AAATTTCATA
7536990 TTTTATATTTTATTGTAATTTTATAAGT
1 TTTTATATTTT-TTGTAATTTTATAAGT
** *
7537018 TTTTATATTTTTAAT-ATTTTGTAA-T
1 TTTTATATTTTTTGTAATTTTATAAGT
* *
7537043 TTTAAATATTATTTTTGTAATTTTTAATATGT
1 TTT-TATA-T-TTTTTGTAA-TTTT-ATAAGT
7537075 ATTTT-TATTTTTTGTAATTTTATAA
1 -TTTTATATTTTTTGTAATTTTATAA
7537100 TTATTATTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
25 4 0.06
26 11 0.17
27 6 0.09
28 20 0.31
29 10 0.16
30 5 0.08
31 4 0.06
32 1 0.02
33 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (27 bp):
TTTTATATTTTTTGTAATTTTATAAGT
Found at i:7537060 original size:21 final size:22
Alignment explanation
Indices: 7537034--7537080 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
7537024 ATTTTTAATA
7537034 TTTTGTAATTTTAAATAT-TAT
1 TTTTGTAATTTTAAATATGTAT
*
7537055 TTTTGTAATTTTTAATATGTAT
1 TTTTGTAATTTTAAATATGTAT
7537077 TTTT
1 TTTT
7537081 ATTTTTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (22 bp):
TTTTGTAATTTTAAATATGTAT
Found at i:7537065 original size:29 final size:28
Alignment explanation
Indices: 7537033--7537101 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
7537023 TATTTTTAAT
*
7537033 ATTTTGTAATTTTAAATATTA-TTTTTGTA
1 ATTTT-TAATTGT-AATATTATTTTTTGTA
* *
7537062 ATTTTTAATATGTATTTTTATTTTTTGTA
1 ATTTTTAAT-TGTAATATTATTTTTTGTA
7537091 ATTTTATAATT
1 ATTTT-TAATT
7537102 ATTATTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 9 0.26
29 21 0.62
30 4 0.12
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (28 bp):
ATTTTTAATTGTAATATTATTTTTTGTA
Found at i:7538836 original size:8 final size:7
Alignment explanation
Indices: 7538802--7538834 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
7538792 CTTTTCATTC
*
7538802 TTTTTGT
1 TTTTTAT
7538809 TTTTTAT
1 TTTTTAT
7538816 TTTTTAT
1 TTTTTAT
7538823 TTTTTAT
1 TTTTTAT
7538830 TTTTT
1 TTTTT
7538835 TAAAAAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:7540047 original size:16 final size:16
Alignment explanation
Indices: 7540026--7540057 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7540016 TTTTCTTTTC
7540026 ATAAATATATATATAT
1 ATAAATATATATATAT
*
7540042 ATAAATATTTATATAT
1 ATAAATATATATATAT
7540058 TTCTATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATATATATATAT
Found at i:7540402 original size:27 final size:27
Alignment explanation
Indices: 7540372--7540431 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
7540362 GAAAGAGAAA
*
7540372 ATTTTGAAAATAAAGGCAATACTCGGT
1 ATTTGGAAAATAAAGGCAATACTCGGT
*
7540399 ATTTGGGAAATAAAGGCAATACTCGGT
1 ATTTGGAAAATAAAGGCAATACTCGGT
7540426 ATTTGG
1 ATTTGG
7540432 GATCTTCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (27 bp):
ATTTGGAAAATAAAGGCAATACTCGGT
Found at i:7540432 original size:27 final size:27
Alignment explanation
Indices: 7540379--7540433 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
7540369 AAAATTTTGA
7540379 AAATAAAGGCAATACTCGGTATTTGGG
1 AAATAAAGGCAATACTCGGTATTTGGG
7540406 AAATAAAGGCAATACTCGGTATTTGGG
1 AAATAAAGGCAATACTCGGTATTTGGG
7540433 A
1 A
7540434 TCTTCGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.25
Consensus pattern (27 bp):
AAATAAAGGCAATACTCGGTATTTGGG
Found at i:7542014 original size:20 final size:19
Alignment explanation
Indices: 7541989--7542053 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
7541979 AAAATAATCA
7541989 AAAATAATTTTCAAAAATTC
1 AAAATAATTTT-AAAAATTC
* *
7542009 AAAATAATTTTTAAAATTA
1 AAAATAATTTTAAAAATTC
7542028 AAAAT-ATTTATAAAAAATTC
1 AAAATAATTT-T-AAAAATTC
7542048 TAAAAT
1 -AAAAT
7542054 TTATATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 4 0.11
19 12 0.32
20 17 0.45
21 5 0.13
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTC
Found at i:7542043 original size:19 final size:19
Alignment explanation
Indices: 7541988--7542043 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
7541978 CAAAATAATC
7541988 AAAAATAATTTTCAAAAATT
1 AAAAATAATTTT-AAAAATT
* *
7542008 CAAAATAATTTTTAAAATT
1 AAAAATAATTTTAAAAATT
7542027 AAAAAT-ATTTATAAAAA
1 AAAAATAATTT-TAAAAA
7542044 ATTCTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 4 0.13
19 16 0.52
20 11 0.35
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATAATTTTAAAAATT
Found at i:7543549 original size:31 final size:31
Alignment explanation
Indices: 7543496--7543560 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
7543486 TACAATTTGA
** * *
7543496 TCACTAAACTATTTGAACGTTTTCATTTAAG
1 TCACTAAACTATTCAAAAGTTTTCATGTAAG
*
7543527 TCACTAAACTATTCAAAAGTTTTTATGTAAG
1 TCACTAAACTATTCAAAAGTTTTCATGTAAG
7543558 TCA
1 TCA
7543561 ATGGGTGGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGTTTTCATGTAAG
Found at i:7544563 original size:223 final size:221
Alignment explanation
Indices: 7544159--7544566 Score: 516
Period size: 223 Copynumber: 1.8 Consensus size: 221
7544149 TGCACACCCC
* * * *
7544159 TAATCATACAATCATTAATTATATGATCTTAATAAAATGAATTATAAATAGTCGTACATTTAACG
1 TAATCATACAATCATTAATTATACGAACTAAATAAAATGAATTATAAATAGTCGTACATTCAACG
* * * *
7544224 ATCCAATTGAATAGTCTCTATACAAGTGTAATGAAATTACTTGCATTTGCATTTACCTAATTATG
66 ATCCAATTGAATAGTCTATATACAAGTGTAATGAAATTACTTGCATATACATTTACCTAACTATG
** * * *
7544289 AATGTAATAAAATGAATTATAATATTAATCATATAATCATTGATCCAATTGAATTGAACTATGTA
131 AACCTAATAAAATGAATTATAAAATTAATCATATAAGCATTAATCCAATTGAATTGAACTATGTA
7544354 AAAAATTAATTAAATGAATATACTAT
196 AAAAATTAATTAAATGAATATACTAT
*
7544380 TAATCATACAATCATTAATTATACGAACGTAAAT-GAATGAATTATATAATTAGTCGTACATTCA
1 TAATCATACAATCATTAATTATACGAAC-TAAATAAAATGAATTATA-AA-TAGTCGTACATTCA
* * * * * * * *
7544444 ATGATCCAATTGTATTGTTTATGTACTAGTGTAATGACATTA-TGTGCATATACATTTTCCTAAC
63 ACGATCCAATTGAATAGTCTATATACAAGTGTAATGAAATTACT-TGCATATACATTTACCTAAC
** * *
7544508 TATGAACCTAATTGAATGAATTATAAAATTAATCGTACT-AGCATTAATTCAATTGAATT
127 TATGAACCTAATAAAATGAATTATAAAATTAATCATA-TAAGCATTAATCCAATTGAATT
7544567 TGTTTATGTA
Statistics
Matches: 156, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
221 37 0.24
222 7 0.04
223 111 0.71
224 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (221 bp):
TAATCATACAATCATTAATTATACGAACTAAATAAAATGAATTATAAATAGTCGTACATTCAACG
ATCCAATTGAATAGTCTATATACAAGTGTAATGAAATTACTTGCATATACATTTACCTAACTATG
AACCTAATAAAATGAATTATAAAATTAATCATATAAGCATTAATCCAATTGAATTGAACTATGTA
AAAAATTAATTAAATGAATATACTAT
Found at i:7550662 original size:13 final size:14
Alignment explanation
Indices: 7550635--7550709 Score: 61
Period size: 13 Copynumber: 5.6 Consensus size: 14
7550625 TAGGCCTTGC
*
7550635 TTTCTTCTT-TCTT
1 TTTCTTTTTCTCTT
7550648 TTT-TTTTTCTCTT
1 TTTCTTTTTCTCTT
7550661 TTTCCTTTTTC-CTT
1 TTT-CTTTTTCTCTT
* *
7550675 TTTCCTTTT-TCGT
1 TTTCTTTTTCTCTT
*
7550688 TTTCTGTTTCT-TT
1 TTTCTTTTTCTCTT
7550701 CTTTCTTTT
1 -TTTCTTTT
7550710 CCTATTTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
12 4 0.08
13 25 0.51
14 14 0.29
15 6 0.12
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTCTTTTTCTCTT
Found at i:7550669 original size:6 final size:7
Alignment explanation
Indices: 7550651--7550690 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
7550641 CTTTCTTTTT
7550651 TTTTTCTC
1 TTTTTC-C
7550659 TTTTTCC
1 TTTTTCC
7550666 TTTTTCC
1 TTTTTCC
7550673 TTTTTCC
1 TTTTTCC
*
7550680 TTTTTCG
1 TTTTTCC
7550687 TTTT
1 TTTT
7550691 CTGTTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (7 bp):
TTTTTCC
Found at i:7550718 original size:20 final size:21
Alignment explanation
Indices: 7550667--7550724 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
7550657 TCTTTTTCCT
* *
7550667 TTTTCCTTTTTCCTT-TTTCG
1 TTTTCCTATTTCTTTCTTTCG
*
7550687 TTTT-CTGTTTCTTTCTTTC-
1 TTTTCCTATTTCTTTCTTTCG
7550706 TTTTCCTATTTCTTTCTTT
1 TTTTCCTATTTCTTTCTTT
7550725 TTATCTTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.02, C:0.22, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTCCTATTTCTTTCTTTCG
Found at i:7552077 original size:5 final size:5
Alignment explanation
Indices: 7552067--7552092 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
7552057 TGAGCATTCG
7552067 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
7552093 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:7553010 original size:9 final size:9
Alignment explanation
Indices: 7552996--7553032 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
7552986 TATAGTTTGA
7552996 TATTCGAAT
1 TATTCGAAT
7553005 TATTCGAAT
1 TATTCGAAT
*
7553014 TATTCGAGT
1 TATTCGAAT
7553023 TATTCGAAT
1 TATTCGAAT
7553032 T
1 T
7553033 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:7553102 original size:9 final size:9
Alignment explanation
Indices: 7553085--7553115 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
7553075 TCGAGTTGAT
7553085 TCGAATAAC
1 TCGAATAAC
*
7553094 TCGATTAAC
1 TCGAATAAC
7553103 TCGAATAAC
1 TCGAATAAC
7553112 TCGA
1 TCGA
7553116 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:7553387 original size:19 final size:18
Alignment explanation
Indices: 7553363--7553405 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
7553353 TAATATTAAT
*
7553363 AAAAATTTAAT-ATAAATA
1 AAAAAATTAATAATAAA-A
7553381 AAAAAATTAATCAATAAAA
1 AAAAAATTAAT-AATAAAA
7553400 AAAAAA
1 AAAAAA
7553406 CTAAAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAATTAATAATAAAA
Found at i:7553822 original size:6 final size:6
Alignment explanation
Indices: 7553811--7553836 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7553801 ATAATTATCA
7553811 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
7553837 AAGTTATCAT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:7554387 original size:30 final size:29
Alignment explanation
Indices: 7554328--7554392 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
7554318 TCCCTCTCAA
7554328 TCCCCAACTCCCTTAATCTTAATCTCTTC
1 TCCCCAACTCCCTTAATCTTAATCTCTTC
*
7554357 TCCCCAACTCCTTTAACCTCTTAA-CTCTTC
1 TCCCCAACTCCCTTAA--TCTTAATCTCTTC
*
7554387 TTCCCA
1 TCCCCA
7554393 TTCCTTCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 15 0.47
30 11 0.34
31 6 0.19
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.37
Consensus pattern (29 bp):
TCCCCAACTCCCTTAATCTTAATCTCTTC
Found at i:7556179 original size:16 final size:16
Alignment explanation
Indices: 7556158--7556203 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
7556148 TCTACCTCCG
7556158 TTATATTTTAAATTTT
1 TTATATTTTAAATTTT
* * *
7556174 TTATATATTATATATT
1 TTATATTTTAAATTTT
*
7556190 TTATATTTTTAATT
1 TTATATTTTAAATT
7556204 AATATAATAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTTTAAATTTT
Found at i:7556213 original size:25 final size:25
Alignment explanation
Indices: 7556159--7556209 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
7556149 CTACCTCCGT
* *
7556159 TATATTTTAAATTTTTTATATATTA
1 TATATTTTAAATTTTTAATATAATA
*
7556184 TATATTTTATATTTTTAAT-TAATA
1 TATATTTTAAATTTTTAATATAATA
7556208 TA
1 TA
7556210 ATATATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATATTTTAAATTTTTAATATAATA
Found at i:7558147 original size:18 final size:19
Alignment explanation
Indices: 7558115--7558150 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
7558105 AGTAAATAAC
*
7558115 TTAAAATTTATAAAAATAT
1 TTAAAATTTAAAAAAATAT
7558134 TTAAAA-TTAAAAAAATA
1 TTAAAATTTAAAAAAATA
7558151 GTATGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAATTTAAAAAAATAT
Found at i:7559929 original size:34 final size:34
Alignment explanation
Indices: 7559886--7559952 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
7559876 TAAGTACATC
7559886 CATTAACCACTTTAAATCATACCAAACATACCTT
1 CATTAACCACTTTAAATCATACCAAACATACCTT
7559920 CATTAACCACTTTAAATCATACCAAACATACCT
1 CATTAACCACTTTAAATCATACCAAACATACCT
7559953 CCAAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (34 bp):
CATTAACCACTTTAAATCATACCAAACATACCTT
Found at i:7559965 original size:13 final size:13
Alignment explanation
Indices: 7559947--7559976 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
7559937 CATACCAAAC
7559947 ATACCTCCAAAAT
1 ATACCTCCAAAAT
*
7559960 ATACCTCTAAAAT
1 ATACCTCCAAAAT
7559973 ATAC
1 ATAC
7559977 ATGAGAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (13 bp):
ATACCTCCAAAAT
Found at i:7560289 original size:25 final size:25
Alignment explanation
Indices: 7560234--7560299 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
7560224 AAGCGAGAAA
*
7560234 CGGTAAGCTCTTTCGAGCTGAATAT
1 CGGTAAGCTCTTACGAGCTGAATAT
* * *
7560259 CAGTAAGCTCTTACGATCTTTAA-AT
1 CGGTAAGCTCTTACGAGC-TGAATAT
*
7560284 CGGTAAGCTCATACGA
1 CGGTAAGCTCTTACGA
7560300 ACTGTGGTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 31 0.91
26 3 0.09
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (25 bp):
CGGTAAGCTCTTACGAGCTGAATAT
Found at i:7562615 original size:26 final size:23
Alignment explanation
Indices: 7562585--7562666 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 23
7562575 GAGCCATGAT
7562585 CGGTAAGCTC-ATTCTGAGATGATAAA
1 CGGTAAGCTCTA-TC-GAGAT-A-AAA
*
7562611 CGGTAAGCTCTATCGAGCTAAAA
1 CGGTAAGCTCTATCGAGATAAAA
** * * *
7562634 CGGTAAGCTCCGTAGAGCTGAAA
1 CGGTAAGCTCTATCGAGATAAAA
7562657 CGGTAAGCTC
1 CGGTAAGCTC
7562667 ATACAAGCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
23 32 0.64
24 1 0.02
25 4 0.08
26 12 0.24
27 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (23 bp):
CGGTAAGCTCTATCGAGATAAAA
Done.