Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 16 of 345
Found at i:4974670 original size:10 final size:10
Alignment explanation
Indices: 4974642--4974671 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
4974632 TGTATTACGT
4974642 TTTTTTTTCTC
1 TTTTTTTT-TC
4974653 TTTTTTTTTC
1 TTTTTTTTTC
4974663 TTTTTTTTT
1 TTTTTTTTT
4974672 TTCTGATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:4975960 original size:21 final size:21
Alignment explanation
Indices: 4975921--4975961 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4975911 CAGTTAAGTG
*
4975921 TTTGATTATTTTCTATTTTGC
1 TTTGATTATTTTATATTTTGC
* *
4975942 TTTGATTTTTTTATTTTTTG
1 TTTGATTATTTTATATTTTG
4975962 ATACTAACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTGATTATTTTATATTTTGC
Found at i:4978254 original size:15 final size:16
Alignment explanation
Indices: 4978234--4978264 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4978224 TAGTTTTGCG
4978234 TTCATTTCAT-GCATT
1 TTCATTTCATCGCATT
4978249 TTCATTTCATCGCATT
1 TTCATTTCATCGCATT
4978265 ATGTGCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.52
Consensus pattern (16 bp):
TTCATTTCATCGCATT
Found at i:4983214 original size:177 final size:177
Alignment explanation
Indices: 4982918--4983528 Score: 1008
Period size: 177 Copynumber: 3.5 Consensus size: 177
4982908 GACATTGGTG
* *
4982918 AAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATC-AGAAACGGTGAGTCTTATCT
1 AAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGA-AAATGGCGAGTCTTATCT
* *
4982982 CCATGTATCAGCTATGGAGTATATTTTAGCCACCAGCCTTATCTCTCTGAAGTTGCAGTGGAGCA
65 CCATGTATCGGCTATGGAGTAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTTGCAGTGGAGCA
*
4983047 GGTTGAAGATACAAGTCTTATCTTTCTGAAGTTGCAGGAAGTAGACTA
130 GGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTA
*
4983095 AAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCAAGTCTTATCTC
1 AAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTC
* * *
4983160 CACGTATTGGCTATGGAGTAGATTTTAGCCACCAGCCTTATCTTTCTGAAGTTGCAGTGGAGCAG
66 CATGTATCGGCTATGGAGTAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTTGCAGTGGAGCAG
* *
4983225 GTTGAAGATACAAGTCTTATCTTCCTGAAGTTACAGGAAGCAGACTA
131 GTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTA
** *
4983272 AAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATAAAAAATGGCGAGTCTTATCTT
1 AAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTC
* * * *
4983337 CATGTATCGGTTATGGAGTAGATTTTAGCCACCATCCTTATCTCTCTAAAGTTGCAGAGGAGCAG
66 CATGTATCGGCTATGGAGTAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTTGCAGTGGAGCAG
* *
4983402 ATTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTG
131 GTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTA
* *
4983449 AAAATTACAGATCTTATCTCCATCTATCTGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTC
1 AAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTC
4983514 CATGTATCGGCTATG
66 CATGTATCGGCTATG
4983529 AAACAAATCA
Statistics
Matches: 401, Mismatches: 32, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
177 400 1.00
178 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (177 bp):
AAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTC
CATGTATCGGCTATGGAGTAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTTGCAGTGGAGCAG
GTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGACTA
Found at i:4983509 original size:45 final size:45
Alignment explanation
Indices: 4983460--4983581 Score: 174
Period size: 45 Copynumber: 2.7 Consensus size: 45
4983450 AAATTACAGA
* *
4983460 TCTTATCTCCATCTATCTGCTATGGAGCAGATCGAAA-ATGGCGAG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATC-AAAGATGGCGAG
* * *
4983505 TCTTATCTCCATGTATCGGCTATGAAACAAATCAAAGATGGCGAG
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAGATGGCGAG
*
4983550 TCTTATTTCCATGTATCGGCTATGGAGCAGAT
1 TCTTATCTCCATGTATCGGCTATGGAGCAGAT
4983582 TTTAGCCACC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
44 3 0.04
45 64 0.96
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (45 bp):
TCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAGATGGCGAG
Found at i:4985044 original size:21 final size:22
Alignment explanation
Indices: 4985004--4985044 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4984994 TATGCGTGTA
4985004 TATATATATATATATGGTTTGG
1 TATATATATATATATGGTTTGG
* *
4985026 TATAT-TATCTATATTGTTT
1 TATATATATATATATGGTTT
4985045 TGTTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.56
Consensus pattern (22 bp):
TATATATATATATATGGTTTGG
Found at i:4985151 original size:14 final size:15
Alignment explanation
Indices: 4985124--4985162 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
4985114 GTATTCTATG
4985124 TTTTTGTATATATTA
1 TTTTTGTATATATTA
*
4985139 TTTTTTTAT-TATTA
1 TTTTTGTATATATTA
4985153 TTTTATGTAT
1 TTTT-TGTAT
4985163 TTTCTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (15 bp):
TTTTTGTATATATTA
Found at i:4985291 original size:17 final size:17
Alignment explanation
Indices: 4985271--4985312 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
4985261 AATGTTTTTA
*
4985271 TATTTTTAATTCTATAG
1 TATTTTTAATTATATAG
*
4985288 TA-TTTTATTTATATAG
1 TATTTTTAATTATATAG
*
4985304 TTTTTTTAA
1 TATTTTTAA
4985313 AATCTTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (17 bp):
TATTTTTAATTATATAG
Found at i:4985336 original size:26 final size:26
Alignment explanation
Indices: 4985299--4985395 Score: 74
Period size: 26 Copynumber: 3.7 Consensus size: 26
4985289 ATTTTATTTA
*
4985299 TATAGTTT-TTTTAAAATCTTTAATG
1 TATATTTTCTTTTAAAATCTTTAATG
* *
4985324 TATATTTTCTTTTCAAATCTGTT-GTG
1 TATATTTTCTTTTAAAATCT-TTAATG
** * *
4985350 TAAATATTTTCTTTTAATTTATTTATATA
1 T--ATATTTTCTTTTAAAATCTTTA-ATG
4985379 TATATTTTC-TTTAAAAT
1 TATATTTTCTTTTAAAAT
4985396 TATTCGTATA
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
25 7 0.13
26 19 0.35
27 12 0.22
28 15 0.27
29 2 0.04
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (26 bp):
TATATTTTCTTTTAAAATCTTTAATG
Found at i:4985405 original size:27 final size:27
Alignment explanation
Indices: 4985353--4985411 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
4985343 TGTTGTGTAA
* * *
4985353 ATATTTTCTTTTAATTTATTTATATAT
1 ATATTTTCTTTAAAATTATTCATATAT
*
4985380 ATATTTTCTTTAAAATTATTCGTATAT
1 ATATTTTCTTTAAAATTATTCATATAT
4985407 A-ATTT
1 ATATTT
4985412 GGTTGTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (27 bp):
ATATTTTCTTTAAAATTATTCATATAT
Found at i:4987017 original size:21 final size:19
Alignment explanation
Indices: 4986992--4987030 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
4986982 CAGTTAGGTG
4986992 TTTGATTATTTTCTATTTTTC
1 TTTGATT-TTTT-TATTTTTC
4987013 TTTGATTTTTTTATTTTT
1 TTTGATTTTTTTATTTTT
4987031 TGATACTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTGATTTTTTTATTTTTC
Found at i:4987031 original size:21 final size:21
Alignment explanation
Indices: 4986992--4987031 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4986982 CAGTTAGGTG
*
4986992 TTTGATTATTTTCTATTTTTC
1 TTTGATTATTTTATATTTTTC
*
4987013 TTTGATTTTTTTAT-TTTTT
1 TTTGATTATTTTATATTTTT
4987032 GATACTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTGATTATTTTATATTTTTC
Found at i:4995451 original size:46 final size:46
Alignment explanation
Indices: 4995387--4995655 Score: 358
Period size: 46 Copynumber: 5.6 Consensus size: 46
4995377 TTTGAGTACT
* *
4995387 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
4995433 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
4995479 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
4995531 TCTGATCAAGTGATAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTG---A---CAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
4995583 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
4995629 TCTGATCAAGTGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
4995656 GCTACACTTA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
49 1 0.01
52 85 0.43
55 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:4995512 original size:52 final size:51
Alignment explanation
Indices: 4995447--4995655 Score: 293
Period size: 52 Copynumber: 4.1 Consensus size: 51
4995437 ATCAAGTGAC
4995447 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
* *
4995499 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * *
4995550 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
4995597 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGTG
4995649 ATAAGTG
1 A-AAGTG
4995656 GCTACACTTA
Statistics
Matches: 140, Mismatches: 9, Indels: 15
0.85 0.05 0.09
Matches are distributed among these distances:
46 42 0.30
51 1 0.01
52 92 0.66
53 5 0.04
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:4995550 original size:7 final size:7
Alignment explanation
Indices: 4995533--4995566 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
4995523 TACACTTATC
4995533 TGATCAAG
1 TGAT-AAG
4995541 TGATAAG
1 TGATAAG
*
4995548 TGAAAAG
1 TGATAAG
4995555 TGATAAG
1 TGATAAG
4995562 TGATA
1 TGATA
4995567 GCTTCGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.26
Consensus pattern (7 bp):
TGATAAG
Found at i:4995663 original size:37 final size:37
Alignment explanation
Indices: 4995619--4995764 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
4995609 GATAGCTTTA
**
4995619 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
4995656 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
4995693 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
4995730 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
4995765 ATCATACGTA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 88 0.85
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:4996479 original size:46 final size:46
Alignment explanation
Indices: 4996411--4996668 Score: 338
Period size: 46 Copynumber: 5.6 Consensus size: 46
4996401 TTTCTAAAAT
*
4996411 GAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAACATGATAC
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
* * * *
4996457 AAAATGTGTAAGACTATGGTTGAAAGATACCATGGAAACATGATAT
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
*
4996503 GAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATGATAC
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
* ***
4996549 GAAATGTGTAAGACCATGGTTGAAAGATACCACGGCAACATGACGGG
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-TAC
** * *
4996596 GAAATGAATAAGATCATGGTTGAAAGATACCATGGCAACATGACA-
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
* * *
4996641 GAAAATGAGTAAGACCATAGTTTAAAGA
1 G-AAATGTGTAAGACCATGGTTGAAAGA
4996669 CAGTATGGCA
Statistics
Matches: 185, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
45 1 0.01
46 145 0.78
47 39 0.21
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.22
Consensus pattern (46 bp):
GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
Found at i:4997841 original size:22 final size:23
Alignment explanation
Indices: 4997811--4997855 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
4997801 ATTAAATTGT
4997811 AAAGAGTGTAAAAGT-ATTATGCG
1 AAAGAGTGTAAAAGTGA-TATGCG
4997834 AAAG-GTGTAAAAGTGATATGCG
1 AAAGAGTGTAAAAGTGATATGCG
4997856 TGCATGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.42, C:0.04, G:0.29, T:0.24
Consensus pattern (23 bp):
AAAGAGTGTAAAAGTGATATGCG
Found at i:4999477 original size:22 final size:22
Alignment explanation
Indices: 4999452--4999494 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4999442 TATCCAAACA
4999452 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
4999474 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
4999495 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:4999498 original size:11 final size:11
Alignment explanation
Indices: 4999459--4999499 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
4999449 ACAATAACAA
4999459 CAAAATAGTAG
1 CAAAATAGTAG
* *
4999470 CAACATAATAG
1 CAAAATAGTAG
*
4999481 TAAAATAGTAG
1 CAAAATAGTAG
4999492 CAAAATAG
1 CAAAATAG
4999500 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:5000609 original size:46 final size:46
Alignment explanation
Indices: 5000501--5000726 Score: 296
Period size: 46 Copynumber: 5.0 Consensus size: 46
5000491 TTATCTTCGA
* * * * *
5000501 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTT--TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
5000545 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
** * *
5000591 CACATTTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
5000637 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACAT-ATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTCATAT
* * *
5000683 CATGTTGCCATGATATTTTTCAACTATGGTCTTACTCATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
5000727 TTCAGAAAGC
Statistics
Matches: 160, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
44 36 0.22
45 1 0.01
46 123 0.77
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:5001581 original size:51 final size:50
Alignment explanation
Indices: 5001505--5001625 Score: 188
Period size: 51 Copynumber: 2.4 Consensus size: 50
5001495 CTCAAACTTA
* * *
5001505 CTTCATACTTCATCTGGAATTATTACTTTGTTGCTTTAGCTTCAACAAGAG
1 CTTCATATTTCATC-CGAATTATTACTTTGTTGCTCTAGCTTCAACAAGAG
5001556 CTTCATATTTCATCCAGAATTATTACTTTGTTGCTCTAGCTTCAACAAGAG
1 CTTCATATTTCATCC-GAATTATTACTTTGTTGCTCTAGCTTCAACAAGAG
*
5001607 CTTTATATTTCATCCGAAT
1 CTTCATATTTCATCCGAAT
5001626 AACTTGGTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
50 4 0.06
51 61 0.94
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (50 bp):
CTTCATATTTCATCCGAATTATTACTTTGTTGCTCTAGCTTCAACAAGAG
Found at i:5002869 original size:31 final size:31
Alignment explanation
Indices: 5002829--5002922 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
5002819 TCTTTTTATA
5002829 CTAA-TAAAATAATAAAAAATAATAAAATAT
1 CTAATTAAAATAATAAAAAATAATAAAATAT
* * **
5002859 CTTATTAAAATATTAATAAAATAAT-ATTTAT
1 CTAATTAAAATAATAA-AAAATAATAAAATAT
*
5002890 CTAATT-AAATAATTATAAAAT-ATCAAAATAT
1 CTAATTAAAATAA-TAAAAAATAAT-AAAATAT
5002921 CT
1 CT
5002923 CTAGCATCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
29 2 0.04
30 13 0.26
31 27 0.54
32 8 0.16
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (31 bp):
CTAATTAAAATAATAAAAAATAATAAAATAT
Found at i:5002880 original size:11 final size:11
Alignment explanation
Indices: 5002830--5002884 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
5002820 CTTTTTATAC
5002830 TAATAAAATAA
1 TAATAAAATAA
5002841 TAA-AAAATAA
1 TAATAAAATAA
* **
5002851 TAA-AATATCT
1 TAATAAAATAA
* *
5002861 TATTAAAATAT
1 TAATAAAATAA
5002872 TAATAAAATAA
1 TAATAAAATAA
5002883 TA
1 TA
5002885 TTTATCTAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
10 16 0.46
11 19 0.54
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:5004095 original size:16 final size:16
Alignment explanation
Indices: 5004074--5004108 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5004064 CTTTGTGTGT
5004074 CTCTTCTAAGTTCCTC
1 CTCTTCTAAGTTCCTC
5004090 CTCTTCTAAGTTCCTC
1 CTCTTCTAAGTTCCTC
5004106 CTC
1 CTC
5004109 AGGTGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.40, G:0.06, T:0.43
Consensus pattern (16 bp):
CTCTTCTAAGTTCCTC
Found at i:5008047 original size:46 final size:45
Alignment explanation
Indices: 5007995--5008206 Score: 264
Period size: 46 Copynumber: 4.6 Consensus size: 45
5007985 TTTCTGAAAT
* *
5007995 GAAATGTGTAAGACCATGGTTGAAAGATACCACGGCAACATGATA
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA
5008040 CGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA
1 -GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA
** * * * *
5008086 TGAAATGAATAAGATCATGGTTGAAAAATACTATGGCAACATGACGGG
1 -GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC--A
*
5008134 GAAAT-TAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA
1 GAAATGT-GTAAGACCATGGTTGAAAGATACCATGGCAACATGACA
* *
5008179 GAAAATGAGTAAGACCATAGTTGAAAGA
1 G-AAATGTGTAAGACCATGGTTGAAAGA
5008207 CACTATGACA
Statistics
Matches: 144, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
45 1 0.01
46 104 0.72
47 39 0.27
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (45 bp):
GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA
Found at i:5009557 original size:25 final size:24
Alignment explanation
Indices: 5009521--5009571 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
5009511 GCACTTTAAA
5009521 TTTTCCAACTTGTTGTC-TCAAGTG
1 TTTTCCAACTTGTTGTCAT-AAGTG
5009545 TTTTCCTAACTTGTTGTCATAAGTG
1 TTTTCC-AACTTGTTGTCATAAGTG
5009570 TT
1 TT
5009572 GTTTAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.24
25 18 0.72
26 1 0.04
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (24 bp):
TTTTCCAACTTGTTGTCATAAGTG
Found at i:5018346 original size:15 final size:17
Alignment explanation
Indices: 5018334--5018365 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5018324 AAATATTAAT
5018334 CTTT-TTATAATTAAAA
1 CTTTATTATAATTAAAA
5018350 CTTTATTATAA-TAAAA
1 CTTTATTATAATTAAAA
5018366 AGGAACACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
CTTTATTATAATTAAAA
Found at i:5020031 original size:106 final size:107
Alignment explanation
Indices: 5019846--5020122 Score: 333
Period size: 106 Copynumber: 2.6 Consensus size: 107
5019836 CAATGAAGAT
* * * * * *
5019846 GCATCCATTGTGTCTCTACATCTAGTTAGTGGAGACGCATTTACGTGACTCTATAGCTCAATCTA
1 GCATCCATTGTGTCTCTACCTCTAGTTAGTGGAGACGCATGTATGCGACACTATAGCTCAGTCTA
* * *
5019911 TGGTGATGCGAGACATGCATCTTCACT-G-TGTCAGTAGAGAA
66 TGGTGACGCGAGACATGCATCTTCA-TAGATATCAATAGAGAA
* ** *
5019952 GCATCCACTGTGTCTCTACCTCTAGTTAGTTAAGACGCATGTATGCGACGCTATAGCTCAGTCTA
1 GCATCCATTGTGTCTCTACCTCTAGTTAGTGGAGACGCATGTATGCGACACTATAGCTCAGTCTA
* *
5020017 TGGTGACGCGAGACATGCATCTTCATAAGCATATCAATTGAGAC
66 TGGTGACGCGAGACATGCATCTTCAT-AG-ATATCAATAGAGAA
* * * * *
5020061 GTATCCATTGTGTCTCTACCTTTAGTTAGTGGGGACACATGTGTGCGACACTATAGCTCAGT
1 GCATCCATTGTGTCTCTACCTCTAGTTAGTGGAGACGCATGTATGCGACACTATAGCTCAGT
5020123 TTGTAGAGAC
Statistics
Matches: 144, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
105 1 0.01
106 80 0.56
107 1 0.01
109 62 0.43
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (107 bp):
GCATCCATTGTGTCTCTACCTCTAGTTAGTGGAGACGCATGTATGCGACACTATAGCTCAGTCTA
TGGTGACGCGAGACATGCATCTTCATAGATATCAATAGAGAA
Found at i:5021064 original size:22 final size:23
Alignment explanation
Indices: 5021036--5021096 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
5021026 TATGCACTAT
5021036 TAAACAGAGAGCACTAAA-GTGC
1 TAAACAGAGAGCACTAAATGTGC
* *
5021058 TATACAGATAGCAC-AAATGTGC
1 TAAACAGAGAGCACTAAATGTGC
5021080 TAAACAGAGAGCACTAA
1 TAAACAGAGAGCACTAA
5021097 TATACTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.09
22 28 0.85
23 2 0.06
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (23 bp):
TAAACAGAGAGCACTAAATGTGC
Found at i:5021104 original size:22 final size:22
Alignment explanation
Indices: 5021036--5021104 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
5021026 TATGCACTAT
5021036 TAAACAGAGAGCACTAA-AGTGC
1 TAAACAGAGAGCACTAATA-TGC
* * * *
5021058 TATACAGATAGCACAAATGTGC
1 TAAACAGAGAGCACTAATATGC
*
5021080 TAAACAGAGAGCACTAATATAC
1 TAAACAGAGAGCACTAATATGC
5021102 TAA
1 TAA
5021105 TAATCTAAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.19
Consensus pattern (22 bp):
TAAACAGAGAGCACTAATATGC
Found at i:5024078 original size:11 final size:11
Alignment explanation
Indices: 5024062--5024119 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
5024052 TTTAATCACT
5024062 TTAATATTAAA
1 TTAATATTAAA
5024073 TTAATA-TAATA
1 TTAATATTAA-A
* *
5024084 TAAATATTAAG
1 TTAATATTAAA
5024095 TTAATATTAAA
1 TTAATATTAAA
5024106 TTAA-ATTAAA
1 TTAATATTAAA
5024116 TTAA
1 TTAA
5024120 ATTTAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
10 13 0.32
11 25 0.61
12 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:5024108 original size:5 final size:5
Alignment explanation
Indices: 5024062--5024122 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
5024052 TTTAATCACT
* *
5024062 TTAATA TTAAA TT-AA TATAATA TAAATA TTAAG TTAATA TTAAA TTAAA
1 TTAA-A TTAAA TTAAA T-TAA-A TTAA-A TTAAA TTAA-A TTAAA TTAAA
5024111 TTAAA TTAAA TT
1 TTAAA TTAAA TT
5024123 TAATATTAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
4 3 0.06
5 26 0.55
6 16 0.34
7 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:5024121 original size:33 final size:32
Alignment explanation
Indices: 5024062--5024125 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
5024052 TTTAATCACT
5024062 TTAATATTAAATTAATATAATATAAATATTAAG
1 TTAATATTAAATTAATATAATATAAAT-TTAAG
5024095 TTAATATTAAATTAA-ATTAA-ATTAAATTTAA
1 TTAATATTAAATTAATA-TAATA-TAAATTTAA
5024126 TATTAAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 6 0.21
33 23 0.79
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (32 bp):
TTAATATTAAATTAATATAATATAAATTTAAG
Found at i:5024205 original size:38 final size:34
Alignment explanation
Indices: 5024063--5024218 Score: 100
Period size: 38 Copynumber: 4.2 Consensus size: 34
5024053 TTAATCACTT
* *
5024063 TAATATTAAATT-AATATAATATAAATATTAAGT
1 TAATATTAAATTAAATTTAATATAAATATTAAGA
* *
5024096 TAATATTAAATTAAATTAAATTAAATTTAATATTAAGA
1 TAATATTAAATTAAATTTAA-T--A-TAAATATTAAGA
* *
5024134 TAATCACTTTAATATCAAA-TTAATAAAATACTATTAAGA
1 TAAT-A--TTAA-ATTAAATTTAATATAA-A-TATTAAGA
*
5024173 TAAGTATTAAATTAAATTTTAATATTAAACTATTAAAA
1 TAA-TATTAAATTAAA-TTTAATA-TAAA-TATTAAGA
*
5024211 TATTATTA
1 TAATATTA
5024219 TTTTTGGAAT
Statistics
Matches: 96, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
33 12 0.12
34 5 0.05
35 1 0.01
36 5 0.05
37 11 0.11
38 33 0.34
39 15 0.16
40 2 0.02
41 7 0.07
42 5 0.05
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (34 bp):
TAATATTAAATTAAATTTAATATAAATATTAAGA
Found at i:5029740 original size:21 final size:21
Alignment explanation
Indices: 5029716--5029755 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5029706 GGCGTATATA
*
5029716 AAAATGTATACGTA-ATATAAT
1 AAAATATATA-GTATATATAAT
5029737 AAAATATATAGTATATATA
1 AAAATATATAGTATATATA
5029756 CATGTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAATATATAGTATATATAAT
Found at i:5047264 original size:20 final size:22
Alignment explanation
Indices: 5047229--5047269 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5047219 AAACAATAAG
5047229 AATCGATTTAAAATAA-CAAAC
1 AATCGATTTAAAATAAGCAAAC
*
5047250 AATCGA-TTCAAATAAGCAAA
1 AATCGATTTAAAATAAGCAAA
5047270 AAATAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (22 bp):
AATCGATTTAAAATAAGCAAAC
Found at i:5048740 original size:17 final size:17
Alignment explanation
Indices: 5048718--5048774 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
5048708 ACGTATGAGA
5048718 AAAACAAAAAACGTGGG
1 AAAACAAAAAACGTGGG
* * *
5048735 AAAAC-AAAATC--AGA
1 AAAACAAAAAACGTGGG
5048749 AAAACAAAAAACGTGGG
1 AAAACAAAAAACGTGGG
5048766 AAAACAAAA
1 AAAACAAAA
5048775 TCAAGAAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 5 0.16
17 15 0.48
ACGTcount: A:0.67, C:0.12, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAACAAAAAACGTGGG
Found at i:5048753 original size:31 final size:32
Alignment explanation
Indices: 5048715--5048783 Score: 131
Period size: 31 Copynumber: 2.2 Consensus size: 32
5048705 ATTACGTATG
5048715 AGAAAAACAAAAAACGTGGGAAAACAAAATC-
1 AGAAAAACAAAAAACGTGGGAAAACAAAATCA
5048746 AGAAAAACAAAAAACGTGGGAAAACAAAATCA
1 AGAAAAACAAAAAACGTGGGAAAACAAAATCA
5048778 AGAAAA
1 AGAAAA
5048784 CACCCAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 31 0.84
32 6 0.16
ACGTcount: A:0.67, C:0.12, G:0.16, T:0.06
Consensus pattern (32 bp):
AGAAAAACAAAAAACGTGGGAAAACAAAATCA
Found at i:5053785 original size:15 final size:15
Alignment explanation
Indices: 5053762--5053791 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5053752 CTTAATTTAG
*
5053762 TTAAGTCGGGAGTCA
1 TTAACTCGGGAGTCA
5053777 TTAACTCGGGAGTCA
1 TTAACTCGGGAGTCA
5053792 AATTGTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (15 bp):
TTAACTCGGGAGTCA
Found at i:5056290 original size:18 final size:18
Alignment explanation
Indices: 5056267--5056327 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
5056257 CTAATAACAT
*
5056267 TAAAATATATATATAATA
1 TAAAATACATATATAATA
5056285 TAAAATACATATAATATATA
1 TAAAATACATAT-ATA-ATA
*
5056305 TTAGAAAT-GATA-ATAATA
1 -TA-AAATACATATATAATA
5056323 TAAAA
1 TAAAA
5056328 CTATTCATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 3 0.08
17 2 0.05
18 14 0.38
19 6 0.16
20 3 0.08
21 5 0.14
22 4 0.11
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (18 bp):
TAAAATACATATATAATA
Found at i:5056396 original size:19 final size:19
Alignment explanation
Indices: 5056372--5056408 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5056362 TATAAATAAT
*
5056372 AATGATGTTAGAAATATAC
1 AATGATATTAGAAATATAC
5056391 AATGATATTAGAAATATA
1 AATGATATTAGAAATATA
5056409 TATAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (19 bp):
AATGATATTAGAAATATAC
Found at i:5056506 original size:24 final size:24
Alignment explanation
Indices: 5056465--5056520 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
5056455 ACACAATAAT
*
5056465 ATATATAACATACAATAT-TGAAAA
1 ATATAT-ACATACAATATACGAAAA
5056489 CATATATACATA-ATATATACGAAAA
1 -ATATATACATACA-ATATACGAAAA
5056514 ATATATA
1 ATATATA
5056521 GATATACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.57
25 11 0.39
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (24 bp):
ATATATACATACAATATACGAAAA
Found at i:5056545 original size:30 final size:30
Alignment explanation
Indices: 5056492--5056566 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
5056482 TTGAAAACAT
*
5056492 ATATACATAATATATACGAAAAATATATAG
1 ATATACATAATATATACGAAAAATATATAC
** *
5056522 ATATACATAATATAATA-TTAAAATATTTAC
1 ATATACATAATAT-ATACGAAAAATATATAC
5056552 ATAATACATAA-ATAT
1 AT-ATACATAATATAT
5056567 TAGGGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 26 0.67
31 11 0.28
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.35
Consensus pattern (30 bp):
ATATACATAATATATACGAAAAATATATAC
Found at i:5056636 original size:29 final size:27
Alignment explanation
Indices: 5056604--5056660 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
5056594 CTACATAAGT
* *
5056604 ATATACATAAATATATTAAAAACATATAC
1 ATATACATAAA-A-ATAAAAAAAATATAC
*
5056633 ATATATATAAAAATAAAAAAAATATAC
1 ATATACATAAAAATAAAAAAAATATAC
5056660 A
1 A
5056661 CTAATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.56
28 1 0.04
29 10 0.40
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (27 bp):
ATATACATAAAAATAAAAAAAATATAC
Found at i:5056640 original size:21 final size:21
Alignment explanation
Indices: 5056604--5056645 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
5056594 CTACATAAGT
5056604 ATATACATAAATATATTAAAAAC
1 ATATACAT-AATATA-TAAAAAC
5056627 ATATACAT-ATATATAAAAA
1 ATATACATAATATATAAAAA
5056646 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
23 8 0.42
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (21 bp):
ATATACATAATATATAAAAAC
Found at i:5058602 original size:13 final size:13
Alignment explanation
Indices: 5058564--5058602 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
5058554 AATATGAGTT
5058564 GATTGTTGAAAACA
1 GATT-TTGAAAACA
*
5058578 GAATTTGCAAAACA
1 GATTTTG-AAAACA
5058592 GATTTTGAAAA
1 GATTTTGAAAA
5058603 TACCTCGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (13 bp):
GATTTTGAAAACA
Found at i:5058728 original size:89 final size:88
Alignment explanation
Indices: 5058511--5058843 Score: 333
Period size: 89 Copynumber: 3.8 Consensus size: 88
5058501 GAAATTGAAA
* * ** * *
5058511 AAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTGTTGAAAA
1 AAAATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
* * * *
5058576 CA-GAATTTGCAAAACAGATTTTG
65 CATAAATTTGAAAAAAACATTTTG
* *
5058599 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
5058664 GCATAAATTT-AAAAAAACATTAATTG
65 -CATAAATTTGAAAAAAACATT--TTG
* *
5058690 AAAATATCTCAGC-GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 AAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA
* *
5058754 CATAAA-TTGAACAGAA-A--TTG
65 CATAAATTTGAAAAAAACATTTTG
* * ** ** *
5058774 AAAATACCTCAACA-TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAGTTTTG-AAAC
1 AAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAC
*
5058837 AAAAATT
66 ATAAATT
5058844 AACAATACCT
Statistics
Matches: 209, Mismatches: 28, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
82 8 0.04
83 1 0.00
84 53 0.25
88 59 0.28
89 65 0.31
90 9 0.04
91 14 0.07
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (88 bp):
AAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAC
ATAAATTTGAAAAAAACATTTTG
Found at i:5058884 original size:71 final size:71
Alignment explanation
Indices: 5058763--5058902 Score: 192
Period size: 71 Copynumber: 2.0 Consensus size: 71
5058753 ACATAAATTG
* ** **
5058763 AACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAG
1 AACAAAAATTGAAAATACCTCAACATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAG
5058828 TTTTGA
66 TTTTGA
* *
5058834 AACAAAAATT-AACAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AACAAAAATTGAA-AATACCTCAACATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
5058898 TTTTT
65 GTTTT
5058903 TTGAAAAGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 2 0.03
71 58 0.97
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (71 bp):
AACAAAAATTGAAAATACCTCAACATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAG
TTTTGA
Found at i:5058990 original size:92 final size:90
Alignment explanation
Indices: 5058865--5059103 Score: 311
Period size: 90 Copynumber: 2.6 Consensus size: 90
5058855 AGCGTGTCCC
**
5058865 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCATAAATTAAAAAACATTA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA-CATAAATTAAAAAACAGAA
* *
5058930 ATTGAAAATACCTCGGCATGTGATCTT
65 ATTGAAAATACCTCGACATGTGA-CCT
* * * * * *
5058957 GAGGCTCAATTCACCTCTAGTAATATGAATTGA--TTTTTGAAAAACAGAAATTGAAAAACAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACATAAATTAAAAAACAGAA
*
5059020 ATTGTAAATACCTCGACATGTGACCT
65 ATTGAAAATACCTCGACATGTGACCT
* *
5059046 GAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATGAACATAAATTAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-AAACATAAATTAAAA
5059104 CTACCTCAGT
Statistics
Matches: 124, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
89 30 0.24
90 43 0.35
91 22 0.18
92 29 0.23
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (90 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACATAAATTAAAAAACAGAAA
TTGAAAATACCTCGACATGTGACCT
Found at i:5059012 original size:14 final size:14
Alignment explanation
Indices: 5058993--5059023 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5058983 GAATTGATTT
5058993 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
5059007 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
5059021 TTG
1 TTG
5059024 TAAATACCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:5059143 original size:75 final size:74
Alignment explanation
Indices: 5059007--5059238 Score: 313
Period size: 74 Copynumber: 3.1 Consensus size: 74
5058997 AAAACAGAAA
* * *
5059007 TTGAAAAACAGAAATTGTAAATACCTCGACATGTGACCTGAGGTTCAACTCACCTCTCGCAATAT
1 TTGAAAAA-ATAAATTGAAAATACCTC-A-ATGTGTCCTGAGGTTCAACTCACCTCTCGCAATAT
5059072 GAGTTGATTTTT
63 GAGTTGATTTTT
* * *
5059084 TTGATGAACATAAATT-AAAACTACCTCAGTGTGTCCTGAGGTTCAACTCACCTCTCGCAATATG
1 TTGA-AAAAATAAATTGAAAA-TACCTCAATGTGTCCTGAGGTTCAACTCACCTCTCGCAATATG
5059148 AGTTGATTTTT
64 AGTTGATTTTT
* * * * *
5059159 TTGAAAAAATAGATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGAG
1 TTGAAAAAATAAATTGAAAATACCTCAATGTGTCCTGAGGTTCAACTCACCTCTCGCAATATGAG
5059224 TTGATTTTT
66 TTGATTTTT
5059233 TTGAAA
1 TTGAAA
5059239 CAGAAATAAA
Statistics
Matches: 138, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
74 63 0.46
75 53 0.38
76 4 0.03
77 16 0.12
78 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (74 bp):
TTGAAAAAATAAATTGAAAATACCTCAATGTGTCCTGAGGTTCAACTCACCTCTCGCAATATGAG
TTGATTTTT
Found at i:5157075 original size:27 final size:25
Alignment explanation
Indices: 5157038--5157095 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
5157028 AGCATGGCTG
*
5157038 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATG-GACAGAGCCA
* *
5157064 CCAGATACAGATAGTGGGCAGAGCCA
1 CCAGA-ACAGATAATGGACAGAGCCA
5157090 CCAGAA
1 CCAGAA
5157096 TAAAGTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 18 0.64
27 9 0.32
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (25 bp):
CCAGAACAGATAATGGACAGAGCCA
Found at i:5158829 original size:26 final size:26
Alignment explanation
Indices: 5158784--5158951 Score: 221
Period size: 26 Copynumber: 6.2 Consensus size: 26
5158774 ATGAAATTCT
5158784 TTATCATGAAAACATTTACCTAACCCA
1 TTATCATG-AAACATTTACCTAACCCA
5158811 TTATCATGAAACATTTACCTAAACCC-
1 TTATCATGAAACATTTACCT-AACCCA
*
5158837 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
5158863 TTATCATGAAGCATTTACCTAAACCCA
1 TTATCATGAAACATTTACCT-AACCCA
* *
5158890 TTATCATGGAAACATGTACCTAACCTA
1 TTATCAT-GAAACATTTACCTAACCCA
*
5158917 TTTATCATGGAAACATTTACTCTAACCTA
1 -TTATCAT-GAAACATTTAC-CTAACCCA
5158946 TTATCA
1 TTATCA
5158952 AATTTTATGA
Statistics
Matches: 128, Mismatches: 7, Indels: 11
0.88 0.05 0.08
Matches are distributed among these distances:
25 5 0.04
26 49 0.38
27 31 0.24
28 35 0.27
29 8 0.06
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5170111 original size:27 final size:26
Alignment explanation
Indices: 5170074--5170188 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
5170064 AGCATGGCTG
* *
5170074 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
5170100 CCAGATACAGATAGTCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
5170128 CCAGAATAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
5170155 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
5170182 CCAGAAC
1 CCAGAAC
5170189 GCTTCCTCCA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 5 0.07
27 55 0.72
28 16 0.21
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5170133 original size:54 final size:54
Alignment explanation
Indices: 5170074--5170188 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
5170064 AGCATGGCTG
*
5170074 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAGTCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAGTCGTGGCAGAGCCA
* * * * *
5170128 CCAGAATAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAGTCGTGGCAGAGCCA
5170182 CCAGAAC
1 CCAGAAC
5170189 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAGTCGTGGCAGAGCCA
Found at i:5171806 original size:26 final size:26
Alignment explanation
Indices: 5171770--5171931 Score: 261
Period size: 26 Copynumber: 6.2 Consensus size: 26
5171760 CATGAAATTC
5171770 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5171796 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
5171822 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
5171848 TTATCATGAAGCATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
5171874 TTATCATGGAACATGTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
5171900 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5171926 TTATCA
1 TTATCA
5171932 ATTTGTATGA
Statistics
Matches: 128, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 128 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5175941 original size:27 final size:26
Alignment explanation
Indices: 5175904--5176018 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
5175894 AGCATGGCTG
* *
5175904 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
5175930 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
5175958 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
5175985 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
5176012 CCAGAAC
1 CCAGAAC
5176019 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5175963 original size:54 final size:54
Alignment explanation
Indices: 5175904--5176018 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
5175894 AGCATGGCTG
*
5175904 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
5175958 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
5176012 CCAGAAC
1 CCAGAAC
5176019 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:5176148 original size:26 final size:27
Alignment explanation
Indices: 5176119--5176194 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 27
5176109 CAAAATTAAC
* *
5176119 CCTAGGGGTATAACAGTAATTTTGC-A
1 CCTAGGGGTATAATAGTAATTTTCCAA
*
5176145 CCTAAGGGTATAATAGTAATTTTCCATA
1 CCTAGGGGTATAATAGTAATTTTCCA-A
* *
5176173 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATAATAGTAATTT
5176195 AGCTACTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 22 0.52
28 20 0.48
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (27 bp):
CCTAGGGGTATAATAGTAATTTTCCAA
Found at i:5177642 original size:26 final size:26
Alignment explanation
Indices: 5177602--5177711 Score: 159
Period size: 26 Copynumber: 4.2 Consensus size: 26
5177592 CATGAAATTC
*
5177602 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
5177628 TTATCAT-GAAGCATTTACCTAACCCA
1 TTATCATGGAA-CATTTACCTAACCCA
* * *
5177654 TTATCATGGAACATGTACTTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
*
5177680 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
5177706 TTATCA
1 TTATCA
5177712 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
25 2 0.03
26 71 0.93
27 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:5192996 original size:75 final size:75
Alignment explanation
Indices: 5192904--5193416 Score: 534
Period size: 75 Copynumber: 6.6 Consensus size: 75
5192894 TGATGTTTTT
5192904 ATTTCTG--TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGA
1 ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGA
*
5192967 GGTAATTTCA
66 GGTATTTTCA
* ** *
5192977 ATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
1 ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGA
5193042 GGTATTTTCA
66 GGTATTTTCA
* ** *
5193052 ATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
1 ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGA
*
5193117 GCTATTTTCA
66 GGTATTTTCA
** ** *
5193127 ATTTCTGTCTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGATTCACATGC
1 ATTTCTGT-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-A-AGACACGC
*
5193192 TGAGGTATTTTTA
63 TGAGGTATTTTCA
** * * **
5193205 ATTTCTACTTTTCAAAAAAATCAATCAACTGATATTGCGAGGGGTGAGTTGAATCTCAA-ATCAC
1 ATTTCTGTTTTTC--AAAAA--AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA-CAC
5193269 GCACTGAGGTATTTTCA
61 G--CTGAGGTATTTTCA
* * *
5193286 ATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTTAGGTCACAC
1 ATTTCTGTTTTTC---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACAC
*
5193351 GCTGAGATATTTTCA
61 GCTGAGGTATTTTCA
* * *
5193366 TTTTTTTTTTGCTTTTTC--AAAGATCAACTCATAATT-CGAGAGGTGAGTTGA
1 ----ATTTCTG-TTTTTCAAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGA
5193417 ACTTCGGGTC
Statistics
Matches: 374, Mismatches: 44, Indels: 37
0.82 0.10 0.08
Matches are distributed among these distances:
73 6 0.02
75 142 0.38
76 40 0.11
77 4 0.01
78 22 0.06
79 8 0.02
80 71 0.19
81 58 0.16
82 11 0.03
83 1 0.00
84 5 0.01
85 6 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (75 bp):
ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGA
GGTATTTTCA
Found at i:5193356 original size:80 final size:77
Alignment explanation
Indices: 5192915--5193365 Score: 545
Period size: 75 Copynumber: 5.8 Consensus size: 77
5192905 TTTCTGTTTC
*
5192915 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
*
5192980 TCTATTTTTC--
66 TCTGTTTTTCAA
** *
5192990 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
*
5193055 TCTGTCTTTC--
66 TCTGTTTTTCAA
** * *
5193065 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGCTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
*
5193130 TCTGTCTTT-AA
66 TCTGTTTTTCAA
** * *
5193141 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGATTCACATGCTGAGGTATTTTTAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-A-AGACACGCTGAGGTATTTTCAA
**
5193206 TTTCTACTTTTCAA
64 TTTCTGTTTTTCAA
* * **
5193220 AAAAATCAATCAACTGATATTGCGAGGGGTGAGTTGAATCTCAA-ATCACGCACTGAGGTATTTT
1 AAAAA--AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA-CACG--CTGAGGTATTTT
5193284 CAATTTCTGTTTTTCAAA
61 CAATTTCTGTTTTTC-AA
* * * *
5193302 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTTAGGTCACACGCTGAGATATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACACGCTGAGGTATTTTCA
5193366 TTTTTTTTTT
Statistics
Matches: 327, Mismatches: 35, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
75 142 0.43
76 38 0.12
77 1 0.00
78 25 0.08
79 10 0.03
80 44 0.13
81 55 0.17
82 11 0.03
83 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (77 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
TCTGTTTTTCAA
Found at i:5193626 original size:13 final size:13
Alignment explanation
Indices: 5193608--5193632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5193598 CCAAAATTTC
5193608 AAAAAAATAAAAT
1 AAAAAAATAAAAT
5193621 AAAAAAATAAAA
1 AAAAAAATAAAA
5193633 AAATTTTCAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:5193708 original size:29 final size:31
Alignment explanation
Indices: 5193644--5193715 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
5193634 AATTTTCAAA
*
5193644 AAAAATTACATCTTAGACCCTAAACTTTCCTT
1 AAAAATTACATTTTAGACCCTAAACTTT-CTT
*
5193676 --AAATTACATTTTA-ACCTTAAACTTT-TT
1 AAAAATTACATTTTAGACCCTAAACTTTCTT
5193703 AAAAATTACATTT
1 AAAAATTACATTT
5193716 AGCCCCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 2 0.06
29 22 0.61
30 12 0.33
ACGTcount: A:0.40, C:0.18, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAAATTACATTTTAGACCCTAAACTTTCTT
Found at i:5194173 original size:19 final size:20
Alignment explanation
Indices: 5194149--5194191 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
5194139 TGTTTTCATA
*
5194149 TTTTCTTTCCTT-GGTTTTT
1 TTTTCTTTCCTTAGATTTTT
*
5194168 TTTTCTTTCTTTAGATTTTT
1 TTTTCTTTCCTTAGATTTTT
5194188 TTTT
1 TTTT
5194192 TATTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.77
Consensus pattern (20 bp):
TTTTCTTTCCTTAGATTTTT
Found at i:5209694 original size:22 final size:21
Alignment explanation
Indices: 5209651--5209694 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
5209641 TTATCACTTG
5209651 AAAATTAAAAAAAAAAGTATAT
1 AAAATTAAAAAAAAAAG-ATAT
5209673 AAAATTTAAAAATAAAAA-ATAT
1 AAAA-TTAAAAA-AAAAAGATAT
5209695 TTTAGAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAATTAAAAAAAAAAGATAT
Found at i:5210368 original size:24 final size:25
Alignment explanation
Indices: 5210324--5210375 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
5210314 TTTTGGAGAA
5210324 AAAAAGAGAGAGATTCGAATACAAG
1 AAAAAGAGAGAGATTCGAATACAAG
*
5210349 AAAAAGAGAGA-CTCTC-AATACAAG
1 AAAAAGAGAGAGAT-TCGAATACAAG
5210373 AAA
1 AAA
5210376 TACACGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.58, C:0.12, G:0.19, T:0.12
Consensus pattern (25 bp):
AAAAAGAGAGAGATTCGAATACAAG
Found at i:5211011 original size:3 final size:3
Alignment explanation
Indices: 5211005--5211305 Score: 92
Period size: 3 Copynumber: 101.0 Consensus size: 3
5210995 ATTAACCTAC
* * * * *
5211005 TAT TAT TAT TTT TAT CAA TA- TAG TAT TAT T-T TTT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
5211050 TGT TAT TAG CAT GTA- TAT TAT TAT TAAT GTAT CAT TGT TAT TTT CTAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT T-AT -TAT TAT TAT TAT TAT -TAT
* *
5211098 T-T TAT TAT TAGT T-T TAT TAC TAT T-T TTT CTAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * * * *
5211142 T-T TCAT TACT T-T TGT TAT TAT TAT CAT TAT TTT CTAT TAT CAT TAA
1 TAT T-AT TA-T TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * *
5211188 TAT GTCGT T-T GT-T TAT TAT TAT TAT TAT TAT TAT TTT TAA CAT TAT
1 TAT -T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
5211234 TAT CAT CAT TA- TAT ATAT T-T TTT TAA TAT TAT TAC CAT TAT T-T
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
5211277 T-T TAA AAT TAT TAT TAA TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5211306 AATCCATCCT
Statistics
Matches: 217, Mismatches: 55, Indels: 52
0.67 0.17 0.16
Matches are distributed among these distances:
2 28 0.13
3 165 0.76
4 22 0.10
5 2 0.01
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5211019 original size:23 final size:22
Alignment explanation
Indices: 5210993--5211041 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
5210983 ATTACAATTA
* *
5210993 TTATTAACCTACTATTATTATTT
1 TTATCAACATACTATTATT-TTT
* *
5211016 TTATCAATATAGTATTATTTTT
1 TTATCAACATACTATTATTTTT
5211038 TTAT
1 TTAT
5211042 ATTATTATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATCAACATACTATTATTTTT
Found at i:5211150 original size:33 final size:31
Alignment explanation
Indices: 5211090--5211180 Score: 107
Period size: 30 Copynumber: 2.9 Consensus size: 31
5211080 ATCATTGTTA
5211090 TTTTCTATT-TTATTATTAGTTTT-ATTACTATT
1 TTTTCTATTATTATTATTA-TTTTCATTAC--TT
5211122 TTTTCTATTATTATTATTATTTTCATTACTT
1 TTTTCTATTATTATTATTATTTTCATTACTT
* *
5211153 TTGT-TATTATTATCATTATTTTCTATTA
1 TTTTCTATTATTATTATTATTTTC-ATTA
5211181 TCATTAATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
30 18 0.33
31 9 0.17
32 13 0.24
33 14 0.26
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTTCTATTATTATTATTATTTTCATTACTT
Found at i:5211447 original size:15 final size:16
Alignment explanation
Indices: 5211416--5211450 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5211406 GTTATTCCAT
*
5211416 TTTTATCTCTATATTA
1 TTTTATCTATATATTA
5211432 TTTTATCTAT-TATTA
1 TTTTATCTATATATTA
5211447 TTTT
1 TTTT
5211451 TGTCTAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTATCTATATATTA
Found at i:5211451 original size:16 final size:17
Alignment explanation
Indices: 5211414--5211456 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
5211404 TTGTTATTCC
*
5211414 ATTTTTATCTCTATATT
1 ATTTTTATCTATATATT
5211431 A-TTTTATCTAT-TATT
1 ATTTTTATCTATATATT
*
5211446 ATTTTTGTCTA
1 ATTTTTATCTA
5211457 GATTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 5 0.22
16 17 0.74
17 1 0.04
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTTATCTATATATT
Found at i:5211652 original size:125 final size:127
Alignment explanation
Indices: 5211468--5211729 Score: 343
Period size: 125 Copynumber: 2.1 Consensus size: 127
5211458 ATTTTTCAAG
* * *
5211468 TAAAGGCAATATTCGATACTTGAAAATTCGAGAAATCGTGTCCTAACGTACTGGTTTTCGGTTTT
1 TAAAGGCAATATTCCATACTTGAAAATTCGAGAAATCGTGTCCTAACGTACTGGGTTTCGATTTT
* * * *
5211533 TCGTTTGATCTAAGTAACCGATTATCC-TTTT-AAATTAAAATATATGAGTTTTAAATAAAA
66 TCGTTTGAACTAAATAACCGAATATCCATTTTAAAATTAAAATACATGAGTTTTAAATAAAA
* * * *
5211593 TAAAGGCAATATTCCATA-TTTAGAAATTCGAGTAGTCGT-TCCCTAACGTATTGGGTTTCGATT
1 TAAAGGCAATATTCCATACTTGA-AAATTCGAGAAATCGTGT-CCTAACGTACTGGGTTTCGATT
* * *
5211656 TTTCGTTTGAACTAAATATCCGAATATCCATTTTAAAATTTAAATACATGAGTTTTAAATGAAA
64 TTTCGTTTGAACTAAATAACCGAATATCCATTTTAAAATTAAAATACATGAGTTTTAAATAAAA
5211720 TAGAAGGCAA
1 TA-AAGGCAA
5211730 GTTCATACTC
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
124 4 0.03
125 75 0.64
126 4 0.03
127 28 0.24
128 7 0.06
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (127 bp):
TAAAGGCAATATTCCATACTTGAAAATTCGAGAAATCGTGTCCTAACGTACTGGGTTTCGATTTT
TCGTTTGAACTAAATAACCGAATATCCATTTTAAAATTAAAATACATGAGTTTTAAATAAAA
Found at i:5213462 original size:50 final size:50
Alignment explanation
Indices: 5213404--5213511 Score: 137
Period size: 51 Copynumber: 2.2 Consensus size: 50
5213394 GAAGTACTTC
* * * * *
5213404 ACCTAAAAAGGGGAGAGGCCAAGGTGAAAACCCATAAAGGGCGCTTTGAG
1 ACCTAAAAAAGAGAGAAGCCAAGGCGAAAACCCACAAAGGGCGCTTTGAG
* *
5213454 ACCTAAAAAAATAGAGAAGTCAAGGCGAAAACCCACAAAGGGCGCTTTGAG
1 ACCT-AAAAAAGAGAGAAGCCAAGGCGAAAACCCACAAAGGGCGCTTTGAG
5213505 ACC-AAAA
1 ACCTAAAA
5213512 GGGTTTTGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 4 0.08
50 4 0.08
51 42 0.84
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.11
Consensus pattern (50 bp):
ACCTAAAAAAGAGAGAAGCCAAGGCGAAAACCCACAAAGGGCGCTTTGAG
Found at i:5213918 original size:16 final size:18
Alignment explanation
Indices: 5213892--5213925 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5213882 ACTTACATTA
5213892 CACTAAACCCA-AAACCC
1 CACTAAACCCACAAACCC
5213909 CACT-AACCCACAAACCC
1 CACTAAACCCACAAACCC
5213926 AAACAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (18 bp):
CACTAAACCCACAAACCC
Found at i:5213957 original size:26 final size:25
Alignment explanation
Indices: 5213914--5213962 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
5213904 AACCCCACTA
5213914 ACCCACAAACCCAAACAATAACCCTT
1 ACCCACAAACCCAAACAA-AACCCTT
*
5213940 ACCCA-AAACCCATTACAAAACCC
1 ACCCACAAACCCA-AACAAAACCC
5213963 AAATACCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.47, C:0.43, G:0.00, T:0.10
Consensus pattern (25 bp):
ACCCACAAACCCAAACAAAACCCTT
Found at i:5214993 original size:21 final size:19
Alignment explanation
Indices: 5214957--5215000 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
5214947 CTACGTTCTA
*
5214957 TATATATTTTTATATTATG
1 TATATATTTTAATATTATG
5214976 TATATATTTTAA-ATTAT-
1 TATATATTTTAATATTATG
5214993 TATATATT
1 TATATATT
5215001 AAGTATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.33
18 5 0.21
19 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATATATTTTAATATTATG
Found at i:5214996 original size:17 final size:18
Alignment explanation
Indices: 5214957--5215000 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5214947 CTACGTTCTA
*
5214957 TATATATTTTTATATTATG
1 TATATA-TTTTAAATTATG
5214976 TATATATTTTAAATTAT-
1 TATATATTTTAAATTATG
5214993 TATATATT
1 TATATATT
5215001 AAGTATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.33
18 10 0.42
19 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TATATATTTTAAATTATG
Found at i:5215128 original size:16 final size:15
Alignment explanation
Indices: 5215096--5215140 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
5215086 ATTTCTAGTA
5215096 TATGTATA-TATTA-
1 TATGTATATTATTAT
*
5215109 TATGTATTTTATATAT
1 TATGTATATTAT-TAT
5215125 TATGTATATTATTAT
1 TATGTATATTATTAT
5215140 T
1 T
5215141 TTTATCATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.26
14 3 0.11
15 6 0.22
16 11 0.41
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TATGTATATTATTAT
Found at i:5215134 original size:18 final size:19
Alignment explanation
Indices: 5215100--5215139 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
5215090 CTAGTATATG
*
5215100 TATATATTATATGTATT-T
1 TATATATTATATATATTAT
*
5215118 TATATATTATGTATATTAT
1 TATATATTATATATATTAT
5215137 TAT
1 TAT
5215140 TTTTATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TATATATTATATATATTAT
Found at i:5215223 original size:21 final size:22
Alignment explanation
Indices: 5215184--5215236 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
5215174 TCATGTTATT
*
5215184 TATATAT-TTTATTACATAT-G
1 TATATATCTTTAATACATATAG
*
5215204 TATATATCTTTAATATATATAG
1 TATATATCTTTAATACATATAG
*
5215226 -GTATATCTTTA
1 TATATATCTTTA
5215237 TGTAAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.25
21 20 0.71
22 1 0.04
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (22 bp):
TATATATCTTTAATACATATAG
Found at i:5221509 original size:109 final size:109
Alignment explanation
Indices: 5221315--5221516 Score: 343
Period size: 109 Copynumber: 1.9 Consensus size: 109
5221305 TAAATTCAAT
* *
5221315 AGGATATTTGACAATTTGGTTAAACGAGAAATCGGAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
5221380 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
66 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
* *
5221424 AGGATATTT-AGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTTGA-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
*
5221488 ATTTCCAAACGCAAAATATTGCCTTATTT
65 ATTTCCAAACGCAAAACATTGCCTTATTT
5221517 GGAAATATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 1 0.01
109 86 0.99
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (109 bp):
AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
Found at i:5221742 original size:9 final size:9
Alignment explanation
Indices: 5221713--5221746 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5221703 AAAATAAAGG
5221713 AAAATATAT
1 AAAATATAT
5221722 GAAAAT-TAT
1 -AAAATATAT
5221731 AAAATATAT
1 AAAATATAT
5221740 AAAATAT
1 AAAATAT
5221747 GTATGTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAATATAT
Found at i:5221816 original size:13 final size:13
Alignment explanation
Indices: 5221798--5221855 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
5221788 ATTATGAAAA
5221798 ATATAAAATATAT
1 ATATAAAATATAT
*
5221811 ATAT-AAGTATAT
1 ATATAAAATATAT
*
5221823 ATTTTAAAAT-TACT
1 A-TATAAAATATA-T
*
5221837 ATATAAAATATAC
1 ATATAAAATATAT
5221850 ATATAA
1 ATATAA
5221856 GTACGCATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
12 8 0.22
13 21 0.58
14 7 0.19
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATAAAATATAT
Found at i:5222080 original size:6 final size:6
Alignment explanation
Indices: 5222071--5222103 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5222061 ATATAAGTAT
5222071 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATA
5222104 CACTCCTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:5222133 original size:3 final size:3
Alignment explanation
Indices: 5222125--5222161 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
5222115 ATATAAAAGC
*
5222125 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5222162 GGACTAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5223831 original size:44 final size:45
Alignment explanation
Indices: 5223717--5223848 Score: 126
Period size: 45 Copynumber: 3.0 Consensus size: 45
5223707 TTGAAAACTA
* * * * *
5223717 TGGTTTCTTTGATCTGCTTCGTTGTTAGTACAAGAAGGCAAGATC
1 TGGTATCTTCGATCTGCTTCGCTGTCAGTACAAGAAGGCAAGAGC
* * * *
5223762 TGCTATCTTC-ATTCTACTCCGCTGTCAGTACAGGAAGGCAAG-GC
1 TGGTATCTTCGA-TCTGCTTCGCTGTCAGTACAAGAAGGCAAGAGC
* *
5223806 TGGTGTCTTCGATCTGCTTCGCTGTCAAG-GCAAGAAGGCAAGA
1 TGGTATCTTCGATCTGCTTCGCTGTC-AGTACAAGAAGGCAAGA
5223849 TCTGCTGTCT
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
44 33 0.49
45 35 0.51
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (45 bp):
TGGTATCTTCGATCTGCTTCGCTGTCAGTACAAGAAGGCAAGAGC
Found at i:5223921 original size:88 final size:89
Alignment explanation
Indices: 5223797--5224464 Score: 883
Period size: 88 Copynumber: 7.6 Consensus size: 89
5223787 CAGTACAGGA
* * * * **
5223797 AGGCAAGGCTGGTGTCTTCGA-TCTGCTTCGCTGTCAAGGCAAGAAGGCAAGATCTGCTGTCTTC
1 AGGCAAGGTTTGTGTCTTCGACTCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
* *
5223861 AACCATCTCCA-CTACAACCGAGAG
66 AACCAGCTCCATC-ACAACCGACAG
* *
5223885 AGGCAAAGTTTGTGTCTTCGACT-TGCTTCGCCGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
1 AGGCAAGGTTTGTGTCTTCGACTCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
*
5223949 AACCAGCTCCATCACAACCGAGAG
66 AACCAGCTCCATCACAACCGACAG
* * * *
5223973 AGGCAAGGTTTGTGTCTTCGACT-TGCTTCGCCGTCAATACAGGAAGGCAAGATCTTTTATTTTC
1 AGGCAAGGTTTGTGTCTTCGACTCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
5224037 AACCAGCTCCATCACAACCGACAG
66 AACCAGCTCCATCACAACCGACAG
* * ** *
5224061 ATGCAAGGTTTGTGTCTTTGAC-CTGCTTCGCTGTCAACCCAGGAAGGCAAGATCTTTTGTTTTC
1 AGGCAAGGTTTGTGTCTTCGACTCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
*
5224125 AAACAGCTCCATCACAACCGACAG
66 AACCAGCTCCATCACAACCGACAG
* * ** *
5224149 ATGCAAGGTTTGTGTCTTTGAC-CTGCTTCGCTGTCAACCCAGGAAGGCAAGATCTATTGTCTTC
1 AGGCAAGGTTTGTGTCTTCGACTCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
5224213 AACCAGCTCCATCACAACCGACAG
66 AACCAGCTCCATCACAACCGACAG
* *
5224237 AGGCAAGGTTTG-GTTTTCGA-TCTGCTTCGCTGTCAATGCAGGAAGGTAAGATCTTTTGTCTTC
1 AGGCAAGGTTTGTGTCTTCGACTCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
*
5224300 AACCAGCTCCATCACAACCGAAAG
66 AACCAGCTCCATCACAACCGACAG
* * * * *
5224324 AGGCAAGGTTT-TGTTTTC-AATCTGCTTCACTGTTAATGCAGAAAGGCAAGATCTTTTGTCTTC
1 AGGCAAGGTTTGTGTCTTCGACTCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
*
5224387 AACCAGCTCCATCACAACCGAAAG
66 AACCAGCTCCATCACAACCGACAG
* * * * *
5224411 AGGCAAGGTTT-TGTTTTC-AATCTGCTTCACTGTTAATGCAGAAAGGCAAGATCT
1 AGGCAAGGTTTGTGTCTTCGACTCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
5224465 GCTATCTTCA
Statistics
Matches: 538, Mismatches: 36, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
86 1 0.00
87 201 0.37
88 334 0.62
89 2 0.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (89 bp):
AGGCAAGGTTTGTGTCTTCGACTCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
AACCAGCTCCATCACAACCGACAG
Found at i:5223933 original size:44 final size:44
Alignment explanation
Indices: 5223885--5224022 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 44
5223875 CAACCGAGAG
*
5223885 AGGCAAAGTTTGTGTCTTCGACTTGCTTCGCCGTCAATGCAGGA
1 AGGCAAAGTTTGTGTCTTCGACTTGCTTCGCCGTCAATACAGGA
* * ** * *
5223929 AGGC-AAGATCTTTTGTCTTCAACCAGC-T--CCATCACA-ACCGAGA
1 AGGCAAAG-T-TTGTGTCTTCGACTTGCTTCGCCGTCA-ATACAG-GA
*
5223972 GAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCCGTCAATACAGGA
1 -AGGCAAAGTTTGTGTCTTCGACTTGCTTCGCCGTCAATACAGGA
5224017 AGGCAA
1 AGGCAA
5224023 GATCTTTTAT
Statistics
Matches: 70, Mismatches: 14, Indels: 20
0.67 0.13 0.19
Matches are distributed among these distances:
42 7 0.10
43 19 0.27
44 18 0.26
45 18 0.26
46 8 0.11
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (44 bp):
AGGCAAAGTTTGTGTCTTCGACTTGCTTCGCCGTCAATACAGGA
Found at i:5224023 original size:44 final size:44
Alignment explanation
Indices: 5223885--5224023 Score: 133
Period size: 44 Copynumber: 3.2 Consensus size: 44
5223875 CAACCGAGAG
* *
5223885 AGGCAAAGTTTGTGTCTTCGACTTGCTTCGCCGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACTTGCTTCGCCGTCAATACAGGA
* * * ** * *
5223929 AGGCAAGATCTTTTGTCTTCAACCAGC-T--CCATCACA-ACCGAGA
1 AGGCAAGGT-TTGTGTCTTCGACTTGCTTCGCCGTCA-ATACAG-GA
5223972 GAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCCGTCAATACAGGA
1 -AGGCAAGGTTTGTGTCTTCGACTTGCTTCGCCGTCAATACAGGA
5224017 AGGCAAG
1 AGGCAAG
5224024 ATCTTTTATT
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
42 7 0.10
43 16 0.23
44 24 0.34
45 16 0.23
46 8 0.11
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.26
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGACTTGCTTCGCCGTCAATACAGGA
Found at i:5224381 original size:45 final size:45
Alignment explanation
Indices: 5224332--5224464 Score: 132
Period size: 45 Copynumber: 3.0 Consensus size: 45
5224322 AGAGGCAAGG
5224332 TTTTGTTTTCAATCTGCTTCACTGTTAATGCAGAAAGGCAAGATC
1 TTTTGTTTTCAATCTGCTTCACTGTTAATGCAGAAAGGCAAGATC
* * * * *** * *
5224377 TTTTGTCTTCAACCAGCTCCA-TCACAA--CCGAAAGAGGCAAG--G
1 TTTTGTTTTCAATCTGCTTCACTGTTAATGCAG-AA-AGGCAAGATC
5224419 TTTTGTTTTCAATCTGCTTCACTGTTAATGCAGAAAGGCAAGATC
1 TTTTGTTTTCAATCTGCTTCACTGTTAATGCAGAAAGGCAAGATC
5224464 T
1 T
5224465 GCTATCTTCA
Statistics
Matches: 63, Mismatches: 18, Indels: 14
0.66 0.19 0.15
Matches are distributed among these distances:
42 19 0.30
43 12 0.19
44 12 0.19
45 20 0.32
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (45 bp):
TTTTGTTTTCAATCTGCTTCACTGTTAATGCAGAAAGGCAAGATC
Found at i:5226119 original size:6 final size:6
Alignment explanation
Indices: 5226108--5226149 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
5226098 TTGACCCCTC
*
5226108 CTTTTT CTTTTT CTTTTT C-TTCT CTTTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT CTTTTT CTTTTT
5226150 TTCTATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 4 0.12
6 24 0.75
7 4 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:5226140 original size:24 final size:23
Alignment explanation
Indices: 5226109--5226158 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
5226099 TGACCCCTCC
*
5226109 TTTTTCTTTTTCTTTTTCTTCTCT
1 TTTTTCTTTTTCTTTTT-TTCTAT
5226133 TTTTTCTTTTTCTTTTTTTCTAT
1 TTTTTCTTTTTCTTTTTTTCTAT
5226156 TTT
1 TTT
5226159 GACTTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTCTTTTTCTTTTTTTCTAT
Found at i:5226164 original size:23 final size:24
Alignment explanation
Indices: 5226114--5226164 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
5226104 CCTCCTTTTT
* **
5226114 CTTTTTCTTTTTCTTCTCTTTTTT
1 CTTTTTCTTTTTCTTCTATTTTGA
5226138 CTTTTTCTTTTT-TTCTATTTTGA
1 CTTTTTCTTTTTCTTCTATTTTGA
5226161 CTTT
1 CTTT
5226165 GATTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (24 bp):
CTTTTTCTTTTTCTTCTATTTTGA
Found at i:5226177 original size:8 final size:8
Alignment explanation
Indices: 5226162--5226203 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
5226152 CTATTTTGAC
5226162 TTTGATTT
1 TTTGATTT
*
5226170 TTTTA-TT
1 TTTGATTT
5226177 TTTGATTT
1 TTTGATTT
5226185 TTTGATTT
1 TTTGATTT
*
5226193 TTTAATTT
1 TTTGATTT
5226201 TTT
1 TTT
5226204 TCTAGTCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (8 bp):
TTTGATTT
Found at i:5226202 original size:15 final size:15
Alignment explanation
Indices: 5226162--5226194 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5226152 CTATTTTGAC
*
5226162 TTTGATTTTTTTATT
1 TTTGATTTTTTGATT
5226177 TTTGATTTTTTGATT
1 TTTGATTTTTTGATT
5226192 TTT
1 TTT
5226195 TAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTGATTTTTTGATT
Found at i:5228808 original size:19 final size:20
Alignment explanation
Indices: 5228779--5228827 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5228769 CACTTCGTGA
* *
5228779 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
5228798 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
5228818 AAATG-AATGC
1 AAATGTAATGC
5228828 CTAAAGGACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:5230385 original size:109 final size:109
Alignment explanation
Indices: 5230191--5230392 Score: 343
Period size: 109 Copynumber: 1.9 Consensus size: 109
5230181 TAAATTCAAT
* *
5230191 AGGATATTTGACAATTTGGTTAAACGAGAAATCGGAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
5230256 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
66 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
* *
5230300 AGGATATTT-AGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTTGA-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
*
5230364 ATTTCCAAACGCAAAATATTGCCTTATTT
65 ATTTCCAAACGCAAAACATTGCCTTATTT
5230393 GGAAATATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 1 0.01
109 86 0.99
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (109 bp):
AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
Found at i:5230618 original size:9 final size:9
Alignment explanation
Indices: 5230589--5230622 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5230579 AAAATAAAGG
5230589 AAAATATAT
1 AAAATATAT
5230598 GAAAAT-TAT
1 -AAAATATAT
5230607 AAAATATAT
1 AAAATATAT
5230616 AAAATAT
1 AAAATAT
5230623 GTATGTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAATATAT
Found at i:5230955 original size:6 final size:6
Alignment explanation
Indices: 5230946--5230978 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5230936 ATATAAGTAT
5230946 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATA
5230979 CACTCCTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:5231008 original size:3 final size:3
Alignment explanation
Indices: 5231000--5231033 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
5230990 ATATAAAAGA
*
5231000 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5231034 GGACTAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5234153 original size:36 final size:36
Alignment explanation
Indices: 5234106--5234177 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
5234096 ATTTGTAGCC
*
5234106 GTTGAATGCGATCCCTTTCCTCTTTATGATACCTTT
1 GTTGAATGCGATCCCCTTCCTCTTTATGATACCTTT
5234142 GTTGAATGCGATCCCCTTCCTCTTTATGATACCTTT
1 GTTGAATGCGATCCCCTTCCTCTTTATGATACCTTT
5234178 TACTGTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (36 bp):
GTTGAATGCGATCCCCTTCCTCTTTATGATACCTTT
Found at i:5234809 original size:14 final size:14
Alignment explanation
Indices: 5234790--5234823 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5234780 CGCTGAGGTA
*
5234790 TTTCAATCTCTATT
1 TTTCAATCTATATT
*
5234804 TTTCAATTTATATT
1 TTTCAATCTATATT
5234818 TTTCAA
1 TTTCAA
5234824 AAATCAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTCAATCTATATT
Found at i:5234859 original size:86 final size:83
Alignment explanation
Indices: 5234728--5235029 Score: 276
Period size: 86 Copynumber: 3.6 Consensus size: 83
5234718 TTGATGTTTT
* **
5234728 TATTTTTCAAAATTCAACTCATATTGCGAGAAAT-AAGTTGAGCCTCAGGATACGCTGAGGTATT
1 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAA-TTGAGCCTCAGGATACGCTGAGGTATT
5234792 TCAATCTCTATTTTTCAATTTA
65 TC-AT-T-TATTTTTCAATTTA
** *
5234814 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGGCACGCTGAGGAATTT
1 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGATACGCTGAGGTA-TT
* * *
5234879 TCATTTTTGCTTTTCAATCTC
65 TCATTTAT--TTTTCAATTTA
* * * * *
5234900 TGCTTTTTAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGTTTACATGCTGAG
1 T-ATTTTT-CAAAAA-TCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGG-ATAC--GCTGAG
5234964 GTA-TT--TTTAGTTTTT--ATTTA
60 GTATTTCATTTA-TTTTTCAATTTA
* * *
5234984 TACTTTTCAAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTC
1 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTC
5235030 GGGTCACATG
Statistics
Matches: 181, Mismatches: 23, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
81 31 0.17
82 5 0.03
83 4 0.02
84 6 0.03
85 1 0.01
86 69 0.38
87 14 0.08
88 8 0.04
89 35 0.19
91 8 0.04
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (83 bp):
TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGATACGCTGAGGTATTT
CATTTATTTTTCAATTTA
Found at i:5235040 original size:81 final size:83
Alignment explanation
Indices: 5234803--5235311 Score: 306
Period size: 87 Copynumber: 6.0 Consensus size: 83
5234793 CAATCTCTAT
* *
5234803 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGG-CAC
1 TTTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGTCAC
5234867 --GCTGAGGAATTTTCATTTTT-GC
65 ATGCTGAGG-----T-ATTTTTAGC
* * * * * * *
5234889 TTTTCAATCTCTGCTTTTTAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGTTT
1 TTTTCAATTTATAC-TTTT-CAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
5234954 ACATGCTGAGGTATTTTTAG-
63 ACATGCTGAGGTATTTTTAGC
* *
5234974 TTTT-TATTTATACTTTTCAAAAATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
* *
5235038 TGCCGAGGTATTTTTAAATTC
66 TGCTGAGGTATTTTT--A-GC
*
5235059 TGTTGTTCAAATTTTATTTTTAATTCCTACTTTTCCAAAATCAACTCATATTGCGAGAGGTGAGT
1 --TT-TTC--A----A--TTT-A----TACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
* * * *
5235124 TGAGCCTCAGG--ACACGCTGAGGTAATTTCAATTTCTGT
50 TGAGCCTCGGGTCACATGCTGAGGT-A-TT---TTT-AGC
* *
5235162 TTTTCAATTTCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACA
1 TTTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
5235225 CGCTGAGGTA-----A--
66 TGCTGAGGTATTTTTAGC
* * * *
5235236 -TTTCAATTTCTA-TGTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGGGCCTCCGGG-GA
1 TTTTCAATTTATACT-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-CGGGTCA
5235298 CA--CTGAGGTATTTT
64 CATGCTGAGGTATTTT
5235312 CAAATGCTAT
Statistics
Matches: 347, Mismatches: 36, Indels: 89
0.74 0.08 0.19
Matches are distributed among these distances:
72 1 0.00
73 59 0.17
74 3 0.01
75 3 0.01
81 51 0.15
82 5 0.01
83 5 0.01
84 5 0.01
85 10 0.03
86 13 0.04
87 66 0.19
88 9 0.03
89 33 0.10
91 7 0.02
92 3 0.01
94 1 0.00
95 1 0.00
97 3 0.01
98 2 0.01
100 13 0.04
101 3 0.01
102 48 0.14
105 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (83 bp):
TTTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
TGCTGAGGTATTTTTAGC
Found at i:5235179 original size:14 final size:14
Alignment explanation
Indices: 5235149--5235182 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5235139 GCTGAGGTAA
**
5235149 TTTCAATTTCTGTT
1 TTTCAATTTCTACT
5235163 TTTCAATTTCTACT
1 TTTCAATTTCTACT
5235177 TTTCAA
1 TTTCAA
5235183 AAATCAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.59
Consensus pattern (14 bp):
TTTCAATTTCTACT
Found at i:5235209 original size:87 final size:87
Alignment explanation
Indices: 5235068--5235255 Score: 326
Period size: 87 Copynumber: 2.2 Consensus size: 87
5235058 CTGTTGTTCA
*
5235068 AATTT-TATTTTT-AATTCCTACTTTTCCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AATTTCTATTTTTCAATTCCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5235131 CAGGACACGCTGAGGTAATTTC
66 CAGGACACGCTGAGGTAATTTC
* *
5235153 AATTTCTGTTTTTCAATTTCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AATTTCTATTTTTCAATTCCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5235218 CAGGACACGCTGAGGTAATTTC
66 CAGGACACGCTGAGGTAATTTC
*
5235240 AATTTCTATGTTTCAA
1 AATTTCTATTTTTCAA
5235256 AAATCAACTC
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 5 0.05
86 6 0.06
87 85 0.89
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (87 bp):
AATTTCTATTTTTCAATTCCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
CAGGACACGCTGAGGTAATTTC
Found at i:5235282 original size:73 final size:72
Alignment explanation
Indices: 5235162--5235399 Score: 289
Period size: 73 Copynumber: 3.2 Consensus size: 72
5235152 CAATTTCTGT
5235162 TTTTCAATTTCTACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTTCAATTTCTA-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
5235227 CTGAGGTA
65 CTGAGGTA
* * * * ** *
5235235 ATTTCAATTTCTATGTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGGGCCTCCGGGGACA
1 TTTTCAATTTCTAT-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
5235300 CTGAGGTA
65 CTGAGGTA
* * * * * *
5235308 TTTTCAAATGCTATTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACCT-GGGTTCAC
1 TTTTCAATTTCTA-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC
5235372 GTACTGAGGTA
64 G--CTGAGGTA
*
5235383 TTTTCAATTTCTTTTTT
1 TTTTCAATTTCTATTTT
5235400 TTTTCAATTT
Statistics
Matches: 139, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
72 3 0.02
73 113 0.81
74 5 0.04
75 18 0.13
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (72 bp):
TTTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTA
Found at i:5235416 original size:17 final size:17
Alignment explanation
Indices: 5235383--5235417 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5235373 TACTGAGGTA
* *
5235383 TTTTCAATTTCTTTTTT
1 TTTTCAATTTATGTTTT
5235400 TTTTCAATTTATGTTTT
1 TTTTCAATTTATGTTTT
5235417 T
1 T
5235418 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTCAATTTATGTTTT
Found at i:5235528 original size:76 final size:76
Alignment explanation
Indices: 5235400--5235794 Score: 236
Period size: 77 Copynumber: 5.1 Consensus size: 76
5235390 TTTCTTTTTT
*
5235400 TTTTCAATTTATGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCA
1 TTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
5235463 CA-CTGAGGAA
66 CATCTGAGGTA
* * * *
5235473 TTTTCAATTTCTGCTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGATTTGAGCCTCGGCTC
1 TTTTCAATTTATGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
5235538 ACATGCTGAGGTA
65 ACAT-CTGAGGTA
* * **** * * * * * *
5235551 TTTTCAGTTTCTGTTTTTCAAATTTCTGTTTGTTAAAAATCA-ACT-C-ATATTGCGAGAGGTGA
1 TTTTCAATTTATGTTTTTCAAA-------AAAAT-CAACTCATATTGCGAGA--G-GTGAGTTGA
* *
5235613 G--TTGAGTCTCAGGGCATACTGAGGTA
55 GCCTCG-G-GTCA---CAT-CTGAGGTA
* * *
5235639 TTTTCAATTTATGTTTTTC--AAAAATCAA-TGCATATTGCTAGAGGTGATTTGAGCCGCGGGTC
1 TTTTCAATTTATGTTTTTCAAAAAAATCAACT-CATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
5235701 ACATGTCGAGGTA
65 ACATCT-GAGGTA
* * * * * *
5235714 TTTTCAATTTATATTTTTCGAAAAAGTCAACTCATATTACGAGAAGTGAGTTGAGCCGCGGGTCA
1 TTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
5235779 CATGTCGAGGTA
66 CATCT-GAGGTA
5235791 TTTT
1 TTTT
5235795 TAAAATCTTT
Statistics
Matches: 248, Mismatches: 43, Indels: 58
0.71 0.12 0.17
Matches are distributed among these distances:
73 17 0.07
74 1 0.00
75 27 0.11
76 43 0.17
77 57 0.23
78 39 0.16
79 5 0.02
80 2 0.01
81 2 0.01
82 2 0.01
83 3 0.01
84 5 0.02
85 16 0.06
86 1 0.00
88 28 0.11
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (76 bp):
TTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
CATCTGAGGTA
Found at i:5235636 original size:166 final size:162
Alignment explanation
Indices: 5235236--5235723 Score: 604
Period size: 165 Copynumber: 3.0 Consensus size: 162
5235226 GCTGAGGTAA
* * * * * * *
5235236 TTTCAATTTCTATGTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGGGCCTCCGGGGACAC
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACAC
* * * * * *
5235301 TGAGGTATTTTCAAATGCTATTTTTCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACCTGG
66 TGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAA-TCATATTGCGAGAGGTGATTTGAGCCTCG
* * * *
5235366 GTTCACGTACTGAGGTATTTTCAATTTCTTTTTTT
130 GCTCACATGCTGAGGTATTTTCAATTTC--TTGTT
*
5235401 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACAC
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACAC
* *
5235466 TGAGGAATTTTCAATTTCTGCTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGATTTGAGCC
66 TGAGGTATTTTCAATTTCTGTTTTTC---AAAAATCAA-TCATATTGCGAGAGGTGATTTGAGCC
*
5235531 TCGGCTCACATGCTGAGGTATTTTCAGTTTC-TGTT
127 TCGGCTCACATGCTGAGGTATTTTCAATTTCTTGTT
* * *
5235566 TTTCAAATTTCTGTTTGTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGGGCAT
1 TTTC-AATTTATGTTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
* * *
5235630 ACTGAGGTATTTTCAATTTATGTTTTTCAAAAATCAATGCATATTGCTAGAGGTGATTTGAGCCG
64 ACTGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAAT-CATATTGCGAGAGGTGATTTGAGCCT
*
5235695 CGGGTCACATG-TCGAGGTATTTTCAATTT
128 CGGCTCACATGCT-GAGGTATTTTCAATTT
5235724 ATATTTTTCG
Statistics
Matches: 284, Mismatches: 32, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
162 2 0.01
163 58 0.20
165 86 0.30
166 77 0.27
167 2 0.01
168 59 0.21
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (162 bp):
TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACAC
TGAGGTATTTTCAATTTCTGTTTTTCAAAAATCAATCATATTGCGAGAGGTGATTTGAGCCTCGG
CTCACATGCTGAGGTATTTTCAATTTCTTGTT
Found at i:5235781 original size:77 final size:75
Alignment explanation
Indices: 5235585--5235794 Score: 275
Period size: 77 Copynumber: 2.8 Consensus size: 75
5235575 TCTGTTTGTT
* * * *
5235585 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGGG-CATA-CT-GAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCGC-GGGTCACATGTCGAGGTATTTTCAAT
*
5235647 TTATGTTTTTC
65 TTATATTTTTC
* *
5235658 AAAAATCAA-TGCATATTGCTAGAGGTGATTTGAGCCGCGGGTCACATGTCGAGGTATTTTCAAT
1 AAAAATCAACT-CATATTGCGAGAGGTGAGTTGAGCCGCGGGTCACATGTCGAGGTATTTTCAAT
5235722 TTATATTTTTC
65 TTATATTTTTC
* *
5235733 GAAAAAGTCAACTCATATTACGAGAAGTGAGTTGAGCCGCGGGTCACATGTCGAGGTATTTT
1 -AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCGCGGGTCACATGTCGAGGTATTTT
5235795 TAAAATCTTT
Statistics
Matches: 119, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
72 4 0.03
73 35 0.29
74 1 0.01
75 24 0.20
76 5 0.04
77 49 0.41
78 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCGCGGGTCACATGTCGAGGTATTTTCAATT
TATATTTTTC
Found at i:5236068 original size:44 final size:44
Alignment explanation
Indices: 5236005--5236109 Score: 156
Period size: 44 Copynumber: 2.4 Consensus size: 44
5235995 GGCCTCTCTA
* * *
5236005 AAGTTGCAGCGGAGCAGGTCAAAGTTGCAAGTTTTGTCTCCCTG
1 AAGTTGCAGTGAAGCAGGTCAAAGTTGCAAGTCTTGTCTCCCTG
**
5236049 AAGTTGCAGTGAAGCAGGTCAAAGTTGCAAGTCTTGTCTTTCTG
1 AAGTTGCAGTGAAGCAGGTCAAAGTTGCAAGTCTTGTCTCCCTG
*
5236093 AAGTTACAGTGAAGCAG
1 AAGTTGCAGTGAAGCAG
5236110 ATCGAAGCCA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (44 bp):
AAGTTGCAGTGAAGCAGGTCAAAGTTGCAAGTCTTGTCTCCCTG
Found at i:5236405 original size:16 final size:18
Alignment explanation
Indices: 5236379--5236412 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5236369 ACTTACATTA
5236379 CACTAAACCCA-AAACCC
1 CACTAAACCCACAAACCC
5236396 CACT-AACCCACAAACCC
1 CACTAAACCCACAAACCC
5236413 AAACAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (18 bp):
CACTAAACCCACAAACCC
Found at i:5236444 original size:26 final size:25
Alignment explanation
Indices: 5236401--5236449 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
5236391 AACCCCACTA
5236401 ACCCACAAACCCAAACAATAACCCTT
1 ACCCACAAACCCAAACAA-AACCCTT
*
5236427 ACCCA-AAACCCATTACAAAACCC
1 ACCCACAAACCCA-AACAAAACCC
5236450 AAATACCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.47, C:0.43, G:0.00, T:0.10
Consensus pattern (25 bp):
ACCCACAAACCCAAACAAAACCCTT
Found at i:5237434 original size:30 final size:31
Alignment explanation
Indices: 5237398--5237461 Score: 121
Period size: 30 Copynumber: 2.1 Consensus size: 31
5237388 TATATATTTC
5237398 TTTACTATTCCATGTATATATTGGG-TTATA
1 TTTACTATTCCATGTATATATTGGGTTTATA
5237428 TTTACTATTCCATGTATATATTGGGTTTATA
1 TTTACTATTCCATGTATATATTGGGTTTATA
5237459 TTT
1 TTT
5237462 TAATACTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 25 0.76
31 8 0.24
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.53
Consensus pattern (31 bp):
TTTACTATTCCATGTATATATTGGGTTTATA
Found at i:5237498 original size:18 final size:17
Alignment explanation
Indices: 5237475--5237517 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
5237465 TACTACGTTC
*
5237475 TATATATTTTATATTAT
1 TATATATTTTAAATTAT
5237492 GTATATATTTTAAATTAT
1 -TATATATTTTAAATTAT
5237510 TATATATT
1 TATATATT
5237518 AAGTATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATATATTTTAAATTAT
Found at i:5237740 original size:21 final size:22
Alignment explanation
Indices: 5237701--5237753 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
5237691 TCATGTTATT
*
5237701 TATATAT-TTTATTACATAT-G
1 TATATATCTTTAATACATATAG
*
5237721 TATATATCTTTAATATATATAG
1 TATATATCTTTAATACATATAG
*
5237743 -GTATATCTTTA
1 TATATATCTTTA
5237754 TGTAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.25
21 20 0.71
22 1 0.04
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (22 bp):
TATATATCTTTAATACATATAG
Found at i:5239386 original size:41 final size:41
Alignment explanation
Indices: 5239329--5239622 Score: 237
Period size: 41 Copynumber: 6.7 Consensus size: 41
5239319 GAAATTATAG
5239329 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAAAACAA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAAAACAA
* * * * * *
5239370 ATCTTATTTCCCTGAAGTTGTAGTGGAACAAATTGAAGCTATAAATTACAT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGC--A--G-A--TA-AAA--ACAA
*
5239421 ATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATAAAAACAA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAAAACAA
* * * * * *
5239462 ATCTTATTTCCCTGAAGTTGCAGTGGGATGGATTGAAGTTACAATATCAG
1 ATCTTATCTCTCTGAAGTTGCAGT---A--GA--GCAGATA-AA-AACAA
* * *
5239512 ATCTTATCTCTCTAAAGTTGCAGTAGAGCAAATCAAAACAA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAAAACAA
* *
5239553 ATCTTATTTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAAAACAA
* *
5239594 ATCCTATCTCTCTGAAGTTGCAGTGGAGC
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGC
5239623 GGATTAAGGT
Statistics
Matches: 199, Mismatches: 35, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
41 115 0.58
42 2 0.01
43 7 0.04
44 3 0.02
45 3 0.02
46 4 0.02
47 2 0.01
48 7 0.04
49 6 0.03
50 24 0.12
51 26 0.13
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (41 bp):
ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAAAACAA
Done.