Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 13 of 135
Found at i:5807508 original size:7 final size:7
Alignment explanation
Indices: 5807496--5807536 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
5807486 TTACACCCTT
5807496 TTTTTTC
1 TTTTTTC
5807503 TTTTTTC
1 TTTTTTC
5807510 TTTTTTC
1 TTTTTTC
5807517 TTTTTTC
1 TTTTTTC
5807524 TTTTTTC
1 TTTTTTC
5807531 TTTTTT
1 TTTTTT
5807537 AATTCTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:5811364 original size:68 final size:68
Alignment explanation
Indices: 5811255--5811394 Score: 253
Period size: 68 Copynumber: 2.1 Consensus size: 68
5811245 GTATAGGACC
*
5811255 TCTTTATAATGGTAGTTCTTGTATGTGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
1 TCTTTATAATGGTAGTTCTTGTATGCGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
5811320 ATG
66 ATG
* *
5811323 TCTTTATAATGGTAGTTCTTGTATGCGTTAATGATCAAATTGGTATGAATATGCTTTTGGAGTTT
1 TCTTTATAATGGTAGTTCTTGTATGCGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
5811388 ATG
66 ATG
5811391 TCTT
1 TCTT
5811395 GTTTGATGGA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (68 bp):
TCTTTATAATGGTAGTTCTTGTATGCGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
ATG
Found at i:5812808 original size:51 final size:51
Alignment explanation
Indices: 5812739--5812846 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 51
5812729 AATATTATTC
*
5812739 CAATATTTGATAGTACAAAATTAGTCGAAAGCT-TCAGAAGAGTTAATATAT
1 CAATATTTGATAGTACAAAATTAGTCGAAAGCTCT-AGAAGAGCTAATATAT
* *
5812790 CAATATTTGGTAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAATATAT
1 CAATATTTGATAGTACAAAATTAGTCGAAAGCTCTAGAAGAGCTAATATAT
5812841 CAATAT
1 CAATAT
5812847 CTAAAAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
51 52 0.98
52 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (51 bp):
CAATATTTGATAGTACAAAATTAGTCGAAAGCTCTAGAAGAGCTAATATAT
Found at i:5815888 original size:27 final size:27
Alignment explanation
Indices: 5815856--5815944 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
5815846 ATTCGTGGGC
*
5815856 AAATGACTGAAATACCCTCGATGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
5815883 AAATGA-TAGAAATACCCT-GAAGGGTA
1 AAATGACT-GAAATACCCTCGAAGGGTA
* * * *
5815909 AAATGACCGAAATACCCCCAAAAGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
5815936 AAATGACTG
1 AAATGACTG
5815945 TTATACCCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 23 0.43
27 30 0.57
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (27 bp):
AAATGACTGAAATACCCTCGAAGGGTA
Found at i:5816148 original size:26 final size:26
Alignment explanation
Indices: 5816119--5816172 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
5816109 TTGCCACATA
* *
5816119 TACTGTTACTGGTAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
5816145 TACTATTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
5816171 TA
1 TA
5816173 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCGT
Found at i:5816212 original size:45 final size:45
Alignment explanation
Indices: 5816148--5816233 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
5816138 GCTGCGTTAC
* * *
5816148 TATTACTGGCAGCTTTGCTGCGTTATTGGTGTGTTGGCTGGTCAT
1 TATTACTAGCAGCTTTGCTGCGATATTGGTGTATTGGCTGGTCAT
5816193 TATTACTAGCAGCTTTGCTGCGATATTGGTGTATTGGCTGG
1 TATTACTAGCAGCTTTGCTGCGATATTGGTGTATTGGCTGG
5816234 GTGGGTCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.14, C:0.15, G:0.30, T:0.41
Consensus pattern (45 bp):
TATTACTAGCAGCTTTGCTGCGATATTGGTGTATTGGCTGGTCAT
Found at i:5816360 original size:28 final size:28
Alignment explanation
Indices: 5816320--5816381 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
5816310 ACTGCATTGT
5816320 ACTGTTACGGTATTAGGCTAAGGCCCAC
1 ACTGTTACGGTATTAGGCTAAGGCCCAC
* *
5816348 ACTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACGGTATTAGGCTAAGGCCCAC
5816376 ACTGTT
1 ACTGTT
5816382 GCCGCATAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (28 bp):
ACTGTTACGGTATTAGGCTAAGGCCCAC
Found at i:5816393 original size:28 final size:28
Alignment explanation
Indices: 5816335--5816416 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
5816325 TACGGTATTA
* * *
5816335 GGCTAAGGCCCACACTGTTACTGTATTG
1 GGCTAAGGCCCACACTGTTACCGCATAG
*
5816363 GGCTAAGGCCCACACTGTTGCCGCATAG
1 GGCTAAGGCCCACACTGTTACCGCATAG
* * * *
5816391 GGCTCAGGCCCAGACTGCTACTGCAT
1 GGCTAAGGCCCACACTGTTACCGCAT
5816417 GTTGTATACT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.21, C:0.30, G:0.27, T:0.22
Consensus pattern (28 bp):
GGCTAAGGCCCACACTGTTACCGCATAG
Found at i:5820913 original size:34 final size:33
Alignment explanation
Indices: 5820840--5820951 Score: 138
Period size: 34 Copynumber: 3.4 Consensus size: 33
5820830 GATTTAGTGT
*
5820840 TATTTTTTAAAAATTAATTAAA-TTAGGGTTTAG
1 TATTTTTAAAAAATTAATTAAATTTA-GGTTTAG
**
5820873 -GGTTTTAAATAAATTAATTAAATTTAGGTTTAG
1 TATTTTTAAA-AAATTAATTAAATTTAGGTTTAG
*
5820906 TATTTTTAAGAAAATTAATTAAATTTTGGTTTAG
1 TATTTTTAA-AAAATTAATTAAATTTAGGTTTAG
*
5820940 TTTTTTTAAAAA
1 TATTTTTAAAAA
5820952 TAATATTGTG
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
32 6 0.09
33 22 0.32
34 39 0.57
35 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (33 bp):
TATTTTTAAAAAATTAATTAAATTTAGGTTTAG
Found at i:5821367 original size:125 final size:125
Alignment explanation
Indices: 5821011--5821649 Score: 879
Period size: 125 Copynumber: 5.1 Consensus size: 125
5821001 GGATTTTGAT
*
5821011 TTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAA
1 TTTTTT-TACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAA
* ** *
5821076 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACATAGACGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTG-AAAAAGCTCCCATGTGGACGCTC
* * *
5821138 ATTTTCTT-CAGTAGTTCCTGAAAAAATAATTTTGAGATGACGGTTCTGAACAAATAGTGTCAAA
1 -TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAA
5821202 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAGAGCTCCCATGTGGACGCT-
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAA-AGCTCCCATGTGGACGCTC
*
5821263 TTTTTTTACTGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAA
1 TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAA
* * *
5821328 ACACTTCAAGTAGGATGCACTATCAGCAAAATTGA-TGAAAAAAGCTCCCATGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTG-AAAAAGCTCCCATGTGGACGCTC
* *
5821389 TTTTTATACAGTAGTTCCTG-AAAAATAATTTTGAGAAGA-TGTTTCTGAACAAATAGTGTCAAA
1 TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTT-TGAACAAATAGTGTCAAA
* * * * *
5821452 AATGCTTCAAGAAGTATGCACTGTCAGCAAAATTACTG-AAAA--T---AGGTGGACACTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCCCATGTGGACGCTC
* * * *
5821507 TTTTTCTACAGTAGTTCCTGAAAAGATAATTTTGAGAAGAC-ATTTCTGAAAAAATAGTGTCAAA
1 TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTT-TGAACAAATAGTGTCAAA
*
5821571 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAGAAAAGCTCCCATGTGGGCGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGA-AAAAGCTCCCATGTGGACGCTC
* *
5821633 TTTTTCTACAATAGTTC
1 TTTTTTTACAGTAGTTC
5821650 GTGTTTGGCC
Statistics
Matches: 461, Mismatches: 34, Indels: 34
0.87 0.06 0.06
Matches are distributed among these distances:
118 29 0.06
119 74 0.16
121 5 0.01
123 5 0.01
124 11 0.02
125 176 0.38
126 155 0.34
127 1 0.00
128 5 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (125 bp):
TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAGCTCCCATGTGGACGCTC
Found at i:5824603 original size:26 final size:25
Alignment explanation
Indices: 5824555--5824603 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
5824545 ACTTCTATTT
*
5824555 TATTAAAAATATAAAAATAATTTAC
1 TATTAAAAATATAAAAAGAATTTAC
5824580 TATT-AAAATATTAAAAACGAATTT
1 TATTAAAAATA-TAAAAA-GAATTT
5824604 TATTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 10 0.48
26 5 0.24
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (25 bp):
TATTAAAAATATAAAAAGAATTTAC
Found at i:5824607 original size:24 final size:23
Alignment explanation
Indices: 5824551--5824607 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 23
5824541 AAGAACTTCT
*
5824551 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAAGA
5824574 ATTTACTATT-AAAATATTAAAAACGA
1 ATTT--TATTAAAAATA-TAAAAA-GA
5824600 ATTTTATT
1 ATTTTATT
5824608 TTATTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 10 0.34
26 5 0.17
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAAGA
Found at i:5826857 original size:30 final size:30
Alignment explanation
Indices: 5826803--5826867 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
5826793 ATTAATTAAA
*
5826803 GAGAGCTTTGAGAAATTTAAGGAGAAGTTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
**
5826833 GAGAGCTTTGAGAAATTTTGGGAGAAATTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
*
5826863 TAGAG
1 GAGAG
5826868 TTTTTTGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.31, T:0.31
Consensus pattern (30 bp):
GAGAGCTTTGAGAAATTTAAGGAGAAATTT
Found at i:5827698 original size:22 final size:22
Alignment explanation
Indices: 5827670--5827721 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
5827660 TGGGCATCGA
*
5827670 AAATTGACCA-AATAAACCAATT
1 AAATTGAACATAA-AAACCAATT
* *
5827692 AAATTGAACATGAAAATCAATT
1 AAATTGAACATAAAAACCAATT
5827714 AAATTGAA
1 AAATTGAA
5827722 AAATCGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.25
Consensus pattern (22 bp):
AAATTGAACATAAAAACCAATT
Found at i:5827724 original size:17 final size:17
Alignment explanation
Indices: 5827704--5827741 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5827694 ATTGAACATG
*
5827704 AAAATC-AATTAAATTGA
1 AAAATCGAA-TAAACTGA
5827721 AAAATCGAATAAACTGA
1 AAAATCGAATAAACTGA
5827738 AAAA
1 AAAA
5827742 ATTCAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAATCGAATAAACTGA
Found at i:5830653 original size:19 final size:19
Alignment explanation
Indices: 5830573--5830653 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
5830563 GGGTAATTAA
* *
5830573 CACACAACGTGCATACTTG
1 CACACAAAGTGCATACTAG
* *
5830592 CATACAAAAG-GCATCCTAG
1 CACAC-AAAGTGCATACTAG
** * *
5830611 TGCACAAAGCGCATACTGG
1 CACACAAAGTGCATACTAG
*
5830630 CACACAAAGTGCATCCTAG
1 CACACAAAGTGCATACTAG
5830649 CACAC
1 CACAC
5830654 GAAGCGTATA
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
18 4 0.09
19 39 0.85
20 3 0.07
ACGTcount: A:0.36, C:0.31, G:0.17, T:0.16
Consensus pattern (19 bp):
CACACAAAGTGCATACTAG
Found at i:5830659 original size:38 final size:38
Alignment explanation
Indices: 5830573--5830685 Score: 102
Period size: 38 Copynumber: 2.9 Consensus size: 38
5830563 GGGTAATTAA
* * * *
5830573 CACACAACGTGCATACTTGCATACAAAAG-GCATCCTAG
1 CACACAAAGCGCATACTGGCACAC-AAAGTGCATCCTAG
**
5830611 TGCACAAAGCGCATACTGGCACACAAAGTGCATCCTAG
1 CACACAAAGCGCATACTGGCACACAAAGTGCATCCTAG
* * * * *
5830649 CACACGAAGCGTATATTTGGCACACGAGGTGCATCCT
1 CACACAAAGCGCATA-CTGGCACACAAAGTGCATCCT
5830686 GACAAATTAA
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
37 4 0.07
38 38 0.63
39 18 0.30
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (38 bp):
CACACAAAGCGCATACTGGCACACAAAGTGCATCCTAG
Found at i:5831838 original size:25 final size:25
Alignment explanation
Indices: 5831803--5831939 Score: 134
Period size: 25 Copynumber: 5.4 Consensus size: 25
5831793 CCACAAAAGG
* *
5831803 TTTTCCAGATAATACACCATATAGGC
1 TTTT-CAGATAATACGCCACATAGGC
* *
5831829 TTTTCAGATAATATGCAACATAGGC
1 TTTTCAGATAATACGCCACATAGGC
* * *
5831854 -TTTCTAGATAATACACCACATATGT
1 TTTTC-AGATAATACGCCACATAGGC
* * *
5831879 TTTTTAGATAACT-TGCCACAAAGGC
1 TTTTCAGATAA-TACGCCACATAGGC
*
5831904 TTTTCAGATAATACGCCACATAGTC
1 TTTTCAGATAATACGCCACATAGGC
5831929 TTTTCAGATAA
1 TTTTCAGATAA
5831940 CTTACCACAA
Statistics
Matches: 88, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
24 5 0.06
25 75 0.85
26 8 0.09
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (25 bp):
TTTTCAGATAATACGCCACATAGGC
Found at i:5831888 original size:50 final size:49
Alignment explanation
Indices: 5831782--5831953 Score: 168
Period size: 50 Copynumber: 3.4 Consensus size: 49
5831772 ACAGGCTTTC
* * * * * *
5831782 CAGATGACTTGCCACAAAAGGTTTTCCAGATAATACACCATATAGGCTTTT
1 CAGATAACTTGCAAC-AAAGGCTTTCTAGATAATACACCACATA-GTTTTT
*
5831833 CAGATAA-TATGCAACATAGGCTTTCTAGATAATACACCACATATGTTTTT
1 CAGATAACT-TGCAACAAAGGCTTTCTAGATAATACACCACATA-GTTTTT
* * *
5831883 TAGATAACTTGCCACAAAGGCTTT-TCAGATAATACGCCACATAGTCTTTT
1 CAGATAACTTGCAACAAAGGCTTTCT-AGATAATACACCACATAGT-TTTT
* *
5831933 CAGATAACTTACCACAAAGGC
1 CAGATAACTTGCAACAAAGGC
5831954 ACTGCATAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.03
50 88 0.85
51 12 0.12
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (49 bp):
CAGATAACTTGCAACAAAGGCTTTCTAGATAATACACCACATAGTTTTT
Found at i:5831947 original size:25 final size:25
Alignment explanation
Indices: 5831868--5831948 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
5831858 TAGATAATAC
*
5831868 ACCACATATGT-TTTTTAGATAACTT
1 ACCACATA-GTCTTTTCAGATAACTT
* * *
5831893 GCCACAAAGGCTTTTCAGATAA--T
1 ACCACATAGTCTTTTCAGATAACTT
5831916 ACGCCACATAGTCTTTTCAGATAACTT
1 A--CCACATAGTCTTTTCAGATAACTT
5831943 ACCACA
1 ACCACA
5831949 AAGGCACTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 40 0.91
27 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (25 bp):
ACCACATAGTCTTTTCAGATAACTT
Found at i:5839860 original size:29 final size:29
Alignment explanation
Indices: 5839774--5839876 Score: 88
Period size: 27 Copynumber: 3.7 Consensus size: 29
5839764 TTGCATCACG
* * *
5839774 AAGGCATTTCTTTTTCAGATATAGCTACA
1 AAGGCATTTCTTTTACAGAGATAGCCACA
* * **
5839803 AAGGC--TTCTTTTACGGAGATTGTGACA
1 AAGGCATTTCTTTTACAGAGATAGCCACA
*
5839830 AAGGC-TTTCTTTTGACAGAGATCGCCACA
1 AAGGCATTTCTTTT-ACAGAGATAGCCACA
*
5839859 AAGGCATTTCATTT-CAGA
1 AAGGCATTTCTTTTACAGA
5839877 TATTTTCCAC
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
27 21 0.35
28 11 0.18
29 21 0.35
30 7 0.12
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (29 bp):
AAGGCATTTCTTTTACAGAGATAGCCACA
Found at i:5840005 original size:29 final size:29
Alignment explanation
Indices: 5839967--5840068 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
5839957 ACATCCAGTA
5839967 TTTGCCACAAAGGCTTTCCTGTCTAAAGT
1 TTTGCCACAAAGGCTTTCCTGTCTAAAGT
* * * **
5839996 TTTGCCACAAATGCTATCCTTTACATCCAGT
1 TTTGCCACAAAGGCTTTCCTGT-C-TAAAGT
* * * *
5840027 ACTCGCCACAAAGGCTTTCCTGTCCAAAGA
1 -TTTGCCACAAAGGCTTTCCTGTCTAAAGT
*
5840057 TTTACCACAAAG
1 TTTGCCACAAAG
5840069 ACTATGCTTT
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
29 28 0.53
30 3 0.06
31 5 0.09
32 17 0.32
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
TTTGCCACAAAGGCTTTCCTGTCTAAAGT
Found at i:5840035 original size:61 final size:59
Alignment explanation
Indices: 5839931--5840129 Score: 227
Period size: 61 Copynumber: 3.3 Consensus size: 59
5839921 TTACCTTTCC
* * * * *
5839931 AAAGTTTCGCCACAAAGGTTGTCTTTACATCCAGTATTTGCCACAAAGGCTTTCCTGTCT
1 AAAGTTTTGCCACAAA-GCTATCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
*
5839991 AAAGTTTTGCCACAAATGCTATCCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCC
1 AAAGTTTTGCCACAAA-GCTAT-CTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
* * * * * *
5840052 AAAGATTTACCACAAAGACTATGCTTTATATCCATTACTCGCCAAAAAGGCTTTCCTATCT
1 AAAGTTTTGCCACAAAG-CTAT-CTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
* *
5840113 AGAGTTTTGCCAAAAAG
1 AAAGTTTTGCCACAAAG
5840130 GCGTTCCTTA
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
60 19 0.16
61 99 0.84
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (59 bp):
AAAGTTTTGCCACAAAGCTATCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
Found at i:5840357 original size:53 final size:53
Alignment explanation
Indices: 5840260--5840403 Score: 148
Period size: 53 Copynumber: 2.7 Consensus size: 53
5840250 TCCCCACAAA
* * * *
5840260 ATGCCATAACTCACTAGTTACAGTCTTACACT-ATATCGTCTTCTTCCCACATG
1 ATGCCATAACTCACCAGTTACGGTCTTACA-TGATATGGTATTCTTCCCACATG
* * *
5840313 ATGCCATAAAC-CACCAGTTACGGTCTTACATGATATGGTATTCTTTCTATATG
1 ATGCCAT-AACTCACCAGTTACGGTCTTACATGATATGGTATTCTTCCCACATG
** * * *
5840366 ATGTTATAACTCACCAATTACGGCCTTACACGATATGG
1 ATGCCATAACTCACCAGTTACGGTCTTACATGATATGG
5840404 CCATGGACAT
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
52 4 0.05
53 69 0.91
54 3 0.04
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (53 bp):
ATGCCATAACTCACCAGTTACGGTCTTACATGATATGGTATTCTTCCCACATG
Found at i:5869315 original size:43 final size:43
Alignment explanation
Indices: 5869188--5869316 Score: 129
Period size: 44 Copynumber: 3.0 Consensus size: 43
5869178 TTAGGATTCT
*
5869188 GTTATGTG-TTATCGTGTAAGACCACGTCTGGGATGTTGGCATC
1 GTTATGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCATC
* * **
5869231 GACT-TGTGACTTACGTGTAAGACC-CTATCTGGGACAATGGCATC
1 G-TTATGTGA-TTACGTGTAAGACCAC-GTCTGGGACGTTGGCATC
* **
5869275 GTTATGTGATTACATGTAAGACCACGTCTAAGACGTTGGCAT
1 GTTATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
5869317 TTTATGAAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
43 32 0.47
44 33 0.49
45 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
GTTATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:5873410 original size:13 final size:14
Alignment explanation
Indices: 5873392--5873420 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5873382 AAAATTGCTT
5873392 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
5873405 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
5873419 AA
1 AA
5873421 GCCACTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Found at i:5873575 original size:11 final size:11
Alignment explanation
Indices: 5873538--5873575 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
5873528 TCCTTCGTTG
5873538 ATCATCCCTCA
1 ATCATCCCTCA
*
5873549 AGCATCCCTCA
1 ATCATCCCTCA
5873560 ATCATCCCTCA
1 ATCATCCCTCA
*
5873571 TTCAT
1 ATCAT
5873576 TCTCATCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.26, C:0.42, G:0.03, T:0.29
Consensus pattern (11 bp):
ATCATCCCTCA
Found at i:5875787 original size:29 final size:30
Alignment explanation
Indices: 5875736--5875797 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
5875726 AATTATTTTA
5875736 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
5875766 TTGTTAATTTT-TTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
5875795 TTG
1 TTG
5875798 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:5875954 original size:13 final size:11
Alignment explanation
Indices: 5875919--5875948 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5875909 TATATATATT
5875919 TAAAAATTATA
1 TAAAAATTATA
*
5875930 TAAAAATCATA
1 TAAAAATTATA
5875941 TAAAAATT
1 TAAAAATT
5875949 TAATATGGGC
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:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:5886058 original size:29 final size:30
Alignment explanation
Indices: 5886007--5886068 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
5885997 AATTATTTTA
5886007 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
5886037 TTGTTAATTTT-TTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
5886066 TTG
1 TTG
5886069 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:5886225 original size:13 final size:11
Alignment explanation
Indices: 5886190--5886219 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5886180 TATATATATT
5886190 TAAAAATTATA
1 TAAAAATTATA
*
5886201 TAAAAATCATA
1 TAAAAATTATA
5886212 TAAAAATT
1 TAAAAATT
5886220 TAATATGGGC
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:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:5889722 original size:58 final size:60
Alignment explanation
Indices: 5889658--5889773 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 60
5889648 ATCACTTTAA
*
5889658 TATTAAATTAATATAATACTTA-T-CAAGATAA-ATATTAGATTAAA-TATAATATTAAATC
1 TATTAAATTAATATAATACTTACTACAAGATAATA-ATTAAATTAAATTA-AATATTAAATC
*
5889716 TATTAAATTAATATAATATTTATCTACAAGATAATAATTAAATTAAATTAAATATTAA
1 TATTAAATTAATATAATACTTA-CTACAAGATAATAATTAAATTAAATTAAATATTAA
5889774 GATAATTGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
58 21 0.41
60 1 0.02
61 26 0.51
62 3 0.06
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (60 bp):
TATTAAATTAATATAATACTTACTACAAGATAATAATTAAATTAAATTAAATATTAAATC
Found at i:5889773 original size:61 final size:58
Alignment explanation
Indices: 5889658--5889858 Score: 158
Period size: 61 Copynumber: 3.2 Consensus size: 58
5889648 ATCACTTTAA
*
5889658 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATATAATATTAAATC
1 TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATATAATATTAAATC
*
5889716 TATTAAATTAATATAATATTTATCTACAAGAT-AATAATTAAATTAAAT-TAAATATTAAGATAA
1 TATTAAATTAATATAATACTTA--T-CAAGATAAAT-ATTAAATTAAATAT-AATATT---A-AA
5889779 TTGC
57 -T-C
* * * *
5889783 TTTAATATTAAATTAATAAAATAC-TATTAAGATAATTATTAAA-TCAATAGTAATATTAAATC
1 -----TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATA-TAATATTAAATC
*
5889845 TATTAAAATAATAT
1 TATTAAATTAATAT
5889859 CATTTTTGGA
Statistics
Matches: 115, Mismatches: 9, Indels: 39
0.71 0.06 0.24
Matches are distributed among these distances:
57 12 0.10
58 21 0.18
60 5 0.04
61 23 0.20
62 1 0.01
63 1 0.01
64 3 0.03
65 3 0.03
66 1 0.01
67 5 0.04
68 17 0.15
69 4 0.03
71 2 0.02
72 17 0.15
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (58 bp):
TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATATAATATTAAATC
Found at i:5892208 original size:54 final size:54
Alignment explanation
Indices: 5892127--5892248 Score: 154
Period size: 54 Copynumber: 2.3 Consensus size: 54
5892117 TCCACCTGTA
* * * * *
5892127 TAACTCACTGAGTAGGGTCACATGGCCATGTCACAGGCCGTGTGCTAGACAAAG
1 TAACTCACTGACTTGCGACACACGGCCATGTCACAGGCCGTGTGCTAGACAAAG
* * * * *
5892181 TAACTCTCTGACTTGCGACACACGGCCATGTCGCAGGCCGTGTGCTAGGCCATG
1 TAACTCACTGACTTGCGACACACGGCCATGTCACAGGCCGTGTGCTAGACAAAG
5892235 TAACTCACTGACTT
1 TAACTCACTGACTT
5892249 AAAACATTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (54 bp):
TAACTCACTGACTTGCGACACACGGCCATGTCACAGGCCGTGTGCTAGACAAAG
Found at i:5894295 original size:23 final size:23
Alignment explanation
Indices: 5894250--5894295 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5894240 TGACATATTC
* **
5894250 TTTTATCTTTTATTTACTTAACT
1 TTTTATCTTTTAATTACCAAACT
*
5894273 TTTTTTCTTTTAATTACCAAACT
1 TTTTATCTTTTAATTACCAAACT
5894296 ACTACTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTATCTTTTAATTACCAAACT
Found at i:5898949 original size:18 final size:20
Alignment explanation
Indices: 5898918--5898956 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5898908 TTAAAAATAA
5898918 ATTTTCTAAAAATATT-TTT
1 ATTTTCTAAAAATATTATTT
5898937 ATTTTCT-AAAATATTATTT
1 ATTTTCTAAAAATATTATTT
5898956 A
1 A
5898957 CCAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTCTAAAAATATTATTT
Found at i:5902267 original size:26 final size:26
Alignment explanation
Indices: 5902231--5902287 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
5902221 ATAAACAAGT
5902231 AAAATAAAATTTAAAA-AAAAT-TAAA
1 AAAATAAAA-TTAAAATAAAATATAAA
*
5902256 AAAACTAAAATTAAAATAAAATATAAG
1 AAAA-TAAAATTAAAATAAAATATAAA
5902283 AAAAT
1 AAAAT
5902288 CAATATGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 10 0.36
26 11 0.39
27 7 0.25
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (26 bp):
AAAATAAAATTAAAATAAAATATAAA
Found at i:5903460 original size:11 final size:11
Alignment explanation
Indices: 5903436--5903468 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5903426 TTCGGGTCTC
5903436 TAAACTAATA-A
1 TAAA-TAATATA
5903447 TAAATAATATA
1 TAAATAATATA
5903458 TAAATAATATA
1 TAAATAATATA
5903469 ATTAGTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATAATATA
Found at i:5904233 original size:3 final size:3
Alignment explanation
Indices: 5904225--5904265 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5904215 CCGCTGCCCT
5904225 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5904266 TTCAAGTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5904729 original size:1 final size:1
Alignment explanation
Indices: 5904725--5904755 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
5904715 TTTTTGCTTC
5904725 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5904756 GCTTAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5910879 original size:15 final size:17
Alignment explanation
Indices: 5910841--5910879 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
5910831 AAAAAATATC
5910841 AATTAAATTTCTACAAA
1 AATTAAATTTCTACAAA
5910858 AA-T-AATTT-TA-AAA
1 AATTAAATTTCTACAAA
5910871 AATTAAATT
1 AATTAAATT
5910880 CTAAGAGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.25
14 3 0.15
15 9 0.45
16 1 0.05
17 2 0.10
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATTTCTACAAA
Found at i:5915008 original size:23 final size:23
Alignment explanation
Indices: 5914982--5915027 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5914972 TTTTAAACTC
5914982 AATCATTATGTTAGCCAAAGTTA
1 AATCATTATGTTAGCCAAAGTTA
5915005 AATCATTATGTTAGCCAAAGTTA
1 AATCATTATGTTAGCCAAAGTTA
5915028 TTTAAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
AATCATTATGTTAGCCAAAGTTA
Found at i:5916440 original size:14 final size:14
Alignment explanation
Indices: 5916421--5916460 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5916411 TTGATTGGCA
5916421 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
5916435 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
5916449 GGAAAATGTTTT
1 GTAAAATGTTTT
5916461 ACATTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:5916482 original size:20 final size:20
Alignment explanation
Indices: 5916443--5916482 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5916433 CCGTAAAATG
**
5916443 ATTTCTGGAAAATGTTTTAC
1 ATTTCTGGAAAATGACTTAC
*
5916463 ATTTCTGTAAAATGACTTAC
1 ATTTCTGGAAAATGACTTAC
5916483 TGGAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
ATTTCTGGAAAATGACTTAC
Found at i:5916490 original size:35 final size:34
Alignment explanation
Indices: 5916430--5916495 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
5916420 AGTAAAATGT
* *
5916430 TTTCCGTAAAATGATTTCTGGAAAATGTTTTACA
1 TTTCCGTAAAATGATTACTGGAAAATATTTTACA
*
5916464 TTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTCCGTAAAATGA-TTACTGGAAAATATTTT
5916496 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (34 bp):
TTTCCGTAAAATGATTACTGGAAAATATTTTACA
Found at i:5918888 original size:15 final size:15
Alignment explanation
Indices: 5918868--5918899 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5918858 GGACGGATAT
5918868 GGAGAAGAGGGAACC
1 GGAGAAGAGGGAACC
5918883 GGAGAAGAGGGAACC
1 GGAGAAGAGGGAACC
5918898 GG
1 GG
5918900 GGAAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.50, T:0.00
Consensus pattern (15 bp):
GGAGAAGAGGGAACC
Found at i:5920481 original size:29 final size:30
Alignment explanation
Indices: 5920448--5920504 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
5920438 GGGGTGGGAT
5920448 GGGAGCAAAAGTTATGGG-GGAAAGTGAGA
1 GGGAGCAAAAGTTATGGGAGGAAAGTGAGA
* *
5920477 GGGAGTAAAAGTTTTGGGAGGAAAGTGA
1 GGGAGCAAAAGTTATGGGAGGAAAGTGA
5920505 AGAAGTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.37, C:0.02, G:0.44, T:0.18
Consensus pattern (30 bp):
GGGAGCAAAAGTTATGGGAGGAAAGTGAGA
Found at i:5922442 original size:21 final size:21
Alignment explanation
Indices: 5922416--5922455 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5922406 TTACCATTAT
*
5922416 TGTTG-TAGTTGTTATTATTCA
1 TGTTGTTAGTTATT-TTATTCA
5922437 TGTTGTTAGTTATTTTATT
1 TGTTGTTAGTTATTTTATT
5922456 TATTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.62
Consensus pattern (21 bp):
TGTTGTTAGTTATTTTATTCA
Found at i:5926480 original size:10 final size:10
Alignment explanation
Indices: 5926436--5926499 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
5926426 AAAATTATTA
5926436 TTTTAGAAAAT
1 TTTTAG-AAAT
*
5926447 TTTTA-AATT
1 TTTTAGAAAT
* *
5926456 TTTTAATGTATT
1 TTTT-A-GAAAT
5926468 TTTTAGAAAT
1 TTTTAGAAAT
5926478 TTTTAGAAA-
1 TTTTAGAAAT
*
5926487 TTTTATAAAT
1 TTTTAGAAAT
5926497 TTT
1 TTT
5926500 ATAATTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.34
10 16 0.36
11 6 0.14
12 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (10 bp):
TTTTAGAAAT
Found at i:5927852 original size:25 final size:25
Alignment explanation
Indices: 5927817--5927883 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
5927807 CTCACCACAA
* *
5927817 CTCGTATGAGCTTATCGAT-TTGCAC
1 CTCGTAGGAGCTTACCGATATT-CAC
*
5927842 CTCGTAGGAGCTTACCGATATTCAG
1 CTCGTAGGAGCTTACCGATATTCAC
*
5927867 CTCGGAGGAGCTTACCG
1 CTCGTAGGAGCTTACCG
5927884 TTTATCGTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 35 0.95
26 2 0.05
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.28
Consensus pattern (25 bp):
CTCGTAGGAGCTTACCGATATTCAC
Found at i:5930495 original size:2 final size:2
Alignment explanation
Indices: 5930488--5930525 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5930478 TTTGTAAGTG
5930488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5930526 AAAAAAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5936236 original size:23 final size:23
Alignment explanation
Indices: 5936187--5936241 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
5936177 TTTTTAGAAA
* * *
5936187 ATTCTGCAAAGCCTTTGTGGCGC
1 ATTCTGTAAAGCCTTTGTAGCAC
* *
5936210 ATTCTGTAAAGTCTTTGTAGCAT
1 ATTCTGTAAAGCCTTTGTAGCAC
5936233 ATTCTGTAA
1 ATTCTGTAA
5936242 CACCCTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (23 bp):
ATTCTGTAAAGCCTTTGTAGCAC
Found at i:5940343 original size:26 final size:27
Alignment explanation
Indices: 5940293--5940353 Score: 115
Period size: 26 Copynumber: 2.3 Consensus size: 27
5940283 TAAAAATAAG
5940293 CAAAATATTATAACTTTTTTTATTTAC
1 CAAAATATTATAACTTTTTTTATTTAC
5940320 CAAAATATTATAA-TTTTTTTATTTAC
1 CAAAATATTATAACTTTTTTTATTTAC
5940346 CAAAATAT
1 CAAAATAT
5940354 ACAAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.62
27 13 0.38
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
CAAAATATTATAACTTTTTTTATTTAC
Found at i:5940442 original size:27 final size:27
Alignment explanation
Indices: 5940412--5940463 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
5940402 GGCCAATCAC
5940412 ATTGGCGGCACCAAAGGTGCCAAAGAT
1 ATTGGCGGCACCAAAGGTGCCAAAGAT
*
5940439 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
5940464 GACTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAT
Found at i:5940644 original size:19 final size:19
Alignment explanation
Indices: 5940617--5940686 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
5940607 TCAACTCACT
*
5940617 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
5940636 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
5940654 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
5940673 TTTTAATTTAATAA
1 TTTTAATTTAATAA
5940687 ACTATTCTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:5940654 original size:18 final size:19
Alignment explanation
Indices: 5940613--5940692 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
5940603 CCCTTCAACT
*
5940613 CACT-TTTTTATTTAATAA
1 CACTATTTTAATTTAATAA
*
5940631 CTCTATTTTAATTTAATAA
1 CACTATTTTAATTTAATAA
* *
5940650 -ACTATTCTCATTTAATAA
1 CACTATTTTAATTTAATAA
*
5940668 CTCTATTTTAATTTAATAA
1 CACTATTTTAATTTAATAA
5940687 -ACTATT
1 CACTATT
5940693 CTCATNNNNN
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
18 23 0.45
19 28 0.55
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.51
Consensus pattern (19 bp):
CACTATTTTAATTTAATAA
Found at i:5940667 original size:37 final size:37
Alignment explanation
Indices: 5940622--5940697 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
5940612 TCACTTTTTT
5940622 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
5940659 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
5940696 AT
1 AT
5940698 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:5941550 original size:26 final size:28
Alignment explanation
Indices: 5941521--5941585 Score: 107
Period size: 29 Copynumber: 2.4 Consensus size: 28
5941511 ATTTTTTGGC
5941521 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
5941547 ATATTTTGGTAAATAAAAAAAAAGTTATA
1 ATATTTTGGTAAAT-AAAAAAAAGTTATA
5941576 ATATTTTGGT
1 ATATTTTGGT
5941586 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 14 0.39
28 7 0.19
29 15 0.42
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:5950105 original size:27 final size:27
Alignment explanation
Indices: 5950069--5950190 Score: 118
Period size: 27 Copynumber: 4.5 Consensus size: 27
5950059 ATTTGCCAAT
* * *
5950069 AAGGTCATTCTCTCAGAGTTCACCATA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* **
5950096 AAGTTTATTCTTTCAGAGTTCGTCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* **
5950123 AAGGTTATTCTTTCAAAGTTCGTCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* * *
5950150 AAGGTTATTCTTTTAGAGCTCGCCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* *
5950177 AAGGCTATTATTTC
1 AAGGTTATTCTTTC
5950191 CTAATGTGTT
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (27 bp):
AAGGTTATTCTTTCAGAGTTCACCACA
Found at i:5950133 original size:54 final size:54
Alignment explanation
Indices: 5950069--5950185 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 54
5950059 ATTTGCCAAT
* * * * * *
5950069 AAGGTCATTCTCTCAGAGTTCACCATAAAGTTTATTCTTTCAGAGTTCGTCACA
1 AAGGTTATTCTCTCAAAGTTCACCACAAAGGTTATTCTTTCAGAGCTCGCCACA
* ** *
5950123 AAGGTTATTCTTTCAAAGTTCGTCACAAAGGTTATTCTTTTAGAGCTCGCCACA
1 AAGGTTATTCTCTCAAAGTTCACCACAAAGGTTATTCTTTCAGAGCTCGCCACA
*
5950177 AAGGCTATT
1 AAGGTTATT
5950186 ATTTCCTAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (54 bp):
AAGGTTATTCTCTCAAAGTTCACCACAAAGGTTATTCTTTCAGAGCTCGCCACA
Found at i:5962301 original size:26 final size:26
Alignment explanation
Indices: 5962272--5962340 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
5962262 ATCCTCTCTC
5962272 AAGCCATATAACAGGAAGCTCACAAA
1 AAGCCATATAACAGGAAGCTCACAAA
*
5962298 AAGCTAT-TAATC-GGAAAGCTCACAAA
1 AAGCCATATAA-CAGG-AAGCTCACAAA
*
5962324 GAGCC-TAT--CAGGAAGCT
1 AAGCCATATAACAGGAAGCT
5962341 TATCCGGGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
23 6 0.17
24 2 0.06
25 6 0.17
26 22 0.61
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (26 bp):
AAGCCATATAACAGGAAGCTCACAAA
Found at i:5962423 original size:26 final size:26
Alignment explanation
Indices: 5962377--5962454 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
5962367 ATAAGAGTCA
* * * *
5962377 TAATCATGAAGTTCAAAAAGAACTTT
1 TAATCAGGAAGCTCAAGAAGAACCTT
* *
5962403 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCAAGAAGAACCTT
* *
5962429 TAATCGGGAAGCTCAAGAAGAGCCTT
1 TAATCAGGAAGCTCAAGAAGAACCTT
5962455 ATAACGGGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (26 bp):
TAATCAGGAAGCTCAAGAAGAACCTT
Found at i:5962462 original size:26 final size:26
Alignment explanation
Indices: 5962401--5962463 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
5962391 AAAAAGAACT
* *
5962401 TTTAATCAGGAAGCTCACGAAGAGCC
1 TTTAATCGGGAAGCTCAAGAAGAGCC
5962427 TTTAATCGGGAAGCTCAAGAAGAGCC
1 TTTAATCGGGAAGCTCAAGAAGAGCC
5962453 TTATAA-CGGGA
1 TT-TAATCGGGA
5962464 GCTTCGGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 31 0.91
27 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (26 bp):
TTTAATCGGGAAGCTCAAGAAGAGCC
Found at i:5965383 original size:50 final size:50
Alignment explanation
Indices: 5965272--5965520 Score: 264
Period size: 50 Copynumber: 4.8 Consensus size: 50
5965262 ATTTGGGCAA
*
5965272 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* * * *
5965328 AGAGGTCCCATGTAAGGCCATGTCTGGGATATGGCGTTGACACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * ***
5965378 AGAGGTCCCATGTAAGACTAAGTCTGGGACATGATGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
5965428 AGAGGTCCCCCGTAAGACCCTGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
5965478 AGAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
5965521 TCTTATGATC
Statistics
Matches: 162, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
50 88 0.54
51 32 0.20
53 3 0.02
55 2 0.01
56 37 0.23
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:5967105 original size:42 final size:42
Alignment explanation
Indices: 5967048--5967160 Score: 181
Period size: 42 Copynumber: 2.7 Consensus size: 42
5967038 GTTTACAAAC
* *
5967048 AAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAA
*
5967090 AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAA
* *
5967132 AAAAACGCCGCTAAAGATCATGTTATTTA
1 AAAAACGCCGCTAAAGACCATGTTCTTTA
5967161 ACAGCGTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAA
Found at i:5967254 original size:42 final size:42
Alignment explanation
Indices: 5967134--5967255 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
5967124 GCTTAGAGAA
* * *
5967134 AAACGCCGCTAAAGATCATGTTATTTAACAGCG-TTTTTTCTT
1 AAACGCCGCTAAAGAACAT-TTCTTTAGCAGCGCTTTTTTCTT
* * * * *
5967176 AAACACCGCTAAAGAACATGGTCTTTTGCGGTGCTTTTTTC-T
1 AAACGCCGCTAAAGAACAT-TTCTTTAGCAGCGCTTTTTTCTT
*
5967218 AAGCGCCGCTAAAGAACATTATCTTTAGCAGCGCTTTT
1 AAACGCCGCTAAAGAACATT-TCTTTAGCAGCGCTTTT
5967256 ATACAAAAAC
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 57 0.89
43 7 0.11
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATTTCTTTAGCAGCGCTTTTTTCTT
Found at i:5967594 original size:21 final size:21
Alignment explanation
Indices: 5967570--5967661 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
5967560 TTTTGCTCTG
* *
5967570 CTCTGCTTCTCTCGTTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
5967591 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
5967612 CGCTGCTTCCCTCGCTGCAG-
1 CTCTGCTTCCCTCGCTGCAGC
*
5967632 CTGCTGCTTCCCTCGCTGCTGC
1 CT-CTGCTTCCCTCGCTGCAGC
5967654 CTCTGCTT
1 CTCTGCTT
5967662 TAAGTTGTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.02
21 59 0.95
22 2 0.03
ACGTcount: A:0.03, C:0.42, G:0.21, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:5972577 original size:16 final size:16
Alignment explanation
Indices: 5972556--5972632 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
5972546 GATTTTAGTA
5972556 AAGTATATATTCCAGC
1 AAGTATATATTCCAGC
**
5972572 AAGTATATATT-TGGC
1 AAGTATATATTCCAGC
*
5972587 ---CATATATTCCAGC
1 AAGTATATATTCCAGC
*
5972600 AACTGGAATATATTCCAGC
1 AA---GTATATATTCCAGC
5972619 AAGTATATATTCCA
1 AAGTATATATTCCA
5972633 AAGTTATAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
12 7 0.15
13 2 0.04
15 2 0.04
16 22 0.47
19 14 0.30
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.32
Consensus pattern (16 bp):
AAGTATATATTCCAGC
Found at i:5973281 original size:148 final size:148
Alignment explanation
Indices: 5973096--5973399 Score: 380
Period size: 148 Copynumber: 2.1 Consensus size: 148
5973086 AAGCTAAAAC
* * *
5973096 TTGTGGCGCTTAGAGCAAAAATGCCACAAATACCATGGACAAAACGACA-CTGTTATTGGATAAC
1 TTGTGGCGCTTAGAGCAAAAACGCCACAAATAACATGGACAAAACGACATC-GTTATTAGATAAC
* * * *
5973160 CATAAACATTTTTACGGCGTTTTATCAAAAGCGCCACTAATAAAAATAGGAAACGGCGTCGTTAC
65 CATAAACATTTTTACGGCGCTTTAGCAAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTAC
5973225 CTCAAC-CACTAATAAATAT
130 CTCAACTC-CTAATAAATAT
* * * *
5973244 TTGTGGCGCTT-GCAGTAAAAACGCCACTAATAACATGGACAAAATGGCATCGTTATTAGATAAC
1 TTGTGGCGCTTAG-AGCAAAAACGCCACAAATAACATGGACAAAACGACATCGTTATTAGATAAC
* * ** * * *
5973308 CTTAAACATTTTTGCGGCGCTTTAGCTGAAGCGCCACTAATAAAAGTAGGAAATGACGCCGTTTC
65 CATAAACATTTTTACGGCGCTTTAGCAAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTAC
* *
5973373 CTCAACTCGTAGTAAATAT
130 CTCAACTCCTAATAAATAT
5973392 TTGTGGCG
1 TTGTGGCG
5973400 TTTTTAAAAT
Statistics
Matches: 133, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
147 1 0.01
148 130 0.98
149 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (148 bp):
TTGTGGCGCTTAGAGCAAAAACGCCACAAATAACATGGACAAAACGACATCGTTATTAGATAACC
ATAAACATTTTTACGGCGCTTTAGCAAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTACC
TCAACTCCTAATAAATAT
Found at i:5973855 original size:7 final size:7
Alignment explanation
Indices: 5973843--5973918 Score: 64
Period size: 7 Copynumber: 10.3 Consensus size: 7
5973833 TTTGGGATTT
5973843 AACCTTA
1 AACCTTA
5973850 AACCTTA
1 AACCTTA
*
5973857 AACCCCTA
1 AA-CCTTA
5973865 AACCTTAA
1 AACCTT-A
5973873 AATCC-TA
1 AA-CCTTA
*
5973880 AGCCATTA
1 AACC-TTA
5973888 AACCCTTA
1 AA-CCTTA
*
5973896 AACCCTA
1 AACCTTA
5973903 AACCTTA
1 AACCTTA
*
5973910 AATCTTA
1 AACCTTA
5973917 AA
1 AA
5973919 ACCAACAACC
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
6 2 0.04
7 32 0.57
8 18 0.32
9 4 0.07
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.25
Consensus pattern (7 bp):
AACCTTA
Found at i:5973898 original size:8 final size:8
Alignment explanation
Indices: 5973845--5973911 Score: 54
Period size: 8 Copynumber: 8.9 Consensus size: 8
5973835 TGGGATTTAA
5973845 CCTTAAA-
1 CCTTAAAC
5973852 CCTTAAAC
1 CCTTAAAC
*
5973860 CCCTAAA-
1 CCTTAAAC
*
5973867 CCTTAAAAT
1 CCTT-AAAC
*
5973876 CC-TAAGC
1 CCTTAAAC
*
5973883 CATTAAAC
1 CCTTAAAC
5973891 CCTTAAAC
1 CCTTAAAC
5973899 CC-TAAA-
1 CCTTAAAC
5973905 CCTTAAA
1 CCTTAAA
5973912 TCTTAAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
6 2 0.04
7 21 0.44
8 23 0.48
9 2 0.04
ACGTcount: A:0.42, C:0.33, G:0.01, T:0.24
Consensus pattern (8 bp):
CCTTAAAC
Found at i:5973920 original size:15 final size:15
Alignment explanation
Indices: 5973843--5973921 Score: 72
Period size: 15 Copynumber: 5.3 Consensus size: 15
5973833 TTTGGGATTT
5973843 AACCTTAAACCTTAA
1 AACCTTAAACCTTAA
* *
5973858 ACCCCTAAACCTTAA
1 AACCTTAAACCTTAA
*
5973873 AATCC-TAAGCCATTAA
1 AA-CCTTAAACC-TTAA
* *
5973889 ACCCTTAAACCCT-A
1 AACCTTAAACCTTAA
*
5973903 AACCTTAAATCTTAA
1 AACCTTAAACCTTAA
5973918 AACC
1 AACC
5973922 AACAACCAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
14 11 0.22
15 27 0.54
16 12 0.24
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.24
Consensus pattern (15 bp):
AACCTTAAACCTTAA
Found at i:5974384 original size:21 final size:20
Alignment explanation
Indices: 5974317--5974384 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
5974307 GACTAAATGG
5974317 CCTAAACCCCAAACCTC-AAA
1 CCTAAACCCCAAACC-CAAAA
**
5974337 CCTTAAACCCCAAACTCCTAACC
1 CC-TAAACCCCAAAC-CC-AAAA
*
5974360 CCTAAACCCAAAACACCAAAA
1 CCTAAACCCCAAAC-CCAAAA
5974381 CCTA
1 CCTA
5974385 CATCATAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 19 0.50
22 14 0.37
23 3 0.08
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (20 bp):
CCTAAACCCCAAACCCAAAA
Found at i:5975093 original size:115 final size:113
Alignment explanation
Indices: 5974742--5975382 Score: 569
Period size: 115 Copynumber: 5.6 Consensus size: 113
5974732 TGGTTTCCCG
* * ** * * * *
5974742 TAAGCGCCACAAATTTTAGTATACATCAAGACCAAAACGCTGCGTTTTGGTTAAGGTATTCTACG
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
** * * * * **
5974807 GCGCTAGCCACAAATCTCCGCTACTACTATGCTTTAGCGGCG-TTTCACCG
66 GCGCT-TTCAAAAAGCGCCGCTAATACTAT-CTTTAGCGGCGTTTTC-CTA
* * * * * * *
5974857 TAAGCGGCAATAATTC-AAGTATACATCCAGACCAAAACGCTGCGTTTTGGTTCAGATATTTTGT
1 TAAGCGCCACTAATTCTAA-CATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGC
* * * *
5974921 GGCTCATCCAAAAAGCGCCGCTAATACTATCCTTTAGCGGCGTTTTCCAA
65 GGCGCTTTCAAAAAGCGCCGCTAATACTAT-CTTTAGCGGCGTTTTCCTA
** * *
5974971 TAAGCGCCACTAACGCTAACATACCTTAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
* * * * * *
5975036 GCGCTTTTACTAAAGCGCCGCTAATACTATCCTTTAACGGCATTTTACTG
66 GCGCTTTCA-AAAAGCGCCGCTAATACTAT-CTTTAGCGGCGTTTTCCTA
** * * *
5975086 TAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGCTGTGTTTTGGTTAAGATATTTTGCA
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
** ** ** * * *
5975151 GCGCTAGCCACGACTCACCGCTAATACTATGTTATAGCGGCGTTTTCGGTA
66 GCGCT-TTCAAAAAGCGCCGCTAATACTATCTT-TAGCGGCGTTTTC-CTA
* ** * * * **
5975202 -AA-CGCCGCTAATTCTAGTATA-AGCAAGACCAAAA-TGATGCGTTTTGGTTCAGATATTTCAC
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACT-CTGCGTTTTGGTTAAGATATTTTGC
* *
5975263 GGCGCTTTCAAAAAGCGCCGTTAATACTATCTGTTTGCGGCGTTTTCCTA
65 GGCGCTTTCAAAAAGCGCCGCTAATACTATCT-TTAGCGGCGTTTTCCTA
5975313 TAAGCGCCACTAATTCTAACATACATCAAGACC-AAACTCTGCG-TTTGGTTAAGATATTTTGCG
1 TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
5975376 GCGCTTT
66 GCGCTTT
5975383 GCCATGCCTT
Statistics
Matches: 420, Mismatches: 93, Indels: 29
0.77 0.17 0.05
Matches are distributed among these distances:
111 2 0.00
112 55 0.13
113 61 0.15
114 117 0.28
115 183 0.44
116 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (113 bp):
TAAGCGCCACTAATTCTAACATACATCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCG
GCGCTTTCAAAAAGCGCCGCTAATACTATCTTTAGCGGCGTTTTCCTA
Found at i:5975145 original size:229 final size:226
Alignment explanation
Indices: 5974768--5975380 Score: 637
Period size: 229 Copynumber: 2.7 Consensus size: 226
5974758 TAGTATACAT
* * * ** * * *
5974768 CAAGACCAAAACGCTGCGTTTTGGTTAAGGTATTCTACGGCGCTAGCCACAAATCTCCGCTACTA
1 CAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTACGGCGCT-TTCACAAAGCGCCGCTAATA
* * * * * *
5974833 CTATGCTTTAGCGGCGTTTCACCGTAAGCGGCAATAATTCAAGTATACATCCAGACCAAAACGCT
65 CTAT-CTTTAGCGGCGTTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGCT
* * * *
5974898 GCGTTTTGGTTCAGATATTTTG-TG-GCTCATCCAAAAAGCGCCGCTAATACTATCCTT-TAGCG
129 GCGTTTTGGTTAAGATATTTTGCAGCGCT-AGCCAAAAAGCACCGCTAATACTAT-CTTATAGCG
*
5974960 GCGTTTTCCAATAAGCGCCACTAACGCTAACAT-AC
192 GCGTTTT-CAATAAACGCCACTAACGCTAACATAAC
* *
5974995 CTTAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTACTAAAGCGCCGCTAA
1 C--AAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTACGGCGCTTTCAC-AAAGCGCCGCTAA
* *
5975060 TACTATCCTTTAACGGCATTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACG
63 TACTAT-CTTTAGCGGCGTTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACG
* ** ** *
5975125 CTGTGTTTTGGTTAAGATATTTTGCAGCGCTAGCCACGACTCACCGCTAATACTATGTTATAGCG
127 CTGCGTTTTGGTTAAGATATTTTGCAGCGCTAGCCAAAAAGCACCGCTAATACTATCTTATAGCG
** * ** ** *
5975190 GCGTTTTCGGTAAACGCCGCTAATTCTAGTATAAG
192 GCGTTTTCAATAAACGCCACTAACGCTAACATAAC
* * * * *
5975225 CAAGACCAAAA-TGATGCGTTTTGGTTCAGATATTTCACGGCGCTTTCAAAAAGCGCCGTTAATA
1 CAAGACCAAAACT-CTGCGTTTTGGTTAAGATATTTTACGGCGCTTTCACAAAGCGCCGCTAATA
* * * ** *
5975289 CTATCTGTTTGCGGCGTTTTCCTATAAGCGCCACTAATTCTAACATACATCAAGACC-AAACTCT
65 CTATCT-TTAGCGGCGTTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGCT
*
5975353 GCG-TTTGGTTAAGATATTTTGCGGCGCT
129 GCGTTTTGGTTAAGATATTTTGCAGCGCT
5975381 TTGCCATGCC
Statistics
Matches: 322, Mismatches: 55, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
225 24 0.07
226 10 0.03
227 63 0.20
228 42 0.13
229 146 0.45
230 34 0.11
231 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (226 bp):
CAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTACGGCGCTTTCACAAAGCGCCGCTAATAC
TATCTTTAGCGGCGTTTTACTGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGCTGC
GTTTTGGTTAAGATATTTTGCAGCGCTAGCCAAAAAGCACCGCTAATACTATCTTATAGCGGCGT
TTTCAATAAACGCCACTAACGCTAACATAAC
Found at i:5977330 original size:50 final size:50
Alignment explanation
Indices: 5977225--5978203 Score: 1859
Period size: 50 Copynumber: 19.6 Consensus size: 50
5977215 CATGCCAAAA
* ** * * *
5977225 CCATGTCTCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAATG
* * * *
5977276 CCATGTCCCAAACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977326 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977376 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977426 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977476 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977526 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977576 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977626 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977676 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977726 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977776 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977826 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977876 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977926 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5977976 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5978026 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5978076 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5978126 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
5978176 CCATGTCCCAGACATGGTCTTACATGGG
1 CCATGTCCCAGACATGGTCTTACATGGG
5978204 NNNNNNNNNN
Statistics
Matches: 914, Mismatches: 14, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
50 889 0.97
51 25 0.03
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
Found at i:5979335 original size:21 final size:21
Alignment explanation
Indices: 5979305--5979372 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
5979295 ATGCTAAACT
5979305 GAAACCCATAAGGGTTGAACG
1 GAAACCCATAAGGGTTGAACG
* * * *
5979326 GAAGCTCAT-AGGAGCTGAACA
1 GAAACCCATAAGG-GTTGAACG
*
5979347 GAAACCCATAAGGGTTAAACG
1 GAAACCCATAAGGGTTGAACG
*
5979368 AAAAC
1 GAAAC
5979373 TCTTATGAGT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
20 3 0.09
21 29 0.83
22 3 0.09
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (21 bp):
GAAACCCATAAGGGTTGAACG
Found at i:5979497 original size:24 final size:24
Alignment explanation
Indices: 5979470--5979581 Score: 188
Period size: 24 Copynumber: 4.7 Consensus size: 24
5979460 TAATTTTTCA
*
5979470 TCAATTCATCCTTTGTATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
*
5979494 TCAATTCATCATTTGCATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
*
5979518 TCAATTCATCCTTTACATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
5979542 TCAATTCATCCTTTGCATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
*
5979566 TCAATTCATCATTTGC
1 TCAATTCATCCTTTGC
5979582 CATAGAACTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 82 1.00
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (24 bp):
TCAATTCATCCTTTGCATTTACCG
Found at i:5983998 original size:26 final size:26
Alignment explanation
Indices: 5983963--5984023 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
5983953 CAATCAACTC
*
5983963 AAACTTAAGGGTCATCCAACCCATTT
1 AAACTCAAGGGTCATCCAACCCATTT
* * * *
5983989 AAGCTCAAGGGTCTTTCGACCCATTT
1 AAACTCAAGGGTCATCCAACCCATTT
5984015 AAACTCAAG
1 AAACTCAAG
5984024 CTCGCTAGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (26 bp):
AAACTCAAGGGTCATCCAACCCATTT
Found at i:5990987 original size:4 final size:4
Alignment explanation
Indices: 5990972--5991000 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
5990962 TTGGTAAGGG
5990972 AATA AA-A AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
5991001 AGGTTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:5991481 original size:17 final size:18
Alignment explanation
Indices: 5991448--5991483 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5991438 TAATGAATAC
*
5991448 ATAAAATAATATTATATA
1 ATAAAAGAATATTATATA
5991466 ATAAAAGAAT-TTATATA
1 ATAAAAGAATATTATATA
5991483 A
1 A
5991484 AAATTAGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAAGAATATTATATA
Found at i:5993781 original size:21 final size:21
Alignment explanation
Indices: 5993757--5993811 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
5993747 TAGAAAAAAA
* *
5993757 ATAAATATATATAAAATTATC
1 ATAAATATAAATAAAACTATC
* *
5993778 ATAAAGATAAATAATACTATC
1 ATAAATATAAATAAAACTATC
5993799 ATAAATATAAATA
1 ATAAATATAAATA
5993812 TTAATTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAATATAAATAAAACTATC
Found at i:5997921 original size:17 final size:16
Alignment explanation
Indices: 5997901--5997937 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
5997891 TTGTTTTACA
5997901 TTTTTTCCTTGTTCTGT
1 TTTTTTCCTTGTTCT-T
*
5997918 TTTTTTCCTTTTTCTT
1 TTTTTTCCTTGTTCTT
5997934 TTTT
1 TTTT
5997938 ATTTGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTTTCCTTGTTCTT
Found at i:5997976 original size:33 final size:33
Alignment explanation
Indices: 5997925--5998024 Score: 116
Period size: 33 Copynumber: 3.0 Consensus size: 33
5997915 TGTTTTTTTC
5997925 CTTTTTC-TTTTTTATTTGTTTTTCTTTATTTA
1 CTTTTTCATTTTTTATTTGTTTTTCTTTATTTA
*
5997957 CTTTTTCAGTTTTTT-TTTGTTTTTCTTTATTTT
1 CTTTTTCA-TTTTTTATTTGTTTTTCTTTATTTA
*
5997990 CTTTATT-ATTTTCTTTATTTGTTTATCATTTATTT
1 CTTT-TTCA-TTT-TTTATTTGTTTTTC-TTTATTT
5998025 TATAATATTT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
32 7 0.12
33 25 0.42
34 11 0.19
35 9 0.15
36 7 0.12
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (33 bp):
CTTTTTCATTTTTTATTTGTTTTTCTTTATTTA
Found at i:5998000 original size:12 final size:12
Alignment explanation
Indices: 5997983--5998008 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5997973 TTGTTTTTCT
5997983 TTATTTTCTTTA
1 TTATTTTCTTTA
5997995 TTATTTTCTTTA
1 TTATTTTCTTTA
5998007 TT
1 TT
5998009 TGTTTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTTCTTTA
Found at i:5998071 original size:23 final size:22
Alignment explanation
Indices: 5998022--5998098 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
5998012 TTATCATTTA
*
5998022 TTTTATAATATTTT-AAATGTATA
1 TTTTA-AATATTTTAAAAT-TATT
5998045 TTTTAAATATTTTAAAAATTATT
1 TTTTAAATATTTT-AAAATTATT
*
5998068 TTTTAAA-ATTTTGAATATTATTT
1 TTTTAAATATTTT-AAAATTA-TT
5998091 TTTTAAAT
1 TTTTAAAT
5998099 TATTATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
22 19 0.40
23 24 0.51
24 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (22 bp):
TTTTAAATATTTTAAAATTATT
Found at i:5998093 original size:22 final size:20
Alignment explanation
Indices: 5998019--5998115 Score: 76
Period size: 22 Copynumber: 4.8 Consensus size: 20
5998009 TGTTTATCAT
* *
5998019 TTATTTTATAATATTTTAAA
1 TTATTTTTTAAAATTTTAAA
*
5998039 TGTATATTTTAAATATTTTAAAAA
1 T-TATTTTTTAAA-ATTTT--AAA
5998063 TTATTTTTTAAAATTTTGAATA
1 TTATTTTTTAAAATTTT-AA-A
*
5998085 TTATTTTTTTAAA--TT--A
1 TTATTTTTTAAAATTTTAAA
5998101 TTATTTTTTAAAATT
1 TTATTTTTTAAAATT
5998116 ATTTTAAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
16 13 0.21
20 3 0.05
21 10 0.16
22 23 0.37
23 10 0.16
24 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATTTTTTAAAATTTTAAA
Found at i:5998104 original size:16 final size:16
Alignment explanation
Indices: 5998083--5998118 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
5998073 AAATTTTGAA
*
5998083 TATTATTTTTTTAAAT
1 TATTATTTTTTAAAAT
5998099 TATTATTTTTTAAAAT
1 TATTATTTTTTAAAAT
5998115 TATT
1 TATT
5998119 TTAAAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATTTTTTAAAAT
Found at i:5998193 original size:11 final size:10
Alignment explanation
Indices: 5998177--5998222 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 10
5998167 TAATACTTTA
5998177 TTTATTTGTCT
1 TTTATTTGT-T
5998188 TTTATTTGTT
1 TTTATTTGTT
5998198 TATTATTTGTTT
1 T-TTATTTG-TT
5998210 TTTAATTTGTT
1 TTT-ATTTGTT
5998221 TT
1 TT
5998223 ACAATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.06
11 22 0.69
12 8 0.25
ACGTcount: A:0.13, C:0.02, G:0.09, T:0.76
Consensus pattern (10 bp):
TTTATTTGTT
Found at i:5998199 original size:23 final size:23
Alignment explanation
Indices: 5998173--5998221 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
5998163 AAAATAATAC
5998173 TTTATTTATTTGTCTTTT-ATTTG
1 TTTA-TTATTTGTCTTTTAATTTG
*
5998196 TTTATTATTTGTTTTTTAATTTG
1 TTTATTATTTGTCTTTTAATTTG
5998219 TTT
1 TTT
5998222 TACAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (23 bp):
TTTATTATTTGTCTTTTAATTTG
Found at i:6005955 original size:10 final size:10
Alignment explanation
Indices: 6005925--6005971 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
6005915 ATTTTTAGAG
6005925 ATTATATAAAA
1 ATTATA-AAAA
* *
6005936 ATTCTCAAAA
1 ATTATAAAAA
6005946 ATTAT-AAAA
1 ATTATAAAAA
*
6005955 ATAATAAAAA
1 ATTATAAAAA
6005965 ATTATAA
1 ATTATAA
6005972 TAGGGGTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 8 0.27
10 18 0.60
11 4 0.13
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:6006010 original size:10 final size:10
Alignment explanation
Indices: 6005995--6006019 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6005985 TTAAATTTTT
6005995 ATAACATTTA
1 ATAACATTTA
6006005 ATAACATTTA
1 ATAACATTTA
6006015 ATAAC
1 ATAAC
6006020 TTATATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAACATTTA
Found at i:6006366 original size:20 final size:19
Alignment explanation
Indices: 6006332--6006387 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
6006322 AATTTTTACA
*
6006332 AATTTTTATACTTTTAATT
1 AATTTTTATATTTTTAATT
* *
6006351 AGTTTTTTATATTTTTTTATT
1 A-ATTTTTATA-TTTTTAATT
6006372 AATTTTTATATTTTTA
1 AATTTTTATATTTTTA
6006388 TCATTTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.20
20 16 0.53
21 8 0.27
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
AATTTTTATATTTTTAATT
Found at i:6006385 original size:48 final size:49
Alignment explanation
Indices: 6006333--6006427 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 49
6006323 ATTTTTACAA
* * *
6006333 ATTTTTAT-ACTTTTAATTAGTTTTT-TATATTTTTTTATTAATTTTTAT
1 ATTTTTATCA-TTTTAATTAGTTTTTGTATAATATTTTAATAATTTTTAT
*
6006381 ATTTTTATCATTTTAATTATTTTTTGTATAATATTTTAATAATTTTT
1 ATTTTTATCATTTTAATTAGTTTTTGTATAATATTTTAATAATTTTT
6006428 GGGCTAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
48 22 0.54
49 19 0.46
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (49 bp):
ATTTTTATCATTTTAATTAGTTTTTGTATAATATTTTAATAATTTTTAT
Found at i:6006438 original size:22 final size:23
Alignment explanation
Indices: 6006390--6006439 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
6006380 TATTTTTATC
* * *
6006390 ATTTTAATTATTTTTTGTATAAT
1 ATTTTAATAATTTTTGGGATAAT
*
6006413 ATTTTAATAATTTTTGGGCTAA-
1 ATTTTAATAATTTTTGGGATAAT
6006435 ATTTT
1 ATTTT
6006440 TAGAATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (23 bp):
ATTTTAATAATTTTTGGGATAAT
Found at i:6008350 original size:5 final size:5
Alignment explanation
Indices: 6008322--6008402 Score: 65
Period size: 5 Copynumber: 15.8 Consensus size: 5
6008312 TATAGTGAAA
* * * * * *
6008322 CATAT CTTAT CATAC CAGAG CATAT CATAAAT TATAC CATAT CA-ATT
1 CATAT CATAT CATAT CATAT CATAT CAT--AT CATAT CATAT CATA-T
*
6008369 CATAT CATAT CATAT CAGAT CATAT CATAT CATA
1 CATAT CATAT CATAT CATAT CATAT CATAT CATA
6008403 CAAAATCATA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
4 1 0.02
5 53 0.90
6 1 0.02
7 4 0.07
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.35
Consensus pattern (5 bp):
CATAT
Found at i:6009116 original size:48 final size:48
Alignment explanation
Indices: 6009031--6009122 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
6009021 AGCCCGTGTC
* * *
6009031 TGCACGATTTCACACGGCTGTGTGCCCCACATAGCCTACCCACAGGCT
1 TGCACGATTTCACACGACCGTGTGCCCCACACAGCCTACCCACAGGCT
* * * *
6009079 TGCATGATTTCACATGACCGTGTGCCCCGCACGGCCTACCCACA
1 TGCACGATTTCACACGACCGTGTGCCCCACACAGCCTACCCACA
6009123 CTACCGTGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (48 bp):
TGCACGATTTCACACGACCGTGTGCCCCACACAGCCTACCCACAGGCT
Found at i:6009282 original size:5 final size:5
Alignment explanation
Indices: 6009272--6009298 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6009262 TGAGCATTCG
6009272 ATCGA ATCGA ATCGA ATCGA ATCGA AT
1 ATCGA ATCGA ATCGA ATCGA ATCGA AT
6009299 AAAAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
ATCGA
Found at i:6010076 original size:30 final size:31
Alignment explanation
Indices: 6010037--6010096 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
6010027 TTGGGGTAGA
*
6010037 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
6010068 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
6010097 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:6010320 original size:18 final size:18
Alignment explanation
Indices: 6010297--6010333 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6010287 TATAGTTTGA
*
6010297 TATTCGAGTTATTTGAAT
1 TATTCGAGTTATTCGAAT
6010315 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
6010333 T
1 T
6010334 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:6014706 original size:51 final size:51
Alignment explanation
Indices: 6014620--6014991 Score: 593
Period size: 51 Copynumber: 7.3 Consensus size: 51
6014610 GCTTCTAATC
* *
6014620 AGTGACAAGTGACAAGTAGTAGCTTCAGCTGCGCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
*
6014671 AGTGGCAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
* *
6014722 AGTGACAAGTGATAAGTAGTAGCTTCAACTACGCTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
6014773 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
6014824 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
* * * *
6014875 AGTGACAAGTGATAAGTGGTAGCTTTAACTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
* * * * * *
6014926 AGTAAGAAGTGATAAGT-GATAGCTTTAGCTACACTTATTTGATCAGGGACA
1 AGTGACAAGTGATAAGTAG-TAGCTTCAGCTACGCTTATCTGATCAGTGACA
6014977 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
6014992 ATGTGATCCG
Statistics
Matches: 301, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
50 1 0.00
51 300 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATCAGTGACA
Found at i:6016995 original size:31 final size:31
Alignment explanation
Indices: 6016959--6017028 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
6016949 ACTTAATAAC
*
6016959 CAGTGACTTAAATAAAAACTTTCAAATAGTT
1 CAGTGACTTAAATAAAAACTTTCAAATAATT
*
6016990 CAGTGACTTAAATGAAAACTTTCAAATAATT
1 CAGTGACTTAAATAAAAACTTTCAAATAATT
*
6017021 AAGTGACT
1 CAGTGACT
6017029 ATTTTATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAACTTTCAAATAATT
Found at i:6018424 original size:31 final size:29
Alignment explanation
Indices: 6018365--6018426 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
6018355 GTTTCACGTG
*
6018365 TATAATTGCACCAAATTAAAATTCATGTA
1 TATAATTGCACCAAAGTAAAATTCATGTA
* *
6018394 TATAATTGCACATTAAAGTAAAGTTCATGTA
1 TATAATTGCAC--CAAAGTAAAATTCATGTA
6018425 TA
1 TA
6018427 ATTTTGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
31 17 0.61
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (29 bp):
TATAATTGCACCAAAGTAAAATTCATGTA
Found at i:6018426 original size:29 final size:27
Alignment explanation
Indices: 6018363--6018429 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
6018353 AAGTTTCACG
*
6018363 TGTATAATTGCACCAAATTAAAATTCA
1 TGTATAATTGCACCAAAGTAAAATTCA
* *
6018390 TGTATATAATTGCACATTAAAGTAAAGTTCA
1 TG--TATAATTGCAC--CAAAGTAAAATTCA
6018421 TGTATAATT
1 TGTATAATT
6018430 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
29 18 0.55
31 13 0.39
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (27 bp):
TGTATAATTGCACCAAAGTAAAATTCA
Found at i:6020099 original size:21 final size:20
Alignment explanation
Indices: 6020073--6020117 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
6020063 TTTTATTTTA
6020073 TTTTTTAATTTTAAAATTATT
1 TTTTTTAATTTTAAAA-TATT
*
6020094 TTTTTTATTTTTAAAATATT
1 TTTTTTAATTTTAAAATATT
6020114 TTTT
1 TTTT
6020118 GTGTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTAATTTTAAAATATT
Found at i:6020128 original size:21 final size:21
Alignment explanation
Indices: 6020073--6020130 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
6020063 TTTTATTTTA
*
6020073 TTTTT-TAATTTTAAAATTAT
1 TTTTTGTATTTTTAAAATTAT
*
6020093 TTTTTTTATTTTTAAAA-TAT
1 TTTTTGTATTTTTAAAATTAT
*
6020113 TTTTTGTGTTTATTAAAA
1 TTTTTGTATTT-TTAAAA
6020131 ATAGGGCCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTTTGTATTTTTAAAATTAT
Found at i:6021331 original size:28 final size:27
Alignment explanation
Indices: 6021292--6021348 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
6021282 AGAAACTAAA
* *
6021292 AACAAACATTCAACTAAAAAGAATGAT
1 AACAAACATTCAACTAAAAAAAATCAT
6021319 AACAAATCATTCAACTAAAAAAAATCAT
1 AACAAA-CATTCAACTAAAAAAAATCAT
6021347 AA
1 AA
6021349 AACGACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.61, C:0.16, G:0.04, T:0.19
Consensus pattern (27 bp):
AACAAACATTCAACTAAAAAAAATCAT
Found at i:6026089 original size:17 final size:15
Alignment explanation
Indices: 6026053--6026109 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 15
6026043 TATAAACAAT
6026053 ACAAAAATATTAAAA
1 ACAAAAATATTAAAA
*
6026068 ACAAAACTATTAAAATA
1 ACAAAAATATT-AAA-A
*
6026085 ACAAAAAAATATAAAA
1 ACAAAAATAT-TAAAA
*
6026101 ATAAAAATA
1 ACAAAAATA
6026110 AATTACAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 10 0.29
16 11 0.32
17 12 0.35
18 1 0.03
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (15 bp):
ACAAAAATATTAAAA
Found at i:6026183 original size:20 final size:18
Alignment explanation
Indices: 6026160--6026233 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 18
6026150 ATTTAAAAGC
6026160 TATAGAAAATTATTAAAATT
1 TATA-AAAA-TATTAAAATT
*
6026180 TATATAAAATATAAAAATAT
1 TATA-AAAATATTAAAAT-T
6026200 TATAAAAAGTA-TAAAA-T
1 TATAAAAA-TATTAAAATT
*
6026217 TATAAAACAAATTAAAA
1 TATAAAA-ATATTAAAA
6026234 ATATAAGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
17 9 0.20
18 6 0.13
19 16 0.35
20 15 0.33
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (18 bp):
TATAAAAATATTAAAATT
Found at i:6026203 original size:18 final size:19
Alignment explanation
Indices: 6026183--6026252 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 19
6026173 TAAAATTTAT
*
6026183 ATAAAA-TATAAAAATATT
1 ATAAAAGTATAAAAATATA
*
6026201 ATAAAAAGTATAAAATTATA
1 AT-AAAAGTATAAAAATATA
*
6026221 A-AACAAAT-TAAAAATATA
1 ATAA-AAGTATAAAAATATA
* *
6026239 AGAAAATTATAAAA
1 ATAAAAGTATAAAA
6026253 CTAATATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 17 0.40
19 14 0.33
20 11 0.26
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (19 bp):
ATAAAAGTATAAAAATATA
Found at i:6026230 original size:29 final size:28
Alignment explanation
Indices: 6026171--6026253 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
6026161 ATAGAAAATT
* *
6026171 ATTAAAATTTATATAAAA-TATAAAA-AT
1 ATTAAAA-ATATATAAAATTATAAAACAA
6026198 ATTATAAAA-AGTATAAAATTATAAAACAA
1 ATTA-AAAATA-TATAAAATTATAAAACAA
*
6026227 ATTAAAAATATAAGAAAATTATAAAAC
1 ATTAAAAATAT-ATAAAATTATAAAAC
6026254 TAATATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 1 0.02
27 11 0.23
28 15 0.32
29 20 0.43
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
ATTAAAAATATATAAAATTATAAAACAA
Found at i:6026430 original size:16 final size:17
Alignment explanation
Indices: 6026398--6026438 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
6026388 TTTGTTCATC
6026398 AAAAA-AAATATAAAAT
1 AAAAATAAATATAAAAT
*
6026414 AAAAATAAAT-TACAAT
1 AAAAATAAATATAAAAT
6026430 AAAAATAAA
1 AAAAATAAA
6026439 AATATTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAAATAAATATAAAAT
Found at i:6026435 original size:311 final size:312
Alignment explanation
Indices: 6026087--6026709 Score: 1239
Period size: 311 Copynumber: 2.0 Consensus size: 312
6026077 TTAAAATAAC
6026087 AAAAAAATATAAAAATAAAAATAAATTACAATAAAAATAAAAATATTGTAAAAAATGGAATATAT
1 AAAAAAATATAAAAATAAAAATAAATTACAATAAAAATAAAAATATTGTAAAAAATGGAATATAT
6026152 TTAAAAGCTATAGAAAATTATTAAAATTTATATAAAATATAAAAATATTATAAAAAGTATAAAAT
66 TTAAAAGCTATAGAAAATTATTAAAATTTATATAAAATATAAAAATATTATAAAAAGTATAAAAT
6026217 TATAAAACAAATTAAAAATATAAGAAAATTATAAAACTAATATTTTTTTCATTTGCACACTAACC
131 TATAAAACAAATTAAAAATATAAGAAAATTATAAAACTAATATTTTTTTCATTTGCACACTAACC
6026282 ATTGTTAACAATACAGCACCTATTAAAAATTATATAAAAAATTATTTAATTCCTTAAGCTATCTA
196 ATTGTTAACAATACAGCACCTATTAAAAATTATATAAAAAATTATTTAATTCCTTAAGCTATCTA
6026347 TTGTGTTCATCTTACACAGACCTCCCCAATGCTTGCACCCCTTTGTTCATCA
261 TTGTGTTCATCTTACACAGACCTCCCCAATGCTTGCACCCCTTTGTTCATCA
6026399 AAAAAAATAT-AAAATAAAAATAAATTACAATAAAAATAAAAATATTGTAAAAAATGGAATATAT
1 AAAAAAATATAAAAATAAAAATAAATTACAATAAAAATAAAAATATTGTAAAAAATGGAATATAT
6026463 TTAAAAGCTATAGAAAATTATTAAAATTTATATAAAATATAAAAATATTATAAAAAGTATAAAAT
66 TTAAAAGCTATAGAAAATTATTAAAATTTATATAAAATATAAAAATATTATAAAAAGTATAAAAT
6026528 TATAAAACAAATTAAAAATATAAGAAAATTATAAAACTAATATTTTTTTCATTTGCACACTAACC
131 TATAAAACAAATTAAAAATATAAGAAAATTATAAAACTAATATTTTTTTCATTTGCACACTAACC
6026593 ATTGTTAACAATACAGCACCTATTAAAAATTATATAAAAAATTATTTAATTCCTTAAGCTATCTA
196 ATTGTTAACAATACAGCACCTATTAAAAATTATATAAAAAATTATTTAATTCCTTAAGCTATCTA
6026658 TTGTGTTCATCTTACACAGACCTCCCCAATGCTTGCACCCCTTTGTTCATCA
261 TTGTGTTCATCTTACACAGACCTCCCCAATGCTTGCACCCCTTTGTTCATCA
6026710 TCGATGACAA
Statistics
Matches: 311, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
311 301 0.97
312 10 0.03
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (312 bp):
AAAAAAATATAAAAATAAAAATAAATTACAATAAAAATAAAAATATTGTAAAAAATGGAATATAT
TTAAAAGCTATAGAAAATTATTAAAATTTATATAAAATATAAAAATATTATAAAAAGTATAAAAT
TATAAAACAAATTAAAAATATAAGAAAATTATAAAACTAATATTTTTTTCATTTGCACACTAACC
ATTGTTAACAATACAGCACCTATTAAAAATTATATAAAAAATTATTTAATTCCTTAAGCTATCTA
TTGTGTTCATCTTACACAGACCTCCCCAATGCTTGCACCCCTTTGTTCATCA
Found at i:6026494 original size:20 final size:18
Alignment explanation
Indices: 6026471--6026544 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 18
6026461 ATTTAAAAGC
6026471 TATAGAAAATTATTAAAATT
1 TATA-AAAA-TATTAAAATT
*
6026491 TATATAAAATATAAAAATAT
1 TATA-AAAATATTAAAAT-T
6026511 TATAAAAAGTA-TAAAA-T
1 TATAAAAA-TATTAAAATT
*
6026528 TATAAAACAAATTAAAA
1 TATAAAA-ATATTAAAA
6026545 ATATAAGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
17 9 0.20
18 6 0.13
19 16 0.35
20 15 0.33
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (18 bp):
TATAAAAATATTAAAATT
Found at i:6026514 original size:18 final size:19
Alignment explanation
Indices: 6026494--6026563 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 19
6026484 TAAAATTTAT
*
6026494 ATAAAA-TATAAAAATATT
1 ATAAAAGTATAAAAATATA
*
6026512 ATAAAAAGTATAAAATTATA
1 AT-AAAAGTATAAAAATATA
*
6026532 A-AACAAAT-TAAAAATATA
1 ATAA-AAGTATAAAAATATA
* *
6026550 AGAAAATTATAAAA
1 ATAAAAGTATAAAA
6026564 CTAATATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 17 0.40
19 14 0.33
20 11 0.26
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (19 bp):
ATAAAAGTATAAAAATATA
Found at i:6026541 original size:29 final size:28
Alignment explanation
Indices: 6026482--6026564 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
6026472 ATAGAAAATT
* *
6026482 ATTAAAATTTATATAAAA-TATAAAA-AT
1 ATTAAAA-ATATATAAAATTATAAAACAA
6026509 ATTATAAAA-AGTATAAAATTATAAAACAA
1 ATTA-AAAATA-TATAAAATTATAAAACAA
*
6026538 ATTAAAAATATAAGAAAATTATAAAAC
1 ATTAAAAATAT-ATAAAATTATAAAAC
6026565 TAATATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 1 0.02
27 11 0.23
28 15 0.32
29 20 0.43
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
ATTAAAAATATATAAAATTATAAAACAA
Found at i:6031912 original size:35 final size:35
Alignment explanation
Indices: 6031873--6031954 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 35
6031863 TATGTATTTT
**
6031873 TACTTTTTTTTTCTTTCTATTTTTTAAAATTTGAA
1 TACTTTTTTAATCTTTCTATTTTTTAAAATTTGAA
*
6031908 TACTTTTTTAATGTTTCTATTTTTTAAAATTTGAA
1 TACTTTTTTAATCTTTCTATTTTTTAAAATTTGAA
6031943 TACTTTTTTAAT
1 TACTTTTTTAAT
6031955 GTTCTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (35 bp):
TACTTTTTTAATCTTTCTATTTTTTAAAATTTGAA
Found at i:6031914 original size:18 final size:18
Alignment explanation
Indices: 6031893--6031950 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
6031883 TTCTTTCTAT
6031893 TTTTTAAAATTTGAATAC
1 TTTTTAAAATTTGAATAC
* ** *
6031911 TTTTT-TAATGTT-TCTAT
1 TTTTTAAAAT-TTGAATAC
6031928 TTTTTAAAATTTGAATAC
1 TTTTTAAAATTTGAATAC
6031946 TTTTT
1 TTTTT
6031951 TAATGTTCTC
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTTAAAATTTGAATAC
Found at i:6031916 original size:19 final size:19
Alignment explanation
Indices: 6031892--6031953 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
6031882 TTTCTTTCTA
6031892 TTTTTTAAAATTTGAATAC
1 TTTTTTAAAATTTGAATAC
** *
6031911 TTTTTTAATGTTT--CTA-
1 TTTTTTAAAATTTGAATAC
6031927 TTTTTTAAAATTTGAATAC
1 TTTTTTAAAATTTGAATAC
6031946 TTTTTTAA
1 TTTTTTAA
6031954 TGTTCTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 11 0.32
17 2 0.06
18 2 0.06
19 19 0.56
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTTTAAAATTTGAATAC
Found at i:6031955 original size:35 final size:35
Alignment explanation
Indices: 6031886--6031957 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
6031876 TTTTTTTTTC
6031886 TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
1 TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
6031921 TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
1 TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
6031956 TT
1 TT
6031958 CTCATAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (35 bp):
TTTCTATTTTTTAAAATTTGAATACTTTTTTAATG
Done.