Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 16 of 66
Found at i:5574795 original size:29 final size:29
Alignment explanation
Indices: 5574749--5574817 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
5574739 AATGTTATTT
* * * *
5574749 AGAGGTTATACTTCATCCTTGA-AAAGGCC
1 AGAGGTTATGCCTCATCC-TCATAAAGGCA
*
5574778 AGAGGTTATGCCTGATCCTCATAAAGGCA
1 AGAGGTTATGCCTCATCCTCATAAAGGCA
5574807 AGAGGTTATGC
1 AGAGGTTATGC
5574818 TTGCTCTCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 2 0.06
29 32 0.94
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (29 bp):
AGAGGTTATGCCTCATCCTCATAAAGGCA
Found at i:5577405 original size:39 final size:40
Alignment explanation
Indices: 5577351--5577443 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 40
5577341 TTTCGCTGAA
* * *
5577351 TCTCGCTGTAGCGAAATTTCTACCTAG-AAACAGAATGTT
1 TCTCGCTGCAGCGAAATTTCAACCTAGAAAACAGAAAGTT
5577390 TCTCGCTGCAGCGAAATTTCAACCTAGAAAACAGAAAGTT
1 TCTCGCTGCAGCGAAATTTCAACCTAGAAAACAGAAAGTT
* *
5577430 TCTTGCTACAGCGA
1 TCTCGCTGCAGCGA
5577444 GAATGCATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 25 0.52
40 23 0.48
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (40 bp):
TCTCGCTGCAGCGAAATTTCAACCTAGAAAACAGAAAGTT
Found at i:5577733 original size:2 final size:2
Alignment explanation
Indices: 5577728--5577754 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5577718 ACACATATTT
5577728 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
5577755 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5579872 original size:19 final size:19
Alignment explanation
Indices: 5579845--5579887 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5579835 AAACCGGGAA
*
5579845 CAAAATCTAGGATGAAATT
1 CAAAATCTAAGATGAAATT
*
5579864 CAAATTCTAAGATGAAATT
1 CAAAATCTAAGATGAAATT
*
5579883 TAAAA
1 CAAAA
5579888 GAAAAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (19 bp):
CAAAATCTAAGATGAAATT
Found at i:5580969 original size:28 final size:29
Alignment explanation
Indices: 5580928--5580987 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
5580918 GTCTATGGGC
*
5580928 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
5580956 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
5580986 AA
1 AA
5580988 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:5583559 original size:22 final size:22
Alignment explanation
Indices: 5583531--5583574 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5583521 TTCTATTGGT
5583531 ATAAGAGCTTTTGGTTTTAAAG
1 ATAAGAGCTTTTGGTTTTAAAG
*
5583553 ATAAGAGTTTTTGGTTTTAAAG
1 ATAAGAGCTTTTGGTTTTAAAG
5583575 TGGTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (22 bp):
ATAAGAGCTTTTGGTTTTAAAG
Found at i:5589148 original size:28 final size:29
Alignment explanation
Indices: 5589107--5589166 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
5589097 GTCTATGGGC
*
5589107 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
5589135 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
5589165 AA
1 AA
5589167 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:5592772 original size:48 final size:48
Alignment explanation
Indices: 5592647--5592769 Score: 142
Period size: 49 Copynumber: 2.5 Consensus size: 48
5592637 AATTTTTAGA
* *
5592647 AATTTTTA-TTATATATACTTATATTTTAATGGCCCCTTCAAAATTTATGG
1 AATTTTTATTTAT-TATA--TATTTTTTAATGGCCCCTCCAAAATTTATGG
* *
5592697 AATTTTTGTTTATTATATATTTTTTAATGGTCCTCTCCAAAATTTATGG
1 AATTTTTATTTATTATATATTTTTTAATGG-CCCCTCCAAAATTTATGG
*
5592746 AGTTATTTATTTATTATAT-TTTTT
1 AATT-TTTATTTATTATATATTTTT
5592770 AATAACTTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
48 12 0.19
49 24 0.38
50 24 0.38
51 4 0.06
ACGTcount: A:0.28, C:0.09, G:0.08, T:0.54
Consensus pattern (48 bp):
AATTTTTATTTATTATATATTTTTTAATGGCCCCTCCAAAATTTATGG
Found at i:5593105 original size:17 final size:16
Alignment explanation
Indices: 5593085--5593117 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5593075 TCTTTTTTTT
5593085 CTATTTATATTATTTAA
1 CTATTTATA-TATTTAA
5593102 CTATTTATATATTTAA
1 CTATTTATATATTTAA
5593118 TCATTGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
CTATTTATATATTTAA
Found at i:5594769 original size:2 final size:2
Alignment explanation
Indices: 5594762--5594793 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5594752 GAGAAATAAA
5594762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5594794 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5595401 original size:5 final size:5
Alignment explanation
Indices: 5595378--5595418 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
5595368 AGGAAGAAGG
*
5595378 AAGAGA AAG-A AAG-A AAGAA AAGAA AAGAA AGGAA AAGAA AA
1 AAGA-A AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA
5595419 TAACAAGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
4 8 0.25
5 21 0.66
6 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:5595529 original size:26 final size:25
Alignment explanation
Indices: 5595455--5595525 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
5595445 CAAGCAAGAA
*
5595455 AAAAATTGGACATAGTCCAATAAAG
1 AAAAATTGGACATGGTCCAATAAAG
*
5595480 AAAAATTAGACATGGTCCAATAAAGG
1 AAAAATTGGACATGGTCCAATAAA-G
*
5595506 AAAAA-TGGATATGGTCCAAT
1 AAAAATTGGACATGGTCCAAT
5595526 TAAAAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 35 0.85
26 6 0.15
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.21
Consensus pattern (25 bp):
AAAAATTGGACATGGTCCAATAAAG
Found at i:5595536 original size:25 final size:24
Alignment explanation
Indices: 5595455--5595538 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 24
5595445 CAAGCAAGAA
* *
5595455 AAAAATTGGACATAGTCCAATAAAG
1 AAAAA-TGGATATGGTCCAATAAAG
* *
5595480 AAAAATTAGACATGGTCCAATAAAGG
1 AAAAA-TGGATATGGTCCAATAAA-G
5595506 AAAAATGGATATGGTCCAATTAAA-
1 AAAAATGGATATGGTCCAA-TAAAG
5595530 AAGAAATGG
1 AA-AAATGG
5595539 GAGAAGTCCA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.04
25 40 0.77
26 10 0.19
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.20
Consensus pattern (24 bp):
AAAAATGGATATGGTCCAATAAAG
Found at i:5597566 original size:11 final size:11
Alignment explanation
Indices: 5597550--5597590 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5597540 AGAACTTTTG
5597550 GGTTTAAAGTT
1 GGTTTAAAGTT
*
5597561 GGTTTAAAATT
1 GGTTTAAAGTT
*
5597572 GTTTTAAAGTT
1 GGTTTAAAGTT
*
5597583 GTTTTAAA
1 GGTTTAAA
5597591 ATTTACAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.49
Consensus pattern (11 bp):
GGTTTAAAGTT
Found at i:5597577 original size:22 final size:22
Alignment explanation
Indices: 5597552--5597593 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5597542 AACTTTTGGG
5597552 TTTAAAGTTGGTTTAAAATTGT
1 TTTAAAGTTGGTTTAAAATTGT
*
5597574 TTTAAAGTTGTTTTAAAATT
1 TTTAAAGTTGGTTTAAAATT
5597594 TACAGTGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TTTAAAGTTGGTTTAAAATTGT
Found at i:5597630 original size:5 final size:5
Alignment explanation
Indices: 5597620--5597659 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
5597610 CCCCAAGTCC
* * *
5597620 AGTTA AGTTA AGATA AGTTA AATTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
5597660 GGTTGAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (5 bp):
AGTTA
Found at i:5602074 original size:34 final size:34
Alignment explanation
Indices: 5602021--5602103 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
5602011 CCATTTAAGG
* *
5602021 GCTGATTTTTGAGGCTGGAAAGAGCTATTTTTCT
1 GCTGATTTTGGAGGCTGGAAAGAGCCATTTTTCT
* * *
5602055 GCTGGTTTTGGAGGTTGGAAAGTGCCATTTTTCT
1 GCTGATTTTGGAGGCTGGAAAGAGCCATTTTTCT
5602089 GCTGATTTTGGAGGC
1 GCTGATTTTGGAGGC
5602104 CAAAAAGTGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.17, C:0.12, G:0.31, T:0.40
Consensus pattern (34 bp):
GCTGATTTTGGAGGCTGGAAAGAGCCATTTTTCT
Found at i:5602111 original size:34 final size:34
Alignment explanation
Indices: 5602047--5602113 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
5602037 GGAAAGAGCT
* ****
5602047 ATTTTTCTGCTGGTTTTGGAGGTTGGAAAGTGCC
1 ATTTTTCTGCTGATTTTGGAGGCCAAAAAGTGCC
5602081 ATTTTTCTGCTGATTTTGGAGGCCAAAAAGTGC
1 ATTTTTCTGCTGATTTTGGAGGCCAAAAAGTGC
5602114 AGAATTTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.39
Consensus pattern (34 bp):
ATTTTTCTGCTGATTTTGGAGGCCAAAAAGTGCC
Found at i:5602454 original size:17 final size:19
Alignment explanation
Indices: 5602432--5602466 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5602422 AAAGGAAGAG
5602432 AAAGAAA-G-AAAGAAAAA
1 AAAGAAAGGAAAAGAAAAA
5602449 AAAGAAAGGAAAAGAAAA
1 AAAGAAAGGAAAAGAAAA
5602467 TAACAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAGAAAGGAAAAGAAAAA
Found at i:5602539 original size:25 final size:24
Alignment explanation
Indices: 5602501--5602582 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 24
5602491 AACAAGCAAG
5602501 AAAAAAATTGGACATGGTCCAATA
1 AAAAAAATTGGACATGGTCCAATA
*
5602525 AAGAAAAATTAGACATGGTCCAATA
1 AA-AAAAATTGGACATGGTCCAATA
*
5602550 AAAAAAA-TGGATATGGTCCAATTA
1 AAAAAAATTGGACATGGTCCAA-TA
5602574 AAAAGAAAT
1 AAAA-AAAT
5602583 GGGAGAAGTC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
23 12 0.24
24 13 0.25
25 26 0.51
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.21
Consensus pattern (24 bp):
AAAAAAATTGGACATGGTCCAATA
Found at i:5605296 original size:20 final size:20
Alignment explanation
Indices: 5605271--5605316 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
5605261 TTTTGACCCC
5605271 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
5605291 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
5605311 ATTTGA
1 ATTTGA
5605317 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:5605392 original size:28 final size:27
Alignment explanation
Indices: 5605361--5605413 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
5605351 TTTGGAGTAT
*
5605361 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
5605389 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
5605414 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:5605419 original size:28 final size:28
Alignment explanation
Indices: 5605361--5605419 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5605351 TTTGGAGTAT
* *
5605361 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
5605389 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
5605417 AGG
1 AGG
5605420 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:5612374 original size:20 final size:20
Alignment explanation
Indices: 5612357--5612394 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5612347 CCTCAAATCT
5612357 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
5612377 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
5612395 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:5626513 original size:16 final size:15
Alignment explanation
Indices: 5626474--5626518 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
5626464 ATATAAAATT
5626474 AAAATAACTTAATAAA
1 AAAATAAC-TAATAAA
*
5626490 AATA-AACTAATCAAA
1 AAAATAACTAAT-AAA
5626505 AAAATAACTAATAA
1 AAAATAACTAATAA
5626519 GCCTAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 4 0.16
15 11 0.44
16 10 0.40
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATAACTAATAAA
Found at i:5630930 original size:14 final size:14
Alignment explanation
Indices: 5630891--5630923 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
5630881 ATTTATTTAA
5630891 AGTATATATACTAAT
1 AGTATATATA-TAAT
5630906 AGTATATATATAAT
1 AGTATATATATAAT
5630920 AGTA
1 AGTA
5630924 ATTATATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (14 bp):
AGTATATATATAAT
Found at i:5633505 original size:2 final size:2
Alignment explanation
Indices: 5633498--5633548 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5633488 NNNNNNNNNN
5633498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5633540 AT AT AT AT A
1 AT AT AT AT A
5633549 CTATGTCATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5633701 original size:54 final size:54
Alignment explanation
Indices: 5633643--5633754 Score: 190
Period size: 54 Copynumber: 2.1 Consensus size: 54
5633633 GATGGAGATG
5633643 GATGGGATGTCCGGCTATGTGCACGACT-TGGTGGGATGCACATGAGATGGGTGA
1 GATGGGATGTCCGGCTATGTGCACGA-TGTGGTGGGATGCACATGAGATGGGTGA
* *
5633697 GATGGGATGTCCGGCTATGTGCATGATGTGGTGGGATGCACATGAGCTGGGTGA
1 GATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGATGGGTGA
5633751 GATG
1 GATG
5633755 CAGATAATGA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
53 1 0.02
54 54 0.98
ACGTcount: A:0.20, C:0.13, G:0.42, T:0.25
Consensus pattern (54 bp):
GATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGATGGGTGA
Found at i:5635556 original size:22 final size:22
Alignment explanation
Indices: 5635511--5635556 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
5635501 GGGCATTTTG
*
5635511 TCTTCTAAGTATCAATACTTAT
1 TCTTCTAAGTATCAATACTCAT
5635533 TCTTC-AAGTATCAATACGTCAT
1 TCTTCTAAGTATCAATAC-TCAT
5635555 TC
1 TC
5635557 ATAAAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (22 bp):
TCTTCTAAGTATCAATACTCAT
Found at i:5636638 original size:28 final size:28
Alignment explanation
Indices: 5636599--5636725 Score: 109
Period size: 30 Copynumber: 4.4 Consensus size: 28
5636589 CTCACACTGT
5636599 CTTTTCAAGGATCAAGCATAACCTTAGC
1 CTTTTCAAGGATCAAGCATAACCTTAGC
* * *
5636627 TTTTTCAAGGATCAAGCAAAAGCTCTTTGC
1 CTTTTCAAGGATCAAGCATAA-C-CTTAGC
5636657 CTTTTCAAGGATC-AGACATAACCTTTTTA-C
1 CTTTTCAAGGATCAAG-CATAACC---TTAGC
* * *
5636687 CTTTTCAAAGATC-AGACATAA-ATTGGC
1 CTTTTCAAGGATCAAG-CATAACCTTAGC
5636714 CTTTTCAAGGAT
1 CTTTTCAAGGAT
5636726 TAGACAAAAC
Statistics
Matches: 82, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
26 2 0.02
27 12 0.15
28 20 0.24
29 4 0.05
30 42 0.51
31 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (28 bp):
CTTTTCAAGGATCAAGCATAACCTTAGC
Found at i:5636664 original size:30 final size:28
Alignment explanation
Indices: 5636599--5636670 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
5636589 CTCACACTGT
*
5636599 CTTTTCAAGGATCAAGCATAACCTTAGC
1 CTTTTCAAGGATCAAGCAAAACCTTAGC
* *
5636627 TTTTTCAAGGATCAAGCAAAAGCTCTTTGC
1 CTTTTCAAGGATCAAGCAAAA-C-CTTAGC
5636657 CTTTTCAAGGATCA
1 CTTTTCAAGGATCA
5636671 GACATAACCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 19 0.50
29 1 0.03
30 18 0.47
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (28 bp):
CTTTTCAAGGATCAAGCAAAACCTTAGC
Found at i:5637534 original size:21 final size:21
Alignment explanation
Indices: 5637500--5637539 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5637490 CTTCATGTTG
5637500 ATTCATTCTCCAAGGTTTTCTT
1 ATTCATTCTCCAA-GTTTTCTT
*
5637522 ATTC-TTCTTCAAGTTTTC
1 ATTCATTCTCCAAGTTTTC
5637540 AAATTTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.17, C:0.23, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTCATTCTCCAAGTTTTCTT
Found at i:5637795 original size:20 final size:20
Alignment explanation
Indices: 5637770--5637808 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5637760 CATAAAAAGC
5637770 ATTCAAGGATCACTTAAACT
1 ATTCAAGGATCACTTAAACT
*
5637790 ATTCAAGGATTACTTAAAC
1 ATTCAAGGATCACTTAAAC
5637809 AAGAATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTCAAGGATCACTTAAACT
Found at i:5639231 original size:38 final size:40
Alignment explanation
Indices: 5639145--5639247 Score: 142
Period size: 38 Copynumber: 2.6 Consensus size: 40
5639135 ACCCGGCTCA
*
5639145 TGTACATCCCCCCACATCGTGCAC-ATAGCTGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACAATAGATGG-ACCATCG
*
5639185 TGTGCATCCCCCCACATCGTGCACAATCA-AT-G-CCATCG
1 TGTACATCCCCCCACATCGTGCACAAT-AGATGGACCATCG
5639223 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
5639248 CGGGCACTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
38 30 0.52
40 24 0.41
41 3 0.05
42 1 0.02
ACGTcount: A:0.23, C:0.41, G:0.16, T:0.20
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACAATAGATGGACCATCG
Found at i:5644145 original size:43 final size:43
Alignment explanation
Indices: 5644077--5644169 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 43
5644067 TTGTGTGATA
*
5644077 ATGATGACCCAGCTATCTACGGTGTGGGAATGCACATGAGCTG
1 ATGATGACCCAGCTATCTACAGTGTGGGAATGCACATGAGCTG
* * * *
5644120 ATGATGACCTAGCTATGTGCAGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATCTACAGTGTGGGAATGCACATGAGCTG
5644163 ATGATGA
1 ATGATGA
5644170 TGATATTGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (43 bp):
ATGATGACCCAGCTATCTACAGTGTGGGAATGCACATGAGCTG
Found at i:5644188 original size:43 final size:44
Alignment explanation
Indices: 5644097--5644186 Score: 109
Period size: 43 Copynumber: 2.1 Consensus size: 44
5644087 AGCTATCTAC
* *
5644097 GGTGTGGGAATGCACATGAGCTGATGATGACCTAGCTATGTGCA-
1 GGTGTGGGAGTGCACATGAGCTGATGATGA-CTAGATATGTGCAT
5644141 -GTGTGGGAGTGCACATGAGCTGATGATGA-T-GATAT-TGCAT
1 GGTGTGGGAGTGCACATGAGCTGATGATGACTAGATATGTGCAT
*
5644181 TGTGTG
1 GGTGTG
5644187 TGTAGGGAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 4 0.10
40 4 0.10
41 6 0.14
43 28 0.67
ACGTcount: A:0.23, C:0.12, G:0.36, T:0.29
Consensus pattern (44 bp):
GGTGTGGGAGTGCACATGAGCTGATGATGACTAGATATGTGCAT
Found at i:5645927 original size:36 final size:34
Alignment explanation
Indices: 5645887--5645956 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
5645877 TATGCTTTAC
* *
5645887 ACATTACCTTTTCAAGTGGATCAAGCATAACCTCAG
1 ACATTACATTTTCAA--GGATCAAACATAACCTCAG
* *
5645923 ACATTGCATTTTTAAGGATCAAACATAACCTCAG
1 ACATTACATTTTCAAGGATCAAACATAACCTCAG
5645957 CCTTTTCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 18 0.60
36 12 0.40
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.29
Consensus pattern (34 bp):
ACATTACATTTTCAAGGATCAAACATAACCTCAG
Found at i:5653547 original size:80 final size:80
Alignment explanation
Indices: 5653403--5653550 Score: 201
Period size: 80 Copynumber: 1.9 Consensus size: 80
5653393 GATTCTAACT
* * *
5653403 TGTATGCCATGAGATATATGTGCTAAGCATATCATGTACATTATGGGCTAAGCATGTAAGTGATT
1 TGTATGCCATGAGATATATGTGCTAAGCATATCATATACACTATGGGCTAAGCATATAAGTGATT
5653468 TATAAGGTTATGAAA
66 TATAAGGTTATGAAA
* * * *
5653483 TGTATGCCATGAGATTTATGTGTTAAG-ATAGTCATATACACTATGGGTTAAGTATAATAA-TGA
1 TGTATGCCATGAGATATATGTGCTAAGCATA-TCATATACACTATGGGCTAAGCAT-ATAAGTGA
5653546 TTTAT
64 TTTAT
5653551 GGAAATGTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
79 3 0.05
80 53 0.90
81 3 0.05
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (80 bp):
TGTATGCCATGAGATATATGTGCTAAGCATATCATATACACTATGGGCTAAGCATATAAGTGATT
TATAAGGTTATGAAA
Found at i:5661497 original size:21 final size:21
Alignment explanation
Indices: 5661451--5661497 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
5661441 GTTTTTGGGT
* *
5661451 TTCAAGTATCAATATCTGTTC
1 TTCAAGCATCAATATCTGATC
*
5661472 ATCAAGCATCAATA-CTTGATC
1 TTCAAGCATCAATATC-TGATC
5661493 TTCAA
1 TTCAA
5661498 AATTCTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (21 bp):
TTCAAGCATCAATATCTGATC
Found at i:5672226 original size:2 final size:2
Alignment explanation
Indices: 5672219--5672246 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5672209 CATGAATTTC
5672219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5672247 TAACAAGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5677592 original size:22 final size:21
Alignment explanation
Indices: 5677550--5677592 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5677540 TTAGAATTAT
*
5677550 GGAAAAAAACTTCCAATGAAA
1 GGAAAAAAACTTCAAATGAAA
5677571 GGAAAAAAA-TTACAAATAGAAA
1 GGAAAAAAACTT-CAAAT-GAAA
5677593 TCAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 13 0.68
22 4 0.21
ACGTcount: A:0.63, C:0.09, G:0.14, T:0.14
Consensus pattern (21 bp):
GGAAAAAAACTTCAAATGAAA
Found at i:5680557 original size:37 final size:37
Alignment explanation
Indices: 5680510--5680591 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
5680500 AATGCAATAT
* * * *
5680510 CATCTTCATGTGTGCACTCCCTACTCGCGCATTTCAA
1 CATCATCATGTGTGCACCCCCTACTCGCACAGTTCAA
5680547 CATCATCATGTGTGCACCCCCTACTCGCACAGTTCAA
1 CATCATCATGTGTGCACCCCCTACTCGCACAGTTCAA
*
5680584 TATCATCA
1 CATCATCA
5680592 CACAACATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.23, C:0.35, G:0.12, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACCCCCTACTCGCACAGTTCAA
Found at i:5689888 original size:3 final size:3
Alignment explanation
Indices: 5689867--5689905 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
5689857 CTTTCTTTGA
*
5689867 CTT CTCT CTT GTT -TT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
5689906 TCAACTCCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:5694144 original size:42 final size:42
Alignment explanation
Indices: 5694085--5694226 Score: 221
Period size: 42 Copynumber: 3.4 Consensus size: 42
5694075 TGTTGATTTG
*
5694085 GACCCTGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
5694127 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCATTACT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
** *
5694169 GACCAAGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
*
5694211 GACCCGGCTATATGCG
1 GACCCGGCTATGTGCG
5694227 CATAAGCCGT
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.22
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Found at i:5694280 original size:26 final size:26
Alignment explanation
Indices: 5694246--5694307 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
5694236 TTGCATATGA
*
5694246 GATGTTGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGGTGTGCAT
5694272 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGGTGTGCAT
*
5694298 GTTGATGATG
1 GATGATGATG
5694308 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.34
Consensus pattern (26 bp):
GATGATGATGATGGGATGGTGTGCAT
Found at i:5699223 original size:21 final size:21
Alignment explanation
Indices: 5699181--5699230 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5699171 ATACGGAAAG
*
5699181 ATTTTGAAAACACGATACATTT
1 ATTTT-AAAACACAATACATTT
5699203 ATTTTAAAA-ACAATACAATTT
1 ATTTTAAAACACAATAC-ATTT
*
5699224 AGTTTAA
1 ATTTTAA
5699231 TTTCTTGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 14 0.56
22 5 0.20
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (21 bp):
ATTTTAAAACACAATACATTT
Found at i:5699517 original size:35 final size:35
Alignment explanation
Indices: 5699478--5699568 Score: 116
Period size: 34 Copynumber: 2.6 Consensus size: 35
5699468 CTTACTCAGC
5699478 TCATGTGCACTCCTTACACGTACA-A-GGCAATATCA
1 TCATGTGCACTCCTTACAC--ACATATGGCAATATCA
* **
5699513 TCATGTGCA-TCCCTACACACATATTTCAATATCA
1 TCATGTGCACTCCTTACACACATATGGCAATATCA
5699547 TCATGTGCACTCCTTACACACA
1 TCATGTGCACTCCTTACACACA
5699569 CATTTCAACA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 3 0.06
33 1 0.02
34 25 0.51
35 20 0.41
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (35 bp):
TCATGTGCACTCCTTACACACATATGGCAATATCA
Found at i:5699574 original size:35 final size:35
Alignment explanation
Indices: 5699478--5699584 Score: 135
Period size: 35 Copynumber: 3.1 Consensus size: 35
5699468 CTTACTCAGC
** ***
5699478 TCATGTGCACTCCTTACACGTACAAGGCAATATCA
1 TCATGTGCACTCCTTACACACACATTTCAATATCA
* *
5699513 TCATGTGCA-TCCCTACACACATATTTCAATATCA
1 TCATGTGCACTCCTTACACACACATTTCAATATCA
*
5699547 TCATGTGCACTCCTTACACACACATTTCAACATCA
1 TCATGTGCACTCCTTACACACACATTTCAATATCA
5699582 TCA
1 TCA
5699585 CACGCACTCT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
34 27 0.44
35 34 0.56
ACGTcount: A:0.32, C:0.31, G:0.08, T:0.29
Consensus pattern (35 bp):
TCATGTGCACTCCTTACACACACATTTCAATATCA
Found at i:5699592 original size:35 final size:35
Alignment explanation
Indices: 5699526--5699593 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
5699516 TGTGCATCCC
* * ***
5699526 TACACACATATTTCAATATCATCATGTGCACTCCT
1 TACACACACATTTCAACATCATCACACGCACTCCT
5699561 TACACACACATTTCAACATCATCACACGCACTC
1 TACACACACATTTCAACATCATCACACGCACTC
5699594 TCGCCCACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (35 bp):
TACACACACATTTCAACATCATCACACGCACTCCT
Found at i:5707542 original size:42 final size:42
Alignment explanation
Indices: 5707127--5707538 Score: 619
Period size: 42 Copynumber: 9.8 Consensus size: 42
5707117 GTTGATTTGA
*
5707127 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGTTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
*
5707169 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTCCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
*
5707211 ACCCGGCTATGTGC-AGTAGAAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* ** *
5707252 ACCCGACTATGTGCGAGTAGGAGTGCACATAAGATGTAGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
5707294 ACCCGGCTATGTGCGAGTAAGAGTGCACGTAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
5707336 ACCCGGCTATGTGCGAGTCGGAGTGCACATAAGTCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
**
5707378 ACTTGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
5707420 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* * * * *
5707462 ACCTGGCTATGTGTGAGTAGGAGTGCACATAAGTCATTGCTA
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* * * *
5707504 ACCCGACTATGTGTGAGTGGGAGTACACATAAGCC
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCC
5707539 ATTGTTGCCT
Statistics
Matches: 334, Mismatches: 35, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 38 0.11
42 296 0.89
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
Found at i:5707813 original size:26 final size:26
Alignment explanation
Indices: 5707777--5707838 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
5707767 TTGCATATGA
5707777 GATGATGATGATGGAATGATGTGCAT
1 GATGATGATGATGGAATGATGTGCAT
* *
5707803 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGAATGATGTGCAT
*
5707829 GTTGATGATG
1 GATGATGATG
5707839 GGTATATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.26, C:0.03, G:0.39, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGAATGATGTGCAT
Found at i:5709004 original size:22 final size:20
Alignment explanation
Indices: 5708964--5709004 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
5708954 TACTTTTTTG
*
5708964 ATCGATTAAACCTTGTGTTA
1 ATCGATTAAACCTTCTGTTA
5708984 ATCGATTAAAATCCTTCTGTT
1 ATCGATT-AAA-CCTTCTGTT
5709005 TGTCTCAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (20 bp):
ATCGATTAAACCTTCTGTTA
Found at i:5709104 original size:71 final size:71
Alignment explanation
Indices: 5708959--5709142 Score: 239
Period size: 72 Copynumber: 2.6 Consensus size: 71
5708949 TCCAATACTT
* * *
5708959 TTTTGATCGATTAAACCTTGTGTTAATCGATTAAAATCCTTCTGTTTGTCTCAGTGTGCCTTTCA
1 TTTTAATCGATTAAACCTTGTGTTAATTGATTAAAATCCTTCTGTTTGTCTCAATGTGCCTTTCA
*
5709024 ATTTTG
66 ATGTTG
* * * * *
5709030 TTTTAATCGATTAAAATCTTTTGTCAATTGATTAAAA-CCTTTTTGTTTGTTTCAATGTGCC-TT
1 TTTTAATCGATT-AAACCTTGTGTTAATTGATTAAAATCC-TTCTGTTTGTCTCAATGTGCCTTT
5709093 CAATGTTG
64 CAATGTTG
*
5709101 TTTTAATTGATTAAACCTTGTGTTAATTGATTAAAAT-CTTCT
1 TTTTAATCGATTAAACCTTGTGTTAATTGATTAAAATCCTTCT
5709143 ATGAAGTTCT
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
69 3 0.03
70 22 0.23
71 33 0.34
72 38 0.40
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (71 bp):
TTTTAATCGATTAAACCTTGTGTTAATTGATTAAAATCCTTCTGTTTGTCTCAATGTGCCTTTCA
ATGTTG
Found at i:5709126 original size:20 final size:20
Alignment explanation
Indices: 5709098--5709135 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5709088 GCCTTCAATG
*
5709098 TTGTTTTAATTGATTAAACC
1 TTGTGTTAATTGATTAAACC
5709118 TTGTGTTAATTGATTAAA
1 TTGTGTTAATTGATTAAA
5709136 ATCTTCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (20 bp):
TTGTGTTAATTGATTAAACC
Found at i:5714695 original size:25 final size:25
Alignment explanation
Indices: 5714603--5714755 Score: 125
Period size: 25 Copynumber: 6.1 Consensus size: 25
5714593 TGGTAATGAT
* *
5714603 TGTTATCTATAAGGCATTGTGTGAC
1 TGTTATCTTTAAGGCATTGCGTGAC
*
5714628 TGTTATCTGTT--GGACATTGTGTGAC
1 TGTTATCT-TTAAGG-CATTGCGTGAC
* *
5714653 TATTAT-TTGT-AGTTCATTGCGTGAC
1 TGTTATCTT-TAAG-GCATTGCGTGAC
*
5714678 TGTTATCTTTAAGGCATTACGTGAC
1 TGTTATCTTTAAGGCATTGCGTGAC
* * *
5714703 TGTTTTCTTTAAGGCATTACATGAC
1 TGTTATCTTTAAGGCATTGCGTGAC
* * * *
5714728 TGCTATGTGTATGGCATTGCGTGAC
1 TGTTATCTTTAAGGCATTGCGTGAC
5714753 TGT
1 TGT
5714756 CATTGCTTGG
Statistics
Matches: 104, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.01
24 4 0.04
25 94 0.90
26 5 0.05
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (25 bp):
TGTTATCTTTAAGGCATTGCGTGAC
Found at i:5716209 original size:18 final size:18
Alignment explanation
Indices: 5716177--5716223 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5716167 TCAATGTCTA
* *
5716177 TCTTGCTGCTTTTGAAGC
1 TCTTGCTACTCTTGAAGC
*
5716195 TCTTGCTACTCTTGAGGC
1 TCTTGCTACTCTTGAAGC
5716213 T-TATGCTACTC
1 TCT-TGCTACTC
5716224 AATAGTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.43
Consensus pattern (18 bp):
TCTTGCTACTCTTGAAGC
Found at i:5718028 original size:43 final size:44
Alignment explanation
Indices: 5717937--5718033 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 44
5717927 TGCACTAGAG
*
5717937 ATTTTTGCTAATAATGTTGACACTTAAGTTTTGTAACTTTGTTT
1 ATTTTTGCTAATAATGTTGACACTTAAGTTTTGTAACTTTGTTC
* **
5717981 ATTTTTGTTAATGGTGTTGACACTTAAG-TTTGTAACTTTGTTC
1 ATTTTTGCTAATAATGTTGACACTTAAGTTTTGTAACTTTGTTC
5718024 ATTTTTGCTA
1 ATTTTTGCTA
5718034 GTAGGTAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 23 0.48
44 25 0.52
ACGTcount: A:0.23, C:0.09, G:0.15, T:0.53
Consensus pattern (44 bp):
ATTTTTGCTAATAATGTTGACACTTAAGTTTTGTAACTTTGTTC
Found at i:5718290 original size:23 final size:23
Alignment explanation
Indices: 5718246--5718290 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5718236 CTTTTTTTTA
* *
5718246 GGCATTGCCTGACTAGTTGATAT
1 GGCATTGCCTGACTACTAGATAT
**
5718269 GGCATTGTGTGACTACTAGATA
1 GGCATTGCCTGACTACTAGATA
5718291 AGCATTACGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (23 bp):
GGCATTGCCTGACTACTAGATAT
Found at i:5718379 original size:83 final size:83
Alignment explanation
Indices: 5718248--5718442 Score: 225
Period size: 83 Copynumber: 2.3 Consensus size: 83
5718238 TTTTTTTAGG
* *** * *
5718248 CATTGCCTGACTAGTTGATATGGCATTGTGTGACTACTAGATAAGCATTACGTGACTTAGGCATT
1 CATTGCATGACTAGTTGATATGGCATTGCACGACTACTAGACAAGCATTACGTGACTTACGCATT
5718313 ACT-TGAATGGTTTTTAAT
66 A-TGTGAATGGTTTTTAAT
* * * *
5718331 CATTGCATGACTAGTTGATATGACATTGCACGAC-AGGTAGACAGGCATTGCGTGACTTACGCAT
1 CATTGCATGACTAGTTGATATGGCATTGCACGACTA-CTAGACAAGCATTACGTGACTTACGCAT
*
5718395 TATGTGAATGGTTTTTAGT
65 TATGTGAATGGTTTTTAAT
* *
5718414 CGA-TACGTGACTAGTTGATATGGCATTGC
1 C-ATTGCATGACTAGTTGATATGGCATTGC
5718443 GTGACTTAGG
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
82 2 0.02
83 92 0.97
84 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (83 bp):
CATTGCATGACTAGTTGATATGGCATTGCACGACTACTAGACAAGCATTACGTGACTTACGCATT
ATGTGAATGGTTTTTAAT
Found at i:5718488 original size:38 final size:38
Alignment explanation
Indices: 5718437--5718517 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
5718427 GTTGATATGG
*
5718437 CATTGCGTGACTTAGGCATGGTGTGAATGGTTTGTAGT
1 CATTGCGTGACTTAGGCATGATGTGAATGGTTTGTAGT
*
5718475 CATTGCGTGACTTATGCATGATGTGAATGGTTTGTAGT
1 CATTGCGTGACTTAGGCATGATGTGAATGGTTTGTAGT
*
5718513 AATTG
1 CATTG
5718518 TGAGACTGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (38 bp):
CATTGCGTGACTTAGGCATGATGTGAATGGTTTGTAGT
Found at i:5718560 original size:60 final size:60
Alignment explanation
Indices: 5718475--5718644 Score: 223
Period size: 60 Copynumber: 2.8 Consensus size: 60
5718465 GGTTTGTAGT
* * * * * * * *
5718475 CATTGCGTGACTTATGCATGATGTGAATGGTTTGTAGTAATTGTGAGACTGGTAGATAGG
1 CATTGCATGACTTAGGCATGGTGTGAATGGTTTGTAGTCATTGTGTGACTGGTAAACAGA
* *
5718535 CATTGCATGCCTTAGGCATGGTGTGAATGGTTTGTAGTCATTGCGTGACTGGTAAACAGA
1 CATTGCATGACTTAGGCATGGTGTGAATGGTTTGTAGTCATTGTGTGACTGGTAAACAGA
** *
5718595 CATTGCATGACTTAGGCATGGCATGAAAGGTTTGTAGTCATTGTGTGACT
1 CATTGCATGACTTAGGCATGGTGTGAATGGTTTGTAGTCATTGTGTGACT
5718645 ACTTGATATG
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.34
Consensus pattern (60 bp):
CATTGCATGACTTAGGCATGGTGTGAATGGTTTGTAGTCATTGTGTGACTGGTAAACAGA
Found at i:5718563 original size:98 final size:99
Alignment explanation
Indices: 5718376--5718584 Score: 298
Period size: 98 Copynumber: 2.1 Consensus size: 99
5718366 GGTAGACAGG
* * * *
5718376 CATTGCGTGACTTACGCATTATGTGAATGGTTTTTAGTCGATACGTGACTAGTTGATATGGCATT
1 CATTGCGTGACTTACGCATGATGTGAATGGTTTGTAGTCAATACGTGACTAGTAGATATGGCATT
*
5718441 GCGTGACTTAGGCATGGTGTGAATGGTTTGTAGT
66 GCATGACTTAGGCATGGTGTGAATGGTTTGTAGT
* * *
5718475 CATTGCGTGACTTATGCATGATGTGAATGGTTTGTAGT-AAT-TGTGAGACTGGTAGATA-GGCA
1 CATTGCGTGACTTACGCATGATGTGAATGGTTTGTAGTCAATACGT--GACTAGTAGATATGGCA
*
5718537 TTGCATGCCTTAGGCATGGTGTGAATGGTTTGTAGT
64 TTGCATGACTTAGGCATGGTGTGAATGGTTTGTAGT
5718573 CATTGCGTGACT
1 CATTGCGTGACT
5718585 GGTAAACAGA
Statistics
Matches: 99, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
97 2 0.02
98 52 0.53
99 45 0.45
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (99 bp):
CATTGCGTGACTTACGCATGATGTGAATGGTTTGTAGTCAATACGTGACTAGTAGATATGGCATT
GCATGACTTAGGCATGGTGTGAATGGTTTGTAGT
Found at i:5718712 original size:83 final size:83
Alignment explanation
Indices: 5718573--5718727 Score: 249
Period size: 83 Copynumber: 1.9 Consensus size: 83
5718563 GGTTTGTAGT
* *
5718573 CATTGCGTGACTGGTAAACAGACATTGCATGACTTAGGCATGGCATGAAAGGTTTGTAGTCATTG
1 CATTGCGTGACTGGTAAACAGACATTACATGACTTAGGCATGGCATCAAAGGTTTGTAGTCATTG
*
5718638 TGTGACTACTTGATATGG
66 AGTGACTACTTGATATGG
* *
5718656 CATTGCGTGACTGGTAGACA-AGCATTACATGACTTAGGCATGGCATCAATGGTTTGTAGTCATT
1 CATTGCGTGACTGGTAAACAGA-CATTACATGACTTAGGCATGGCATCAAAGGTTTGTAGTCATT
5718720 GAGTGACT
65 GAGTGACT
5718728 GGTAGACAGG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
82 1 0.02
83 65 0.98
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.31
Consensus pattern (83 bp):
CATTGCGTGACTGGTAAACAGACATTACATGACTTAGGCATGGCATCAAAGGTTTGTAGTCATTG
AGTGACTACTTGATATGG
Found at i:5718749 original size:60 final size:60
Alignment explanation
Indices: 5718656--5718787 Score: 237
Period size: 60 Copynumber: 2.2 Consensus size: 60
5718646 CTTGATATGG
5718656 CATTGCGTGACTGGTAGACAAGCATTACATGACTTAGGCATGGCATCAATGGTTTGTAGT
1 CATTGCGTGACTGGTAGACAAGCATTACATGACTTAGGCATGGCATCAATGGTTTGTAGT
* * *
5718716 CATTGAGTGACTGGTAGACAGGCATTACATGACTTAGGCATGGCATGAATGGTTTGTAGT
1 CATTGCGTGACTGGTAGACAAGCATTACATGACTTAGGCATGGCATCAATGGTTTGTAGT
5718776 CATTGCGTGACT
1 CATTGCGTGACT
5718788 ATTTAATATG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (60 bp):
CATTGCGTGACTGGTAGACAAGCATTACATGACTTAGGCATGGCATCAATGGTTTGTAGT
Found at i:5718779 original size:143 final size:143
Alignment explanation
Indices: 5718521--5718853 Score: 468
Period size: 143 Copynumber: 2.3 Consensus size: 143
5718511 GTAATTGTGA
* ** *
5718521 GACTGGTAGATAGGCATTGCATGCCTTAGGCATGGTGTGAATGGTTTGTAGTCATTGCGTGACTG
1 GACTGGTAGATAGGCATTGCATGACTTAGGCATGGCATGAATGGTTTGTAGTCATTGAGTGACTG
* * *
5718586 GTAAACAGACATTGCATGACTTAGGCATGGCATGAAAGGTTTGTAGTCATTGTGTGACTACTTGA
66 GTAAACAGACATTACATGACTTAGGCATGGCATGAAAGGTTTGTAGTCATTGCGTGACTACTTAA
* *
5718651 TATGGCATTGCGT
131 TATGGCATTACAT
* * * *
5718664 GACTGGTAGACAAGCATTACATGACTTAGGCATGGCATCAATGGTTTGTAGTCATTGAGTGACTG
1 GACTGGTAGATAGGCATTGCATGACTTAGGCATGGCATGAATGGTTTGTAGTCATTGAGTGACTG
* * * *
5718729 GTAGACAGGCATTACATGACTTAGGCATGGCATGAATGGTTTGTAGTCATTGCGTGACTATTTAA
66 GTAAACAGACATTACATGACTTAGGCATGGCATGAAAGGTTTGTAGTCATTGCGTGACTACTTAA
5718794 TATGGCATTACAT
131 TATGGCATTACAT
* * * **
5718807 GATTGGCAGATAGGCATTGCATGATTTAGGCATTACATGAATGGTTT
1 GACTGGTAGATAGGCATTGCATGACTTAGGCATGGCATGAATGGTTT
5718854 TTGTGTTTCA
Statistics
Matches: 164, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
143 164 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (143 bp):
GACTGGTAGATAGGCATTGCATGACTTAGGCATGGCATGAATGGTTTGTAGTCATTGAGTGACTG
GTAAACAGACATTACATGACTTAGGCATGGCATGAAAGGTTTGTAGTCATTGCGTGACTACTTAA
TATGGCATTACAT
Found at i:5719681 original size:21 final size:19
Alignment explanation
Indices: 5719631--5719672 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5719621 AGATTCTCAA
5719631 CATTTTGTATC-CTCTCTTC
1 CATTTT-TATCACTCTCTTC
5719650 CATTTTTATCACTCTCTT-
1 CATTTTTATCACTCTCTTC
5719668 CATTT
1 CATTT
5719673 GCTTAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.14, C:0.29, G:0.02, T:0.55
Consensus pattern (19 bp):
CATTTTTATCACTCTCTTC
Found at i:5721423 original size:20 final size:19
Alignment explanation
Indices: 5721398--5721470 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 19
5721388 GCACCGAAAC
5721398 TATCGATACATTATTGAATG
1 TATCGATACATTATT-AATG
* *
5721418 TATCGATACTTTCA-TACATC
1 TATCGATACATT-ATTA-ATG
*
5721438 TATCGATACATTAGTAAAATG
1 TATCGATACATTA-T-TAATG
*
5721459 TATAGATACATT
1 TATCGATACATT
5721471 TCACATAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
19 2 0.05
20 25 0.60
21 14 0.33
22 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
TATCGATACATTATTAATG
Found at i:5721985 original size:67 final size:67
Alignment explanation
Indices: 5721857--5721997 Score: 158
Period size: 67 Copynumber: 2.1 Consensus size: 67
5721847 CATAAGGTAC
* * * * * **
5721857 ATGGAAAATACGTCATATACATAATCTCATGGCACTCATTTGCTTTCTCAATCATTTCATATAGT
1 ATGGAATATACATCATATACATAATCTCATGGCACTCATATGCATACTCAATCATCCCATATAGT
5721922 AT
66 AT
* * * *
5721924 ATGGAATATACATCATATACATTATCTCATGGCATTTATCATGCATACTCAATCA-CCCATATGG
1 ATGGAATATACATCATATACATAATCTCATGGCACTCAT-ATGCATACTCAATCATCCCATATAG
5721988 TAT
65 TAT
*
5721991 AAGGAAT
1 ATGGAAT
5721998 TTATATCGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
67 49 0.80
68 12 0.20
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (67 bp):
ATGGAATATACATCATATACATAATCTCATGGCACTCATATGCATACTCAATCATCCCATATAGT
AT
Found at i:5724486 original size:16 final size:15
Alignment explanation
Indices: 5724463--5724492 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5724453 AAAAATATTT
5724463 AAAAAATAAAAATCC
1 AAAAAATAAAAATCC
5724478 AAAAGAATAAAAATC
1 AAAA-AATAAAAATC
5724493 TAATTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.10, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAATCC
Found at i:5728714 original size:23 final size:23
Alignment explanation
Indices: 5728682--5728746 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
5728672 ATTTGTAACA
* *
5728682 CAATGTCTAACAAACCAATTAAG
1 CAATGCCTAACAAACCAATCAAG
* * *
5728705 CAATGCCTAACAAACTAGTCATG
1 CAATGCCTAACAAACCAATCAAG
*
5728728 CAATGCCTAA-AAATCAATC
1 CAATGCCTAACAAACCAATC
5728747 CCGCAAGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 6 0.18
23 28 0.82
ACGTcount: A:0.45, C:0.25, G:0.09, T:0.22
Consensus pattern (23 bp):
CAATGCCTAACAAACCAATCAAG
Found at i:5728780 original size:22 final size:22
Alignment explanation
Indices: 5728704--5728790 Score: 70
Period size: 22 Copynumber: 3.9 Consensus size: 22
5728694 AACCAATTAA
5728704 GCAATGCCTAACAAACTAGTCAT
1 GCAATGCCT-ACAAACTAGTCAT
* * **
5728727 GCAATGCCTA-AAAATCAATCCC
1 GCAATGCCTACAAACT-AGTCAT
*
5728749 GCAA-GCCCTACAACCTAGTCAT
1 GCAATG-CCTACAAACTAGTCAT
* *
5728771 GCAATGCCTAAAAATTAGTC
1 GCAATGCCTACAAACTAGTC
5728791 TCAAAATCCT
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
21 5 0.10
22 30 0.62
23 13 0.27
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.21
Consensus pattern (22 bp):
GCAATGCCTACAAACTAGTCAT
Found at i:5728815 original size:44 final size:44
Alignment explanation
Indices: 5728723--5728824 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
5728713 AACAAACTAG
** * *
5728723 TCATGCAATGCCTAAAAATCAATCCCGCAAGCCCTACAACCTAG
1 TCATGCAATGCCTAAAAATCAATCCCAAAAGCCCTACAACCCAA
* * * * *
5728767 TCATGCAATGCCTAAAAATTAGTCTCAAAATCCTTACAACCCAA
1 TCATGCAATGCCTAAAAATCAATCCCAAAAGCCCTACAACCCAA
* *
5728811 TCATGAAATCCCTA
1 TCATGCAATGCCTA
5728825 TAACCTAATC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.23
Consensus pattern (44 bp):
TCATGCAATGCCTAAAAATCAATCCCAAAAGCCCTACAACCCAA
Found at i:5728829 original size:22 final size:22
Alignment explanation
Indices: 5728794--5728846 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
5728784 ATTAGTCTCA
*
5728794 AAATCCTTACAACCCAATCATG
1 AAATCCCTACAACCCAATCATG
* *
5728816 AAATCCCTATAACCTAATCATG
1 AAATCCCTACAACCCAATCATG
* *
5728838 TAATGCCTA
1 AAATCCCTA
5728847 AAAATTGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.28, G:0.06, T:0.26
Consensus pattern (22 bp):
AAATCCCTACAACCCAATCATG
Found at i:5728865 original size:66 final size:66
Alignment explanation
Indices: 5728754--5728879 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
5728744 ATCCCGCAAG
* **
5728754 CCCTACAACCTAGTCATGCAATGCCTAAAAATTAGTCTCAAAATCCTTACAACCCAATCATGAAA
1 CCCTACAACCTAATCATGCAATGCCTAAAAATTAGTCTCAAAATCCCAACAACCCAATCATGAAA
5728819 T
66 T
* * * **
5728820 CCCTATAACCTAATCATGTAATGCCTAAAAATT-GTTTCTGCAATCCCAACAACCCAATCA
1 CCCTACAACCTAATCATGCAATGCCTAAAAATTAGTCTC-AAAATCCCAACAACCCAATCA
5728880 CACAATGCCT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 4 0.08
66 47 0.92
ACGTcount: A:0.38, C:0.29, G:0.07, T:0.25
Consensus pattern (66 bp):
CCCTACAACCTAATCATGCAATGCCTAAAAATTAGTCTCAAAATCCCAACAACCCAATCATGAAA
T
Found at i:5730805 original size:13 final size:13
Alignment explanation
Indices: 5730787--5730811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5730777 GGAGAAATTG
5730787 TGATTTTATAAAA
1 TGATTTTATAAAA
5730800 TGATTTTATAAA
1 TGATTTTATAAA
5730812 TTTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:5735415 original size:25 final size:25
Alignment explanation
Indices: 5735381--5735441 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
5735371 TGTGGTCGCA
* **
5735381 ACCACATATATCAACTGGTGGCC-T
1 ACCACGTATATCAACCCGTGGCCTT
*
5735405 AGCCACGTATATCATCCCGTGGCCTT
1 A-CCACGTATATCAACCCGTGGCCTT
5735431 ACCACGTATAT
1 ACCACGTATAT
5735442 ATATCACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 1 0.03
25 28 0.90
26 2 0.06
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.26
Consensus pattern (25 bp):
ACCACGTATATCAACCCGTGGCCTT
Found at i:5738487 original size:21 final size:21
Alignment explanation
Indices: 5738440--5738495 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
5738430 CCTATTCCCC
5738440 AAATAAAAATTAATCAAAAAAT
1 AAAT-AAAATTAATCAAAAAAT
*
5738462 AAATAAAA-TAATCAAATAAT
1 AAATAAAATTAATCAAAAAAT
5738482 ACAATAAAAATTAA
1 A-AAT-AAAATTAA
5738496 AATTAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 8 0.27
23 3 0.10
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAAAATTAATCAAAAAAT
Found at i:5739613 original size:80 final size:82
Alignment explanation
Indices: 5739486--5739643 Score: 268
Period size: 80 Copynumber: 2.0 Consensus size: 82
5739476 TGTTTATTAG
*
5739486 GGCTTACCCACTTGTAATTTAGAAAAAAAACTTAGTGTTTAAAATTTTTGTTTCATTT-AATT-A
1 GGCTTACCCACTTGTAATCTAGAAAAAAAACTTAGTGTTTAAAATTTTTGTTTCATTTAAATTAA
5739549 AATATATTATAAANTTGA
66 AATATATTATAAA-TTGA
*
5739567 GGCTTACCCACTTGTAATCTAG-AGAAAAACTTAGTGTTTAAAATTTTTGTTTCATTTAAATTAA
1 GGCTTACCCACTTGTAATCTAGAAAAAAAACTTAGTGTTTAAAATTTTTGTTTCATTTAAATTAA
5739631 AATATATTATAAA
66 AATATATTATAAA
5739644 ATTATATGAT
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
80 34 0.47
81 25 0.34
82 14 0.19
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.41
Consensus pattern (82 bp):
GGCTTACCCACTTGTAATCTAGAAAAAAAACTTAGTGTTTAAAATTTTTGTTTCATTTAAATTAA
AATATATTATAAATTGA
Found at i:5739734 original size:2 final size:2
Alignment explanation
Indices: 5739722--5739757 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5739712 ATAGATTTAG
*
5739722 TA TA AA 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
5739758 ATGAATGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5742252 original size:19 final size:20
Alignment explanation
Indices: 5742227--5742273 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5742217 TAAAGAAAGG
5742227 AAAAAAAAAGAGAGGTATT-T
1 AAAAAAAAA-AGAGGTATTCT
*
5742247 AAAAAAAAAAGAGGTCTTCT
1 AAAAAAAAAAGAGGTATTCT
5742267 AAAAAAA
1 AAAAAAA
5742274 TAAACAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.64, C:0.04, G:0.15, T:0.17
Consensus pattern (20 bp):
AAAAAAAAAAGAGGTATTCT
Found at i:5746003 original size:9 final size:9
Alignment explanation
Indices: 5745989--5746054 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
5745979 ACAATCAATG
5745989 AAAAAAGAA
1 AAAAAAGAA
5745998 AAAAAAGAGA
1 AAAAAAGA-A
** *
5746008 TGAAAAG-G
1 AAAAAAGAA
*
5746016 AAAATA-AA
1 AAAAAAGAA
5746024 AAAAAAGAA
1 AAAAAAGAA
5746033 AAAAAGAGAA
1 AAAAA-AGAA
*
5746043 AAAAGAGAA
1 AAAAAAGAA
5746052 AAA
1 AAA
5746055 TGAGCTCTAG
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
8 8 0.18
9 22 0.50
10 14 0.32
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:5748224 original size:31 final size:30
Alignment explanation
Indices: 5747253--5748216 Score: 330
Period size: 31 Copynumber: 31.4 Consensus size: 30
5747243 GATTTGAGTC
*
5747253 TTAAGTCCAATTTAGCTGGCATCCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* * * *
5747284 TTAAGTCCAGTTACGTTGGCA-CAAAGATGT
1 TTAAGCCCAATTA-GCTGGCATCCAAGATGT
** *
5747314 TTAATACCAATTTAGCTAGCATCCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* ** * * *
5747345 TTAAGCCTAGCTATGTTGCCA-CAAAGA-GAT
1 TTAAGCCCAATTA-GCTGGCATCCAAGATG-T
* *
5747375 TTAAGCCTAAGTTATACTGGCATCCAAGATGT
1 TTAAGCCCAA-TTA-GCTGGCATCCAAGATGT
* * *
5747407 ATAA-CTCCAGTTA-CTTTGGCA-CGAAAGA-GT
1 TTAAGC-CCAATTAGC--TGGCATC-CAAGATGT
* *
5747437 TTAAGCCCAATTTCGCTGGCATTCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* ** * * * *
5747468 TTAAGCCCAGTTATATTAGCAT-AAAGACGA
1 TTAAGCCCAATTA-GCTGGCATCCAAGATGT
* *
5747498 TTAAGCCTAATTTAGCTAGCATCCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
** ** * * *
5747529 TTAAGCATAGCTATGTTGACA-CAAAGA-GAT
1 TTAAGCCCAATTA-GCTGGCATCCAAGATG-T
* *
5747559 TTAAGCCTAATTTCGCTGGCATCCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* ** * * *
5747590 TTAAGCCCAGTTATATTGGCA-CAAAGACGA
1 TTAAGCCCAATTA-GCTGGCATCCAAGATGT
*
5747620 TTAAGCCCAATTTAGCTAGCATCCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
** ** * * *
5747651 TTAAGCATAGCTATGTTGGTA-CAAAGA-GAT
1 TTAAGCCCAATTA-GCTGGCATCCAAGATG-T
*
5747681 TTAAGCCCAATTTATCTGGCATCCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* * * *
5747712 ATAAGTCCAGTTA-CTTTGGCA-CAAAGGA-GT
1 TTAAGCCCAATTAGC--TGGCATCCAA-GATGT
* *
5747742 TTAAGCCCAATTTCGCTAGCATCCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* ** *
5747773 TTAAGCCCAGTTATATTGGCA-CAAAGA-GAT
1 TTAAGCCCAATTA-GCTGGCATCCAAGATG-T
**
5747803 TTAAGCCCAATTTAATTGGCATCCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* * *
5747834 ATAAGTCCAATTA-CTTTGGCA-CAAAAGA-GT
1 TTAAGCCCAATTAGC--TGGCATC-CAAGATGT
* * *
5747864 TTAAGCCCAATTTTGTTGGCATCCAAGATGA
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* * ** *
5747895 TTAAGTCCAGTTATATTGGCA-CAAAGA-GAT
1 TTAAGCCCAATTA-GCTGGCATCCAAGATG-T
* *
5747925 TTAAGCCCAATCTAACTGGCATCCAAGATGA
1 TTAAGCCCAAT-TAGCTGGCATCCAAGATGT
* * ** * *
5747956 TTAAGCCTAGTTATATTGGCA-CAAAGA-GA
1 TTAAGCCCAATTA-GCTGGCATCCAAGATGT
* *
5747985 TTAAGCCCAATTTAGCTAGCATCCAAGATAT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* ** * *
5748016 TTAAGCCTAGCTACGTTGGCNCA-CAAAAGATGT
1 TTAAGCCCAATTA-GCTGG--CATC-CAAGATGT
* *
5748049 TTAAGCCCAATTTAAACTGGCATCCAAAATGT
1 TTAAGCCCAA-TT-AGCTGGCATCCAAGATGT
* * * * *
5748081 ATAAGTCCAGTTACGTTGGCA-CAAAAGGA-GT
1 TTAAGCCCAATTA-GCTGGCATC-CAA-GATGT
5748112 TTAAGCCCAATTTAGCTGGCATCCAAGATGT
1 TTAAGCCCAA-TTAGCTGGCATCCAAGATGT
* **
5748143 TTAAGCCCAGTTATATTGGCA-CCAAGATGT
1 TTAAGCCCAATTA-GCTGGCATCCAAGATGT
* *
5748173 TTAAGCCCACTGTAGCTGGCATCCAAGACGT
1 TTAAGCCCAAT-TAGCTGGCATCCAAGATGT
*
5748204 CTAAGCCCAATTA
1 TTAAGCCCAATTA
5748217 TCTTGGCACG
Statistics
Matches: 677, Mismatches: 179, Indels: 155
0.67 0.18 0.15
Matches are distributed among these distances:
29 21 0.03
30 280 0.41
31 315 0.47
32 38 0.06
33 18 0.03
34 4 0.01
35 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (30 bp):
TTAAGCCCAATTAGCTGGCATCCAAGATGT
Found at i:5748237 original size:61 final size:61
Alignment explanation
Indices: 5747253--5748238 Score: 1041
Period size: 61 Copynumber: 16.1 Consensus size: 61
5747243 GATTTGAGTC
* * **
5747253 TTAAGTCCAATTTAGCTGGCATCCAAGATGTTTAAGTCCAGTTACGTTGGCACAAAGATG-T
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGA-GAT
** * * * * *
5747314 TTAATACCAATTTAGCTAGCATCCAAGATGTTTAAGCCTAGCTATGTTGCCACAAAGAGAT
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAGAT
* *
5747375 TTAAGCCTAAGTTATA-CTGGCATCCAAGATGTATAA-CTCCAGTTACT-TTGGCACGAAAGAG-
1 TTAAGCCCAA-TT-TAGCTGGCATCCAAGATGTTTAAGC-CCAGTTA-TATTGGCAC-AAAGAGA
5747436 T
61 T
* * * *
5747437 TTAAGCCCAATTTCGCTGGCATTCAAGATGTTTAAGCCCAGTTATATTAGCATAAAGACGA-
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGA-GAT
* * ** * * *
5747498 TTAAGCCTAATTTAGCTAGCATCCAAGATGTTTAAGCATAGCTATGTTGACACAAAGAGAT
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAGAT
* *
5747559 TTAAGCCTAATTTCGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGACGA-
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGA-GAT
* ** * * *
5747620 TTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGCATAGCTATGTTGGTACAAAGAGAT
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAGAT
* * *
5747681 TTAAGCCCAATTTATCTGGCATCCAAGATGTATAAGTCCAGTTACT-TTGGCACAAAG-GAGT
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTA-TATTGGCACAAAGAGA-T
* *
5747742 TTAAGCCCAATTTCGCTAGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAGAT
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAGAT
** * * *
5747803 TTAAGCCCAATTTAATTGGCATCCAAGATGTATAAGTCCAATTACT-TTGGCACAAA-AGAGT
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTA-TATTGGCACAAAGAGA-T
* * * *
5747864 TTAAGCCCAATTTTGTTGGCATCCAAGATGATTAAGTCCAGTTATATTGGCACAAAGAGAT
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAGAT
* * * *
5747925 TTAAGCCCAATCTAACTGGCATCCAAGATGATTAAGCCTAGTTATATTGGCACAAAGAGA-
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAGAT
* * * * **
5747985 TTAAGCCCAATTTAGCTAGCATCCAAGATATTTAAGCCTAGCTACGTTGGCNCACAAA-AGATGT
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGG--CACAAAGAGA--T
* * * * **
5748049 TTAAGCCCAATTTAAACTGGCATCCAAAATGTATAAGTCCAGTTACGTTGGCACAAA-AGGAGT
1 TTAAGCCCAATTT-AGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGA-GA-T
*
5748112 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACCAAGATG-T
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGA-GAT
* * * * * * *
5748173 TTAAGCCCACTGTAGCTGGCATCCAAGACGTCTAAGCCCAATTATCTTGGCAC-GAGAGAAT
1 TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAG-AT
5748234 TTAAG
1 TTAAG
5748239 TTACGTAGCC
Statistics
Matches: 783, Mismatches: 110, Indels: 64
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.00
60 64 0.08
61 548 0.70
62 93 0.12
63 33 0.04
64 15 0.02
65 29 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (61 bp):
TTAAGCCCAATTTAGCTGGCATCCAAGATGTTTAAGCCCAGTTATATTGGCACAAAGAGAT
Found at i:5748322 original size:25 final size:25
Alignment explanation
Indices: 5748275--5748325 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
5748265 AACAACCTTT
* *
5748275 TTTTCTTCTAAAACCTCTAGGTACA
1 TTTTCTTCTAAAACCCCCAGGTACA
*
5748300 TTTTCTTCTAAAACCCCCGGGTACA
1 TTTTCTTCTAAAACCCCCAGGTACA
5748325 T
1 T
5748326 CTTCAAAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.37
Consensus pattern (25 bp):
TTTTCTTCTAAAACCCCCAGGTACA
Found at i:5748377 original size:21 final size:21
Alignment explanation
Indices: 5748320--5748378 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
5748310 AAACCCCCGG
*
5748320 GTACATCTTCAAAACCTCCGA
1 GTACATCTTCAAAATCTCCGA
* * *
5748341 GAACA-CTCCTAAAATCTCTGA
1 GTACATCTTC-AAAATCTCCGA
5748362 GTACATCTTCAAAATCT
1 GTACATCTTCAAAATCT
5748379 TTGGGTATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.36, C:0.29, G:0.08, T:0.27
Consensus pattern (21 bp):
GTACATCTTCAAAATCTCCGA
Found at i:5748681 original size:22 final size:22
Alignment explanation
Indices: 5748653--5748709 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 22
5748643 ACTTATTCCC
5748653 TAAATAAAAATTAATCAAAAAA
1 TAAATAAAAATTAATCAAAAAA
*
5748675 TAAAT-AAAA-TAATCAAATAA
1 TAAATAAAAATTAATCAAAAAA
5748695 TACAATAAAAATTAA
1 TA-AATAAAAATTAA
5748710 AATTAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 12 0.39
21 7 0.23
22 9 0.29
23 3 0.10
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAATAAAAATTAATCAAAAAA
Found at i:5752991 original size:21 final size:21
Alignment explanation
Indices: 5752967--5753007 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5752957 CTCCAAGCTT
*
5752967 TTTTCTTTTTTCTCCTTTCTC
1 TTTTCTTTTTTCACCTTTCTC
5752988 TTTTCTTTTTTCACCTTTCT
1 TTTTCTTTTTTCACCTTTCT
5753008 TCCCTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTCTTTTTTCACCTTTCTC
Found at i:5754016 original size:19 final size:20
Alignment explanation
Indices: 5753992--5754031 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5753982 ATTATTTTAA
*
5753992 TATTATTTTA-TCCAAAAAT
1 TATTATCTTATTCCAAAAAT
*
5754011 TATTATCTTATTTCAAAAAT
1 TATTATCTTATTCCAAAAAT
5754031 T
1 T
5754032 TTCTCTAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTATCTTATTCCAAAAAT
Found at i:5754141 original size:11 final size:11
Alignment explanation
Indices: 5754125--5754149 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5754115 CTTAATAAGA
5754125 TATTATTATTT
1 TATTATTATTT
5754136 TATTATTATTT
1 TATTATTATTT
5754147 TAT
1 TAT
5754150 CAAATATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTATTATTT
Found at i:5758289 original size:19 final size:19
Alignment explanation
Indices: 5758249--5758287 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5758239 TTAATGTTTT
*
5758249 AATATTATTTTATTAATAA
1 AATATTATTTTATTAAAAA
5758268 AATATTATTTT-TTAAAAA
1 AATATTATTTTATTAAAAA
5758286 AA
1 AA
5758288 ATTTTGTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATTATTTTATTAAAAA
Found at i:5768285 original size:27 final size:26
Alignment explanation
Indices: 5768225--5768305 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 26
5768215 AATATTTAAA
* *
5768225 TTAAATAAATATTAATATTTTAA-ATAT
1 TTAATTAAATATTAAT-TATTAATAT-T
*
5768252 TT-TTTAAATGATTAATTATTAATATT
1 TTAATTAAAT-ATTAATTATTAATATT
5768278 TTAATTAAAT-TCTAGATTATTAATATT
1 TTAATTAAATAT-TA-ATTATTAATATT
5768305 T
1 T
5768306 AAAAAATCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.02
26 15 0.33
27 29 0.64
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (26 bp):
TTAATTAAATATTAATTATTAATATT
Found at i:5768300 original size:34 final size:34
Alignment explanation
Indices: 5768234--5768301 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
5768224 ATTAAATAAA
** *
5768234 TATTAATATTTTAAATATTTTTTAAATGATTAAT
1 TATTAATATTTTAAATAAATTCTAAATGATTAAT
* * *
5768268 TATTAATATTTTAATTAAATTCTAGATTATTAAT
1 TATTAATATTTTAAATAAATTCTAAATGATTAAT
5768302 ATTTAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (34 bp):
TATTAATATTTTAAATAAATTCTAAATGATTAAT
Found at i:5768315 original size:24 final size:26
Alignment explanation
Indices: 5768266--5768315 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
5768256 TAAATGATTA
*
5768266 ATTATTAATATTTTAATTAAATTCTAG
1 ATTATTAATATTTTAA-TAAAATCTAG
5768293 ATTATTAATA-TTTAA-AAAATCTA
1 ATTATTAATATTTTAATAAAATCTA
5768316 ATAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
26 5 0.23
27 10 0.45
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTATTAATATTTTAATAAAATCTAG
Found at i:5775808 original size:2 final size:2
Alignment explanation
Indices: 5775801--5775872 Score: 90
Period size: 2 Copynumber: 35.5 Consensus size: 2
5775791 TGGTGTGCGT
* * **
5775801 GA GA GA GA GA GA GA GA GA GA GA GA GA GT GA GA GT GTA NT GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA
*
5775844 GA GA GA GA GA GA GA GA GA GA GA GT GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5775873 TGAGTTCTGA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.43, C:0.00, G:0.49, T:0.07
Consensus pattern (2 bp):
GA
Found at i:5779009 original size:34 final size:35
Alignment explanation
Indices: 5778971--5779036 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
5778961 TCGTGCAATG
*
5778971 CCAAGTAAGGC-AAAATATCACTATTTGAGCAACA
1 CCAAGTAAGGCAAAAATAGCACTATTTGAGCAACA
** *
5779005 CCAAGTGGGGCAAAAATAGCACTGTTTGAGCA
1 CCAAGTAAGGCAAAAATAGCACTATTTGAGCA
5779037 CTGCCGGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 9 0.33
35 18 0.67
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (35 bp):
CCAAGTAAGGCAAAAATAGCACTATTTGAGCAACA
Found at i:5779022 original size:69 final size:69
Alignment explanation
Indices: 5778871--5779022 Score: 180
Period size: 69 Copynumber: 2.2 Consensus size: 69
5778861 GCATCGTTGG
* * * * * **
5778871 GTGGGGCAAAAATACTATTGATCGTGTAATGCCAAGTACGGCAGAGAGACCACTGTTTGAGCGCC
1 GTGGGGCAAAAATACCATTGATCGTGCAATGCCAAGTAAGGCAGAAAGACCACTATTTGAGCAAC
*
5778936 ACTA
66 ACAA
* * * *
5778940 GTGAGGCAGAAATACCATTGATCGTGCAATGCCAAGTAAGGCA-AAATATCACTATTTGAGCAAC
1 GTGGGGCAAAAATACCATTGATCGTGCAATGCCAAGTAAGGCAGAAAGACCACTATTTGAGCAAC
5779004 ACCAA
66 A-CAA
5779009 GTGGGGCAAAAATA
1 GTGGGGCAAAAATA
5779023 GCACTGTTTG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
68 16 0.24
69 52 0.76
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (69 bp):
GTGGGGCAAAAATACCATTGATCGTGCAATGCCAAGTAAGGCAGAAAGACCACTATTTGAGCAAC
ACAA
Found at i:5782827 original size:22 final size:22
Alignment explanation
Indices: 5782802--5783240 Score: 131
Period size: 22 Copynumber: 19.6 Consensus size: 22
5782792 TTCGGGTAAG
5782802 CAATTTTCAAATCCTTCGAGTA
1 CAATTTTCAAATCCTTCGAGTA
5782824 CAATTTTCAAATCCTTCGAGTA
1 CAATTTTCAAATCCTTCGAGTA
* * * *
5782846 TAATCTTCAAACTCGTT-GGGTA
1 CAATTTTCAAA-TCCTTCGAGTA
* *
5782868 CAATCTTT-AAATCTTTCAAGTA
1 CAAT-TTTCAAATCCTTCGAGTA
* *
5782890 TC-ATTTTCAAA-CCTCCGGGTAA
1 -CAATTTTCAAATCCTTCGAGT-A
* *
5782912 GCAATTTTTAAATCC-TCTAAGTA
1 -CAATTTTCAAATCCTTC-GAGTA
* * *
5782935 CAGTCTTCAAATCC-TCAAGGTA
1 CAATTTTCAAATCCTTCGA-GTA
*
5782957 CAATCTTTAAAAGT--TTCGAGTAA
1 CAAT-TTTCAAA-TCCTTCGAGT-A
* * *
5782980 GCAACTTTT-AAATCCTCCGGGAA
1 -CAA-TTTTCAAATCCTTCGAGTA
* *
5783003 TAATTTTCAAATTCCTT-GGGTA
1 CAATTTTCAAA-TCCTTCGAGTA
* *
5783025 CAATCTTCAAATCCTGTAG-GTAA
1 CAATTTTCAAATCCT-TCGAGT-A
* *
5783048 CCATTTTCAAA-CC-TCCACGTAA
1 CAATTTTCAAATCCTTCGA-GT-A
* * *
5783070 GCAATCTTTAAAAT-CTCCGTGTA
1 -CAAT-TTTCAAATCCTTCGAGTA
*
5783093 TGCAATTTTCAAATCCTTCAAGTA
1 --CAATTTTCAAATCCTTCGAGTA
* * * *
5783117 CAATCTTCAAAACCTCCAAGTAA
1 CAATTTTCAAATCCTTCGAGT-A
* *
5783140 GCAATTTTTAAATCC-TCTG-CTA
1 -CAATTTTCAAATCCTTC-GAGTA
* * *
5783162 TAATTTTCAAATCCTTTGGGTA
1 CAATTTTCAAATCCTTCGAGTA
* * * *
5783184 CAATCTTCGAATCTTTCGGGTAA
1 CAATTTTCAAATCCTTCGAGT-A
* * *
5783207 CCATTTTCAAA-AC-TCAGGGTA
1 CAATTTTCAAATCCTTC-GAGTA
5783228 CAATTTTCAAATC
1 CAATTTTCAAATC
5783241 GTCTAGGTAA
Statistics
Matches: 307, Mismatches: 71, Indels: 78
0.67 0.16 0.17
Matches are distributed among these distances:
20 1 0.00
21 48 0.16
22 142 0.46
23 68 0.22
24 46 0.15
25 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (22 bp):
CAATTTTCAAATCCTTCGAGTA
Found at i:5783156 original size:24 final size:24
Alignment explanation
Indices: 5783050--5783156 Score: 96
Period size: 24 Copynumber: 4.6 Consensus size: 24
5783040 GTAGGTAACC
*
5783050 ATTTTCAAA-CCTCCACGTAAGCA
1 ATTTTCAAATCCTCCAAGTAAGCA
* ** *
5783073 ATCTTTAAAAT-CTCCGTGTATGCA
1 AT-TTTCAAATCCTCCAAGTAAGCA
*
5783097 ATTTTCAAATCCTTCAAGT-A-CA
1 ATTTTCAAATCCTCCAAGTAAGCA
* *
5783119 ATCTTCAAAACCTCCAAGTAAGCA
1 ATTTTCAAATCCTCCAAGTAAGCA
*
5783143 ATTTTTAAATCCTC
1 ATTTTCAAATCCTC
5783157 TGCTATAATT
Statistics
Matches: 64, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
22 18 0.28
23 10 0.16
24 36 0.56
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (24 bp):
ATTTTCAAATCCTCCAAGTAAGCA
Found at i:5785340 original size:40 final size:37
Alignment explanation
Indices: 5785261--5785400 Score: 144
Period size: 40 Copynumber: 3.7 Consensus size: 37
5785251 TAAAAAAAAT
*
5785261 AATAAA-TTAAATAA-TCAAAAACAAATATCT-TAAAC
1 AATAAACTTAAATAACT-AAAAATAAATATCTATAAAC
5785296 -ATAAACTTAAATAACTAAAAATAAATATCTATACAAC
1 AATAAACTTAAATAACTAAAAATAAATATCTATA-AAC
* * *
5785333 GATATAAACTTAAATAACTATACATAAATATCTAAATAAC
1 -A-ATAAACTTAAATAACTAAAAATAAATATCTATA-AAC
*
5785373 AACATAAACTTAAATAACTAAACATAAA
1 -A-ATAAACTTAAATAACTAAAAATAAA
5785401 GATCCAAACA
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
34 5 0.06
35 21 0.23
36 3 0.03
37 3 0.03
40 58 0.64
ACGTcount: A:0.60, C:0.13, G:0.01, T:0.26
Consensus pattern (37 bp):
AATAAACTTAAATAACTAAAAATAAATATCTATAAAC
Found at i:5785362 original size:14 final size:14
Alignment explanation
Indices: 5785297--5785400 Score: 58
Period size: 14 Copynumber: 7.7 Consensus size: 14
5785287 ATCTTAAACA
*
5785297 TAAACTTAAATAAC
1 TAAACATAAATAAC
* *
5785311 TAAAAATAAATATC
1 TAAACATAAATAAC
* *
5785325 TATACA-ACGAT-A-
1 TAAACATA-AATAAC
*
5785337 TAAACTTAAATAAC
1 TAAACATAAATAAC
* *
5785351 TATACATAAATATC
1 TAAACATAAATAAC
*
5785365 T-AA-AT-AACAAC
1 TAAACATAAATAAC
*
5785376 ATAAACTTAAATAAC
1 -TAAACATAAATAAC
5785391 TAAACATAAA
1 TAAACATAAA
5785401 GATCCAAACA
Statistics
Matches: 63, Mismatches: 19, Indels: 16
0.64 0.19 0.16
Matches are distributed among these distances:
11 4 0.06
12 9 0.14
13 6 0.10
14 39 0.62
15 5 0.08
ACGTcount: A:0.59, C:0.13, G:0.01, T:0.27
Consensus pattern (14 bp):
TAAACATAAATAAC
Found at i:5785413 original size:26 final size:27
Alignment explanation
Indices: 5785384--5785435 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
5785374 ACATAAACTT
*
5785384 AAATAAC-TAAACATAAAGATCCAAAC
1 AAATAACATAAACATAAAGAACCAAAC
**
5785410 AAATAACATAAATTTAAAGAACCAAA
1 AAATAACATAAACATAAAGAACCAAA
5785436 ATTATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.63, C:0.15, G:0.04, T:0.17
Consensus pattern (27 bp):
AAATAACATAAACATAAAGAACCAAAC
Found at i:5785458 original size:16 final size:16
Alignment explanation
Indices: 5785437--5785471 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5785427 AGAACCAAAA
5785437 TTATAATTTTTATAA-G
1 TTATAA-TTTTATAATG
5785453 TTATAATTTTATAATG
1 TTATAATTTTATAATG
5785469 TTA
1 TTA
5785472 GCACAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TTATAATTTTATAATG
Found at i:5785977 original size:19 final size:19
Alignment explanation
Indices: 5785953--5786002 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5785943 TAGAAAGTAA
* * *
5785953 ATATATTTATATTTAAAGT
1 ATATATATATACTAAAAGT
5785972 ATATATATATACTAAAAGT
1 ATATATATATACTAAAAGT
5785991 AT-TAGTATATAC
1 ATATA-TATATAC
5786003 AAATATAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATATATATACTAAAAGT
Found at i:5787270 original size:31 final size:31
Alignment explanation
Indices: 5787232--5787340 Score: 191
Period size: 31 Copynumber: 3.5 Consensus size: 31
5787222 CAATTTTTTG
*
5787232 TTTTTCAATTTAGTCTTCTAACTTTTTTCTC
1 TTTTTCAATTTAGTCCTCTAACTTTTTTCTC
5787263 TTTTTCAATTTAGTCCTCTAACTTTTTTCTC
1 TTTTTCAATTTAGTCCTCTAACTTTTTTCTC
5787294 TTTTTCAATTTAGTCCTCTAACATTTTTTCTC
1 TTTTTCAATTTAGTCCTCTAAC-TTTTTTCTC
*
5787326 TTTTTCAAGTTAGTC
1 TTTTTCAATTTAGTC
5787341 TAATTTTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 52 0.69
32 23 0.31
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.58
Consensus pattern (31 bp):
TTTTTCAATTTAGTCCTCTAACTTTTTTCTC
Found at i:5787412 original size:31 final size:31
Alignment explanation
Indices: 5787224--5787430 Score: 153
Period size: 31 Copynumber: 6.8 Consensus size: 31
5787214 TAGATTCTCA
* * *
5787224 ATTTTT-TGTTTTTCAATTTAGTCTTCTAACT
1 ATTTTTCTCTTTTTCAATTTAGTCCTCCAA-T
*
5787255 -TTTTTCTCTTTTTCAATTTAGTCCTCTAACT
1 ATTTTTCTCTTTTTCAATTTAGTCCTCCAA-T
* *
5787286 -TTTTTCTCTTTTTCAATTTAGTCCTCTAAC
1 ATTTTTCTCTTTTTCAATTTAGTCCTCCAAT
*
5787316 ATTTTTTCTCTTTTTCAAGTTAGT-CT--AATT
1 A-TTTTTCTCTTTTTCAATTTAGTCCTCCAA-T
* * * * * * * *
5787346 TTTTTTATCTTGTTCAATCTAATCTTTCAAC
1 ATTTTTCTCTTTTTCAATTTAGTCCTCCAAT
* *
5787377 ATTTTTCTCTTTTTAAACTTAGTCCTCCAAT
1 ATTTTTCTCTTTTTCAATTTAGTCCTCCAAT
*
5787408 ATTTTT-T-TTTTT-AATTTGGTCCT
1 ATTTTTCTCTTTTTCAATTTAGTCCT
5787431 TCTTCCATTG
Statistics
Matches: 144, Mismatches: 25, Indels: 17
0.77 0.13 0.09
Matches are distributed among these distances:
28 9 0.06
29 24 0.17
30 7 0.05
31 81 0.56
32 23 0.16
ACGTcount: A:0.19, C:0.18, G:0.05, T:0.58
Consensus pattern (31 bp):
ATTTTTCTCTTTTTCAATTTAGTCCTCCAAT
Found at i:5787922 original size:6 final size:6
Alignment explanation
Indices: 5787911--5787937 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5787901 AGGATTTTTA
5787911 ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATA
5787938 CACACACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:5787944 original size:2 final size:2
Alignment explanation
Indices: 5787937--5787962 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5787927 ACATATACAT
5787937 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
5787963 TACGTATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5790556 original size:178 final size:176
Alignment explanation
Indices: 5790258--5790611 Score: 654
Period size: 178 Copynumber: 2.0 Consensus size: 176
5790248 TTAAATCAGT
*
5790258 TAAAGCCGAGTAAAAGGAGACAATTAAAATATTCCATCATTTTAAGTATTTCACAAGTTGAAAAT
1 TAAAGCCGAGTAAAAGGAGACAATTAAAATATCCCATCATTTTAAGTATTTCACAAGTTGAAAAT
5790323 TTATCCCAACCCATGCAAACGATTGTATTTCATTTAATTTCTCATTAAGGCTTATGACTTCCATA
66 TTATCCCAACCCATGCAAACGATTGTATTTCATTTAATTTCTCATTAAGGCTTATGACTTCCATA
5790388 AAAATTTGGCTCATGCCATCAAATAGTACTCGATGACACCTTGATNC
131 AAAATTTGGCTCATGCCATCAAATAGTACTCGATGACACCTTGAT-C
*
5790435 TAAAGCCGAGTAAAAGGAGACAATTAAAATATCCCATCATTTTTAAGTATTTCACAATTTGAAAA
1 TAAAGCCGAGTAAAAGGAGACAATTAAAATATCCCATCA-TTTTAAGTATTTCACAAGTTGAAAA
*
5790500 TTTATCCCAACCCATGCAAACGGTTGTATTTCATTTAATTTCTCATTAAGGCTTATGACTTCCAT
65 TTTATCCCAACCCATGCAAACGATTGTATTTCATTTAATTTCTCATTAAGGCTTATGACTTCCAT
*
5790565 AAACATTTGGCTCATGCCATCAAATAGTACTCGATGACACCTTGATC
130 AAAAATTTGGCTCATGCCATCAAATAGTACTCGATGACACCTTGATC
5790612 CGAGGCGTAC
Statistics
Matches: 172, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
177 39 0.23
178 133 0.77
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.32
Consensus pattern (176 bp):
TAAAGCCGAGTAAAAGGAGACAATTAAAATATCCCATCATTTTAAGTATTTCACAAGTTGAAAAT
TTATCCCAACCCATGCAAACGATTGTATTTCATTTAATTTCTCATTAAGGCTTATGACTTCCATA
AAAATTTGGCTCATGCCATCAAATAGTACTCGATGACACCTTGATC
Found at i:5792810 original size:13 final size:13
Alignment explanation
Indices: 5792794--5792818 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5792784 TTCTAGAAAA
5792794 TTTATAAAATCAT
1 TTTATAAAATCAT
5792807 TTTATAAAATCA
1 TTTATAAAATCA
5792819 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5803332 original size:18 final size:20
Alignment explanation
Indices: 5803309--5803355 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
5803299 TGGAAATATC
5803309 TAAATATTAATTAA-TAT-A
1 TAAATATTAATTAACTATAA
* *
5803327 TTAATATTATTTAACTATAA
1 TAAATATTAATTAACTATAA
5803347 TAAATATTA
1 TAAATATTA
5803356 TAAAGAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.50
19 3 0.12
20 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATATTAATTAACTATAA
Found at i:5803378 original size:45 final size:45
Alignment explanation
Indices: 5803328--5803416 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
5803318 ATTAATATAT
*
5803328 TAATATTATTT-AACTATAATAAATATTATAAAGAATATTATTTAA
1 TAATATTATTTGAA-TATAATAAATATAATAAAGAATATTATTTAA
*
5803373 TAATATTATTTGAATATAATAAATGTAATAAAGAATATTATTTA
1 TAATATTATTTGAATATAATAAATATAATAAAGAATATTATTTA
5803417 GTATTATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (45 bp):
TAATATTATTTGAATATAATAAATATAATAAAGAATATTATTTAA
Found at i:5803488 original size:23 final size:23
Alignment explanation
Indices: 5803462--5803532 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
5803452 TTTTAATATT
5803462 AAATATTATTTAATTATAATAAA
1 AAATATTATTTAATTATAATAAA
* * * *
5803485 AAAT-TTAATTATCTTCTAATACA
1 AAATATTATTTA-ATTATAATAAA
* *
5803508 AAATATTATTAAATTATTATAAA
1 AAATATTATTTAATTATAATAAA
5803531 AA
1 AA
5803533 TATGTTTGTA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
22 6 0.17
23 25 0.69
24 5 0.14
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATTATTTAATTATAATAAA
Found at i:5808295 original size:38 final size:40
Alignment explanation
Indices: 5808209--5808311 Score: 147
Period size: 38 Copynumber: 2.6 Consensus size: 40
5808199 ACCCAGCTCA
* *
5808209 TGTGCATCCCCCCACATCGTGCACATAGCCGGGGTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCCAGGGCCATCG
** *
5808249 TGTGCATCCCCCCACATCGTGCACA-A-TTAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCCAGGGCCATCG
5808287 TGTGCATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
5808312 CGGGCACTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 32 0.55
39 1 0.02
40 25 0.43
ACGTcount: A:0.19, C:0.39, G:0.20, T:0.21
Consensus pattern (40 bp):
TGTGCATCCCCCCACATCGTGCACATAGCCAGGGCCATCG
Found at i:5809235 original size:23 final size:23
Alignment explanation
Indices: 5809197--5809241 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5809187 AGGAAGAAGA
* *
5809197 AGAAGAAGTTGTTGGAAAATGAG
1 AGAAGAAGTAGCTGGAAAATGAG
*
5809220 AGAAGAAGTAGCTGGAAGATGA
1 AGAAGAAGTAGCTGGAAAATGA
5809242 TATTTATAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.36, T:0.18
Consensus pattern (23 bp):
AGAAGAAGTAGCTGGAAAATGAG
Found at i:5813449 original size:43 final size:43
Alignment explanation
Indices: 5813376--5813507 Score: 149
Period size: 43 Copynumber: 3.1 Consensus size: 43
5813366 GAAATTATAT
* * *
5813376 TGACTCAGCTATGTACGAGTAAGGAATGCGCATAAGCTGAG-GA
1 TGACCCAGCTATGTGCGAGTAAGGAGTGCGCATAAGCTG-GTGA
** * * * *
5813419 TGACCTGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCAGCTATGTGCGAGTAAGGAGTGCGCATAAGCTGGTGA
* *
5813462 TGACCCAGCCATGTGCGAGTAAGGAGTGCGCATGAGCTGGTGA
1 TGACCCAGCTATGTGCGAGTAAGGAGTGCGCATAAGCTGGTGA
5813505 TGA
1 TGA
5813508 TGATGATGTG
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (43 bp):
TGACCCAGCTATGTGCGAGTAAGGAGTGCGCATAAGCTGGTGA
Found at i:5813556 original size:26 final size:23
Alignment explanation
Indices: 5813504--5813563 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
5813494 TGAGCTGGTG
* *
5813504 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATGATGTGT
*
5813527 ATGATGATGATGGGATGATGTGC
1 ATGATGATGATGGGATGATGTGT
*
5813550 ATAATGATGATGGG
1 ATGATGATGATGGG
5813564 TATACGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (23 bp):
ATGATGATGATGGGATGATGTGT
Found at i:5814875 original size:15 final size:15
Alignment explanation
Indices: 5814855--5814911 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
5814845 TTTACAATGC
*
5814855 AATGTGATTATAAGT
1 AATGTGATTGTAAGT
*
5814870 AATGTGCTTGTAAGT
1 AATGTGATTGTAAGT
* * *
5814885 AATATGATTGCAAGC
1 AATGTGATTGTAAGT
5814900 AATGTGATTGTA
1 AATGTGATTGTA
5814912 GGGAAGATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (15 bp):
AATGTGATTGTAAGT
Found at i:5815164 original size:33 final size:33
Alignment explanation
Indices: 5815127--5815208 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 33
5815117 TTTTAATGTC
*
5815127 ATATATTTTATTTTCATTCCTTATTATAATCTT
1 ATATATTTTATTTTCATTCCTTAATATAATCTT
* * *
5815160 ATATATTTTATTTTTATTTCTTAATATAATTTT
1 ATATATTTTATTTTCATTCCTTAATATAATCTT
*
5815193 TTATATTATATATTTT
1 ATATATT-T-TATTTT
5815209 ATTTTAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 35 0.83
34 1 0.02
35 6 0.14
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (33 bp):
ATATATTTTATTTTCATTCCTTAATATAATCTT
Found at i:5816533 original size:25 final size:25
Alignment explanation
Indices: 5816492--5816556 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
5816482 CTTTAGTAAG
5816492 AAATTTT-GTTGGAAATTTCCAACA
1 AAATTTTCGTTGGAAATTTCCAACA
5816516 AAATTTTCGTTGGAAATTTCCAACA
1 AAATTTTCGTTGGAAATTTCCAACA
*
5816541 GAATTTTCGTTGGAAA
1 AAATTTTCGTTGGAAA
5816557 AGACAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 7 0.18
25 32 0.82
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (25 bp):
AAATTTTCGTTGGAAATTTCCAACA
Found at i:5820863 original size:69 final size:69
Alignment explanation
Indices: 5820728--5820866 Score: 154
Period size: 69 Copynumber: 2.0 Consensus size: 69
5820718 GCAAAGTATA
* * * * * * *
5820728 GAGATTTCGGGAAACTGAGCAACGCACGGAGATTGGCAGCAACAACCATCTGCTCTCGATACAAC
1 GAGATTTCGGGAAACTGAGCAACGCACGGAGATCGGCAACAACAAACATCTACGCTCGACAAAAC
5820793 AAGG
66 AAGG
* * * * *
5820797 GAGATTTGGGGAAAGTGAGCAATGCACGGAGATCGGCAACAACAAGAC-TCTACGCTTGGCAAAA
1 GAGATTTCGGGAAACTGAGCAACGCACGGAGATCGGCAACAACAA-ACATCTACGCTCGACAAAA
5820861 CAAGG
65 CAAGG
5820866 G
1 G
5820867 GAACCTAGGT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
69 56 0.98
70 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.29, T:0.15
Consensus pattern (69 bp):
GAGATTTCGGGAAACTGAGCAACGCACGGAGATCGGCAACAACAAACATCTACGCTCGACAAAAC
AAGG
Done.