Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 169 of 196
Found at i:49437132 original size:1 final size:1
Alignment explanation
Indices: 49437001--49437116 Score: 52
Period size: 1 Copynumber: 116.0 Consensus size: 1
49436991 TGAAACTCTC
* * * ** * * * * * * *
49437001 TTTTTTTCTTTTTTTCTTCTTTTTTCCTTTTTTTCTCTTTTCTTTTTTCTTTTTTTCTTCTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * *
49437066 TTTTTTCTTTTTTTCTCTTTTCTTTTTTTCTTCTTTCTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
49437117 CTTTCTCTCT
Statistics
Matches: 77, Mismatches: 38, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (1 bp):
T
Found at i:49437134 original size:23 final size:22
Alignment explanation
Indices: 49437002--49437131 Score: 135
Period size: 23 Copynumber: 6.0 Consensus size: 22
49436992 GAAACTCTCT
49437002 TTTTTTCTTTTTTTC----TTC
1 TTTTTTCTTTTTTTCTTTTTTC
*
49437020 TTTTTTCCTTTTTTTCTCTTTTC
1 TTTTTT-CTTTTTTTCTTTTTTC
*
49437043 TTTTTTCTTTTTTTCTTCTTTC
1 TTTTTTCTTTTTTTCTTTTTTC
*
49437065 TTTTTTTCTTTTTTTCTCTTTTC
1 -TTTTTTCTTTTTTTCTTTTTTC
*
49437088 TTTTTT-TCTTCTTTCTTTTTTTC
1 TTTTTTCT-TTTTTTC-TTTTTTC
* *
49437111 TTTTTTCTTTCTCTCTTTTTT
1 TTTTTTCTTTTTTTCTTTTTT
49437132 TCTGGCCTGC
Statistics
Matches: 96, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.06
19 9 0.09
21 1 0.01
22 32 0.33
23 47 0.49
24 1 0.01
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTCTTTTTTTCTTTTTTC
Found at i:49437445 original size:3 final size:3
Alignment explanation
Indices: 49437439--49437466 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49437429 TTTTTTTTCT
49437439 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
49437467 CCTCCTACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:49437553 original size:17 final size:16
Alignment explanation
Indices: 49437531--49437575 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
49437521 GACGCTGGTA
49437531 CTCTTTCTTTTCTTCT
1 CTCTTTCTTTTCTTCT
49437547 CCTCTTTCTCTTTTCTTCT
1 -CTC-TT-TCTTTTCTTCT
49437566 CT-TTTCTTTT
1 CTCTTTCTTTT
49437576 TTTTTCCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.23
16 2 0.08
17 3 0.12
18 4 0.15
19 11 0.42
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
CTCTTTCTTTTCTTCT
Found at i:49437577 original size:17 final size:16
Alignment explanation
Indices: 49437531--49437577 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
49437521 GACGCTGGTA
49437531 CTCTTTCTTTTCTTCTC
1 CTCTTTCTTTT-TTCTC
* *
49437548 CTCTTTCTCTTTTCTT
1 CTCTTTCTTTTTTCTC
49437564 CTCTTTTCTTTTTT
1 CTC-TTTCTTTTTT
49437578 TTTCCTTCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
CTCTTTCTTTTTTCTC
Found at i:49437581 original size:10 final size:10
Alignment explanation
Indices: 49437532--49437573 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
49437522 ACGCTGGTAC
49437532 TCTT-TCTTT
1 TCTTCTCTTT
* *
49437541 TCTTCTCCTC
1 TCTTCTCTTT
49437551 T-TTCTCTTT
1 TCTTCTCTTT
49437560 TCTTCTCTTT
1 TCTTCTCTTT
49437570 TCTT
1 TCTT
49437574 TTTTTTTCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 11 0.41
10 16 0.59
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:49437887 original size:30 final size:30
Alignment explanation
Indices: 49437832--49437948 Score: 139
Period size: 30 Copynumber: 3.9 Consensus size: 30
49437822 TGTAATTTTT
* *
49437832 AGAAAGTTTA-GGATTAAAATGAAATTTAA
1 AGAAAGTTTAGGGGTCAAAATGAAATTTAA
* * *
49437861 TGAAAGTTTAGGGGTCTAAGTGAAATTTAA
1 AGAAAGTTTAGGGGTCAAAATGAAATTTAA
*
49437891 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAGTTTAGGGGTCAAAATGAAATTTAA
* *
49437920 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AG-AAAGTTTAGGGGTCAAAATGAAATTT
49437949 TTATTTTTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
29 11 0.15
30 63 0.85
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (30 bp):
AGAAAGTTTAGGGGTCAAAATGAAATTTAA
Found at i:49437948 original size:60 final size:59
Alignment explanation
Indices: 49437832--49437948 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 59
49437822 TGTAATTTTT
* * * *
49437832 AGAAAGTTTAGGATTAAAATGAAATTTAATGAAAGTTTAGGGGTCTAAGTGAAATTTAA
1 AGAAAGTTTAGGATCAAAATGAAATTTAAGGAAAGTTTAGGGGTCAAAATGAAATTTAA
* *
49437891 AGAAAGTTTAAGGGTCAAAATGAAATTT-AGGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAGTTT-AGGATCAAAATGAAATTTAAGG-AAAGTTTAGGGGTCAAAATGAAATTT
49437949 TTATTTTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 11 0.22
60 39 0.78
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (59 bp):
AGAAAGTTTAGGATCAAAATGAAATTTAAGGAAAGTTTAGGGGTCAAAATGAAATTTAA
Found at i:49438405 original size:54 final size:55
Alignment explanation
Indices: 49438219--49438436 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 55
49438209 CACGTGAGCC
* *
49438219 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
49438274 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* *
49438325 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
49438379 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
49438434 AAG
1 AAG
49438437 TAGAAATTGA
Statistics
Matches: 150, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.09
51 34 0.23
52 1 0.01
54 52 0.35
55 37 0.25
56 6 0.04
57 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:49438434 original size:14 final size:14
Alignment explanation
Indices: 49438415--49438449 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
49438405 GAGTTGATTT
49438415 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
49438429 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
49438443 TTGAAAA
1 TTGAAAA
49438450 TACCTCAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:49438682 original size:85 final size:87
Alignment explanation
Indices: 49438538--49438785 Score: 308
Period size: 85 Copynumber: 2.8 Consensus size: 87
49438528 AACAGAAATT
* * *
49438538 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
49438603 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* * * *
49438625 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
49438688 TTGATTTTTGAAAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
*
49438714 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
49438778 GTTGATTT
64 GTTGATTT
49438786 TTGAAAAACA
Statistics
Matches: 138, Mismatches: 13, Indels: 18
0.82 0.08 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 32 0.23
88 3 0.02
89 31 0.22
91 33 0.24
93 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:49438731 original size:15 final size:16
Alignment explanation
Indices: 49438698--49438731 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49438688 TTGATTTTTG
* *
49438698 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
49438714 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
49438730 AA
1 AA
49438732 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:49438773 original size:91 final size:88
Alignment explanation
Indices: 49438538--49438792 Score: 324
Period size: 91 Copynumber: 2.9 Consensus size: 88
49438528 AACAGAAATT
* * *
49438538 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
49438603 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * *
49438625 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
49438688 TTGATTTTTGAAAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
*
49438714 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
49438778 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
49438793 ACAAAAATTA
Statistics
Matches: 145, Mismatches: 13, Indels: 16
0.83 0.07 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 32 0.22
88 3 0.02
89 28 0.19
91 43 0.30
93 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:49439150 original size:68 final size:68
Alignment explanation
Indices: 49438996--49439174 Score: 216
Period size: 68 Copynumber: 2.6 Consensus size: 68
49438986 AAAAATTAAA
* * * * * * * **
49438996 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAATATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAA-A-AAATTTAAAATACCTCAACGTG
49439060 CCTCG
64 CCTCG
* *
49439065 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAAAATTTAAAATACCTCAACGTGTC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAATTTAAAATACCTCAACGTGCC
*
49439130 TTG
66 TCG
*
49439133 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAA
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAA
49439175 CAAAAATTAA
Statistics
Matches: 96, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
68 61 0.64
69 27 0.28
70 8 0.08
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (68 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAATTTAAAATACCTCAACGTGCC
TCG
Found at i:49439232 original size:190 final size:191
Alignment explanation
Indices: 49438750--49439742 Score: 1823
Period size: 191 Copynumber: 5.2 Consensus size: 191
49438740 CATGTGAGCC
** *
49438750 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
*
49438815 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCTTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTG-CCCGAGGCTC
* **
49438880 AACTCATTTCTCGCAATATGAGTTGATTTTTTT-TTAAATTTAAAAATACCTCAACGTGTCTT
129 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
49438942 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
*
49439007 ACCTCTCGCAATATGAGTCAATTTAAAATATAAACTAAAAATACCTCGGCGTGCCTCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCC-CGAGGCTCA
*
49439072 ACTCACTTCTCGCAATATGAGTTGA-TTTTTAAAAAAATTT-AAAATACCTCAACGTGTCTT
130 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
49439132 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
49439197 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTG-CCCGAGGCTCA
*
49439262 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAAATTAAAAATACCTCAACGTGTCTT
130 ACTCACTTCTCGCAATATGAGTTGATTTTTTT-AAAAAATTTAAAAATACCTCAACGTGTCTT
49439325 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
49439389 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCGAGGCTCAA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCGAGGCTCAA
49439454 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
49439515 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
49439580 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCGAGGCTCAA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCGAGGCTCAA
49439645 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
49439706 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
49439743 CCTTGGAAAG
Statistics
Matches: 781, Mismatches: 13, Indels: 15
0.97 0.02 0.02
Matches are distributed among these distances:
190 240 0.31
191 366 0.47
192 122 0.16
193 53 0.07
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (191 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCGAGGCTCAA
CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:49439281 original size:122 final size:120
Alignment explanation
Indices: 49439065--49439307 Score: 308
Period size: 122 Copynumber: 2.0 Consensus size: 120
49439055 GCGTGCCTCG
* * * * * * *
49439065 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAAAATTTAAAATACCTCAACGTGTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTAAAAAAAACTAAAAATACCTCAACGTGCC
** *
49439130 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 CCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAA-AAAAATTAAA
* **
49439186 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTAAAA-A-AAACTAAAAATACCTCAACGTG
***
49439250 CCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAAATTAAA
64 CCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAA
49439307 A
1 A
49439308 ATACCTCAAC
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
120 8 0.08
121 38 0.37
122 58 0.56
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (120 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTAAAAAAAACTAAAAATACCTCAACGTGCC
CCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAA
Found at i:49439372 original size:71 final size:69
Alignment explanation
Indices: 49439186--49439378 Score: 217
Period size: 71 Copynumber: 2.7 Consensus size: 69
49439176 AAAAATTAAA
* * ** * * **
49439186 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAACAAAAATTAAAAATACCTCAACGTGC
49439251 CCCG
66 CCCG
*
49439255 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAA-AAAAATTAAAAATACCTCAACG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGA---TTTAAAACAAAAATTAAAAATACCTCAACG
* **
49439319 TGTCTTG
63 TGCCCCG
*
49439326 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTT--AAAACAAAAATTAAAA
49439379 GGCTTAACTC
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
68 3 0.03
69 28 0.27
70 3 0.03
71 64 0.62
72 6 0.06
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (69 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAACAAAAATTAAAAATACCTCAACGTGC
CCCG
Found at i:49439454 original size:381 final size:383
Alignment explanation
Indices: 49438750--49439741 Score: 1832
Period size: 381 Copynumber: 2.6 Consensus size: 383
49438740 CATGTGAGCC
** *
49438750 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
*
49438815 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCTTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
* **
49438880 AACTCATTTCTCGCAATATGAGTTGATTTTTTT-TTAAATTTAAAAATACCTCAACGTGTCTTGA
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGA
49438944 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
195 GGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
*
49439009 CTCTCGCAATATGAGTCAATTTAAAATATAAACTAAAAATACCTCGGCGTGCCTCGAGGCTCAAC
259 CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCTCGAGGCTCAAC
49439074 TCACTTCTCGCAATATGAGTTGA-TTTTTAAAAAAATTT-AAAATACCTCAACGTGTCTT
324 TCACTTCTCGCAATATGAGTTGATTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
49439132 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
49439197 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
*
49439262 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAAATTAAAAATACCTCAACGTGTCTTGA
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTT-AAAAAATTTAAAAATACCTCAACGTGTCTTGA
49439327 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTGAAAAACAAAAATTAAAAGGCTTAACTCACC
195 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTGAAAAACAAAAATTAAAAGGCTTAACTCACC
49439392 TCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCC-CGAGGCTCAACT
260 TCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCTCGAGGCTCAACT
*
49439456 CACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
325 CACTTCTCGCAATATGAGTTGATTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
49439515 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
49439580 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTG-CCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
49439644 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGAG
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGAG
49439709 GCTCAACTCATTTCTCGCAATATGAGTTGATTT
196 GCTCAACTCATTTCTCGCAATATGAGTTGATTT
49439742 TCCTTGGAAA
Statistics
Matches: 595, Mismatches: 11, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
381 226 0.38
382 172 0.29
383 197 0.33
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (383 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGAG
GCTCAACTCATTTCTCGCAATATGAGTTGATTTGAAAAACAAAAATTAAAAGGCTTAACTCACCT
CTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCTCGAGGCTCAACTC
ACTTCTCGCAATATGAGTTGATTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:49439472 original size:120 final size:121
Alignment explanation
Indices: 49439255--49439480 Score: 305
Period size: 120 Copynumber: 1.9 Consensus size: 121
49439245 GCGTGCCCCG
* * * *
49439255 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCA--TATTTAAAAAAAACTAAAAATACCTCAACGT
** *
49439320 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTGAAAAACAAAAATTAAA
64 GTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTGAAAAACAAAAATTAAA
* **
49439378 AGGCTTAACTCACCTCTCGCAATATGAG-TCA-ATTTAAAACATAAACTAAAAATACCTCGGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCATATTTAAAA-A-AAACTAAAAATACCTCAACGT
49439441 G-CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTT
64 GTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTT
49439481 TTTTAAAAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
119 7 0.08
120 37 0.41
121 19 0.21
122 2 0.02
123 26 0.29
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (121 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTCATATTTAAAAAAAACTAAAAATACCTCAACGTGT
CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTGAAAAACAAAAATTAAA
Found at i:49443887 original size:17 final size:17
Alignment explanation
Indices: 49443865--49443910 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
49443855 CTCTTCAGTC
49443865 TTTCTA-AATATTTATTG
1 TTTCTACAA-ATTTATTG
49443882 TTTCTACAAATTTATTG
1 TTTCTACAAATTTATTG
49443899 TTTCTACAAATT
1 TTTCTACAAATT
49443911 CTCATGAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTCTACAAATTTATTG
Found at i:49451495 original size:17 final size:16
Alignment explanation
Indices: 49451469--49451541 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
49451459 CGAGATTTTT
*
49451469 TTTTTGAAAACACAAAA
1 TTTTTAAAAACA-AAAA
*
49451486 TTTTCAAAAACAAGGAAA
1 TTTTTAAAAACAA--AAA
* *
49451504 TTTTTGAAAACGAAAA
1 TTTTTAAAAACAAAAA
* *
49451520 TTTTGAAACACAAAAA
1 TTTTTAAAAACAAAAA
49451536 TTTTTA
1 TTTTTA
49451542 GAAGACACTA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
16 21 0.48
17 10 0.23
18 13 0.30
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.32
Consensus pattern (16 bp):
TTTTTAAAAACAAAAA
Found at i:49451507 original size:73 final size:71
Alignment explanation
Indices: 49451378--49451530 Score: 170
Period size: 72 Copynumber: 2.1 Consensus size: 71
49451368 CGTGATCCGA
* * * *
49451378 TTGAAACACGAGAATTTCTTGTTTTGAAAACACGAGAATTTTAAGACATAATATTTTTTTAAAAC
1 TTGAAACACGAGAATTTCTTGTTTTGAAAACACGAAAATTTTAAAACATAA-AATTTTTGAAAAC
49451443 CAAAATT
65 CAAAATT
*
49451450 TATGAAACACGAG-ATTT-TTTTTTTGAAAACAC-AAAATTTTCAAAAACA-AGGAAATTTTTGA
1 T-TGAAACACGAGAATTTCTTGTTTTGAAAACACGAAAATTTT--AAAACATA--AAATTTTTGA
*
49451511 AAACGAAAATT
61 AAACCAAAATT
49451522 TTGAAACAC
1 TTGAAACAC
49451531 AAAAATTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
70 7 0.10
71 23 0.33
72 28 0.40
73 12 0.17
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (71 bp):
TTGAAACACGAGAATTTCTTGTTTTGAAAACACGAAAATTTTAAAACATAAAATTTTTGAAAACC
AAAATT
Found at i:49451513 original size:18 final size:17
Alignment explanation
Indices: 49451469--49451564 Score: 74
Period size: 18 Copynumber: 5.6 Consensus size: 17
49451459 CGAGATTTTT
49451469 TTTTTGAAAACACAAAA
1 TTTTTGAAAACACAAAA
**
49451486 TTTTCAAAAACA-AGGAAA
1 TTTTTGAAAACACA--AAA
*
49451504 TTTTTGAAAAC-GAAAA
1 TTTTTGAAAACACAAAA
49451520 -TTTTG-AAACACAAAAA
1 TTTTTGAAAACAC-AAAA
*
49451536 TTTTTAGAAGACACTAAAA
1 TTTTT-GAAAACAC-AAAA
*
49451555 TTTTGGAAAA
1 TTTTTGAAAA
49451565 TGGATTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
14 4 0.06
15 5 0.08
16 8 0.13
17 14 0.23
18 18 0.29
19 13 0.21
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.29
Consensus pattern (17 bp):
TTTTTGAAAACACAAAA
Found at i:49451523 original size:15 final size:16
Alignment explanation
Indices: 49451500--49451559 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 16
49451490 CAAAAACAAG
*
49451500 GAAATTTTTGAAA-AC
1 GAAAATTTTGAAACAC
49451515 GAAAATTTTGAAACAC
1 GAAAATTTTGAAACAC
*
49451531 AAAAATTTTTAGAAGACAC
1 GAAAA-TTTT-GAA-ACAC
*
49451550 TAAAATTTTG
1 GAAAATTTTG
49451560 GAAAATGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.32
16 6 0.16
17 5 0.13
18 7 0.18
19 8 0.21
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (16 bp):
GAAAATTTTGAAACAC
Found at i:49451554 original size:19 final size:17
Alignment explanation
Indices: 49451469--49451563 Score: 72
Period size: 19 Copynumber: 5.5 Consensus size: 17
49451459 CGAGATTTTT
49451469 TTTTTGAAA-ACACAAAA
1 TTTTTGAAACACA-AAAA
* *
49451486 -TTTTCAAAAACAAGGAAA
1 TTTTTGAAACACAA--AAA
*
49451504 TTTTTGAAA-ACGAAAA
1 TTTTTGAAACACAAAAA
49451520 -TTTTGAAACACAAAAA
1 TTTTTGAAACACAAAAA
*
49451536 TTTTTAGAAGACACTAAAA
1 TTTTT-GAA-ACACAAAAA
*
49451555 TTTTGGAAA
1 TTTTTGAAA
49451564 ATGGATTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
15 8 0.12
16 17 0.27
17 8 0.12
18 12 0.19
19 19 0.30
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (17 bp):
TTTTTGAAACACAAAAA
Found at i:49451774 original size:20 final size:19
Alignment explanation
Indices: 49451736--49451782 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
49451726 GAATATATTT
49451736 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
49451756 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
49451775 -TTTTGAAA
1 TTTTTGAAA
49451783 AATAAGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:49452153 original size:8 final size:8
Alignment explanation
Indices: 49452140--49452226 Score: 93
Period size: 8 Copynumber: 10.1 Consensus size: 8
49452130 TTGAAACTCT
49452140 TTTTTTTC
1 TTTTTTTC
49452148 TTTTTTTC
1 TTTTTTTC
49452156 TTCTTTTTTCC
1 -T-TTTTTT-C
*
49452167 TTTTTTCC
1 TTTTTTTC
49452175 TTTTTTTCTC
1 -TTTTTT-TC
49452185 TTTTTTTC
1 TTTTTTTC
*
49452193 TTCTTTTC
1 TTTTTTTC
*
49452201 TTTTTTTT
1 TTTTTTTC
49452209 TTTTCTTTC
1 TTTT-TTTC
49452218 TTTTTTTC
1 TTTTTTTC
49452226 T
1 T
49452227 GGCCTGTTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
8 33 0.49
9 25 0.37
10 8 0.12
11 1 0.01
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:49452164 original size:18 final size:17
Alignment explanation
Indices: 49452137--49452226 Score: 112
Period size: 17 Copynumber: 5.2 Consensus size: 17
49452127 GAATTGAAAC
49452137 TCTTTTTTTTCTTTTTT
1 TCTTTTTTTTCTTTTTT
49452154 TCTTCTTTTTTCCTTTTTT
1 TCTT-TTTTTT-CTTTTTT
*
49452173 CCTTTTTTTCTCTTTTTT
1 TCTTTTTTT-TCTTTTTT
*
49452191 TC-TTCTTTTCTTTTTT
1 TCTTTTTTTTCTTTTTT
49452207 T-TTTTTCTTTCTTTTTT
1 TCTTTTT-TTTCTTTTTT
49452224 TCT
1 TCT
49452227 GGCCTGTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
16 12 0.19
17 20 0.32
18 20 0.32
19 11 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TCTTTTTTTTCTTTTTT
Found at i:49452178 original size:26 final size:25
Alignment explanation
Indices: 49452141--49452225 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 25
49452131 TGAAACTCTT
*
49452141 TTTTTTCTTTTTTTCTTCTTTTTTCC
1 TTTTTTCCTTTTTT-TTCTTTTTTCC
*
49452167 TTTTTTCCTTTTTTTCTCTTTTTTTC
1 TTTTTTCCTTTTTTT-TCTTTTTTCC
* *
49452193 TTCTTTT-CTTTTTTTTTTTTCTTTCT
1 TT-TTTTCCTTTTTTTTCTTT-TTTCC
49452219 TTTTTTC
1 TTTTTTC
49452226 TGGCCTGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 9 0.18
26 37 0.74
27 4 0.08
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTTTCCTTTTTTTTCTTTTTTCC
Found at i:49452189 original size:35 final size:35
Alignment explanation
Indices: 49452140--49452226 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
49452130 TTGAAACTCT
49452140 TTTTTTTCTTTTTTTCTTCTT-TTTTCCTTTTTTCC
1 TTTTTTTCTTTTTTTCTTCTTCTTTT-CTTTTTTCC
* **
49452175 TTTTTTTCTCTTTTT-TTCTTCTTTTCTTTTTTTT
1 TTTTTTTCTTTTTTTCTTCTTCTTTTCTTTTTTCC
49452209 TTTTCTTTCTTTTTTTCT
1 TTTT-TTTCTTTTTTTCT
49452227 GGCCTGTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
34 16 0.36
35 28 0.62
36 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (35 bp):
TTTTTTTCTTTTTTTCTTCTTCTTTTCTTTTTTCC
Found at i:49452337 original size:15 final size:14
Alignment explanation
Indices: 49452317--49452370 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
49452307 GGCCTGCTTC
*
49452317 TTTTTTCTGGGCTG
1 TTTTTTTTGGGCTG
49452331 TTTTTTTTTGGGCAT-
1 -TTTTTTTTGGGC-TG
49452346 TTTCTTTTTGGGCTG
1 TTT-TTTTTGGGCTG
49452361 CTTTTTTTTG
1 -TTTTTTTTG
49452371 CTTTGGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 4 0.12
15 26 0.76
16 4 0.12
ACGTcount: A:0.02, C:0.11, G:0.22, T:0.65
Consensus pattern (14 bp):
TTTTTTTTGGGCTG
Found at i:49452385 original size:31 final size:32
Alignment explanation
Indices: 49452345--49452418 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
49452335 TTTTTGGGCA
*
49452345 TTTTCTTTTTGGGCTGCTTT-TTTTTGCTTTG-G
1 TTTT-TTTTTGGGCTGATTTGTTTTT-CTTTGTG
*
49452377 TTTTTTTTTGGGCTGATTTGTTTTTTTTTGTG
1 TTTTTTTTTGGGCTGATTTGTTTTTCTTTGTG
49452409 TTGTTTTTTT
1 TT-TTTTTTT
49452419 TAATTAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 18 0.49
32 12 0.32
33 7 0.19
ACGTcount: A:0.01, C:0.07, G:0.20, T:0.72
Consensus pattern (32 bp):
TTTTTTTTTGGGCTGATTTGTTTTTCTTTGTG
Found at i:49452452 original size:6 final size:6
Alignment explanation
Indices: 49452441--49452465 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49452431 TTTTGGGCTG
49452441 TTGGGT TTGGGT TTGGGT TTGGGT T
1 TTGGGT TTGGGT TTGGGT TTGGGT T
49452466 GCTGCTGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TTGGGT
Found at i:49452542 original size:3 final size:3
Alignment explanation
Indices: 49452536--49452573 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
49452526 TTTCTTTTTT
49452536 TTC TTC TTC TTC TTTC TTC TTC TTC -TC TTTC TTC TTC T
1 TTC TTC TTC TTC -TTC TTC TTC TTC TTC -TTC TTC TTC T
49452574 CCTCCTACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 25 0.78
4 5 0.16
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:49452962 original size:29 final size:29
Alignment explanation
Indices: 49452929--49453045 Score: 85
Period size: 30 Copynumber: 3.9 Consensus size: 29
49452919 TGTAATTTTT
*
49452929 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * * *
49452958 TGAAAGTGTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
49452988 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
49453017 GGAAAAGTTTAGGGGTCAAAATGTAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
49453046 TTATTTTTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
29 13 0.19
30 55 0.79
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:49452984 original size:30 final size:30
Alignment explanation
Indices: 49452944--49453045 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
49452934 ATTTAGGATT
* *
49452944 AAAATGAAATTTAATGAAAGTGTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
49452974 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
49453004 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
49453034 AAAATGTAATTT
1 AAAATGAAATTT
49453046 TTATTTTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.44, C:0.03, G:0.24, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:49453045 original size:60 final size:59
Alignment explanation
Indices: 49452916--49453045 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
49452906 TTCTGGGGCT
** * * *
49452916 AAATGTAATTTTTAGAAAATTTAGGATTAAAATGAAATTTAATGAAAGTGTAGGGGTCT
1 AAATGTAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTGTAGGGGTCA
* * * * *
49452975 AAGTGAAATTTAAAGAAAGTTTAAGGGTCAAAATGAAATTT-AGGAAAAGTTTAGGGGTCA
1 AAATGTAATTTAAAGAAAATTT-AGGATCAAAATGAAATTTAAGG-AAAGTGTAGGGGTCA
49453035 AAATGTAATTT
1 AAATGTAATTT
49453046 TTATTTTTTA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
59 19 0.33
60 38 0.67
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.32
Consensus pattern (59 bp):
AAATGTAATTTAAAGAAAATTTAGGATCAAAATGAAATTTAAGGAAAGTGTAGGGGTCA
Found at i:49453366 original size:17 final size:18
Alignment explanation
Indices: 49453327--49453376 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
49453317 TTTAAATTTA
49453327 AATTTATATAATTTAGGG
1 AATTTATATAATTTAGGG
* *
49453345 AATTTATATATTTTATGG
1 AATTTATATAATTTAGGG
49453363 -ATTTATATACATTT
1 AATTTATATA-ATTT
49453377 TTTAAAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (18 bp):
AATTTATATAATTTAGGG
Found at i:49453394 original size:39 final size:37
Alignment explanation
Indices: 49453347--49453419 Score: 101
Period size: 39 Copynumber: 1.9 Consensus size: 37
49453337 ATTTAGGGAA
*
49453347 TTTATATATTTTATGGATTTATATACATTTTTTAAAGAT
1 TTTATATATTTT-TCGATTTATATA-ATTTTTTAAAGAT
* *
49453386 TTTATATATTTTTCTATTTTTATAATTTTTTAAA
1 TTTATATATTTTTCGATTTATATAATTTTTTAAA
49453420 AAAATTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 10 0.32
38 9 0.29
39 12 0.39
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (37 bp):
TTTATATATTTTTCGATTTATATAATTTTTTAAAGAT
Found at i:49453428 original size:38 final size:39
Alignment explanation
Indices: 49453345--49453428 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 39
49453335 TAATTTAGGG
* *
49453345 AATTTATATATTTTATGGATTTATATACATTTTTTAAAG
1 AATTTATATATTTTATCGATTTATATACATTTTTTAAAA
* * *
49453384 ATTTTATATATTTT-TCTATTTTTATA-ATTTTTTAAAAA
1 AATTTATATATTTTATCGATTTATATACATTTTTT-AAAA
49453422 AATTTAT
1 AATTTAT
49453429 GCATATTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 7 0.18
38 18 0.47
39 13 0.34
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (39 bp):
AATTTATATATTTTATCGATTTATATACATTTTTTAAAA
Found at i:49457346 original size:11 final size:11
Alignment explanation
Indices: 49457309--49457340 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
49457299 TAAAGAGAGC
*
49457309 TTTGAGAGGAA
1 TTTGAGAGAAA
49457320 TTTGAGAGAAA
1 TTTGAGAGAAA
49457331 TTTGAGAGAA
1 TTTGAGAGAA
49457341 CATTGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:49458539 original size:28 final size:28
Alignment explanation
Indices: 49458481--49458540 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
49458471 ATTTTTTTGT
* * *
49458481 TTTATTTAACATTATTATTATAGTTATA
1 TTTATTTAACATTAATATTATAGTAAAA
*
49458509 TTTATTTAATATTAATATTAATA-TAAAA
1 TTTATTTAACATTAATATT-ATAGTAAAA
49458537 TTTA
1 TTTA
49458541 AATTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTATTTAACATTAATATTATAGTAAAA
Found at i:49459157 original size:18 final size:19
Alignment explanation
Indices: 49459136--49459183 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
49459126 TTACATATTA
49459136 TTAAAATA-ATAGAAAAGT-
1 TTAAAATATATA-AAAAGTG
49459154 TTAAATATATATAAAAAGTG
1 TTAAA-ATATATAAAAAGTG
49459174 TATAAAATAT
1 T-TAAAATAT
49459184 TATTTAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 8 0.31
21 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
TTAAAATATATAAAAAGTG
Found at i:49462396 original size:23 final size:23
Alignment explanation
Indices: 49462366--49462428 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
49462356 CGGCCCGGCC
*
49462366 TTTTTTAATTAAAATTAAAATTA
1 TTTTTTAATTAAAATTAAAACTA
49462389 TTTTTTAATTAAAATTAAAACTA
1 TTTTTTAATTAAAATTAAAACTA
* *
49462412 ATTGTT-ATTAAAATTAA
1 TTTTTTAATTAAAATTAA
49462429 TTGTTAGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 11 0.30
23 26 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTTTAATTAAAATTAAAACTA
Found at i:49462441 original size:16 final size:16
Alignment explanation
Indices: 49462404--49462443 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
49462394 TAATTAAAAT
* *
49462404 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
49462420 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
49462436 TAAAATTA
1 TAAAATTA
49462444 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:49462549 original size:9 final size:9
Alignment explanation
Indices: 49462516--49462543 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
49462506 TTTATCAAAT
49462516 TATTAATTG
1 TATTAATTG
49462525 TATTAATTG
1 TATTAATTG
49462534 TATTAATTG
1 TATTAATTG
49462543 T
1 T
49462544 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:49462553 original size:68 final size:68
Alignment explanation
Indices: 49462432--49462641 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
49462422 AAATTAATTG
*
49462432 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
49462495 TGA
66 TGA
49462498 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
49462563 TGA
66 TGA
* *
49462566 TTAGTAAATTTATCAAATTATTAATTATATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
49462631 TGA
66 TGA
49462634 TTAGTAAA
1 TTAGTAAA
49462642 ACAAACTTGA
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
66 26 0.19
68 113 0.81
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:49462748 original size:22 final size:24
Alignment explanation
Indices: 49462708--49462751 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
49462698 AAATAAACTT
49462708 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
49462732 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
49462752 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:49463290 original size:28 final size:28
Alignment explanation
Indices: 49463259--49463316 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
49463249 TAATTACATG
*
49463259 TTAAATTAGCCAAATATGTTGATTCTTT
1 TTAAATTAGCCAAATAGGTTGATTCTTT
* * * *
49463287 TT-AATTGGTCAAATAGGTTGTTTTTTT
1 TTAAATTAGCCAAATAGGTTGATTCTTT
49463314 TTA
1 TTA
49463317 TTTTAGGGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (28 bp):
TTAAATTAGCCAAATAGGTTGATTCTTT
Found at i:49465314 original size:46 final size:46
Alignment explanation
Indices: 49465245--49465429 Score: 264
Period size: 46 Copynumber: 4.0 Consensus size: 46
49465235 CATGGCAAAG
* * * *
49465245 TGTGAAACGTAGGTATGGCATTTCAGTGAATAAAACCATACTGATT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
49465291 TGTGAAAAGTAGGTATGGTATTTC-GATAAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAG-TGAAGAAAACCATACTGAGT
*
49465337 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
49465383 TATGAAAAGTAGGTATGGTATTTCCGTGAAGAAAATCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
49465429 T
1 T
49465430 ATAGCAATGT
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
45 1 0.01
46 122 0.98
47 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:49467286 original size:13 final size:12
Alignment explanation
Indices: 49467254--49467284 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49467244 ATTTTAAAAT
49467254 ATTTTTTACATA
1 ATTTTTTACATA
49467266 ATTTTTTACATA
1 ATTTTTTACATA
49467278 ATTTTTT
1 ATTTTTT
49467285 TAATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTTTACATA
Found at i:49467302 original size:11 final size:11
Alignment explanation
Indices: 49467288--49467332 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
49467278 ATTTTTTTAA
49467288 TTTTAAAATAT
1 TTTTAAAATAT
49467299 TTTT--AA-A-
1 TTTTAAAATAT
49467306 TTTTAAAATAT
1 TTTTAAAATAT
49467317 TTTTAAAATACT
1 TTTTAAAATA-T
49467329 TTTT
1 TTTT
49467333 TTTTTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
7 4 0.14
8 1 0.03
9 4 0.14
10 1 0.03
11 14 0.48
12 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:49467321 original size:18 final size:18
Alignment explanation
Indices: 49467280--49467323 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
49467270 TTTACATAAT
*
49467280 TTTTTTAATTTTAAAATA
1 TTTTTAAATTTTAAAATA
49467298 TTTTTAAATTTTAAAATA
1 TTTTTAAATTTTAAAATA
49467316 TTTTTAAA
1 TTTTTAAA
49467324 ATACTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTAAATTTTAAAATA
Found at i:49467332 original size:61 final size:63
Alignment explanation
Indices: 49467237--49467360 Score: 162
Period size: 61 Copynumber: 2.0 Consensus size: 63
49467227 ATATATTTAT
* * * *
49467237 TTTTTTAATTTTAAAATATTTTTTACATAATTTTTTACATAATTTTTT-TAA-TTTTAAAATA
1 TTTTTAAATTTTAAAATATTTTTAAAATAATTTTTTACATAATTTTTTAAAATTTTTAAAATA
* ***
49467298 TTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTTAAATTTTAAAATATTTTTAAAATAATTTTTTACATAATTTTTTAAAATTTTTAAAATA
49467361 AAAATGGGCC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 41 0.77
62 2 0.04
63 10 0.19
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (63 bp):
TTTTTAAATTTTAAAATATTTTTAAAATAATTTTTTACATAATTTTTTAAAATTTTTAAAATA
Found at i:49471279 original size:30 final size:31
Alignment explanation
Indices: 49471224--49471291 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
49471214 ACCCTTAAAA
** * **
49471224 TATTTACACTATTGGTCCTTCAAATTTTTTG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
49471255 TATTTACACT-TTAATCCCTCAAATTTTGAG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
49471285 TATTTAC
1 TATTTAC
49471292 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTGAG
Found at i:49471472 original size:23 final size:23
Alignment explanation
Indices: 49471446--49471490 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
49471436 TTTCTTACTA
*
49471446 TAGTAATTTTCGGGGTATTACAG
1 TAGTAATTTTCGGGATATTACAG
49471469 TAGTAATTTTCGGGATATTACA
1 TAGTAATTTTCGGGATATTACA
49471491 TTGGTCGTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCGGGATATTACAG
Found at i:49472610 original size:20 final size:20
Alignment explanation
Indices: 49472563--49472610 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
49472553 AATGTGCTAC
*
49472563 ATTTGAAAAAGAAAATTTTG
1 ATTTGAAGAAGAAAATTTTG
49472583 ATTTGAAGAAGAAAATTTTG
1 ATTTGAAGAAGAAAATTTTG
*
49472603 GTTTGAAG
1 ATTTGAAG
49472611 TTAAAACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (20 bp):
ATTTGAAGAAGAAAATTTTG
Found at i:49472869 original size:22 final size:23
Alignment explanation
Indices: 49472844--49472900 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
49472834 TTGTATATTA
49472844 TTTTAAATTTTA-AATTATA-GAT
1 TTTTAAATTTTACAATTATATG-T
* *
49472866 TTTTAAAATTTACATTTATATGT
1 TTTTAAATTTTACAATTATATGT
*
49472889 TTTAAAATTTTA
1 TTTTAAATTTTA
49472901 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 11 0.38
23 17 0.59
24 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTAAATTTTACAATTATATGT
Found at i:49472900 original size:23 final size:23
Alignment explanation
Indices: 49472844--49472900 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
49472834 TTGTATATTA
49472844 TTTT-AAATTTTAAATTATAGAT
1 TTTTAAAATTTTAAATTATAGAT
* *
49472866 TTTTAAAA-TTTACATT-TATAT
1 TTTTAAAATTTTAAATTATAGAT
49472887 GTTTTAAAATTTTA
1 -TTTTAAAATTTTA
49472901 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTAAAATTTTAAATTATAGAT
Found at i:49475138 original size:9 final size:9
Alignment explanation
Indices: 49475124--49475160 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
49475114 TATAGTTTGA
49475124 TATTCGAAT
1 TATTCGAAT
49475133 TATTCGAAT
1 TATTCGAAT
*
49475142 TATTCGAGT
1 TATTCGAAT
*
49475151 TATTCAAAT
1 TATTCGAAT
49475160 T
1 T
49475161 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:49475231 original size:9 final size:9
Alignment explanation
Indices: 49475214--49475244 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
49475204 TCGAGTTGAT
49475214 TCGAATAAC
1 TCGAATAAC
*
49475223 TCGATTAAC
1 TCGAATAAC
49475232 TCGAATAAC
1 TCGAATAAC
49475241 TCGA
1 TCGA
49475245 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:49484314 original size:8 final size:7
Alignment explanation
Indices: 49484292--49484325 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
49484282 GATTTTATAT
49484292 AAATAAA
1 AAATAAA
49484299 AAATAAA
1 AAATAAA
49484306 AAATAAA
1 AAATAAA
*
49484313 AAAGATAA
1 AAATA-AA
49484321 AAATA
1 AAATA
49484326 TTTTTAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
AAATAAA
Found at i:49489566 original size:22 final size:21
Alignment explanation
Indices: 49489522--49489562 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
49489512 ATGTCATTAG
*
49489522 GGTTTAAACAAAAAAGGAAAT
1 GGTTCAAACAAAAAAGGAAAT
*
49489543 GGTTCAAACGAAAAAGGAAA
1 GGTTCAAACAAAAAAGGAAA
49489563 ATGGGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.15
Consensus pattern (21 bp):
GGTTCAAACAAAAAAGGAAAT
Found at i:49492250 original size:12 final size:12
Alignment explanation
Indices: 49492205--49492251 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
49492195 CGATGATTTC
*
49492205 ATATTAAAATA-
1 ATATTTAAATAT
*
49492216 ATTATTTAAAAAT
1 A-TATTTAAATAT
*
49492229 ATATTTAAATTT
1 ATATTTAAATAT
49492241 ATATTTAAATA
1 ATATTTAAATA
49492252 AAATTCTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 1 0.03
12 27 0.93
13 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTTAAATAT
Found at i:49502374 original size:26 final size:25
Alignment explanation
Indices: 49502337--49502418 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
49502327 TATTTGATAA
*
49502337 ATTTTT-AGAATAATTTTTATAGAT
1 ATTTTTAAAAATAATTTTTATAGAT
* *
49502361 ATTTTTGAAAAATAAAATTTCA-AGAT
1 ATTTTT-AAAAAT-AATTTTTATAGAT
* * *
49502387 ATGTTTAAAAAAATATTTTTATATAGT
1 ATTTTTAAAAATA-ATTTTTATAGA-T
49502414 ATTTT
1 ATTTT
49502419 AATTTACTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
24 7 0.16
25 10 0.23
26 15 0.35
27 11 0.26
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (25 bp):
ATTTTTAAAAATAATTTTTATAGAT
Found at i:49504866 original size:13 final size:13
Alignment explanation
Indices: 49504848--49504873 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49504838 TTGGATCTGT
49504848 ACCAAAACAATCA
1 ACCAAAACAATCA
49504861 ACCAAAACAATCA
1 ACCAAAACAATCA
49504874 TAAAACATAT
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:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCA
Found at i:49508967 original size:7 final size:7
Alignment explanation
Indices: 49508952--49508990 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
49508942 ACCCAACAAT
*
49508952 AACCTTA
1 AACCCTA
49508959 AACCCTA
1 AACCCTA
*
49508966 AACCTTA
1 AACCCTA
49508973 AACCCTAA
1 AACCCT-A
49508981 AACCCTA
1 AACCCTA
49508988 AAC
1 AAC
49508991 AAAAGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:49508971 original size:14 final size:14
Alignment explanation
Indices: 49508952--49508981 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
49508942 ACCCAACAAT
49508952 AACCTTAAACCCTA
1 AACCTTAAACCCTA
49508966 AACCTTAAACCCTA
1 AACCTTAAACCCTA
49508980 AA
1 AA
49508982 ACCCTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:49518182 original size:20 final size:21
Alignment explanation
Indices: 49518152--49518195 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 21
49518142 GTCAGAAGTT
49518152 AATTAATTTTTTAAAAA-TTAA
1 AATTAA-TTTTTAAAAATTTAA
49518173 AATT-ATTTTTAAAAATTTAA
1 AATTAATTTTTAAAAATTTAA
49518193 AAT
1 AAT
49518196 CTTTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 8 0.36
21 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTAATTTTTAAAAATTTAA
Found at i:49518261 original size:57 final size:57
Alignment explanation
Indices: 49518163--49518270 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
49518153 ATTAATTTTT
49518163 TAAAAATTAAAATTATTTTTAAAAATTTAAAATCTTTAAAATT-ATTAAATAAATTA
1 TAAAAATTAAAATTATTTTTAAAAATTTAAAATCTTTAAAATTAATTAAATAAATTA
* * *
49518219 TAAAAATTTAAAA-TATTTTTTAATATTTTAATAT-TTTAAAAATTAATTAAAT
1 TAAAAA-TTAAAATTA-TTTTTAAAAATTTAAAATCTTT-AAAATTAATTAAAT
49518271 TTTTATGTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
56 11 0.24
57 27 0.60
58 7 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (57 bp):
TAAAAATTAAAATTATTTTTAAAAATTTAAAATCTTTAAAATTAATTAAATAAATTA
Found at i:49518274 original size:19 final size:19
Alignment explanation
Indices: 49518150--49518275 Score: 56
Period size: 19 Copynumber: 6.8 Consensus size: 19
49518140 ACGTCAGAAG
*
49518150 TTAATTAATTTTTTAAAAA
1 TTAATTAAATTTTTAAAAA
49518169 TTAA--AATTATTTTTAAAAA
1 TTAATTAA--ATTTTTAAAAA
* *
49518188 TT--TAAAATCTTTAAAATTA
1 TTAATTAAATTTTTAAAA--A
* *
49518207 TTAAATAAA-TTATAAAAA
1 TTAATTAAATTTTTAAAAA
* *
49518225 TTTAA--AATATTTTTTAATA
1 -TTAATTAA-ATTTTTAAAAA
49518244 TT--TT-AATATTTTAAAAA
1 TTAATTAAAT-TTTTAAAAA
49518261 TTAATTAAATTTTTA
1 TTAATTAAATTTTTA
49518276 TGTGTTATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 34
0.64 0.09 0.27
Matches are distributed among these distances:
16 2 0.03
17 23 0.29
18 4 0.05
19 38 0.48
20 9 0.11
21 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATTAAATTTTTAAAAA
Found at i:49520237 original size:21 final size:22
Alignment explanation
Indices: 49520220--49520265 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
49520210 TCGCACGGCG
49520220 ATGTCCCT-AGCTCACACGGGC
1 ATGTCCCTCAGCTCACACGGGC
* *
49520241 ATGTGCCTCAGC-CACACGGTC
1 ATGTCCCTCAGCTCACACGGGC
49520262 ATGT
1 ATGT
49520266 GACTCTCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.22
Consensus pattern (22 bp):
ATGTCCCTCAGCTCACACGGGC
Found at i:49523513 original size:20 final size:20
Alignment explanation
Indices: 49523488--49523527 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
49523478 CGTAAAATGA
*
49523488 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
49523508 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
49523528 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:49523517 original size:34 final size:35
Alignment explanation
Indices: 49523473--49523539 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
49523463 CAGTAAAATA
*
49523473 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
49523507 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
49523540 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:49523543 original size:14 final size:15
Alignment explanation
Indices: 49523467--49523543 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
49523457 GATTGCCAGT
* *
49523467 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
49523481 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
49523495 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
49523515 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
49523530 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
49523544 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:49524299 original size:47 final size:47
Alignment explanation
Indices: 49524241--49524375 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 47
49524231 AAAATATGCT
* * * *
49524241 AATACATTGTGGATGAACCACTAGTCGAGCAGAT-GACTGTCAACTAA
1 AATACGTTGTGGAT-AACCACTAGTCGAGTAGATAAACTGACAACTAA
* * * *
49524288 AATACGTTGTGGATAAAACATTGGTCGAGTAGATAAACTGACGACTAA
1 AATACGTTGTGGAT-AACCACTAGTCGAGTAGATAAACTGACAACTAA
* * *
49524336 AACATGTTATGGATAATCCACTAGTCGAGTAGATAAACTG
1 AATACGTTGTGGATAA-CCACTAGTCGAGTAGATAAACTG
49524376 TTGACTACTT
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
47 30 0.42
48 41 0.58
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (47 bp):
AATACGTTGTGGATAACCACTAGTCGAGTAGATAAACTGACAACTAA
Found at i:49532985 original size:19 final size:18
Alignment explanation
Indices: 49532957--49533003 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
49532947 ACTTTATGCT
49532957 TTTTTAAATTTTCATTAA
1 TTTTTAAATTTTCATTAA
**
49532975 TTTTTATAATTTTTTTTAA
1 TTTTTA-AATTTTCATTAA
*
49532994 TTTTGAAATT
1 TTTTTAAATT
49533004 CTTTTTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTAAATTTTCATTAA
Found at i:49533008 original size:18 final size:19
Alignment explanation
Indices: 49532971--49533009 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
49532961 TAAATTTTCA
* *
49532971 TTAATTTTTATAATTTTTT
1 TTAATTTTGATAATTCTTT
49532990 TTAATTTTGA-AATTCTTT
1 TTAATTTTGATAATTCTTT
49533008 TT
1 TT
49533010 TTGAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
TTAATTTTGATAATTCTTT
Found at i:49533008 original size:19 final size:19
Alignment explanation
Indices: 49532971--49533010 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
49532961 TAAATTTTCA
*
49532971 TTAATTTTTATAATTTTTT
1 TTAATTTTGATAATTTTTT
49532990 TTAATTTTGA-AATTCTTTT
1 TTAATTTTGATAATT-TTTT
49533009 TT
1 TT
49533011 TGAATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (19 bp):
TTAATTTTGATAATTTTTT
Found at i:49534242 original size:13 final size:13
Alignment explanation
Indices: 49534205--49534255 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
49534195 TTCTTCATTA
49534205 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
49534218 CTGTGGAAAAGTG
1 CTTTTGAAAAGTG
* *
49534231 CTTTTGAGAAGTA
1 CTTTTGAAAAGTG
*
49534244 ATTTTGAAAAGT
1 CTTTTGAAAAGT
49534256 TTGGTTTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:49534819 original size:62 final size:62
Alignment explanation
Indices: 49534745--49534862 Score: 227
Period size: 62 Copynumber: 1.9 Consensus size: 62
49534735 CCTTTTAAGA
*
49534745 AGTATTTTTCAAAAGCACTTCTAAAAAATTAAAAATTTAAGTGAAAAGTAACTTATAAAAGG
1 AGTACTTTTCAAAAGCACTTCTAAAAAATTAAAAATTTAAGTGAAAAGTAACTTATAAAAGG
49534807 AGTACTTTTCAAAAGCACTTCTAAAAAATTAAAAATTTAAGTGAAAAGTAACTTAT
1 AGTACTTTTCAAAAGCACTTCTAAAAAATTAAAAATTTAAGTGAAAAGTAACTTAT
49534863 TCTTCACAGC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (62 bp):
AGTACTTTTCAAAAGCACTTCTAAAAAATTAAAAATTTAAGTGAAAAGTAACTTATAAAAGG
Found at i:49535190 original size:5 final size:5
Alignment explanation
Indices: 49535180--49535205 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
49535170 TATATATAAA
49535180 CAAAC CAAAC CAAAC CAAAC CAAAC C
1 CAAAC CAAAC CAAAC CAAAC CAAAC C
49535206 CTTGCCTTTC
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:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAC
Found at i:49541051 original size:28 final size:28
Alignment explanation
Indices: 49541012--49541069 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
49541002 TGGTCAACAG
49541012 AAAATAACTTAGATGACAACGAAAAATA
1 AAAATAACTTAGATGACAACGAAAAATA
49541040 AAAATAACTTAGATGACAACGAAAAATA
1 AAAATAACTTAGATGACAACGAAAAATA
49541068 AA
1 AA
49541070 CATTTTTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (28 bp):
AAAATAACTTAGATGACAACGAAAAATA
Found at i:49541411 original size:26 final size:25
Alignment explanation
Indices: 49541382--49541436 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
49541372 AATGATATTC
49541382 TTAATATATTACTAA-AAATAATTATA
1 TTAATATATTACTAATAAAT-A-TATA
* *
49541408 TTAATATTTTAGTAATAAATATATA
1 TTAATATATTACTAATAAATATATA
49541433 TTAA
1 TTAA
49541437 AATTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
26 14 0.54
27 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TTAATATATTACTAATAAATATATA
Found at i:49548904 original size:6 final size:6
Alignment explanation
Indices: 49548893--49548952 Score: 52
Period size: 6 Copynumber: 9.7 Consensus size: 6
49548883 AGGCAACCCA
* *
49548893 ATTTTT ATTTTT ATTTTTT ATTTTT GTTATT ATTATTT ATTATTT -TATTTT
1 ATTTTT ATTTTT A-TTTTT ATTTTT ATTTTT ATT-TTT ATT-TTT AT-TTTT
49548944 A-TTTT ATTT
1 ATTTTT ATTT
49548953 ACTTTATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
5 5 0.11
6 24 0.53
7 16 0.36
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:49548909 original size:5 final size:5
Alignment explanation
Indices: 49548895--49548977 Score: 57
Period size: 5 Copynumber: 16.4 Consensus size: 5
49548885 GCAACCCAAT
* *
49548895 TTTTA TTTT- TATT- TTTTA TTTT- TGTTA TTATTA TTTATTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA -TT-TTA TTTTA
* *
49548940 TTTTA TTTTA -TTTA CTTTA TTTATTA CTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA -TT-TTA TTTTA TTTTA TT
49548978 ATTTATTACT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
4 13 0.20
5 35 0.55
6 7 0.11
7 9 0.14
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:49548912 original size:13 final size:13
Alignment explanation
Indices: 49548894--49548948 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
49548884 GGCAACCCAA
49548894 TTTTTATTTTTAT
1 TTTTTATTTTTAT
*
49548907 TTTTTATTTTT-G
1 TTTTTATTTTTAT
*
49548919 TTATTATTATTTAT
1 TTTTTATT-TTTAT
49548933 TATTTTA-TTTTAT
1 T-TTTTATTTTTAT
49548946 TTT
1 TTT
49548949 ATTTACTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
12 9 0.26
13 20 0.57
14 2 0.06
15 4 0.11
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:49548928 original size:22 final size:22
Alignment explanation
Indices: 49548901--49548984 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 22
49548891 CAATTTTTAT
49548901 TTTTATTTTTTATTTT-TGTTA
1 TTTTATTTTTTATTTTATGTTA
* *
49548922 TTATTATTTATTATTTTATTTTA
1 TT-TTATTTTTTATTTTATGTTA
49548945 TTTTATTTACTTTATTTATTACT-TTA
1 TTTTATTT--TTTA-TT-TTA-TGTTA
*
49548971 TTTTATTATTTATT
1 TTTTATTTTTTATT
49548985 ACTTATTTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.04
22 19 0.37
23 8 0.15
24 7 0.13
25 2 0.04
26 13 0.25
27 1 0.02
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.75
Consensus pattern (22 bp):
TTTTATTTTTTATTTTATGTTA
Found at i:49548963 original size:31 final size:28
Alignment explanation
Indices: 49548897--49548992 Score: 99
Period size: 31 Copynumber: 3.3 Consensus size: 28
49548887 AACCCAATTT
*
49548897 TTATT-TTTATT-TTTTATTTT-TGTTA
1 TTATTATTTATTATTTTATTTTATTTTA
49548922 TTATTATTTATTATTTTATTTTATTTTA
1 TTATTATTTATTATTTTATTTTATTTTA
*
49548950 TTTACTTTATTTATTACTTTATTTTATTATTTA
1 -TTA--TTATTTATTATTTTATTTTA-T-TTTA
49548983 TTACTTATTT
1 TTA-TTATTT
49548993 GGATATTAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.08
26 6 0.10
27 9 0.15
28 4 0.07
29 3 0.05
31 25 0.42
32 4 0.07
33 4 0.07
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (28 bp):
TTATTATTTATTATTTTATTTTATTTTA
Found at i:49550197 original size:15 final size:15
Alignment explanation
Indices: 49550172--49550206 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
49550162 GACTCTATTT
*
49550172 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
49550186 TAATTAATATTAAGA
1 TAATTAATATTAAGA
49550201 TAATTA
1 TAATTA
49550207 TTAAGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:49552431 original size:25 final size:26
Alignment explanation
Indices: 49552373--49552433 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
49552363 TACCCCCAAC
* *
49552373 AAAATTTTGATGATTTTACCCTTGGT
1 AAAATTTTGACGATTTTACCCTTAGT
*
49552399 AAAATTTTGACGATTTTTCCC-TAGT
1 AAAATTTTGACGATTTTACCCTTAGT
49552424 AAAATTTTGA
1 AAAATTTTGA
49552434 GAAAATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 13 0.41
26 19 0.59
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (26 bp):
AAAATTTTGACGATTTTACCCTTAGT
Found at i:49552725 original size:9 final size:10
Alignment explanation
Indices: 49552706--49552734 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
49552696 ATTCAATTTT
49552706 TTTCTATTCA
1 TTTCTATTCA
49552716 TTTC-ATTCA
1 TTTCTATTCA
49552725 TTTCTATTCA
1 TTTCTATTCA
49552735 AAACAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:49554775 original size:19 final size:20
Alignment explanation
Indices: 49554738--49554789 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
49554728 AGGTCGCTCC
*
49554738 TACTATAATTTTATTTATAT-
1 TACTTTAATTTT-TTTATATA
49554758 TACTTTAATTTTTTTATATA
1 TACTTTAATTTTTTTATATA
*
49554778 TA-ATTAATTTTT
1 TACTTTAATTTTT
49554790 ATGATTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TACTTTAATTTTTTTATATA
Found at i:49556314 original size:22 final size:22
Alignment explanation
Indices: 49556266--49556314 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
49556256 ATTTGAAATT
*
49556266 TAATTTTTATTTTAATTTGATA
1 TAATTTTTATTTTAATTTCATA
* *
49556288 TAATTTATTTTTTTATTTTCATA
1 TAATTT-TTATTTTAATTTCATA
49556311 -AATT
1 TAATT
49556315 AGTCCGGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TAATTTTTATTTTAATTTCATA
Found at i:49564794 original size:90 final size:92
Alignment explanation
Indices: 49564627--49564796 Score: 236
Period size: 90 Copynumber: 1.8 Consensus size: 92
49564617 TCGCACTTGA
* * * **
49564627 TATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTTTAATCTCACATTGACTA
1 TATAAATAAGTGACAATTTC-T-ACTATTTTCATTAAAAAGTTAATTTTAATCACACATCAACTA
*
49564692 GAGAACATTCTCATATCTTACATTGACCT
64 GAGAACACTCTCATATCTTACATTGACCT
*
49564721 TATAAATAAGTGACAATTTC-ACTATTTTCATTAAAAA-TTAATTTTAATCACACGTCAACTAGA
1 TATAAATAAGTGACAATTTCTACTATTTTCATTAAAAAGTTAATTTTAATCACACATCAACTAGA
*
49564784 GAAGACTCTCATA
66 GAACACTCTCATA
49564797 GCTCACTTCT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 32 0.47
91 17 0.25
94 19 0.28
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (92 bp):
TATAAATAAGTGACAATTTCTACTATTTTCATTAAAAAGTTAATTTTAATCACACATCAACTAGA
GAACACTCTCATATCTTACATTGACCT
Found at i:49564869 original size:68 final size:68
Alignment explanation
Indices: 49564738--49564870 Score: 169
Period size: 69 Copynumber: 2.0 Consensus size: 68
49564728 AAGTGACAAT
* * *
49564738 TTCACTATTTTCATTAAAAATTAATTTTAATCACACGTCAACTAGAGAAGACTCTCATAGCTCAC
1 TTCACTATTTTCATTAAAAATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCAC
49564803 TTC
66 TTC
* * ****
49564806 TTCACTATTTTCATTAAAACGTTAATTTTAATCCCACATTGGTTAGAGAACAATCTCAT-GCTCA
1 TTCACTATTTTCATTAAAA-ATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCA
49564870 C
65 C
49564871 ACTTACACTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 25 0.45
69 30 0.55
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (68 bp):
TTCACTATTTTCATTAAAAATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCAC
TTC
Found at i:49564880 original size:68 final size:68
Alignment explanation
Indices: 49564738--49564881 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 68
49564728 AAGTGACAAT
* * *
49564738 TTCACTATTTTCATTAAAAATTAATTTTAATCACACGTCAACTAGAGAAGACTCTCATAGCTCAC
1 TTCACTATTTTCATTAAAAATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCAC
*
49564803 TTC
66 TAC
* * ****
49564806 TTCACTATTTTCATTAAAACGTTAATTTTAATCCCACATTGGTTAGAGAACAATCTCAT-GCTCA
1 TTCACTATTTTCATTAAAA-ATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCA
49564870 C-AC
65 CTAC
49564873 TTACACTAT
1 TT-CACTAT
49564882 AAATAAGTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
67 3 0.05
68 31 0.48
69 30 0.47
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (68 bp):
TTCACTATTTTCATTAAAAATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCAC
TAC
Found at i:49564931 original size:252 final size:254
Alignment explanation
Indices: 49564487--49565185 Score: 988
Period size: 257 Copynumber: 2.8 Consensus size: 254
49564477 CATAGCTCAC
* *
49564487 TTCTTCACTATTTTTATTAAAAAAATTAATTTTAATCCCACATTAACTAGAGAATACT-TCCATA
1 TTCTTCACTATTTTCATT-AAAAAATTAATTTTAATCCCACATTAACTAGAGAAAACTCT-CATA
* * ** *
49564551 GCTTACTTCTTCACTACTTTT-ATTAAAA-GTTAATTTTAA-CTTAAAAAGTTA-AGAACACTCC
64 GCTCACTTCTTCACTA-TTTTCATTAAAACGTTAATTTTAATCCTAATTAGTTAGAGAACACTCT
* * *
49564612 CATACTCGCACTT-GA-TATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTT
128 CATGCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTT
*
49564675 TAATCTCACATTGACTAGAGAACATTCTCATATCTTACATTGACCTTATAAATAAGTGACAA
193 TAATCTCACATTGACTAGAGAACATTCTCATATCTCACATTGACCTTATAAATAAGTGACAA
* * * *
49564737 -T-TTCACTATTTTCATT-AAAAATTAATTTTAATCACACGTCAACTAGAGAAGACTCTCATAGC
1 TTCTTCACTATTTTCATTAAAAAATTAATTTTAATCCCACATTAACTAGAGAAAACTCTCATAGC
* * *
49564799 TCACTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCCACATTGGTTAGAGAACAATCTCA
66 TCACTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCTA-ATTAGTTAGAGAACACTCTCA
49564864 TGCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTTTA
130 TGCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTTTA
*
49564929 ATCTCACATTGACTAGAGAACATTCTCATATCTCATATTGACCTTATAAATAAGTGACAA
195 ATCTCACATTGACTAGAGAACATTCTCATATCTCACATTGACCTTATAAATAAGTGACAA
*
49564989 TTTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACATTAACTAGGGAAAACTCTCATA
1 -TTCTTCACTATTTTCATTAAAAAA-TTAATTTTAATCCCACATTAACTAGAGAAAACTCTCATA
* *
49565054 GCTCTCTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCTATATTAGTTAGAGAACTCTCT
64 GCTCACTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCTA-ATTAGTTAGAGAACACTCT
* * * * * * * *
49565119 CATGCTCATACTTACACTGTAAATAGGTGTCAATTTCTT-CCTTTTTTTATTAAAAAGATAATTT
128 CATGCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTT
49565183 TAA
193 TAA
49565186 ATTTAAATAA
Statistics
Matches: 399, Mismatches: 37, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
245 4 0.01
246 60 0.15
247 12 0.03
248 16 0.04
249 6 0.02
250 19 0.05
251 1 0.00
252 108 0.27
254 1 0.00
255 15 0.04
256 28 0.07
257 129 0.32
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (254 bp):
TTCTTCACTATTTTCATTAAAAAATTAATTTTAATCCCACATTAACTAGAGAAAACTCTCATAGC
TCACTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCTAATTAGTTAGAGAACACTCTCAT
GCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTTTAA
TCTCACATTGACTAGAGAACATTCTCATATCTCACATTGACCTTATAAATAAGTGACAA
Found at i:49565010 original size:94 final size:94
Alignment explanation
Indices: 49564803--49565057 Score: 329
Period size: 93 Copynumber: 2.7 Consensus size: 94
49564793 CATAGCTCAC
* **
49564803 TTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCCACATTGGTTAGAGAACAATCTCAT-GC
1 TTCTTCACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTGACTAGAGAACAATCTCATAGC
*
49564867 TCACACTTACACTATAAATAAGTGTCAAT
66 TCACACTTACACTATAAATAAGTGACAAT
* * * * *
49564896 TTCTTAACTATTTTCATTAAAAAGTTCATTTTAATCTCACATTGACTAGAGAACATTCTCATATC
1 TTCTTCACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTGACTAGAGAACAATCTCATAGC
*
49564961 TCATA-TTGAC-CTTATAAATAAGTGACAAT
66 TCACACTT-ACAC-TATAAATAAGTGACAAT
* * *
49564990 TTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACATTAACTAGGGAA-AACTCTCATA
1 TTCTTCACTATTTTCATT-AAAAAGTTAATTTTAATCCCACATTGACTAGAGAACAA-TCTCATA
49565054 GCTC
64 GCTC
49565058 TCTTCTTCAC
Statistics
Matches: 139, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
93 58 0.42
94 41 0.29
95 40 0.29
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.38
Consensus pattern (94 bp):
TTCTTCACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTGACTAGAGAACAATCTCATAGC
TCACACTTACACTATAAATAAGTGACAAT
Found at i:49565300 original size:67 final size:65
Alignment explanation
Indices: 49565206--49565329 Score: 187
Period size: 67 Copynumber: 1.9 Consensus size: 65
49565196 ATATTAGTAT
* *
49565206 ATGCACTTAAATTGTAGTGTGTATAAATATTATATATATAAATATGTGAATTAATTAAATCTTTA
1 ATGCACTTAAATTATAGTATGTATAAATATTATATATA-AAATA--TGAATTAATTAAATCTTTA
49565271 TAC
63 TAC
*
49565274 ATGCAC-TAAATTATAGTATGTGTAAATATTATATATAAAATATGAATTAATTAAAT
1 ATGCACTTAAATTATAGTATGTATAAATATTATATATAAAATATGAATTAATTAAAT
49565330 ATATTTTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
64 14 0.26
66 5 0.09
67 28 0.53
68 6 0.11
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (65 bp):
ATGCACTTAAATTATAGTATGTATAAATATTATATATAAAATATGAATTAATTAAATCTTTATAC
Found at i:49565618 original size:19 final size:20
Alignment explanation
Indices: 49565596--49565635 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
49565586 GTTTTTATAA
49565596 TAAAAT-TATCATTTATTTT
1 TAAAATGTATCATTTATTTT
**
49565615 TAAAATGTATTTTTTATTTT
1 TAAAATGTATCATTTATTTT
49565635 T
1 T
49565636 TTTATTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TAAAATGTATCATTTATTTT
Found at i:49565922 original size:10 final size:11
Alignment explanation
Indices: 49565900--49565928 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
49565890 TTGGTCTCTC
49565900 TCTTTTTTCTT
1 TCTTTTTTCTT
49565911 TCTTTTTT-TT
1 TCTTTTTTCTT
49565921 TCTTTTTT
1 TCTTTTTT
49565929 GCAAATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:49566335 original size:31 final size:29
Alignment explanation
Indices: 49566272--49566335 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
49566262 GACAAAGTTA
*
49566272 AATAGTTGAATGACCATAAAAAATATATT
1 AATAGTTGAATGACCAAAAAAAATATATT
*
49566301 AATAGTT-AGATGACCAAAAAAGAAATTTATT
1 AATAGTTGA-ATGACC-AAAAA-AAATATATT
49566332 AATA
1 AATA
49566336 ATTAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 13 0.43
30 4 0.13
31 12 0.40
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.30
Consensus pattern (29 bp):
AATAGTTGAATGACCAAAAAAAATATATT
Found at i:49579104 original size:15 final size:15
Alignment explanation
Indices: 49579060--49579105 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
49579050 TTTTCTGGGC
49579060 AACCAAA-CAACCCA
1 AACCAAACCAACCCA
*
49579074 ATCC-AACCGAACCCA
1 AACCAAACC-AACCCA
*
49579089 AACCAAACCAAACCA
1 AACCAAACCAACCCA
49579104 AA
1 AA
49579106 ATTCCCAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 2 0.08
14 4 0.15
15 16 0.62
16 4 0.15
ACGTcount: A:0.54, C:0.41, G:0.02, T:0.02
Consensus pattern (15 bp):
AACCAAACCAACCCA
Found at i:49579417 original size:18 final size:20
Alignment explanation
Indices: 49579377--49579419 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
49579367 CTTTTATGTT
**
49579377 AAAAATATATAATTTTAGTA
1 AAAAATATATAATTTTAAAA
49579397 AAAAAT-TA-AATTTTAAAA
1 AAAAATATATAATTTTAAAA
49579415 AAAAA
1 AAAAA
49579420 GGGATTGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 2 0.10
20 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAATATATAATTTTAAAA
Found at i:49579738 original size:6 final size:7
Alignment explanation
Indices: 49579711--49579737 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
49579701 GTAAATTTAA
49579711 ATTTTTT
1 ATTTTTT
49579718 ATTTTTT
1 ATTTTTT
49579725 ATTTTTT
1 ATTTTTT
49579732 ATTTTT
1 ATTTTT
49579738 AAGAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:49579773 original size:21 final size:22
Alignment explanation
Indices: 49579734--49579774 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
49579724 TATTTTTTAT
*
49579734 TTTTAAGAATTTAATTTTAAAA
1 TTTTAAGAATTTAAGTTTAAAA
*
49579756 TTTTAA-AATTTAGGTTTAA
1 TTTTAAGAATTTAAGTTTAA
49579775 TGGTTAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTTAAGAATTTAAGTTTAAAA
Found at i:49582018 original size:16 final size:16
Alignment explanation
Indices: 49581997--49582041 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
49581987 GTTTGGTTCA
49581997 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
49582013 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
49582029 TTGTAATGGAATA
1 CTGTAATGGAATA
49582042 ATGATGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:49582049 original size:16 final size:16
Alignment explanation
Indices: 49581998--49582051 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
49581988 TTTGGTTCAC
*
49581998 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGA
* *
49582014 TGTAATTGAATAGAGT
1 TGTAATGGAATAGAGA
49582030 TGTAATGGAATA-ATGA
1 TGTAATGGAATAGA-GA
49582046 TGTAAT
1 TGTAAT
49582052 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGA
Found at i:49598991 original size:16 final size:17
Alignment explanation
Indices: 49598955--49598991 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
49598945 AATTTTATTT
*
49598955 TAATAGTAAGTTTTAAA
1 TAATAATAAGTTTTAAA
49598972 -AATAATAA-TTTTAAA
1 TAATAATAAGTTTTAAA
49598987 TAATA
1 TAATA
49598992 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAATAATAAGTTTTAAA
Found at i:49599041 original size:15 final size:15
Alignment explanation
Indices: 49599023--49599079 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
49599013 TATCAATATT
49599023 AATATTTTAATAATA
1 AATATTTTAATAATA
*
49599038 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
49599057 AATATATTAATAATA
1 AATATTTTAATAATA
*
49599072 AATGTTTT
1 AATATTTT
49599080 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:49602487 original size:5 final size:5
Alignment explanation
Indices: 49602477--49602503 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
49602467 AAGCATGAAG
49602477 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
49602504 ATCTTTTTTA
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:49602510 original size:15 final size:15
Alignment explanation
Indices: 49602477--49602510 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
49602467 AAGCATGAAG
*
49602477 TTTTATTTTATTTTA
1 TTTTATTTTATTATA
*
49602492 TTTTATTTTATTATC
1 TTTTATTTTATTATA
49602507 TTTT
1 TTTT
49602511 TTACAGGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTTATTATA
Found at i:49608110 original size:25 final size:25
Alignment explanation
Indices: 49608082--49608162 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
49608072 ATATAAAAAC
49608082 TTGAACAATGACATGGAAAACTCAA
1 TTGAACAATGACATGGAAAACTCAA
** * *
49608107 TTGAA-AGATTGA-ATATATATA-TAAA
1 TTGAACA-A-TGACATGGA-AAACTCAA
49608132 CTTGAACAATGACATGGAAAACTCAA
1 -TTGAACAATGACATGGAAAACTCAA
49608158 TTGAA
1 TTGAA
49608163 AGATTGAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 1 0.02
25 22 0.54
26 17 0.41
27 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (25 bp):
TTGAACAATGACATGGAAAACTCAA
Found at i:49608133 original size:51 final size:51
Alignment explanation
Indices: 49608068--49608171 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
49608058 ATATATACAT
49608068 ATATATATAAAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
1 ATATATATAAAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
*
49608119 ATATATATATAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
1 ATATATATAAAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
49608170 AT
1 AT
49608172 TCTGAAAAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (51 bp):
ATATATATAAAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
Found at i:49619108 original size:31 final size:31
Alignment explanation
Indices: 49619070--49619128 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
49619060 AGGAGGAAAA
49619070 AAGAGAGAAATAGTCTTAAAGTCAAAAAGTC
1 AAGAGAGAAATAGTCTTAAAGTCAAAAAGTC
*
49619101 AAGAGAGAAATAGTCTTAAAGTGAAAAA
1 AAGAGAGAAATAGTCTTAAAGTCAAAAA
49619129 CTTATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (31 bp):
AAGAGAGAAATAGTCTTAAAGTCAAAAAGTC
Found at i:49622978 original size:22 final size:22
Alignment explanation
Indices: 49622922--49622985 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
49622912 GGGCCGAAAT
49622922 TTAATTATAATTTTATCATATA
1 TTAATTATAATTTTATCATATA
* * *
49622944 TCAAAATATAATTTTAT-ATGTA
1 T-TAATTATAATTTTATCATATA
*
49622966 TTAATTTATAATTTCATCAT
1 TTAA-TTATAATTTTATCAT
49622986 TTTTTAAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.06
22 16 0.48
23 15 0.45
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAATTATAATTTTATCATATA
Found at i:49624310 original size:41 final size:41
Alignment explanation
Indices: 49624248--49624422 Score: 287
Period size: 41 Copynumber: 4.3 Consensus size: 41
49624238 AATTTAACAT
* **
49624248 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAATCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
49624289 ATTCATATCACCGGCATTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
49624330 ATTCAGATCACCGGCACTTAGCCTGCGAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
49624371 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
49624412 ATTCAGATCAC
1 ATTCAGATCAC
49624423 AAATTTTAAT
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:49626401 original size:23 final size:23
Alignment explanation
Indices: 49626375--49626473 Score: 155
Period size: 23 Copynumber: 4.3 Consensus size: 23
49626365 ATAAGTGCAA
49626375 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
49626398 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
49626421 CACT-ATTATGTAGCCGAAGCTAC
1 CACTGA-TATGTAGCCGAAGCTAC
* *
49626444 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
49626467 CACTGAT
1 CACTGAT
49626474 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
22 1 0.01
23 67 0.97
24 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:49626448 original size:46 final size:46
Alignment explanation
Indices: 49626381--49626470 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
49626371 GCAACACTGA
*
49626381 TATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTAT
1 TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTAT
49626427 TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACT
1 TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACT
49626471 GATCAATAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (46 bp):
TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTAT
Done.