Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 178 of 228
Found at i:53242246 original size:28 final size:28
Alignment explanation
Indices: 53242210--53242275 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
53242200 TTTTTTTGGT
*
53242210 ATATTTTGGTAAATAAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
53242238 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
53242266 ATATTTTGGT
1 ATATTTTGGT
53242276 TATTTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:53245366 original size:27 final size:27
Alignment explanation
Indices: 53245329--53245403 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
53245319 ATAACAAAAT
* *
53245329 TTATAAACAGAGTTCCTGTCAATAAGG
1 TTATTAACAGAGTTCCTGTCAACAAGG
* * *
53245356 TTCTTAACAGAGTTTCTATCAACAAGG
1 TTATTAACAGAGTTCCTGTCAACAAGG
*
53245383 TTATTAATAGAGTTCCTGTCA
1 TTATTAACAGAGTTCCTGTCA
53245404 TTCACAGCTC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (27 bp):
TTATTAACAGAGTTCCTGTCAACAAGG
Found at i:53248571 original size:43 final size:43
Alignment explanation
Indices: 53248481--53248599 Score: 134
Period size: 43 Copynumber: 2.8 Consensus size: 43
53248471 ACCGAGATTA
* * * *
53248481 CGTGTAAGACCATATCTGGGATA-TGACATTGATATGAGACTT
1 CGTGTAAGACCATGTCTAGGACATTGACATCGATATGAGACTT
* *
53248523 CGTGTAAGACCATGTCTAGGACATTGACATCGATATGTGATTT
1 CGTGTAAGACCATGTCTAGGACATTGACATCGATATGAGACTT
* * *
53248566 TGTGTAAGACCATGGCTAGG-CTATTGGCATCGAT
1 CGTGTAAGACCATGTCTAGGAC-ATTGACATCGAT
53248600 GCGAGATTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
42 21 0.32
43 45 0.68
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTAGGACATTGACATCGATATGAGACTT
Found at i:53253409 original size:163 final size:163
Alignment explanation
Indices: 53253130--53253457 Score: 559
Period size: 163 Copynumber: 2.0 Consensus size: 163
53253120 CAGGGTGCCA
*
53253130 GTCTTCATTATTTCGGATAGAGATCCGAAGTCTATATAGTGATTCTAAGAGAAAGTACAGTAAGT
1 GTCTTCATTATTTCGGATAGAGATCCGAAGTCTATATAGTGATTCTAAGAGAAAGTACAATAAGT
* *
53253195 TTTGAGTATGAGGTTGTATTGTAATATCGTAATTCATCTTTAAACGAATAGCTAAATAGAGAAAG
66 TTTGAGTATGAGGCTGTATTGTAATATCGTAATTCATCTTTAAACGAATAGCTAAACAGAGAAAG
*
53253260 TGATTCAGGTTCTCGAAAGTATGGTGGATCACT
131 TGATTCAGGTTCTCGAAAGTATGGTGAATCACT
* * *
53253293 GTCTTCATTATTTTGGATAGAGATCCGAAGTTTCTATAGTGATTCTAAGAGAAAGTACAATAAGT
1 GTCTTCATTATTTCGGATAGAGATCCGAAGTCTATATAGTGATTCTAAGAGAAAGTACAATAAGT
*
53253358 TTTGAGTATGAGGCTGTATTGTAATATCGTAATTCATCATTT-AATGAATAGCTAAACAGAGAAA
66 TTTGAGTATGAGGCTGTATTGTAATATCGTAATTCATC-TTTAAACGAATAGCTAAACAGAGAAA
*
53253422 GTGATTTAGGTTCTCGAAAGTATGGTGAATCACT
130 GTGATTCAGGTTCTCGAAAGTATGGTGAATCACT
53253456 GT
1 GT
53253458 GTTTTAGAGT
Statistics
Matches: 155, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
163 152 0.98
164 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (163 bp):
GTCTTCATTATTTCGGATAGAGATCCGAAGTCTATATAGTGATTCTAAGAGAAAGTACAATAAGT
TTTGAGTATGAGGCTGTATTGTAATATCGTAATTCATCTTTAAACGAATAGCTAAACAGAGAAAG
TGATTCAGGTTCTCGAAAGTATGGTGAATCACT
Found at i:53254483 original size:43 final size:43
Alignment explanation
Indices: 53254393--53254511 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 43
53254383 ACCGAGATTA
* * *
53254393 CGTGTAAGACCATATCT--GAGATATGACATTGATATGAGACTT
1 CGTGTAAGACCATGTCTAGGACAT-TGACATCGATATGAGACTT
* *
53254435 CGTGTAAGACCATGTCTAGGACATTGACATCGATATGTGATTT
1 CGTGTAAGACCATGTCTAGGACATTGACATCGATATGAGACTT
* * *
53254478 TGTGTAAGACCATGGCTAGG-CTATTGGCATCGAT
1 CGTGTAAGACCATGTCTAGGAC-ATTGACATCGAT
53254512 GCGAGATTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
42 17 0.26
43 45 0.68
44 4 0.06
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTAGGACATTGACATCGATATGAGACTT
Found at i:53267726 original size:29 final size:30
Alignment explanation
Indices: 53267683--53267763 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
53267673 GAATTGGATC
*
53267683 AAATCAAAATTTCATGTATAAAATTGCACA-
1 AAATC-AAAGTTCATGTATAAAATTGCACAT
*
53267713 AAATCAAAGTTCATGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTGCACA-T
*
53267744 AAATCATAGTTCATGTATAA
1 AAATCAAAGTTCATGTATAA
53267764 TTTTTGTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 22 0.49
30 5 0.11
31 18 0.40
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGCACAT
Found at i:53268338 original size:28 final size:28
Alignment explanation
Indices: 53268306--53268359 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
53268296 GCCTCCAATG
*
53268306 TTCAATTTAGCATCTAAGTTTTTTTTTA
1 TTCAATTAAGCATCTAAGTTTTTTTTTA
* * *
53268334 TTCAATTAAGTATTTATGTTTTTTTT
1 TTCAATTAAGCATCTAAGTTTTTTTT
53268360 ACTAGAGCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.61
Consensus pattern (28 bp):
TTCAATTAAGCATCTAAGTTTTTTTTTA
Found at i:53283436 original size:16 final size:17
Alignment explanation
Indices: 53283415--53283448 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53283405 TCTTCACCTC
53283415 TTCTTTTTGTTT-CTTT
1 TTCTTTTTGTTTACTTT
*
53283431 TTCTTTTTTTTTACTTT
1 TTCTTTTTGTTTACTTT
53283448 T
1 T
53283449 AATTGCTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (17 bp):
TTCTTTTTGTTTACTTT
Found at i:53289292 original size:22 final size:22
Alignment explanation
Indices: 53289247--53289292 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
53289237 TCTTCTCCTC
* *
53289247 TTCTTTTTGTTTCTTTTTATTT
1 TTCTTTTTCTTTCTTTTTACTT
53289269 TTCTTTTTCTTT-TTTCTTACTT
1 TTCTTTTTCTTTCTTT-TTACTT
53289291 TT
1 TT
53289293 GATTATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (22 bp):
TTCTTTTTCTTTCTTTTTACTT
Found at i:53295631 original size:15 final size:15
Alignment explanation
Indices: 53295611--53295645 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
53295601 TAAAAAAAGA
53295611 AATAATGACAATAAT
1 AATAATGACAATAAT
53295626 AATAATGACAATAAT
1 AATAATGACAATAAT
53295641 AATAA
1 AATAA
53295646 AAGACTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAATGACAATAAT
Found at i:53297170 original size:44 final size:44
Alignment explanation
Indices: 53297098--53297766 Score: 575
Period size: 44 Copynumber: 15.0 Consensus size: 44
53297088 GGTATAGGAA
* * ** * *
53297098 TTGTAGTTTCAATCTACTCCGTTGCAACTTCATGGAGATAAGGT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
53297142 TTGTAGCTTTAATCTGCTCCACTACAACTTTAGGGAAATAAGACT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T
** * * * *
53297187 CACTATGGTAAATTTAATCCGAC-CCACTGCAACTTCAGAGG-TATAGGAT
1 ---T-T-GTAGCTTCAATCTG-CTCCACTGCAACTTCAG-GGAGATAAGAT
* *
53297236 TTGTAGCTTC-ATCTTGCTCTACTGCAACTTTAGGGAGATAAGAT
1 TTGTAGCTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
53297280 TCGTAGCTTC-ATCTTGTTCCAC-GTC-ACTTCAAAGG-GATAAGAC
1 TTGTAGCTTCAATC-TGCTCCACTG-CAACTTC-AGGGAGATAAGAT
* *
53297323 TTGTAGCTTCAACCTGCTCCACTGAAACTTCAGGGAGATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
53297367 TTGTAGCTTTAATCTACTCCACTGCAACTTCAGGGGGATAAGACT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T
* * * * * *
53297412 CACTGTGGTAGATTTAATCCGAC-CTACTGCAACTTCAGAGG-TATAGGAT
1 ---T-T-GTAGCTTCAATCTG-CTCCACTGCAACTTCAG-GGAGATAAGAT
* * ** ***
53297461 TCGTCA-CTTCAATCTGCTTCACCACAACTTCAATAAGATAAGAT
1 TTGT-AGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* *
53297505 TTGTAGCTTCAATCTGCTCCATTACAACTTCAGGGAGATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* *
53297549 TTGTAGCTTCAATATGCTCCACTGCAACTTCAAGGAGATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
53297593 TTGTAGCTTCAATCTGCTCCACTGGAACTTCAGGCAGATAAGAC
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
53297637 TTATAGCTTTAATCTGCTCCACTGCAACTTCAAGGAAATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* *
53297681 TTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAACAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
53297725 TTGTAACTTCAATCTGCTCTACTACAACTTCAGGGAGATAAG
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
53297767 GTTCGCTATG
Statistics
Matches: 501, Mismatches: 95, Indels: 58
0.77 0.15 0.09
Matches are distributed among these distances:
43 39 0.08
44 385 0.77
45 4 0.01
46 2 0.00
48 2 0.00
49 4 0.01
50 59 0.12
51 6 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
Found at i:53297502 original size:225 final size:226
Alignment explanation
Indices: 53297123--53297766 Score: 672
Period size: 225 Copynumber: 2.9 Consensus size: 226
53297113 ACTCCGTTGC
* * * * *
53297123 AACTTCATGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTACAACTTTAGGGAAATAAGACTC
1 AACTTCAAGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTC
*
53297188 ACTATGGTAAATTTAATCCGACCCACTGCAACTTCAGAGGTATAGGATTTGTAGCTTCATCTTGC
66 ACTATGGTAAATTTAATCCGACCCACTGCAACTTCAGAGGTATAGGATTCGTAGCTTCATCTTGC
** * * * *
53297253 TCTACTGCAACTTTAGGGAGATAAGATTCGTAGCTTC-ATCTTGTTCCACGT-C-ACTTCAAAGG
131 TCTACCACAACTTCAAGAAGATAAGATTCGTAGCTTCAATC-TGCTCCA-GTACAACTTC-AAGG
*
53297315 -GATAAGACTTGTAGCTTCAACCTGCTCCACTGA
193 AGATAAGACTTGTAGCTTCAACATGCTCCACTGA
* * *
53297348 AACTTCAGGGAGATAAGATTTGTAGCTTTAATCTACTCCACTGCAACTTCAGGGGGATAAGACTC
1 AACTTCAAGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTC
* * *
53297413 ACTGTGGTAGATTTAATCCGACCTACTGCAACTTCAGAGGTATAGGATTCGTCA-CTTCAATC-T
66 ACTATGGTAAATTTAATCCGACCCACTGCAACTTCAGAGGTATAGGATTCGT-AGCTTC-ATCTT
* * * *
53297476 GCT-TCACCACAACTTCAATAAGATAAGATTTGTAGCTTCAATCTGCTCCATTACAACTTCAGGG
129 GCTCT-ACCACAACTTCAAGAAGATAAGATTCGTAGCTTCAATCTGCTCCAGTACAACTTCAAGG
* * *
53297540 AGATAAGATTTGTAGCTTCAATATGCTCCACTGC
193 AGATAAGACTTGTAGCTTCAACATGCTCCACTGA
* * *
53297574 AACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGGAACTTCAGGCAGATAAGACT-
1 AACTTCAAGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTC
** * * * *
53297638 --TA---TAGCTTTAATCTG-CTCCACTGCAACTTCA-AGGAAATAAGATTTGTAGCTTCAATC-
66 ACTATGGTAAATTTAATCCGAC-CCACTGCAACTTCAGAGG-TATAGGATTCGTAGCTTC-ATCT
* * ** * * * * * * * *
53297695 TACTCCACTGCAACTTCAGGGAGATAACATTTGTAACTTCAATCTGCTCTACTACAACTTCAGGG
128 TGCTCTACCACAACTTCAAGAAGATAAGATTCGTAGCTTCAATCTGCTCCAGTACAACTTCAAGG
53297760 AGATAAG
193 AGATAAG
53297767 GTTCGCTATG
Statistics
Matches: 359, Mismatches: 49, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
219 5 0.01
220 101 0.28
223 1 0.00
224 2 0.01
225 151 0.42
226 99 0.28
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (226 bp):
AACTTCAAGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTC
ACTATGGTAAATTTAATCCGACCCACTGCAACTTCAGAGGTATAGGATTCGTAGCTTCATCTTGC
TCTACCACAACTTCAAGAAGATAAGATTCGTAGCTTCAATCTGCTCCAGTACAACTTCAAGGAGA
TAAGACTTGTAGCTTCAACATGCTCCACTGA
Found at i:53307502 original size:16 final size:16
Alignment explanation
Indices: 53307477--53307507 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53307467 TATGAAAATT
*
53307477 ATTTTTAAAAATTAAA
1 ATTTTAAAAAATTAAA
53307493 ATTTTAAAAAATTAA
1 ATTTTAAAAAATTAA
53307508 TTAAATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTTAAAAAATTAAA
Found at i:53312946 original size:7 final size:7
Alignment explanation
Indices: 53312936--53312968 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
53312926 TTTAAATTTT
53312936 AATATTC
1 AATATTC
53312943 AATATTC
1 AATATTC
53312950 AATATTC
1 AATATTC
53312957 AATATTC
1 AATATTC
53312964 AATAT
1 AATAT
53312969 ATATTTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:53315074 original size:7 final size:7
Alignment explanation
Indices: 53315029--53315055 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53315019 GGGAGAACAA
53315029 TTCATGT
1 TTCATGT
53315036 TTCATGT
1 TTCATGT
53315043 TTCATGT
1 TTCATGT
53315050 TTCATG
1 TTCATG
53315056 CAATACTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TTCATGT
Found at i:53315603 original size:17 final size:17
Alignment explanation
Indices: 53315583--53315679 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
53315573 ATTTCAAGAC
53315583 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
53315600 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
*
53315619 CTTATGTAATGTTTTTAA
1 -TTATGTAATATTTTTAA
* ***
53315637 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
53315656 CTTATGTAAT-TTTTTAA
1 -TTATGTAATATTTTTAA
53315673 TTATGTA
1 TTATGTA
53315680 GTGATTCAAA
Statistics
Matches: 56, Mismatches: 18, Indels: 13
0.64 0.21 0.15
Matches are distributed among these distances:
16 7 0.12
17 17 0.30
18 11 0.20
19 5 0.09
20 16 0.29
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:53315677 original size:36 final size:37
Alignment explanation
Indices: 53315578--53315722 Score: 247
Period size: 37 Copynumber: 3.9 Consensus size: 37
53315568 TGTTAATTTC
53315578 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
*
53315615 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
53315652 AAGACTTATGTAAT-TTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
* * *
53315688 AAGACTTATATAATTTTTTTAATTATATAGTGATT
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATT
53315723 TAAATCGGTT
Statistics
Matches: 104, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
36 35 0.34
37 69 0.66
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (37 bp):
AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:53315682 original size:73 final size:74
Alignment explanation
Indices: 53315578--53315722 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 74
53315568 TGTTAATTTC
* *
53315578 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCAAAGACTTATGTAATGTTTTTAATTATGT
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCAAAGACTTATATAATGTTTTTAATTATAT
53315643 AGTGATTCA
66 AGTGATTCA
*
53315652 AAGACTTATGTAAT-TTTTTAATTATGTAGTGATTCAAAGACTTATATAATTTTTTTAATTATAT
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCAAAGACTTATATAATGTTTTTAATTATAT
53315716 AGTGATT
66 AGTGATT
53315723 TAAATCGGTT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
73 54 0.79
74 14 0.21
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (74 bp):
AAGACTTATGTAATATTTTTAATTATGTAGTGATTCAAAGACTTATATAATGTTTTTAATTATAT
AGTGATTCA
Found at i:53315739 original size:9 final size:9
Alignment explanation
Indices: 53315722--53315841 Score: 161
Period size: 9 Copynumber: 13.4 Consensus size: 9
53315712 ATATAGTGAT
53315722 TTAAATCGG
1 TTAAATCGG
*
53315731 TTAAGTCGG
1 TTAAATCGG
53315740 TTAAATCGG
1 TTAAATCGG
53315749 TTAAATCGG
1 TTAAATCGG
*
53315758 TTAAGTCGG
1 TTAAATCGG
53315767 TTAAATCGG
1 TTAAATCGG
*
53315776 TT-AATCAG
1 TTAAATCGG
*
53315784 TTAAATAGG
1 TTAAATCGG
*
53315793 TTAAAACGG
1 TTAAATCGG
*
53315802 TTAAGTCGG
1 TTAAATCGG
*
53315811 TTAAGTCGG
1 TTAAATCGG
*
53315820 TTAAGTCGG
1 TTAAATCGG
53315829 TTAAATCGG
1 TTAAATCGG
53315838 TTAA
1 TTAA
53315842 TTTTTAACCA
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
8 7 0.07
9 91 0.93
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (9 bp):
TTAAATCGG
Found at i:53315752 original size:27 final size:27
Alignment explanation
Indices: 53315722--53315841 Score: 179
Period size: 27 Copynumber: 4.5 Consensus size: 27
53315712 ATATAGTGAT
53315722 TTAAATCGGTTAAGTCGGTTAAATCGG
1 TTAAATCGGTTAAGTCGGTTAAATCGG
53315749 TTAAATCGGTTAAGTCGGTTAAATCGG
1 TTAAATCGGTTAAGTCGGTTAAATCGG
* * * *
53315776 TT-AATCAGTTAAATAGGTTAAAACGG
1 TTAAATCGGTTAAGTCGGTTAAATCGG
* *
53315802 TTAAGTCGGTTAAGTCGGTTAAGTCGG
1 TTAAATCGGTTAAGTCGGTTAAATCGG
53315829 TTAAATCGGTTAA
1 TTAAATCGGTTAA
53315842 TTTTTAACCA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 22 0.27
27 59 0.73
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (27 bp):
TTAAATCGGTTAAGTCGGTTAAATCGG
Found at i:53316289 original size:49 final size:49
Alignment explanation
Indices: 53316232--53316325 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
53316222 TGCTATCCAA
* *
53316232 TGCTAAACTTGGTCTTCCACTGTCTACACTTTTATCACTATTTATACAT
1 TGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATTTATACAT
*
53316281 TGCTAAACTTAGTCTTCTACTGTCTACACTCTTATCACTATTTAT
1 TGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATTTAT
53316326 CCCTTCTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.44
Consensus pattern (49 bp):
TGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATTTATACAT
Found at i:53317775 original size:26 final size:26
Alignment explanation
Indices: 53317739--53317789 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
53317729 CTGATCAAAA
53317739 AGGGGTTGCTAAGTGCAGATTCCCCC
1 AGGGGTTGCTAAGTGCAGATTCCCCC
53317765 AGGGGTTGCTAAGTGCAGATTCCCC
1 AGGGGTTGCTAAGTGCAGATTCCCC
53317790 GAATCACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCAGATTCCCCC
Found at i:53317806 original size:67 final size:67
Alignment explanation
Indices: 53317698--53317830 Score: 230
Period size: 67 Copynumber: 2.0 Consensus size: 67
53317688 ATTGAATGTA
* * * *
53317698 AGGGGTTGCTAAGTGTAGATTCCCTGAATCACTGATCAAAAAGGGGTTGCTAAGTGCAGATTCCC
1 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGGGATTGCTAAGTGAAGATTCCC
53317763 CC
66 CC
53317765 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGGGATTGCTAAGTGAAGATTCCC
1 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGGGATTGCTAAGTGAAGATTCCC
53317830 C
66 C
53317831 GAATCACTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (67 bp):
AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAAAGGGATTGCTAAGTGAAGATTCCC
CC
Found at i:53317827 original size:41 final size:41
Alignment explanation
Indices: 53317765--53317903 Score: 181
Period size: 41 Copynumber: 3.4 Consensus size: 41
53317755 AGATTCCCCC
53317765 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAA
1 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAA
* * *
53317806 AGGGATTGCTAAGTGAAGATTCCCCGAATCACTGATCAAAG
1 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAA
* * * * *
53317847 AGGGGTTGCTAAGTGCTGATTCCCTGAATTATTGATTC-TAA
1 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGA-TCAAAA
53317888 AGGTGGTTGCTAAGTG
1 AGG-GGTTGCTAAGTG
53317904 TTGATTCCAC
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
41 71 0.84
42 14 0.16
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAAA
Found at i:53317939 original size:43 final size:41
Alignment explanation
Indices: 53317765--53317995 Score: 168
Period size: 41 Copynumber: 5.6 Consensus size: 41
53317755 AGATTCCCCC
** * * *
53317765 AGGGGTTGCTAAGTGCAGATTCCCCGAATCAC-TGATCAAAA
1 AGGGGTTGCTAAGTGTTGATTCCCCGTAT-ACTTGATTATAA
* ** * *
53317806 AGGGATTGCTAAGTGAAGATTCCCCGAATCAC-TGATCA-AA
1 AGGGGTTGCTAAGTGTTGATTCCCCGTAT-ACTTGATTATAA
* * * *
53317846 GAGGGGTTGCTAAGTGCTGATTCCCTGAATTA-TTGATTCTAA
1 -AGGGGTTGCTAAGTGTTGATTCCCCGTA-TACTTGATTATAA
* *
53317888 AGGTGGTTGCTAAGTGTTGATTCCACCGTATCCTTGATTGTGAA
1 AGG-GGTTGCTAAGTGTTGATTCC-CCGTATACTTGATTAT-AA
* *
53317932 AGGGGTTGC-AATGTGTTGATTCCCCTTATAAC-TGAATATAA
1 AGGGGTTGCTAA-GTGTTGATTCCCCGTAT-ACTTGATTATAA
*
53317973 AGTGGTTGCTAAGTGTTGATTCC
1 AGGGGTTGCTAAGTGTTGATTCC
53317996 ACCGAGTAAC
Statistics
Matches: 161, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
40 2 0.01
41 89 0.55
42 37 0.23
43 28 0.17
44 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGTTGATTCCCCGTATACTTGATTATAA
Found at i:53321570 original size:3 final size:3
Alignment explanation
Indices: 53321549--53321606 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
53321539 AATGGAAATG
* * * * *
53321549 TAA TGA TAA TAA CAG TAA TAA TAA TAA TAA TAA TAA TAA TCA TCA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53321597 TAA TAA TAA T
1 TAA TAA TAA T
53321607 TGAAGTTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:53326722 original size:21 final size:21
Alignment explanation
Indices: 53326677--53326722 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
53326667 AAAGTAGGTT
*
53326677 ATATATTATTTTTATAATATT
1 ATATATTATTTTTATAATATC
53326698 ATATATTATGATTTT-TAAT-TC
1 ATATATTAT--TTTTATAATATC
53326719 ATAT
1 ATAT
53326723 TATAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 14 0.64
22 4 0.18
23 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATATTATTTTTATAATATC
Found at i:53326769 original size:57 final size:54
Alignment explanation
Indices: 53326699--53326828 Score: 134
Period size: 58 Copynumber: 2.3 Consensus size: 54
53326689 TATAATATTA
* * * *
53326699 TATATTATGATTTTTAATTCATATTATAATAATTATTATATTAAGAATGTTATTAAAT
1 TATA-TATCATTTTTAATT-ATATT-TAATAATAATTATATTAA-AATATGATTAAAT
*
53326757 TATATATCATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAAAT
1 TATATATCA-TTT-TT-AATTATATTTAATAATAATTATATTAAAATATGATTAAAT
* *
53326814 TATTTATTATTTTTA
1 TATATATCATTTTTA
53326829 TTAAAATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
54 1 0.02
55 2 0.03
56 3 0.05
57 22 0.35
58 23 0.37
59 7 0.11
60 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (54 bp):
TATATATCATTTTTAATTATATTTAATAATAATTATATTAAAATATGATTAAAT
Found at i:53326789 original size:58 final size:58
Alignment explanation
Indices: 53326714--53326841 Score: 159
Period size: 58 Copynumber: 2.2 Consensus size: 58
53326704 TATGATTTTT
* * *
53326714 AATTCATATTATAATAATTATTATATTAAGAATGTTATTAAATTATATATCA-TTTTATTA
1 AATT-ATATT-TAATAATAATTATATTAA-AATATGATTAAATTATATATCATTTTTATTA
* * *
53326774 AATTATATTTAATAATAATTATGTTAAAATATGATTAAATTATTTATTATTTTTATTA
1 AATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATATCATTTTTATTA
*
53326832 AAATATATTT
1 AATTATATTT
53326842 TTTTGAAACA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
57 18 0.30
58 33 0.55
59 5 0.08
60 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (58 bp):
AATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATATCATTTTTATTA
Found at i:53327314 original size:18 final size:19
Alignment explanation
Indices: 53327291--53327326 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
53327281 TATTTTTTTA
53327291 TTTTTTA-TTTTAAAATAT
1 TTTTTTATTTTTAAAATAT
53327309 TTTTTTATTTTTAAAATA
1 TTTTTTATTTTTAAAATA
53327327 AATTTTAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTATTTTTAAAATAT
Found at i:53327332 original size:19 final size:18
Alignment explanation
Indices: 53327292--53327332 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
53327282 ATTTTTTTAT
**
53327292 TTTTTATTTTAAAATATT
1 TTTTTATTTTAAAATAAA
53327310 TTTTTATTTTTAAAATAAA
1 TTTTTA-TTTTAAAATAAA
53327329 TTTT
1 TTTT
53327333 AGTGTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTATTTTAAAATAAA
Found at i:53331201 original size:27 final size:25
Alignment explanation
Indices: 53331146--53331196 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
53331136 TTAAATATTT
*
53331146 TTTTATTTTTAATCAAGTATATATA
1 TTTTATTTTTAATCAAATATATATA
53331171 TTTTATTTTTAATCAAATATATATA
1 TTTTATTTTTAATCAAATATATATA
53331196 T
1 T
53331197 ATTTTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTATTTTTAATCAAATATATATA
Found at i:53331205 original size:29 final size:27
Alignment explanation
Indices: 53331140--53331202 Score: 87
Period size: 25 Copynumber: 2.4 Consensus size: 27
53331130 TATATATTAA
*
53331140 ATAT-TTTTTTATTTTTAATCAAGTAT
1 ATATATTTTTTATTTTTAATCAAATAT
53331166 ATATA--TTTTATTTTTAATCAAATAT
1 ATATATTTTTTATTTTTAATCAAATAT
53331191 ATATATATTTTT
1 ATATAT-TTTTT
53331203 TATATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 24 0.75
26 4 0.12
28 4 0.12
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (27 bp):
ATATATTTTTTATTTTTAATCAAATAT
Found at i:53331585 original size:23 final size:22
Alignment explanation
Indices: 53331555--53331599 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
53331545 TTTTCATACT
53331555 TTTATTT-ATTTCTGAGAATTTA
1 TTTATTTAATTT-TGAGAATTTA
*
53331577 TTTATTTTAATTTTGAGATTTTA
1 TTTA-TTTAATTTTGAGAATTTA
53331600 AAATTATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (22 bp):
TTTATTTAATTTTGAGAATTTA
Found at i:53334657 original size:19 final size:19
Alignment explanation
Indices: 53334632--53334677 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
53334622 TCTCTCAATA
*
53334632 AAAAATTCAAAATATTTTT
1 AAAAATTCAAAATATTTAT
*
53334651 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
53334670 AAAAATTC
1 AAAAATTC
53334678 TACAATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:53337838 original size:41 final size:41
Alignment explanation
Indices: 53337706--53337839 Score: 111
Period size: 41 Copynumber: 3.4 Consensus size: 41
53337696 ACCAGTTTGG
* * *
53337706 CACCTAGTGCCTCATC-AAATAATTCGAAGTAATAATTTGA
1 CACCTAGTGCCTCATCGAAATAATCCGAAGTAGTAAATTGA
** * *
53337746 CACCTAGTGTCC-CA--GAGGCTAAACCG-A--AGTAAATTGG
1 CACCTAGTG-CCTCATCGA-AATAATCCGAAGTAGTAAATTGA
* *
53337783 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCTAGTGCCTCATCGAAATAATCCGAAGTAGTAAATTGA
*
53337824 CACCTAGTGTCTCATC
1 CACCTAGTGCCTCATC
53337840 AACTCGAAGT
Statistics
Matches: 71, Mismatches: 14, Indels: 17
0.70 0.14 0.17
Matches are distributed among these distances:
36 2 0.03
37 17 0.24
38 6 0.08
39 5 0.07
40 16 0.23
41 25 0.35
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
CACCTAGTGCCTCATCGAAATAATCCGAAGTAGTAAATTGA
Found at i:53338076 original size:33 final size:32
Alignment explanation
Indices: 53338014--53338079 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
53338004 AATTAAAAAA
* **
53338014 TCAATCCATTCAATATATATATATCTATCAAT
1 TCAATCCATTCAATAAATATATAAATATCAAT
53338046 TCAATCCACTTCAATAAAT-TATCAAATATCAAT
1 TCAATCCA-TTCAATAAATATAT-AAATATCAAT
53338079 T
1 T
53338080 ACTCCTCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (32 bp):
TCAATCCATTCAATAAATATATAAATATCAAT
Found at i:53338766 original size:21 final size:21
Alignment explanation
Indices: 53338718--53338759 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53338708 TGCTTTCTCA
53338718 TTCTTTCCTTCCATTTTTCTT
1 TTCTTTCCTTCCATTTTTCTT
*
53338739 TTCTTTCCTTTC-TTTTTCTT
1 TTCTTTCCTTCCATTTTTCTT
53338759 T
1 T
53338760 CATTTTCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCTTTCCTTCCATTTTTCTT
Found at i:53338859 original size:13 final size:13
Alignment explanation
Indices: 53338837--53338869 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
53338827 ATATTTAATC
*
53338837 ATTAAGAATATAT
1 ATTAATAATATAT
53338850 ATTAATAATATAT
1 ATTAATAATATAT
53338863 A-TAATAA
1 ATTAATAA
53338870 ACTTATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
ATTAATAATATAT
Found at i:53340469 original size:27 final size:27
Alignment explanation
Indices: 53340410--53340473 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
53340400 TCCAAACTTA
*
53340410 TATAAAATGACTGTTATGCCCCCACAT
1 TATAAAATGAATGTTATGCCCCCACAT
** * **
53340437 GGTAAAATGAATGTTATGCCCCTATGT
1 TATAAAATGAATGTTATGCCCCCACAT
53340464 TATAAAATGA
1 TATAAAATGA
53340474 CTGCATGCTC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (27 bp):
TATAAAATGAATGTTATGCCCCCACAT
Found at i:53340775 original size:33 final size:31
Alignment explanation
Indices: 53340738--53340806 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 31
53340728 TATTACTGTC
53340738 ACTGTAATGGGCTAAGG-CCACACTGATACTGA
1 ACTGTAATGGGCTAAGGCCCA-ACTGA-ACTGA
*
53340770 TACTGTAATGGGTTAAGGCCCAACTGAACTGA
1 -ACTGTAATGGGCTAAGGCCCAACTGAACTGA
53340802 ACTGT
1 ACTGT
53340807 TATTGAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 5 0.15
32 5 0.15
33 21 0.62
34 3 0.09
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
ACTGTAATGGGCTAAGGCCCAACTGAACTGA
Found at i:53346712 original size:42 final size:41
Alignment explanation
Indices: 53346656--53346800 Score: 168
Period size: 42 Copynumber: 3.4 Consensus size: 41
53346646 ACTGAGATGT
*
53346656 GATTACGTGTAAGACCATATCTGGGAAATTGGCATCATTATGT
1 GATT-CGTGTAAGACCATATCTGGGAAATTGGCATCA-TATGA
* * *
53346699 GATTCGTGTAAGACCGTGTCTGGGATATTGGCATCAATATGA
1 GATTCGTGTAAGACCATATCTGGGAAATTGGCATC-ATATGA
* *
53346741 GAATT-GTGTAAGATCATGTCT-GGAACATTGGCATCGATATGA
1 G-ATTCGTGTAAGACCATATCTGGGAA-ATTGGCATC-ATATGA
53346783 GATTCGTGTAAGACCATA
1 GATTCGTGTAAGACCATA
53346801 GCTAGCTATT
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
41 6 0.07
42 74 0.84
43 8 0.09
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (41 bp):
GATTCGTGTAAGACCATATCTGGGAAATTGGCATCATATGA
Found at i:53346835 original size:84 final size:83
Alignment explanation
Indices: 53346662--53346846 Score: 200
Period size: 84 Copynumber: 2.2 Consensus size: 83
53346652 ATGTGATTAC
* * *
53346662 GTGTAAGACCATATCTGGGAAATTGGCATCATTATGTGATTCGTGTAAGACCGTGTCTGGGATAT
1 GTGTAAGACCATATCT-GGAAATTGGCATCATTATGAGATTCGTGTAAGACCATGTCTGAGATAT
*
53346727 TGGCATCAATATGAGAATT
65 TGGCATCAATATGAGAATA
* * *
53346746 GTGTAAGATCATGTCTGGAACATTGGCATCGA-TATGAGATTCGTGTAAGACCATAG-CT-AGCT
1 GTGTAAGACCATATCTGGAA-ATTGGCATC-ATTATGAGATTCGTGTAAGACCAT-GTCTGAGAT
*
53346808 ATTGGCATCGATAT-ATG-ATA
63 ATTGGCATCAATATGA-GAATA
53346828 GCATGTAAGACCATATCTG
1 G--TGTAAGACCATATCTG
53346847 AGATATGGCA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
82 4 0.05
83 20 0.24
84 59 0.69
85 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (83 bp):
GTGTAAGACCATATCTGGAAATTGGCATCATTATGAGATTCGTGTAAGACCATGTCTGAGATATT
GGCATCAATATGAGAATA
Found at i:53349164 original size:41 final size:41
Alignment explanation
Indices: 53349119--53349321 Score: 243
Period size: 41 Copynumber: 5.0 Consensus size: 41
53349109 TTGTATAAAA
* * * * *
53349119 CACCGGCA-TAAAGCCTGCTAGGCACAAAGCCCGATACATTC
1 CACCGGCACT-AAGCCTGCTAGACATAAAGTCTGATACATTT
* *
53349160 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATATTT
1 CACCGGCACTAAGCCTGCTAGACATAAAGTCTGATACATTT
53349201 CACCGGCACTAAGCCTGCTAGACATAAAGTCTGATACATTT
1 CACCGGCACTAAGCCTGCTAGACATAAAGTCTGATACATTT
* *
53349242 CACCGGTACTAAGCCTGCTAGACATAAAATCTGAAGTA-A-TT
1 CACCGGCACTAAGCCTGCTAGACATAAAGTCTG-A-TACATTT
* *
53349283 CACCGGCA-TCAAGCCTGCTAGACGTAAAGTCTGAAACAT
1 CACCGGCACT-AAGCCTGCTAGACATAAAGTCTGATACAT
53349322 CTTATTTTCA
Statistics
Matches: 141, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 3 0.02
41 133 0.94
42 2 0.01
43 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (41 bp):
CACCGGCACTAAGCCTGCTAGACATAAAGTCTGATACATTT
Found at i:53349988 original size:16 final size:17
Alignment explanation
Indices: 53349967--53350001 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53349957 ATCTAATAAT
53349967 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
53349983 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
53350000 TT
1 TT
53350002 CAACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:53353495 original size:21 final size:21
Alignment explanation
Indices: 53353456--53353497 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53353446 GAGATTATGA
*
53353456 AATTACAAATGAATTGGATTG
1 AATTACAAATGAATGGGATTG
53353477 AATTA-AAATGAAATGGGATTG
1 AATTACAAATG-AATGGGATTG
53353498 GAAATTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.31
Consensus pattern (21 bp):
AATTACAAATGAATGGGATTG
Found at i:53359758 original size:22 final size:22
Alignment explanation
Indices: 53359733--53359776 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53359723 TTGTTTTGCC
*
53359733 ACTATTTTACT-TTCATTTTATT
1 ACTATGTTACTATT-ATTTTATT
*
53359755 ACTATGTTGCTATTATTTTATT
1 ACTATGTTACTATTATTTTATT
53359777 TTTATTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.23, C:0.11, G:0.05, T:0.61
Consensus pattern (22 bp):
ACTATGTTACTATTATTTTATT
Found at i:53366986 original size:7 final size:7
Alignment explanation
Indices: 53366951--53366975 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53366941 TGATAAATAA
53366951 TAAAAAT
1 TAAAAAT
53366958 TAAAAAT
1 TAAAAAT
53366965 TAAAAAT
1 TAAAAAT
53366972 TAAA
1 TAAA
53366976 TAAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAAAT
Found at i:53367484 original size:7 final size:7
Alignment explanation
Indices: 53367472--53367501 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
53367462 TTTTTTTAAT
53367472 ATATATA
1 ATATATA
53367479 ATATATA
1 ATATATA
53367486 ATATATA
1 ATATATA
53367493 ATATATA
1 ATATATA
53367500 AT
1 AT
53367502 TTAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:53368153 original size:29 final size:30
Alignment explanation
Indices: 53368115--53368176 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
53368105 TGCAAATTTG
53368115 AAATTCAATCCCTATAATTTTAT-TTTCAA
1 AAATTCAATCCCTATAATTTTATATTTCAA
* * *
53368144 AAATTTAATCTCTATACTTTTATAATTTCAA
1 AAATTCAATCCCTATAATTTTAT-ATTTCAA
53368175 AA
1 AA
53368177 TTGAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.71
31 8 0.29
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (30 bp):
AAATTCAATCCCTATAATTTTATATTTCAA
Found at i:53369809 original size:15 final size:15
Alignment explanation
Indices: 53369789--53369820 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
53369779 TATGTTATTG
53369789 CTTGCTAATTAAGTT
1 CTTGCTAATTAAGTT
53369804 CTTGCTAATTAAGTT
1 CTTGCTAATTAAGTT
53369819 CT
1 CT
53369821 CTCATTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (15 bp):
CTTGCTAATTAAGTT
Found at i:53375448 original size:25 final size:25
Alignment explanation
Indices: 53375423--53375471 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
53375413 TTTAAAATTA
*
53375423 AAAAAAATTA-ATTGCAATGTATTT
1 AAAAAAATGATATTGCAATGTATTT
*
53375447 AAAAAAATGATATTGTAATGTATTT
1 AAAAAAATGATATTGCAATGTATTT
53375472 TAATTTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (25 bp):
AAAAAAATGATATTGCAATGTATTT
Found at i:53377717 original size:15 final size:15
Alignment explanation
Indices: 53377697--53377761 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
53377687 TCCTCCAGCT
53377697 CTTCATCATCATCAA
1 CTTCATCATCATCAA
*
53377712 CTTCAT-ATACATCAT
1 CTTCATCAT-CATCAA
**
53377727 CACCATCATCAT-AA
1 CTTCATCATCATCAA
* *
53377741 TCTTCATCATCTTCGA
1 -CTTCATCATCATCAA
53377757 CTTCA
1 CTTCA
53377762 GCTTCATCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
14 3 0.08
15 32 0.84
16 3 0.08
ACGTcount: A:0.31, C:0.32, G:0.02, T:0.35
Consensus pattern (15 bp):
CTTCATCATCATCAA
Found at i:53386484 original size:17 final size:18
Alignment explanation
Indices: 53386462--53386505 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
53386452 ATTAGCTTCA
53386462 TATAAAATA-TTAATTAT
1 TATAAAATATTTAATTAT
**
53386479 TATAAAATATTTTCTTAT
1 TATAAAATATTTAATTAT
53386497 TATAAAATA
1 TATAAAATA
53386506 AATTTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TATAAAATATTTAATTAT
Found at i:53387255 original size:16 final size:16
Alignment explanation
Indices: 53387194--53387263 Score: 79
Period size: 16 Copynumber: 4.4 Consensus size: 16
53387184 TTTGGTTCGC
* *
53387194 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
53387210 CGTAATGGAATAG-GAG
1 TGTAATGGAATAGAG-G
*
53387226 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
53387242 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
53387258 TGTAAT
1 TGTAAT
53387264 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
15 1 0.02
16 45 0.96
17 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:53387263 original size:32 final size:32
Alignment explanation
Indices: 53387194--53387263 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
53387184 TTTGGTTCGC
* *
53387194 TGTATTGGATTAGAGGCGTAATGGAATAGGAG
1 TGTAATGGAATAGAGGCGTAATGGAATAGGAG
* *
53387226 CGTAATGGAATAGAGGTGTAATGGAATA-GATG
1 TGTAATGGAATAGAGGCGTAATGGAATAGGA-G
53387258 TGTAAT
1 TGTAAT
53387264 AGCAAATCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (32 bp):
TGTAATGGAATAGAGGCGTAATGGAATAGGAG
Found at i:53387308 original size:45 final size:44
Alignment explanation
Indices: 53387242--53387332 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 44
53387232 GGAATAGAGG
* *
53387242 TGTAATGGAATAGATGTGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATACATGCGTAATAG-AAAT-AATGTGTTTGGTTGAA
* *
53387287 TGTAATGGAATACA-GACGTAATAGTAATATTGTGTTTGGTTGAA
1 TGTAATGGAATACATG-CGTAATAGAAATAATGTGTTTGGTTGAA
53387331 TG
1 TG
53387333 GAATAGAGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 2 0.05
44 18 0.45
45 20 0.50
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATACATGCGTAATAGAAATAATGTGTTTGGTTGAA
Found at i:53387525 original size:14 final size:15
Alignment explanation
Indices: 53387470--53387527 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
53387460 AAATAATTTA
* *
53387470 ATTATATTTAAACAT
1 ATTATAATTAAATAT
*
53387485 AATTATTATTAAATAT
1 -ATTATAATTAAATAT
53387501 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
53387515 A-TATAATTTAATA
1 ATTATAATTAAATA
53387528 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 9 0.25
14 4 0.11
15 11 0.31
16 12 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:53387629 original size:120 final size:120
Alignment explanation
Indices: 53387480--53387889 Score: 711
Period size: 120 Copynumber: 3.4 Consensus size: 120
53387470 ATTATATTTA
53387480 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
53387545 TATTCTTATATGAATTTACTCAAATCATAATATATTATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATCATACTATAAAATATAAATT
*
53387600 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
53387665 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATCATACTATAAAATATAAATT
53387720 AACAT-A--ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
53387782 TATTCTTATATGAATTTACTCAAATCATAATATATCATACTATAAAAGATAATTTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATCATACTATAAAATATAA-ATT
* * *
53387838 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
53387890 TAAAATAATT
Statistics
Matches: 277, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
117 107 0.39
118 5 0.02
119 1 0.00
120 164 0.59
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATCATACTATAAAATATAAATT
Found at i:53387638 original size:18 final size:17
Alignment explanation
Indices: 53387617--53387651 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53387607 TTATTATTAA
*
53387617 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53387635 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53387652 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53387959 original size:26 final size:28
Alignment explanation
Indices: 53387930--53387990 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
53387920 TATGAATTTG
*
53387930 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
53387956 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
53387984 TAAAATT
1 TATAATT
53387991 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:53387988 original size:47 final size:46
Alignment explanation
Indices: 53387937--53388080 Score: 104
Period size: 47 Copynumber: 3.1 Consensus size: 46
53387927 TTGTATAATT
53387937 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
53387984 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* * *
53388028 TAAAATAATTAATATTAAATTTAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
53388075 TAAAAT
1 TAAAAT
53388081 TCTTAATAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 26
0.65 0.12 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.20
46 12 0.17
47 15 0.21
48 8 0.11
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:53388000 original size:91 final size:90
Alignment explanation
Indices: 53387905--53388112 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 90
53387895 TAATTATAAC
* * * *
53387905 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
53387970 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
*
53387996 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATTTAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
53388061 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
53388087 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
53388113 CTAAAATCAA
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
91 86 0.80
92 21 0.20
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:53388072 original size:44 final size:43
Alignment explanation
Indices: 53387930--53388072 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
53387920 TATGAATTTG
* * *
53387930 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATTTAATTTAATAAT-ATA
** * * *
53387974 TATAATTTCATAAAATTCTTGATAATAAATTT--TCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATTTAAT-TTA-AT-AATATA
*
53388021 TACAATTTAAAATAATTAATATTAAATTTAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATTTAATTTAATAAT-ATA
53388065 TATAATTT
1 TATAATTT
53388073 CATAAAATTC
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
43 3 0.04
44 34 0.45
45 6 0.08
46 6 0.08
47 23 0.31
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATTTAATTTAATAATATA
Found at i:53388088 original size:47 final size:47
Alignment explanation
Indices: 53387958--53388093 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 47
53387948 TTATTACATA
* *
53387958 TAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAAATT
1 TAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAAATT
* * ** *
53388005 T--TCTT-AT-ATGAATTTATACAATT--TAAAATAATTAATATTAAATT
1 TAAT-TTAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAAATT
53388049 TAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAAA
1 TAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAAA
53388094 ATGTTCTTAT
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
44 20 0.29
45 14 0.21
46 14 0.21
47 20 0.29
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (47 bp):
TAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAAATT
Found at i:53390997 original size:21 final size:21
Alignment explanation
Indices: 53390971--53391035 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
53390961 GAAAAAATAT
53390971 ATGAAACTGAGATGGAAAACA
1 ATGAAACTGAGATGGAAAACA
* *
53390992 ATGAAA---AGA--AAAAATA
1 ATGAAACTGAGATGGAAAACA
53391008 TATGAAACTGAGATGGAAAACA
1 -ATGAAACTGAGATGGAAAACA
53391030 ATGAAA
1 ATGAAA
53391036 GTGAACTGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 3 0.09
20 3 0.09
21 12 0.35
22 5 0.15
ACGTcount: A:0.58, C:0.06, G:0.20, T:0.15
Consensus pattern (21 bp):
ATGAAACTGAGATGGAAAACA
Found at i:53391001 original size:38 final size:38
Alignment explanation
Indices: 53390958--53391035 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
53390948 CAGGGCAGAG
53390958 AAAGAAAAAATATATGAAACTGAGATGGAAAACAATGA
1 AAAGAAAAAATATATGAAACTGAGATGGAAAACAATGA
53390996 AAAGAAAAAATATATGAAACTGAGATGGAAAACAATGA
1 AAAGAAAAAATATATGAAACTGAGATGGAAAACAATGA
53391034 AA
1 AA
53391036 GTGAACTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.62, C:0.05, G:0.18, T:0.15
Consensus pattern (38 bp):
AAAGAAAAAATATATGAAACTGAGATGGAAAACAATGA
Found at i:53391635 original size:9 final size:9
Alignment explanation
Indices: 53391621--53391645 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53391611 TCTGAACTAC
53391621 ATTTATCTT
1 ATTTATCTT
53391630 ATTTATCTT
1 ATTTATCTT
53391639 ATTTATC
1 ATTTATC
53391646 AGCAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTATCTT
Found at i:53394340 original size:21 final size:21
Alignment explanation
Indices: 53394314--53394354 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53394304 ATCTGCTCAA
* *
53394314 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
53394335 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
53394355 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:53407539 original size:31 final size:30
Alignment explanation
Indices: 53407504--53407563 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53407494 GGAGGTGGGA
*
53407504 TGGGAAGGAAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGGAAATAAAAATTTTAGGGGAAAAG
* * *
53407535 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGGAAATAAAAATTTTAGGGGAAAA
53407564 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGGAAATAAAAATTTTAGGGGAAAAG
Found at i:53407792 original size:9 final size:9
Alignment explanation
Indices: 53407778--53407814 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53407768 TATAGTTTGA
53407778 TATTCGAAT
1 TATTCGAAT
53407787 TATTCGAAT
1 TATTCGAAT
*
53407796 TATTCGAGT
1 TATTCGAAT
53407805 TATTCGAAT
1 TATTCGAAT
53407814 T
1 T
53407815 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:53410236 original size:39 final size:40
Alignment explanation
Indices: 53410188--53410270 Score: 109
Period size: 39 Copynumber: 2.1 Consensus size: 40
53410178 CTCAACTACA
*
53410188 ATTTTAATAATTTTTA-AT-AAATTCTTATAATT-TTTTAT
1 ATTTGAATAATTTTTATATAAAATTC-TATAATTATTTTAT
*
53410226 CATTTGAATAATTTTTATGTAAAATTCTATAATTATTTTAT
1 -ATTTGAATAATTTTTATATAAAATTCTATAATTATTTTAT
53410267 ATTT
1 ATTT
53410271 TATAAAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
39 15 0.38
40 12 0.31
41 12 0.31
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (40 bp):
ATTTGAATAATTTTTATATAAAATTCTATAATTATTTTAT
Found at i:53410779 original size:22 final size:22
Alignment explanation
Indices: 53410749--53410792 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53410739 TTTGGTATTT
53410749 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
53410771 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
53410793 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:53415015 original size:18 final size:19
Alignment explanation
Indices: 53414990--53415032 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
53414980 CTTTTCATTC
53414990 TCTTTTTTAAATTTTCTTT
1 TCTTTTTTAAATTTTCTTT
* *
53415009 T-TTTTTTCATTTTTCTTT
1 TCTTTTTTAAATTTTCTTT
53415027 TCTTTT
1 TCTTTT
53415033 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (19 bp):
TCTTTTTTAAATTTTCTTT
Found at i:53417611 original size:22 final size:22
Alignment explanation
Indices: 53417581--53417624 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53417571 TTTGGTATTT
53417581 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
53417603 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
53417625 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:53426409 original size:23 final size:21
Alignment explanation
Indices: 53426382--53426445 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 21
53426372 TAATAACAAT
53426382 AAAATAAATAAAAATATAGAAAC
1 AAAATAAATAAAAA-A-AGAAAC
* *
53426405 AAAATGAAAATATAAAAAGAAAT
1 AAAAT--AAATAAAAAAAGAAAC
53426428 AAAATAAA-AAAATAAAGA
1 AAAATAAATAAAA-AAAGA
53426446 TAGTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.09
21 8 0.23
23 15 0.43
24 1 0.03
25 8 0.23
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.16
Consensus pattern (21 bp):
AAAATAAATAAAAAAAGAAAC
Found at i:53426439 original size:17 final size:18
Alignment explanation
Indices: 53426406--53426439 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53426396 TATAGAAACA
*
53426406 AAATGAAAATATAAAAAG
1 AAATGAAAATAAAAAAAG
53426424 AAAT-AAAATAAAAAAA
1 AAATGAAAATAAAAAAA
53426440 TAAAGATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (18 bp):
AAATGAAAATAAAAAAAG
Found at i:53430311 original size:17 final size:17
Alignment explanation
Indices: 53430291--53430325 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
53430281 TTTAAAAAAA
*
53430291 TATAATTTTTTTAATTT
1 TATAATTATTTTAATTT
53430308 TATAATTATTTTAATTT
1 TATAATTATTTTAATTT
53430325 T
1 T
53430326 TAAAAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATAATTATTTTAATTT
Found at i:53430864 original size:61 final size:62
Alignment explanation
Indices: 53430780--53430899 Score: 170
Period size: 62 Copynumber: 2.0 Consensus size: 62
53430770 TTTGATACAC
** * * * *
53430780 ATATTTAGATCATGTTAAGTTTG-AAAAAGCATAAAATGTATTGATATCATACTTAATTAAT
1 ATATTTAGATCACATTAAATTTGAAAAAAACATAAAATATATTAATATCATACTTAATTAAT
*
53430841 ATATTTAGATCACATTAAATTTGAAAAAAATATAAAATATATTAATATCATACTTAATT
1 ATATTTAGATCACATTAAATTTGAAAAAAACATAAAATATATTAATATCATACTTAATT
53430900 CGAAATATGA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 20 0.39
62 31 0.61
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (62 bp):
ATATTTAGATCACATTAAATTTGAAAAAAACATAAAATATATTAATATCATACTTAATTAAT
Found at i:53431464 original size:24 final size:26
Alignment explanation
Indices: 53431444--53431497 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
53431434 AACATATTAT
53431444 TAATACAAATACAAAAAATATAAATA
1 TAATACAAATACAAAAAATATAAATA
* **
53431470 TAATACAAAAACATTAAAT-TAAATA
1 TAATACAAATACAAAAAATATAAATA
53431495 TAA
1 TAA
53431498 AATAGATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (26 bp):
TAATACAAATACAAAAAATATAAATA
Found at i:53431494 original size:20 final size:19
Alignment explanation
Indices: 53431450--53431499 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
53431440 TTATTAATAC
53431450 AAATACAAAAAATATAAAT
1 AAATACAAAAAATATAAAT
53431469 ATAATACAAAAACAT-TAAATT
1 A-AATACAAAAA-ATATAAA-T
*
53431490 AAATATAAAA
1 AAATACAAAA
53431500 TAGATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 22 0.81
21 4 0.15
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATACAAAAAATATAAAT
Found at i:53435097 original size:21 final size:21
Alignment explanation
Indices: 53435071--53435111 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
53435061 CTTTATATTA
* *
53435071 ATTTTTGTTTGGGATGGGTTT
1 ATTTTTATTTAGGATGGGTTT
*
53435092 ATTTTTATTTAGGTTGGGTT
1 ATTTTTATTTAGGATGGGTT
53435112 GTGAATAAAA
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:0.00, G:0.29, T:0.59
Consensus pattern (21 bp):
ATTTTTATTTAGGATGGGTTT
Found at i:53440339 original size:15 final size:15
Alignment explanation
Indices: 53440319--53440349 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53440309 TAACATGACA
53440319 CTTTTCGATATGGCG
1 CTTTTCGATATGGCG
*
53440334 CTTTTCGATGTGGCG
1 CTTTTCGATATGGCG
53440349 C
1 C
53440350 CATTAAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.23, G:0.29, T:0.39
Consensus pattern (15 bp):
CTTTTCGATATGGCG
Found at i:53446562 original size:49 final size:49
Alignment explanation
Indices: 53446496--53446630 Score: 243
Period size: 49 Copynumber: 2.8 Consensus size: 49
53446486 AATGAGAAAG
* *
53446496 AAACAAAAAAAAAGTCATGTTCAAACATGTACGAAACAAAAAAAAAAAC
1 AAACAAACAAAATGTCATGTTCAAACATGTACGAAACAAAAAAAAAAAC
*
53446545 AAACAAACAAAATGTCATGTTCAAACATGTACGAAACAAAAAAAAAACC
1 AAACAAACAAAATGTCATGTTCAAACATGTACGAAACAAAAAAAAAAAC
53446594 AAACAAACAAAATGTCATGTTCAAACATGTACGAAAC
1 AAACAAACAAAATGTCATGTTCAAACATGTACGAAAC
53446631 CAATTAATAT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 83 1.00
ACGTcount: A:0.59, C:0.17, G:0.09, T:0.15
Consensus pattern (49 bp):
AAACAAACAAAATGTCATGTTCAAACATGTACGAAACAAAAAAAAAAAC
Found at i:53457916 original size:276 final size:276
Alignment explanation
Indices: 53457421--53457976 Score: 995
Period size: 276 Copynumber: 2.0 Consensus size: 276
53457411 TCATACAAAA
* *
53457421 TTCAACCACAATTTTTCATAACATATCATTTCCAATAGGCATTAGCATTGCTAAAATCATGCATT
1 TTCAACCACAATTTGTCATAACATATAATTTCCAATAGGCATTAGCATTGCTAAAATCATGCATT
* *
53457486 ATAAAGGTTTCAAGCTAAAACTAACATTTCAAGTTAACATATACAAAACACCATGTACATGTCAC
66 ATAAAGGTTTCAAGCTAAAACTAAAATTTCAAGTTAACATATACAAAACACCATGTAAATGTCAC
* *
53457551 AAAATCATACTTAAAGTGTTTGAAAAGCTCTTGATTCAAAAATAGGACGGAGTGCGCTTCCAGAA
131 AAAATCATACTTAAAGTGTTTGAAAAGCTATTGATTCAAAAATAGGACGGAGTACGCTTCCAGAA
*
53457616 GATCCTCTTGACACATTTCACAAAGTGACAATCTACAAGGAAATGGAGGCAACAGGATAAGCATA
196 GATCCTCTTGACACATTCCACAAAGTGACAATCTACAAGGAAATGGAGGCAACAGGATAAGCATA
53457681 TTGAACGCTTAGCAAG
261 TTGAACGCTTAGCAAG
*
53457697 TTCAACCACAATTTGTCATAACATATAATTTCCAATATGCATTAGCATTGCTAAAATCATGCATT
1 TTCAACCACAATTTGTCATAACATATAATTTCCAATAGGCATTAGCATTGCTAAAATCATGCATT
53457762 ATAAAGGTTTCAAGCTAAAACTAAAATTTCAAGTTAACATATACAAAACACCATGTAAATGTCAC
66 ATAAAGGTTTCAAGCTAAAACTAAAATTTCAAGTTAACATATACAAAACACCATGTAAATGTCAC
* *
53457827 AAAATCATACTTAAAGTGTTTGAAAAGCTATTGATTCAAAAATAGGATGGAGTACGCTTCCGGAA
131 AAAATCATACTTAAAGTGTTTGAAAAGCTATTGATTCAAAAATAGGACGGAGTACGCTTCCAGAA
* *
53457892 GATCCTCTTGACACATTCCACAAAGTGACAATCTACAAGGAAATGGAGGCAACTGGGTAAGCATA
196 GATCCTCTTGACACATTCCACAAAGTGACAATCTACAAGGAAATGGAGGCAACAGGATAAGCATA
*
53457957 TTGAATGCTTAGCAAG
261 TTGAACGCTTAGCAAG
53457973 TTCA
1 TTCA
53457977 TAGACATTAA
Statistics
Matches: 267, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
276 267 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (276 bp):
TTCAACCACAATTTGTCATAACATATAATTTCCAATAGGCATTAGCATTGCTAAAATCATGCATT
ATAAAGGTTTCAAGCTAAAACTAAAATTTCAAGTTAACATATACAAAACACCATGTAAATGTCAC
AAAATCATACTTAAAGTGTTTGAAAAGCTATTGATTCAAAAATAGGACGGAGTACGCTTCCAGAA
GATCCTCTTGACACATTCCACAAAGTGACAATCTACAAGGAAATGGAGGCAACAGGATAAGCATA
TTGAACGCTTAGCAAG
Found at i:53458156 original size:8 final size:8
Alignment explanation
Indices: 53458126--53458155 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
53458116 TACAATTCTC
53458126 AATCAAAT
1 AATCAAAT
53458134 AATCAAAT
1 AATCAAAT
*
53458142 AATCAATT
1 AATCAAAT
53458150 AATCAA
1 AATCAA
53458156 TCAGTTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (8 bp):
AATCAAAT
Found at i:53459378 original size:15 final size:15
Alignment explanation
Indices: 53459360--53459390 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53459350 ATTAATCAAC
53459360 ATTTATTTAATTAAA
1 ATTTATTTAATTAAA
*
53459375 ATTTATTTAGTTAAA
1 ATTTATTTAATTAAA
53459390 A
1 A
53459391 ATTAATGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTAATTAAA
Found at i:53469454 original size:31 final size:32
Alignment explanation
Indices: 53469418--53469480 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
53469408 TTTTAGGCCT
*
53469418 TTAGCGACGCTTT-TAAGCGCCACTAAAAGTA
1 TTAGCGACGCTTTATAAGCGCCACAAAAAGTA
* *
53469449 TTAGCGGCGCTTTCATGAGCGCCACAAAAAGT
1 TTAGCGACGCTTT-ATAAGCGCCACAAAAAGT
53469481 GCCGCTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
33 15 0.56
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (32 bp):
TTAGCGACGCTTTATAAGCGCCACAAAAAGTA
Found at i:53469566 original size:43 final size:43
Alignment explanation
Indices: 53469518--53469644 Score: 182
Period size: 43 Copynumber: 2.9 Consensus size: 43
53469508 GAAAAAACGC
* * *
53469518 CGCTAAATATCATAACCTTTAGCAGTGCTTTTATCACAAATGT
1 CGCTAAAGATCATGACCTTTAGCGGTGCTTTTATCACAAATGT
* * *
53469561 CGCTAAAGACCTTGACCTTTAGCGGTGCTTTTGTCACAAATGT
1 CGCTAAAGATCATGACCTTTAGCGGTGCTTTTATCACAAATGT
*
53469604 CGCTAAAGATCATGACCTTTAGCGGCGCTTTTTATCACAAA
1 CGCTAAAGATCATGACCTTTAGCGGTGC-TTTTATCACAAA
53469645 CACCGCTAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 62 0.85
44 11 0.15
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (43 bp):
CGCTAAAGATCATGACCTTTAGCGGTGCTTTTATCACAAATGT
Found at i:53469665 original size:43 final size:41
Alignment explanation
Indices: 53469531--53469670 Score: 154
Period size: 43 Copynumber: 3.3 Consensus size: 41
53469521 TAAATATCAT
*
53469531 AACCTTTAGCAGTGCTTTTATCACAAATGTCGCTAAAGACC
1 AACCTTTAGCGGTGCTTTTATCACAAATGTCGCTAAAGACC
* * *
53469572 TTGACCTTTAGCGGTGCTTTTGTCACAAATGTCGCTAAAGATC
1 --AACCTTTAGCGGTGCTTTTATCACAAATGTCGCTAAAGACC
* ***
53469615 ATGACCTTTAGCGGCGCTTTTTATCACAAACACCGCTAAAGAACC
1 A--ACCTTTAGCGGTGC-TTTTATCACAAATGTCGCTAAAG-ACC
53469660 AACCTTTAGCG
1 AACCTTTAGCG
53469671 ATGTTTCTCG
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
43 60 0.73
44 19 0.23
45 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (41 bp):
AACCTTTAGCGGTGCTTTTATCACAAATGTCGCTAAAGACC
Found at i:53473938 original size:42 final size:42
Alignment explanation
Indices: 53473806--53473938 Score: 129
Period size: 42 Copynumber: 3.3 Consensus size: 42
53473796 AATGCCACAA
* *
53473806 AAAATCTTTATTTTGTAGAAATTATTAGTTAAGTGATTTTAT
1 AAAATATTTATTTTGTAGAAATTATTAGTTAAGAGATTTTAT
* * * *
53473848 AAAATATTTATTTT-T---TATTATAAATTAA-A-TTTTTATT
1 AAAATATTTATTTTGTAGAAATTATTAGTTAAGAGATTTTA-T
*
53473885 AGAA-A-TTATTTTGTAGAAATTATTAGTTAAGAGATTTTAT
1 AAAATATTTATTTTGTAGAAATTATTAGTTAAGAGATTTTAT
*
53473925 AAAATATTCATTTT
1 AAAATATTTATTTT
53473939 CGATCTAATC
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
35 7 0.10
36 7 0.10
37 4 0.06
38 10 0.14
39 10 0.14
40 5 0.07
41 7 0.10
42 19 0.28
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (42 bp):
AAAATATTTATTTTGTAGAAATTATTAGTTAAGAGATTTTAT
Found at i:53474452 original size:81 final size:80
Alignment explanation
Indices: 53474357--53474516 Score: 257
Period size: 81 Copynumber: 2.0 Consensus size: 80
53474347 TTAATATTAT
*
53474357 CTCTTTTACAATTATATAAGAAATTATTTAATATATAAATTAAAAAACACCAATTAATCTAAACC
1 CTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAAAAAACACCAATTAATCTAAACC
53474422 CTAAACCCCTAACCCC
66 CTAAA-CCCTAACCCC
* * * *
53474438 CTCTTTTATAATTATATAAGAACTTAATTAATATATAAATTAAAAAATACTAATTAATCTAAACC
1 CTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAAAAAACACCAATTAATCTAAACC
*
53474503 TTAAACCCTAACCC
66 CTAAACCCTAACCC
53474517 GACCCCAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 9 0.12
81 64 0.88
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.33
Consensus pattern (80 bp):
CTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAAAAAACACCAATTAATCTAAACC
CTAAACCCTAACCCC
Found at i:53474582 original size:7 final size:7
Alignment explanation
Indices: 53474552--53474617 Score: 78
Period size: 7 Copynumber: 9.4 Consensus size: 7
53474542 CACTAACTCT
*
53474552 TAACCTC
1 TAACCCC
*
53474559 TAACCTC
1 TAACCCC
*
53474566 TAACCTC
1 TAACCCC
*
53474573 TAATCCC
1 TAACCCC
53474580 TAACCCC
1 TAACCCC
53474587 TAACCCC
1 TAACCCC
53474594 TAACCCC
1 TAACCCC
**
53474601 TAACTAC
1 TAACCCC
53474608 TAACCCC
1 TAACCCC
53474615 TAA
1 TAA
53474618 ACTTTATTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (7 bp):
TAACCCC
Found at i:53474596 original size:21 final size:21
Alignment explanation
Indices: 53474542--53474617 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
53474532 AACTCTAAAT
* * *
53474542 CACTAACTCTTAACCTCTAAC
1 CACTAACCCCTAACCCCTAAC
* * *
53474563 CTCTAACCTCTAATCCCTAAC
1 CACTAACCCCTAACCCCTAAC
*
53474584 CCCTAACCCCTAACCCCTAAC
1 CACTAACCCCTAACCCCTAAC
*
53474605 TACTAACCCCTAA
1 CACTAACCCCTAA
53474618 ACTTTATTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.24
Consensus pattern (21 bp):
CACTAACCCCTAACCCCTAAC
Found at i:53474869 original size:40 final size:40
Alignment explanation
Indices: 53474749--53474931 Score: 197
Period size: 41 Copynumber: 4.5 Consensus size: 40
53474739 TTTCAAATTA
* * *
53474749 TTTCTAAAAACGCTGCTAAAGCCCCGAGCATTAGTGGCGCTT
1 TTTC-AAAAACGC-GCTAAATCCTCGAGCATTAGCGGCGCTT
* ** * *
53474791 CTTGGAAAACGCTGCTAAAGCCTCGAGCATTAGCGGCGCTC
1 TTTCAAAAACGC-GCTAAATCCTCGAGCATTAGCGGCGCTT
53474832 TTTCAAAAACGTCGCTAAATCC-CGAGCATTAGCGGCGCTT
1 TTTCAAAAACG-CGCTAAATCCTCGAGCATTAGCGGCGCTT
* *
53474872 TTTCAAAATCGTCGCTAAATCCTCGAGCATTAGCGCCGCTT
1 TTTCAAAAACG-CGCTAAATCCTCGAGCATTAGCGGCGCTT
* *
53474913 TTTAAAAAACACCGCTAAA
1 TTTCAAAAAC-GCGCTAAA
53474932 GCCCCAAAAG
Statistics
Matches: 122, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
40 38 0.31
41 81 0.66
42 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
TTTCAAAAACGCGCTAAATCCTCGAGCATTAGCGGCGCTT
Found at i:53474890 original size:81 final size:81
Alignment explanation
Indices: 53474749--53474936 Score: 220
Period size: 81 Copynumber: 2.3 Consensus size: 81
53474739 TTTCAAATTA
* *
53474749 TTTCTAAAAACGCTGCTAAAGCCCCGAGCATTAGTGGCGCTTCTTGGAAAACGCTGCTAAAGCCT
1 TTTC-AAAAACGC-GCTAAAGCCCCGAGCATTAGCGGCGCTTCTTGCAAAACGCTGCTAAAGCCT
*
53474814 CGAGCATTAGCGGCGCTC
64 CGAGCATTAGCGCCGCTC
* * *
53474832 TTTCAAAAACGTCGCTAAA-TCCCGAGCATTAGCGGCGCTT-TTTCAAAATCG-TCGCTAAATCC
1 TTTCAAAAACG-CGCTAAAGCCCCGAGCATTAGCGGCGCTTCTTGCAAAA-CGCT-GCTAAAGCC
*
53474894 TCGAGCATTAGCGCCGCTT
63 TCGAGCATTAGCGCCGCTC
* *
53474913 TTTAAAAAACACCGCTAAAGCCCC
1 TTTCAAAAAC-GCGCTAAAGCCCC
53474937 AAAAGATCAG
Statistics
Matches: 90, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
80 7 0.08
81 62 0.69
82 16 0.18
83 5 0.06
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (81 bp):
TTTCAAAAACGCGCTAAAGCCCCGAGCATTAGCGGCGCTTCTTGCAAAACGCTGCTAAAGCCTCG
AGCATTAGCGCCGCTC
Found at i:53475062 original size:40 final size:40
Alignment explanation
Indices: 53475018--53475133 Score: 196
Period size: 40 Copynumber: 2.9 Consensus size: 40
53475008 CATTTTTAGG
53475018 AAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTATGT
1 AAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTATGT
* * *
53475058 AAAGCGCCCCTAATGCTCGATCTTTAGCAGTGTTTTATGT
1 AAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTATGT
*
53475098 AAAGCGCCGCTAATGCTCGATTTTTAGCGGCGTTTT
1 AAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTT
53475134 TTATTCAAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (40 bp):
AAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTATGT
Found at i:53493878 original size:18 final size:18
Alignment explanation
Indices: 53493855--53493891 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
53493845 AGTTCTTTTC
53493855 TTTCTATTATATTAGTAT
1 TTTCTATTATATTAGTAT
*
53493873 TTTCTATTCTATTAGTAT
1 TTTCTATTATATTAGTAT
53493891 T
1 T
53493892 AGATTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTCTATTATATTAGTAT
Found at i:53493884 original size:23 final size:23
Alignment explanation
Indices: 53493850--53493893 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
53493840 AAGAAAGTTC
53493850 TTTTCTTTCTATTA-TATTAGTA
1 TTTTCTTTCTATTAGTATTAGTA
53493872 TTTTCTATTCTATTAGTATTAG
1 TTTTCT-TTCTATTAGTATTAG
53493894 ATTAGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTTCTTTCTATTAGTATTAGTA
Found at i:53493891 original size:6 final size:6
Alignment explanation
Indices: 53493882--53493925 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
53493872 TTTTCTATTC
53493882 TATTAG TATTAG -ATTAG TATTAG --TTAG -ATTAG -ATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
53493925 T
1 T
53493926 TAGTGATCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.11
5 14 0.40
6 17 0.49
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (6 bp):
TATTAG
Found at i:53493891 original size:11 final size:11
Alignment explanation
Indices: 53493883--53493929 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
53493873 TTTCTATTCT
53493883 ATTAGTATTAG
1 ATTAGTATTAG
53493894 ATTAGTATTAG
1 ATTAGTATTAG
53493905 -TTAG-ATTAG
1 ATTAGTATTAG
53493914 ATTAGTATTAG
1 ATTAGTATTAG
53493925 -TTAGT
1 ATTAGT
53493930 GATCCCGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 16 0.47
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:53493914 original size:20 final size:21
Alignment explanation
Indices: 53493884--53493929 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
53493874 TTCTATTCTA
53493884 TTAGTATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
53493905 TTAG-ATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
53493925 TTAGT
1 TTAGT
53493930 GATCCCGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (21 bp):
TTAGTATTAGATTAGTATTAG
Found at i:53493928 original size:15 final size:14
Alignment explanation
Indices: 53493890--53493919 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
53493880 TCTATTAGTA
53493890 TTAGATTAGTATTAG
1 TTAGATTAG-ATTAG
53493905 TTAGATTAGATTAG
1 TTAGATTAGATTAG
53493919 T
1 T
53493920 ATTAGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (14 bp):
TTAGATTAGATTAG
Found at i:53495394 original size:21 final size:22
Alignment explanation
Indices: 53495356--53495396 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53495346 TCTGGAACCA
* *
53495356 AAAAATCAATTTAGAAACAAGT
1 AAAAACCAATCTAGAAACAAGT
53495378 AAAAACCAATCTA-AAACAA
1 AAAAACCAATCTAGAAACAA
53495397 AACAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.63, C:0.15, G:0.05, T:0.17
Consensus pattern (22 bp):
AAAAACCAATCTAGAAACAAGT
Found at i:53496146 original size:24 final size:24
Alignment explanation
Indices: 53496119--53496164 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
53496109 ATAGAGTAAA
53496119 CTTACATAAAGCTTAATAAGTTCG
1 CTTACATAAAGCTTAATAAGTTCG
53496143 CTTACATAAAGCTTAATAAGTT
1 CTTACATAAAGCTTAATAAGTT
53496165 TGTAATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (24 bp):
CTTACATAAAGCTTAATAAGTTCG
Found at i:53502766 original size:21 final size:21
Alignment explanation
Indices: 53502740--53502779 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
53502730 AATATTCATC
53502740 TTCTTGACCTTGTAAGACCTT
1 TTCTTGACCTTGTAAGACCTT
53502761 TTCTTGACCTTGTAAGACC
1 TTCTTGACCTTGTAAGACC
53502780 CAGTCCAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTTGACCTTGTAAGACCTT
Found at i:53503453 original size:45 final size:45
Alignment explanation
Indices: 53503389--53503474 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
53503379 AAGCCAAAAA
53503389 GGGAAAGAGAAAACAGAGTTAATTTCCTTAATTCGATGACTTTTT
1 GGGAAAGAGAAAACAGAGTTAATTTCCTTAATTCGATGACTTTTT
* *
53503434 GGGAAAGAGAAAACAGAGTTGATTTCCTTAATTTGATGACT
1 GGGAAAGAGAAAACAGAGTTAATTTCCTTAATTCGATGACT
53503475 ATCTTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (45 bp):
GGGAAAGAGAAAACAGAGTTAATTTCCTTAATTCGATGACTTTTT
Found at i:53507364 original size:17 final size:18
Alignment explanation
Indices: 53507342--53507382 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
53507332 GACTGAGATA
*
53507342 AGAATT-CTGTTCATAAC
1 AGAATTCCTGTTCACAAC
*
53507359 AGAATTCCTGTTTACAAC
1 AGAATTCCTGTTCACAAC
53507377 AGAATT
1 AGAATT
53507383 GTAGATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
AGAATTCCTGTTCACAAC
Found at i:53512169 original size:17 final size:18
Alignment explanation
Indices: 53512147--53512187 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
53512137 GACTGAGATA
*
53512147 AGAATT-CTGTTCATAAC
1 AGAATTCCTGTTCACAAC
*
53512164 AGAATTCCTGTTTACAAC
1 AGAATTCCTGTTCACAAC
53512182 AGAATT
1 AGAATT
53512188 GTAGATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
AGAATTCCTGTTCACAAC
Found at i:53512661 original size:34 final size:34
Alignment explanation
Indices: 53512597--53512677 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
53512587 GTATGGTAGT
*
53512597 ATTAACATGTTTATAACAAGTATATACAGTAGCA
1 ATTAACATGCTTATAACAAGTATATACAGTAGCA
*
53512631 ATTATCATGCTTATAAC-AG-ATCATAGCAGTAGCA
1 ATTAACATGCTTATAACAAGTAT-ATA-CAGTAGCA
* *
53512665 ATAAACTTGCTTA
1 ATTAACATGCTTA
53512678 ACATGTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 2 0.05
33 5 0.12
34 33 0.82
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (34 bp):
ATTAACATGCTTATAACAAGTATATACAGTAGCA
Found at i:53513713 original size:3 final size:3
Alignment explanation
Indices: 53513705--53513739 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
53513695 CATCCACCTT
53513705 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
53513740 GCAACTACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:53515419 original size:22 final size:22
Alignment explanation
Indices: 53515364--53515422 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
53515354 TGGACATGCA
*
53515364 TAATTATTTTTG-TAAATTTTAT
1 TAATTA-TTTTGAAAAATTTTAT
* *
53515386 TGAA-AATATTGAAAAATTTTAT
1 T-AATTATTTTGAAAAATTTTAT
53515408 TAATTATTTTGAAAA
1 TAATTATTTTGAAAA
53515423 TTTATAAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 6 0.21
22 21 0.72
23 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TAATTATTTTGAAAAATTTTAT
Found at i:53516061 original size:40 final size:40
Alignment explanation
Indices: 53516006--53516086 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
53515996 AAATCCGCCT
53516006 AAGTTAGTCTTGCTCTCAAAAATGAGAATTCACAAAGGAA
1 AAGTTAGTCTTGCTCTCAAAAATGAGAATTCACAAAGGAA
*
53516046 AAGTTAGTCTTGCTCTCGAAAATGAGAATTCACAAAGGAA
1 AAGTTAGTCTTGCTCTCAAAAATGAGAATTCACAAAGGAA
53516086 A
1 A
53516087 TTCTCTAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (40 bp):
AAGTTAGTCTTGCTCTCAAAAATGAGAATTCACAAAGGAA
Found at i:53518361 original size:45 final size:45
Alignment explanation
Indices: 53518297--53518403 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 45
53518287 TAATCAGTAA
* * * *
53518297 CGGTAGCAATAACAGTAACAGTATTCAACACATAAAGTGTTGAAT
1 CGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAAT
* * *
53518342 CTGTAACAGTAACGGTAACATTATTCAACACACAAAGTGTCGAAT
1 CGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAAT
*
53518387 CGGTAATAGTAACAGTA
1 CGGTAACAGTAACAGTA
53518404 GTCGGCATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (45 bp):
CGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAAT
Found at i:53518648 original size:40 final size:42
Alignment explanation
Indices: 53518602--53518687 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 42
53518592 AATTCATTAC
* * * *
53518602 TTCAGTAATTTCATAGTTCAATGCAGTACA-C-ATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACATCAAAAACAATA
*
53518642 TTCAGTAACTTCACAATTCAATTCAGTACATCAAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACATCAAAAACAATA
53518684 TTCA
1 TTCA
53518688 ATATTCCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 26 0.67
41 1 0.03
42 12 0.31
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (42 bp):
TTCAGTAACTTCACAATTCAATGCAGTACATCAAAAACAATA
Found at i:53521178 original size:24 final size:24
Alignment explanation
Indices: 53521146--53521194 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
53521136 ATGACTTCCA
53521146 CCTATCCCTAAACCAGTTGAATAT
1 CCTATCCCTAAACCAGTTGAATAT
53521170 CCTATCCCTAAACCAGTTGAATAT
1 CCTATCCCTAAACCAGTTGAATAT
53521194 C
1 C
53521195 TCTTTCTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.29
Consensus pattern (24 bp):
CCTATCCCTAAACCAGTTGAATAT
Found at i:53523734 original size:23 final size:24
Alignment explanation
Indices: 53523699--53523743 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
53523689 AATATGGTAA
53523699 GAAATTAAGTAGAAAAG-AAGTAT
1 GAAATTAAGTAGAAAAGTAAGTAT
53523722 GAAA-TAAGCTAGAAAAGTAAGT
1 GAAATTAAG-TAGAAAAGTAAGT
53523744 GAGCTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (24 bp):
GAAATTAAGTAGAAAAGTAAGTAT
Found at i:53525447 original size:32 final size:32
Alignment explanation
Indices: 53525404--53525469 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
53525394 TGATCTATCG
*
53525404 TAATATGGGAATTAACTATTACTACTTAGACT
1 TAATATAGGAATTAACTATTACTACTTAGACT
*
53525436 TAATATAGGAATTAACTATTACTACTTAGTCT
1 TAATATAGGAATTAACTATTACTACTTAGACT
53525468 TA
1 TA
53525470 TTTTTATGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (32 bp):
TAATATAGGAATTAACTATTACTACTTAGACT
Found at i:53536946 original size:12 final size:12
Alignment explanation
Indices: 53536924--53536954 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
53536914 TTTTAAATAA
53536924 TTTTAAAAATTT
1 TTTTAAAAATTT
53536936 TTTTAAAAATTT
1 TTTTAAAAATTT
53536948 TTTTAAA
1 TTTTAAA
53536955 CCGTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAAAAATTT
Found at i:53538068 original size:7 final size:7
Alignment explanation
Indices: 53538056--53538080 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53538046 AGTCGATTGA
53538056 TATTTAG
1 TATTTAG
53538063 TATTTAG
1 TATTTAG
53538070 TATTTAG
1 TATTTAG
53538077 TATT
1 TATT
53538081 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Done.