Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, whole genome shotgun sequence
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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 31 of 91
Found at i:5378057 original size:20 final size:20
Alignment explanation
Indices: 5378020--5378058 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5378010 GATTGTTTAA
*
5378020 TATTTTTATTTTCGTTTTTC
1 TATTTTTATTTTCATTTTTC
5378040 TATTTTTAATTTT-ATTTTT
1 TATTTTT-ATTTTCATTTTT
5378059 ATTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (20 bp):
TATTTTTATTTTCATTTTTC
Found at i:5378087 original size:15 final size:16
Alignment explanation
Indices: 5377979--5378087 Score: 58
Period size: 15 Copynumber: 7.1 Consensus size: 16
5377969 TTTCGTTTTT
5377979 TTTATTATTTATT-TA
1 TTTATTATTTATTATA
5377994 TTTATTATTATATTATGA
1 TTTATTATT-TATTAT-A
5378012 TTGT-TTAATATT-TT-TA
1 TT-TATT-AT-TTATTATA
** *
5378028 TTT-TCGTTT-TTCTA
1 TTTATTATTTATTATA
* *
5378042 TTT-TTAATT-TTATT
1 TTTATTATTTATTATA
5378056 TTTATTATTTATT-TA
1 TTTATTATTTATTATA
5378071 TTTATTA-TTATTATA
1 TTTATTATTTATTATA
5378086 TT
1 TT
5378088 AGGATTGTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
13 4 0.05
14 20 0.27
15 28 0.37
16 9 0.12
17 2 0.03
18 7 0.09
19 4 0.05
20 1 0.01
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTATTATTTATTATA
Found at i:5378248 original size:58 final size:58
Alignment explanation
Indices: 5378186--5378553 Score: 333
Period size: 58 Copynumber: 6.2 Consensus size: 58
5378176 AAAGTTTTTG
* *
5378186 GTATCAATTTTTCTCGAAATTAAAGTTTTCAAAAAATATTTTTGAAGAAAAGTTAAAA
1 GTATCAATTTTTCTCGAAAATAAAGTTTTCAAAAAATATTTTTGAAGAAAAGTTGAAA
* *** *
5378244 GTATCAATTTTTCT-TAAAGATAAA-TTTTC-AAAGGGATTTTTG-AGAAAAAATTGAAA
1 GTATCAATTTTTCTCGAAA-ATAAAGTTTTCAAAAAATATTTTTGAAG-AAAAGTTGAAA
* * *
5378300 GTATCAATTTTCCTCGAAATTAAAGTTTTCAAAAACAAAAATATTTTT-AGGGAAAAGTTGAAA
1 GTATCAATTTTTCTCGAAAATAAAGTTTTC----A-AAAAATATTTTTGA-AGAAAAGTTGAAA
* * * *
5378363 GTATCAATTTTCCTTGAAAATAAACTTTCCACAAAAAAATATTTTTGGGAA-AAAAGTTGAAA
1 GTATCAATTTTTCTCGAAAATAAAGTTT--TC-AAAAAATATTTTT--GAAGAAAAGTTGAAA
* ** *
5378425 GTATCAATTTTCCTTAAAAAT-AAGTTTTC-AAAAATGGATTTTT-AAGGAAAAGTTAAAA
1 GTATCAATTTTTCTCGAAAATAAAGTTTTCAAAAAAT--ATTTTTGAA-GAAAAGTTGAAA
* *
5378483 GTATCAATTTTTCTCGAAATTAAAG-TTTCAAAAGAATATTTTTGGAGAAAAGTTGAAA
1 GTATCAATTTTTCTCGAAAATAAAGTTTTCAAAA-AATATTTTTGAAGAAAAGTTGAAA
5378541 GTATCAATTTTTC
1 GTATCAATTTTTC
5378554 CTGCACAAAA
Statistics
Matches: 255, Mismatches: 30, Indels: 50
0.76 0.09 0.15
Matches are distributed among these distances:
55 2 0.01
56 38 0.15
57 22 0.09
58 79 0.31
59 14 0.05
60 3 0.01
61 17 0.07
62 33 0.13
63 44 0.17
64 2 0.01
65 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.36
Consensus pattern (58 bp):
GTATCAATTTTTCTCGAAAATAAAGTTTTCAAAAAATATTTTTGAAGAAAAGTTGAAA
Found at i:5383058 original size:29 final size:30
Alignment explanation
Indices: 5383026--5383100 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
5383016 TAAAAAGAAT
5383026 ATTTAAATGTTTAATTTCA-TGAAAATAAA
1 ATTTAAATGTTTAATTTCATTGAAAATAAA
* * * *
5383055 ATTTAAAAGCTTAA-ATCATTTAAAATAAA
1 ATTTAAATGTTTAATTTCATTGAAAATAAA
5383084 ATTTTAAAAT-TTTAATT
1 A-TTT-AAATGTTTAATT
5383101 AATTGTAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
28 3 0.09
29 22 0.63
30 7 0.20
31 3 0.09
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (30 bp):
ATTTAAATGTTTAATTTCATTGAAAATAAA
Found at i:5383127 original size:29 final size:29
Alignment explanation
Indices: 5383049--5383133 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
5383039 ATTTCATGAA
* *
5383049 AATAAAAT-TTAAAAGCTTAAATCATT-T
1 AATAAAATATTAAAAACTTAAATAATTGT
* ** *
5383076 AAAATAAAATTTTAAAATTTTAATTAATTGT
1 --AATAAAATATTAAAAACTTAAATAATTGT
5383107 AATAAAATATTAAAAACTTAAATAATT
1 AATAAAATATTAAAAACTTAAATAATT
5383134 ATTAAATATT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 31 0.67
30 14 0.30
31 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (29 bp):
AATAAAATATTAAAAACTTAAATAATTGT
Found at i:5384568 original size:18 final size:19
Alignment explanation
Indices: 5384542--5384583 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5384532 TTAAATAGAA
*
5384542 TTATATATTTTT-TAATTT
1 TTATATATTTTTAAAATTT
*
5384560 TTATGTATTTTTAAAATTT
1 TTATATATTTTTAAAATTT
5384579 TTATA
1 TTATA
5384584 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATATATTTTTAAAATTT
Found at i:5385562 original size:11 final size:11
Alignment explanation
Indices: 5385546--5385587 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5385536 AATCCTATAA
5385546 GAGATTTGTTT
1 GAGATTTGTTT
*
5385557 GAGATTTGTTA
1 GAGATTTGTTT
*
5385568 GAGATTTATTT
1 GAGATTTGTTT
5385579 GAGATTTGT
1 GAGATTTGT
5385588 CAGATATTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:5385573 original size:22 final size:22
Alignment explanation
Indices: 5385545--5385587 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5385535 AAATCCTATA
*
5385545 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTATTTGAGATTTGTT
5385567 AGAGATTTATTTGAGATTTGT
1 AGAGATTTATTTGAGATTTGT
5385588 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (22 bp):
AGAGATTTATTTGAGATTTGTT
Found at i:5385692 original size:52 final size:52
Alignment explanation
Indices: 5385613--5385768 Score: 170
Period size: 52 Copynumber: 3.0 Consensus size: 52
5385603 GGATAAGAAA
* * **
5385613 ACTTGCAAAAGAAGAATTCTAAGAGAAAGAT-GATTCTTAATAGGTAAGTTTG
1 ACTTGCAAAAGAAGAATTTTAAAAGAAA-ATGGATTCTTAATAGACAAGTTTG
*
5385665 ACTTGTAAAAGAAGAATTTTAAAAGAAAATGGATTCTTAATAGACAAGTTTG
1 ACTTGCAAAAGAAGAATTTTAAAAGAAAATGGATTCTTAATAGACAAGTTTG
* ** * * * * * *
5385717 ACTTACAGGAGAAGAATTTTAAGAGGAGAGGGATTCTTAATGGGCAAGTTTG
1 ACTTGCAAAAGAAGAATTTTAAAAGAAAATGGATTCTTAATAGACAAGTTTG
5385769 TATGGTTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (52 bp):
ACTTGCAAAAGAAGAATTTTAAAAGAAAATGGATTCTTAATAGACAAGTTTG
Found at i:5386299 original size:31 final size:31
Alignment explanation
Indices: 5386260--5386342 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 31
5386250 GCTTTTAGCC
* *
5386260 CAACAAATGGTATTAGAGCTGTGGTGTTCC-
1 CAACAAATGGTATCAGAGCTGTGGTGATCCT
5386290 CTAACAAATGGTATCAGAGCTGTGGTGATCCT
1 C-AACAAATGGTATCAGAGCTGTGGTGATCCT
*
5386322 CAACAAGTGGTATCAGAGCTG
1 CAACAAATGGTATCAGAGCTG
5386343 AAGGTTCGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
30 1 0.02
31 46 0.96
32 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
CAACAAATGGTATCAGAGCTGTGGTGATCCT
Found at i:5386640 original size:11 final size:11
Alignment explanation
Indices: 5386624--5386665 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5386614 AATCCTATAA
5386624 GAGATTTGTTT
1 GAGATTTGTTT
*
5386635 GAGATTTGTTA
1 GAGATTTGTTT
5386646 GAGATTTGTTT
1 GAGATTTGTTT
*
5386657 GGGATTTGT
1 GAGATTTGT
5386666 CAGATATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:5386648 original size:22 final size:22
Alignment explanation
Indices: 5386623--5386665 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5386613 AAATCCTATA
5386623 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTGAGATTTGTT
*
5386645 AGAGATTTGTTTGGGATTTGT
1 AGAGATTTGTTTGAGATTTGT
5386666 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:5386768 original size:52 final size:52
Alignment explanation
Indices: 5386690--5386846 Score: 192
Period size: 52 Copynumber: 3.0 Consensus size: 52
5386680 TGGACAAGAA
*
5386690 GACTTGCAAAAGAAGAATTCTAAAAGAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGAAAGAGGATTCTTAATAGGTAAGTTT
* * *
5386742 GACTTGTAAGAGAAGAATTCTAAAAGAAA-ATAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGAAAGA-GGATTCTTAATAGGTAAGTTT
* * * * * *
5386794 GACTTACAGGAGAAGATTTCTAAGAGGATAG-GGATTCTTAATGGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAA-AAGAAAGAGGATTCTTAATAGGTAAGTTT
5386846 G
1 G
5386847 TATGGTTATA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
51 1 0.01
52 84 0.94
53 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.29
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAAAGAAAGAGGATTCTTAATAGGTAAGTTT
Found at i:5389122 original size:15 final size:16
Alignment explanation
Indices: 5389102--5389132 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5389092 AGACAAAAAA
5389102 AATTAAATTT-TTTAT
1 AATTAAATTTATTTAT
5389117 AATTAAATTTATTTAT
1 AATTAAATTTATTTAT
5389133 TTGCATCATA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTAAATTTATTTAT
Found at i:5390047 original size:9 final size:9
Alignment explanation
Indices: 5390035--5390107 Score: 58
Period size: 9 Copynumber: 7.7 Consensus size: 9
5390025 TTTTAAAATT
5390035 AAATTTAAA
1 AAATTTAAA
5390044 AAATATCTAAA
1 AAAT-T-TAAA
*
5390055 AAGTTTTAAA
1 AA-ATTTAAA
*
5390065 AATTTTAAA
1 AAATTTAAA
5390074 AAATTATAAAA
1 AAATT-T-AAA
5390085 AAATTT-AA
1 AAATTTAAA
*
5390093 AACTTTAAA
1 AAATTTAAA
*
5390102 ATATTT
1 AAATTT
5390108 CTAAAAGTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
8 7 0.13
9 21 0.40
10 9 0.17
11 15 0.28
12 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (9 bp):
AAATTTAAA
Found at i:5390064 original size:10 final size:9
Alignment explanation
Indices: 5390035--5390124 Score: 56
Period size: 10 Copynumber: 9.4 Consensus size: 9
5390025 TTTTAAAATT
*
5390035 AAATTTAAA
1 AAATTTTAA
*
5390044 AAATATCTAA
1 AAAT-TTTAA
5390054 AAAGTTTTAA
1 AAA-TTTTAA
5390064 AAATTTTAAA
1 AAATTTT-AA
*
5390074 AAATTATAAA
1 AAATT-TTAA
*
5390084 AAAATTT-A
1 AAATTTTAA
*
5390092 AAACTTTAA
1 AAATTTTAA
5390101 AATATTTCTAA
1 AA-ATTT-TAA
* *
5390112 AAGTTATAA
1 AAATTTTAA
5390121 AAAT
1 AAAT
5390125 AAAATTTCAA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
8 7 0.11
9 18 0.29
10 31 0.49
11 7 0.11
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
AAATTTTAA
Found at i:5390069 original size:29 final size:28
Alignment explanation
Indices: 5390035--5390124 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
5390025 TTTTAAAATT
5390035 AAATTTAAAAAATATCTAAAAAGTTTTAA
1 AAATTTAAAAAAT-TCTAAAAAGTTTTAA
* **
5390064 AAATTTTAAAAAATTATAAAAAAATTTAA
1 AAA-TTTAAAAAATTCTAAAAAGTTTTAA
* * *
5390093 AACTTTAAAATATTTCT-AAAAGTTATAA
1 AAATTTAAAA-AATTCTAAAAAGTTTTAA
5390121 AAAT
1 AAAT
5390125 AAAATTTCAA
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
28 18 0.37
29 21 0.43
30 10 0.20
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATTTAAAAAATTCTAAAAAGTTTTAA
Found at i:5390191 original size:11 final size:11
Alignment explanation
Indices: 5390172--5390205 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5390162 AAAATATGAT
5390172 AATTTTATTAA
1 AATTTTATTAA
*
5390183 AATTCTATT-A
1 AATTTTATTAA
5390193 AATTTTATTAA
1 AATTTTATTAA
5390204 AA
1 AA
5390206 ATAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTTTATTAA
Found at i:5390215 original size:21 final size:21
Alignment explanation
Indices: 5390172--5390215 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5390162 AAAATATGAT
* ** *
5390172 AATTTTATTAAAATTCTATTA
1 AATTTTATTAAAAATAAAATA
5390193 AATTTTATTAAAAATAAAATA
1 AATTTTATTAAAAATAAAATA
5390214 AA
1 AA
5390216 ATCTTAAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTTATTAAAAATAAAATA
Found at i:5390291 original size:37 final size:36
Alignment explanation
Indices: 5390225--5390295 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
5390215 AATCTTAAAC
*
5390225 TTTTTGAAAAATTTTAAAAAGTAAAAAATTATAAATT
1 TTTTTGAAAAATTCTAAAAAGTAAAAAATT-TAAATT
* *
5390262 TTTTTGAAAAA-TCTAAAAATTGAAGAAATTTAAA
1 TTTTTGAAAAATTCTAAAAAGT-AAAAAATTTAAA
5390296 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 12 0.40
37 18 0.60
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (36 bp):
TTTTTGAAAAATTCTAAAAAGTAAAAAATTTAAATT
Found at i:5390295 original size:17 final size:16
Alignment explanation
Indices: 5390265--5390307 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
5390255 ATAAATTTTT
5390265 TTGAAAAATCTAAAAA
1 TTGAAAAATCTAAAAA
*
5390281 TTGAAGAAATTTAAAAA
1 TTGAA-AAATCTAAAAA
5390298 TTGTAAAAAT
1 TTG-AAAAAT
5390308 AAAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 17 0.71
18 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (16 bp):
TTGAAAAATCTAAAAA
Found at i:5390298 original size:8 final size:8
Alignment explanation
Indices: 5390268--5390351 Score: 78
Period size: 8 Copynumber: 9.9 Consensus size: 8
5390258 AATTTTTTTG
*
5390268 AAAAATCT
1 AAAAATTT
*
5390276 AAAAATTG
1 AAAAATTT
5390284 AAGAAATTT
1 AA-AAATTT
5390293 AAAAATTGT
1 AAAAATT-T
**
5390302 AAAAATAA
1 AAAAATTT
5390310 AAAATATTTT
1 AAAA-A-TTT
5390320 AAAAATTAT
1 AAAAATT-T
5390329 AAAAATTT
1 AAAAATTT
*
5390337 AAAAACTT
1 AAAAATTT
5390345 AAAAATT
1 AAAAATT
5390352 AAATAAAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
8 33 0.53
9 24 0.39
10 5 0.08
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (8 bp):
AAAAATTT
Found at i:5390320 original size:27 final size:26
Alignment explanation
Indices: 5390290--5390377 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 26
5390280 ATTGAAGAAA
*
5390290 TTTAAAAATTGTAAAAATAAAAAATAT
1 TTTAAAAATTATAAAAATAAAAAA-AT
**
5390317 TTTAAAAATTATAAAAATTTAAAAA-
1 TTTAAAAATTATAAAAATAAAAAAAT
*
5390342 CTTAAAAATTAAATAAAAATAAAAAAAT
1 TTTAAAAATT--ATAAAAATAAAAAAAT
*
5390370 TCTAAAAA
1 TTTAAAAA
5390378 AATATATTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
25 9 0.18
26 1 0.02
27 34 0.68
28 6 0.12
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (26 bp):
TTTAAAAATTATAAAAATAAAAAAAT
Found at i:5390364 original size:25 final size:24
Alignment explanation
Indices: 5390275--5390367 Score: 69
Period size: 27 Copynumber: 3.5 Consensus size: 24
5390265 TTGAAAAATC
* *
5390275 TAAAAATTGAAGAAATTTAAAAATTG
1 TAAAAATT-AA-AAACTTAAAAATTA
* *
5390301 TAAAAATAAAAAATATTTTAAAAATTA
1 TAAAAAT-TAAAA-A-CTTAAAAATTA
5390328 TAAAAATTTAAAAACTTAAAAATTAAA
1 TAAAAA-TTAAAAACTTAAAAATT--A
*
5390355 TAAAAATAAAAAA
1 TAAAAATTAAAAA
5390368 ATTCTAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
25 11 0.20
26 17 0.30
27 27 0.48
28 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (24 bp):
TAAAAATTAAAAACTTAAAAATTA
Found at i:5390378 original size:19 final size:18
Alignment explanation
Indices: 5390302--5390381 Score: 65
Period size: 19 Copynumber: 4.4 Consensus size: 18
5390292 TAAAAATTGT
*
5390302 AAAAATAAAAAATATTTTA
1 AAAAATAAAAAA-ATTTAA
* *
5390321 AAAATTATAAAAATTT-A
1 AAAAATAAAAAAATTTAA
* * *
5390338 AAAACT-TAAAAATTAAA
1 AAAAATAAAAAAATTTAA
5390355 TAAAAATAAAAAAATTCTAA
1 -AAAAATAAAAAAATT-TAA
5390375 AAAAATA
1 AAAAATA
5390382 TATTAAATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
16 8 0.16
17 7 0.14
18 9 0.18
19 24 0.48
20 2 0.04
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAATAAAAAAATTTAA
Found at i:5390401 original size:54 final size:55
Alignment explanation
Indices: 5390268--5390409 Score: 127
Period size: 54 Copynumber: 2.6 Consensus size: 55
5390258 AATTTTTTTG
* * * * *
5390268 AAAAATCTAAAAATTGAAGAAA-TTTAAAAATT--GTAAAAATAAAAAATATTTTA
1 AAAAATATAAAAATTTAA-AAACTTAAAAAATTAAATAAAAATAAAAAATATTTAA
*
5390321 AAAATTATAAAAATTTAAAAACTT-AAAAATTAAATAAAAATAAAAAA-ATTCTAA
1 AAAAATATAAAAATTTAAAAACTTAAAAAATTAAATAAAAATAAAAAATATT-TAA
* *
5390375 AAAAATATATTAAA-TTATAAGA-TTAAAAAATTAAA
1 AAAAATATA-AAAATTTA-AAAACTTAAAAAATTAAA
5390410 AATTTTAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
52 10 0.14
53 20 0.27
54 28 0.38
55 16 0.22
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (55 bp):
AAAAATATAAAAATTTAAAAACTTAAAAAATTAAATAAAAATAAAAAATATTTAA
Found at i:5390407 original size:8 final size:8
Alignment explanation
Indices: 5390276--5390421 Score: 51
Period size: 9 Copynumber: 16.6 Consensus size: 8
5390266 TGAAAAATCT
5390276 AAAAATTGA
1 AAAAATT-A
* *
5390285 AGAAATTT
1 AAAAATTA
*
5390293 AAAAATTGT
1 AAAAATT-A
*
5390302 AAAAATAA
1 AAAAATTA
*
5390310 AAAATATTTT
1 AAAA-A-TTA
5390320 AAAAATTA
1 AAAAATTA
5390328 TAAAAATTTA
1 -AAAAA-TTA
*
5390338 AAAACTT-
1 AAAAATTA
5390345 AAAAATTAAA
1 AAAAATT--A
*
5390355 TAAAAATAA
1 -AAAAATTA
5390364 AAAAATTCTAA
1 AAAAA-T-T-A
5390375 AAAAATATA
1 AAAAAT-TA
**
5390384 TTAAATTA
1 AAAAATTA
* *
5390392 TAAGATTA
1 AAAAATTA
5390400 AAAAATTA
1 AAAAATTA
*
5390408 AAAATTTTA
1 AAAA-ATTA
5390417 AAAAA
1 AAAAA
5390422 ATTTGCAATA
Statistics
Matches: 103, Mismatches: 21, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
7 6 0.06
8 37 0.36
9 38 0.37
10 10 0.10
11 12 0.12
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (8 bp):
AAAAATTA
Found at i:5391148 original size:18 final size:19
Alignment explanation
Indices: 5391105--5391149 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5391095 ATTATCTATA
5391105 ATAAAAATATAATAATAAT
1 ATAAAAATATAATAATAAT
*
5391124 -TATAAATATAA-AA-AGAT
1 ATAAAAATATAATAATA-AT
5391141 ATAAAAATA
1 ATAAAAATA
5391150 AAATTAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 1 0.05
17 4 0.18
18 17 0.77
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAAATATAATAATAAT
Found at i:5391357 original size:17 final size:18
Alignment explanation
Indices: 5391337--5391376 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5391327 TATAACTTTA
5391337 ATATTTAT-ATAATATTT
1 ATATTTATAATAATATTT
* *
5391354 ATATTTATAATTATTTTT
1 ATATTTATAATAATATTT
5391372 ATATT
1 ATATT
5391377 AAAATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTATAATAATATTT
Found at i:5392245 original size:22 final size:22
Alignment explanation
Indices: 5392217--5392265 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
5392207 ATTTTGTCTC
5392217 TTCTAATATTATCATATATACA
1 TTCTAATATTATCATATATACA
5392239 TTCTAATATTATCATATATACA
1 TTCTAATATTATCATATATACA
5392261 -TCTAA
1 TTCTAA
5392266 GCATCCTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (22 bp):
TTCTAATATTATCATATATACA
Found at i:5395302 original size:13 final size:14
Alignment explanation
Indices: 5395284--5395315 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
5395274 ATCATACAAC
5395284 AAAAATAAAAA-GA
1 AAAAATAAAAAGGA
5395297 AAAAATAAAAAGGA
1 AAAAATAAAAAGGA
5395311 AAAAA
1 AAAAA
5395316 AAGCAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (14 bp):
AAAAATAAAAAGGA
Found at i:5396282 original size:65 final size:65
Alignment explanation
Indices: 5396205--5396332 Score: 247
Period size: 65 Copynumber: 2.0 Consensus size: 65
5396195 TTAAAAAGAT
*
5396205 TTTTTTTTTTTTTACCTTTTACACATTTTCTATATAAGAAAAAAGAAAATTTTATTATTATTATC
1 TTTTTTTTTTTTTACCTTGTACACATTTTCTATATAAGAAAAAAGAAAATTTTATTATTATTATC
5396270 TTTTTTTTTTTTTACCTTGTACACATTTTCTATATAAGAAAAAAGAAAATTTTATTATTATTA
1 TTTTTTTTTTTTTACCTTGTACACATTTTCTATATAAGAAAAAAGAAAATTTTATTATTATTA
5396333 AAAATTTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (65 bp):
TTTTTTTTTTTTTACCTTGTACACATTTTCTATATAAGAAAAAAGAAAATTTTATTATTATTATC
Found at i:5396490 original size:25 final size:25
Alignment explanation
Indices: 5396462--5396509 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5396452 TTTTCCCTTA
5396462 TTTTTA-TTATTTTTATTAATAAATT
1 TTTTTAGTT-TTTTTATTAATAAATT
*
5396487 TTTTTAGTTTTTTTATTTATAAA
1 TTTTTAGTTTTTTTATTAATAAA
5396510 GAAAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTTAGTTTTTTTATTAATAAATT
Found at i:5397908 original size:13 final size:12
Alignment explanation
Indices: 5397882--5397915 Score: 50
Period size: 12 Copynumber: 2.7 Consensus size: 12
5397872 AGAAAGAAAT
5397882 AATAAAATAATAAA
1 AATAAAA-AAT-AA
5397896 AATAAAAAATAA
1 AATAAAAAATAA
5397908 AATAAAAA
1 AATAAAAA
5397916 TAATAGAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 3 0.15
14 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:5397913 original size:18 final size:19
Alignment explanation
Indices: 5397878--5397933 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
5397868 AGAAAGAAAG
5397878 AAATAATAAAAT--AATAA
1 AAATAATAAAATAAAATAA
5397895 AAATAA-AAAATAAAATAA
1 AAATAATAAAATAAAATAA
* *
5397913 AAATAATAGAGTAAAATAA
1 AAATAATAAAATAAAATAA
5397932 AA
1 AA
5397934 TTTCATTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 11 0.32
19 12 0.35
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.20
Consensus pattern (19 bp):
AAATAATAAAATAAAATAA
Found at i:5397928 original size:24 final size:21
Alignment explanation
Indices: 5397882--5397934 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
5397872 AGAAAGAAAT
5397882 AATAAAATAATAAAAATAAAA
1 AATAAAATAATAAAAATAAAA
5397903 AATAAAATAA-AAATAATAGAGTAA
1 AATAAAATAATAAA-AATA-A--AA
5397927 AATAAAAT
1 AATAAAAT
5397935 TTCATTTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.11
21 14 0.50
22 1 0.04
24 10 0.36
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (21 bp):
AATAAAATAATAAAAATAAAA
Found at i:5398802 original size:26 final size:27
Alignment explanation
Indices: 5398773--5398825 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
5398763 GTTATCTAGC
5398773 AAATAAAAAATAAATCTAATC-CAACA
1 AAATAAAAAATAAATCTAATCACAACA
*
5398799 AAATAAAAGATAAATCTAATCACAACA
1 AAATAAAAAATAAATCTAATCACAACA
5398826 TTATTCTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.64, C:0.15, G:0.02, T:0.19
Consensus pattern (27 bp):
AAATAAAAAATAAATCTAATCACAACA
Found at i:5411665 original size:14 final size:14
Alignment explanation
Indices: 5411636--5411678 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5411626 AATTTTTATC
*
5411636 AATATTTTTACTAAA
1 AATATTTAT-CTAAA
5411651 AATATTTATCTAAA
1 AATATTTATCTAAA
*
5411665 AATATATATC-AAA
1 AATATTTATCTAAA
5411678 A
1 A
5411679 TTTATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 4 0.15
14 14 0.54
15 8 0.31
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATTTATCTAAA
Found at i:5415650 original size:5 final size:6
Alignment explanation
Indices: 5415570--5415647 Score: 59
Period size: 6 Copynumber: 13.2 Consensus size: 6
5415560 AAAGCCCAAA
* * * * * * **
5415570 AATTTT AATTTT GATTGT AATTTT GATTTT GATTTG AAATTT GTTTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
* *
5415618 AATGTT AA-TTT AATTTT AATTTT GATTTT A
1 AATTTT AATTTT AATTTT AATTTT AATTTT A
5415648 TTTCGAGTCA
Statistics
Matches: 53, Mismatches: 18, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
5 4 0.08
6 49 0.92
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:5417400 original size:20 final size:21
Alignment explanation
Indices: 5417375--5417418 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
5417365 ATTTATTACG
**
5417375 TTGCATAATTCTTAA-TATAT
1 TTGCATAATTAATAATTATAT
5417395 TTGCATAATTAATAATTATAT
1 TTGCATAATTAATAATTATAT
5417416 TTG
1 TTG
5417419 TATTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
TTGCATAATTAATAATTATAT
Found at i:5417429 original size:33 final size:34
Alignment explanation
Indices: 5417392--5417455 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
5417382 ATTCTTAATA
*
5417392 TATTTGCATAATTAATAATTA-TATTTGTATTAT
1 TATTTACATAATTAATAATTATTATTTGTATTAT
* *
5417425 TATTTACATGATTAATTATTATTATTTGTAT
1 TATTTACATAATTAATAATTATTATTTGTAT
5417456 ATTTGCATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.56
Consensus pattern (34 bp):
TATTTACATAATTAATAATTATTATTTGTATTAT
Found at i:5417459 original size:30 final size:30
Alignment explanation
Indices: 5417390--5417465 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 30
5417380 TAATTCTTAA
*
5417390 TATATTTGCATAATTAATAATTATATTTGTAT
1 TATATTTGCATGATTAATAATTATATTTG--T
* *
5417422 TATTATTTACATGATTAATTATTATTATTTG-
1 TA-TATTTGCATGATTAATAATTA-TATTTGT
5417453 TATATTTGCATGA
1 TATATTTGCATGA
5417466 CAATTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 10 0.26
31 2 0.05
32 2 0.05
33 18 0.47
34 6 0.16
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (30 bp):
TATATTTGCATGATTAATAATTATATTTGT
Found at i:5420302 original size:13 final size:13
Alignment explanation
Indices: 5420275--5420312 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5420265 ATTTTATGGA
5420275 TTTAAAAT-A-TT
1 TTTAAAATAATTT
5420286 TTTAAAATAATTT
1 TTTAAAATAATTT
*
5420299 TTTAAATTAATTT
1 TTTAAAATAATTT
5420312 T
1 T
5420313 ACTAAACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.33
12 1 0.04
13 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTAAAATAATTT
Found at i:5423170 original size:25 final size:25
Alignment explanation
Indices: 5423142--5423251 Score: 63
Period size: 25 Copynumber: 4.5 Consensus size: 25
5423132 AAATATGAAT
5423142 AGATAAAATAAAAATAAATAAATAA
1 AGATAAAATAAAAATAAATAAATAA
* *
5423167 AGATGAAAT-----TAAGATAAA-AG
1 AGATAAAATAAAAATAA-ATAAATAA
* **
5423187 AGATGAAATAAAAATAAATGGATAA
1 AGATAAAATAAAAATAAATAAATAA
* *
5423212 A-ATAAACATAAAAAAAAAGAAATACA
1 AGATAAA-ATAAAAATAAATAAATA-A
5423238 AGGATAAATATAAA
1 A-GATAAA-ATAAA
5423252 TTATAAAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.21
21 5 0.08
24 7 0.11
25 26 0.41
26 2 0.03
28 10 0.16
ACGTcount: A:0.69, C:0.02, G:0.11, T:0.18
Consensus pattern (25 bp):
AGATAAAATAAAAATAAATAAATAA
Found at i:5423203 original size:20 final size:20
Alignment explanation
Indices: 5423157--5423224 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
5423147 AAATAAAAAT
* *
5423157 AAATAAATAAAGATGAAATTA
1 AAATAAA-AGAGATGAAATAA
*
5423178 AGATAAAAGAGATGAAATAA
1 AAATAAAAGAGATGAAATAA
* *
5423198 AAATAAATG-GATAAAATAA
1 AAATAAAAGAGATGAAATAA
*
5423217 ACATAAAA
1 AAATAAAA
5423225 AAAAAGAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 15 0.38
20 18 0.46
21 6 0.15
ACGTcount: A:0.68, C:0.01, G:0.12, T:0.19
Consensus pattern (20 bp):
AAATAAAAGAGATGAAATAA
Found at i:5423216 original size:19 final size:19
Alignment explanation
Indices: 5423082--5423223 Score: 77
Period size: 19 Copynumber: 6.7 Consensus size: 19
5423072 ACCTTTTGTG
5423082 AAATAAAAATAAATGAGATAA
1 AAATAAAAATAAAT-AGAT-A
* *
5423103 AAAAATAAAATAAATTAGACA
1 AAATA-AAAATAAA-TAGATA
*
5423124 AACTAAGGAAATATGAATAGATA
1 AAATAA--AAATA--AATAGATA
*
5423147 AAATAAAAATAAATAAATA
1 AAATAAAAATAAATAGATA
* *
5423166 AAGATGAAATTAAGATAAAAGAGATG
1 AA-AT--AA--AA-AT-AAATAGATA
*
5423192 AAATAAAAATAAATGGATA
1 AAATAAAAATAAATAGATA
*
5423211 AAATAAACATAAA
1 AAATAAAAATAAA
5423224 AAAAAAGAAA
Statistics
Matches: 94, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
19 27 0.29
20 5 0.05
21 15 0.16
22 18 0.19
23 13 0.14
24 4 0.04
25 4 0.04
26 8 0.09
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.20
Consensus pattern (19 bp):
AAATAAAAATAAATAGATA
Found at i:5427875 original size:6 final size:6
Alignment explanation
Indices: 5427864--5427894 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5427854 TTAATTTAAA
*
5427864 ACACAT ACACAT TCACAT ACACAT ACACAT A
1 ACACAT ACACAT ACACAT ACACAT ACACAT A
5427895 TAATCTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (6 bp):
ACACAT
Found at i:5429290 original size:21 final size:19
Alignment explanation
Indices: 5429264--5429310 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
5429254 TTTCAATAAA
*
5429264 TTTGTATAATATTTTATATTT
1 TTTGTATAA-A-TTTATAATT
5429285 TTTGTA-AAATTTATAATT
1 TTTGTATAAATTTATAATT
*
5429303 TTAGTATA
1 TTTGTATA
5429311 CGTATATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 13 0.57
19 2 0.09
20 2 0.09
21 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
TTTGTATAAATTTATAATT
Found at i:5430226 original size:9 final size:9
Alignment explanation
Indices: 5430212--5430239 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5430202 AGCAATCTCT
5430212 TTTTCTTTA
1 TTTTCTTTA
5430221 TTTTCTTTA
1 TTTTCTTTA
5430230 TTTTCTTTA
1 TTTTCTTTA
5430239 T
1 T
5430240 ATACCTTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCTTTA
Found at i:5431685 original size:42 final size:43
Alignment explanation
Indices: 5431625--5431714 Score: 141
Period size: 42 Copynumber: 2.1 Consensus size: 43
5431615 TGTCCCCTGA
5431625 TTGTT-AGTTTTATGATAGTAGGTAATG-ATTATTAATTTGCT
1 TTGTTAAGTTTTATGATAGTAGGTAATGTATTATTAATTTGCT
*
5431666 TTGTTAAGTTTTACT-ATAGTAGGTAATGTTTTATTAATTTGCT
1 TTGTTAAGTTTTA-TGATAGTAGGTAATGTATTATTAATTTGCT
5431709 TTGTTA
1 TTGTTA
5431715 TGCAATACCT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
41 5 0.11
42 20 0.44
43 20 0.44
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (43 bp):
TTGTTAAGTTTTATGATAGTAGGTAATGTATTATTAATTTGCT
Found at i:5432701 original size:12 final size:12
Alignment explanation
Indices: 5432684--5432719 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5432674 ACTCTGAGTA
*
5432684 CTGTCTCTGTCT
1 CTGTCTCTCTCT
5432696 CTGTCTCTCTCT
1 CTGTCTCTCTCT
*
5432708 CTCTCTCTCTCT
1 CTGTCTCTCTCT
5432720 ATTTTGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (12 bp):
CTGTCTCTCTCT
Found at i:5434763 original size:26 final size:24
Alignment explanation
Indices: 5434712--5434777 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
5434702 TGATCTATTT
*
5434712 ATAAAATTTATATGAAGTTTTTTTA
1 ATAAAATTTATA-GAAATTTTTTTA
5434737 ATTAAAATTTATA-AAATTTTATCTTA
1 A-TAAAATTTATAGAAATTTT-T-TTA
*
5434763 AAAAAATTTA-AGAAA
1 ATAAAATTTATAGAAA
5434778 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
24 7 0.20
25 13 0.37
26 15 0.43
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (24 bp):
ATAAAATTTATAGAAATTTTTTTA
Found at i:5438118 original size:35 final size:35
Alignment explanation
Indices: 5438070--5438140 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
5438060 TGTCACTTAC
*
5438070 AATTATTGAATTATAATTAATCGATCACAATTTAA
1 AATTATTGAATTATAATTAATCGATCACAATCTAA
* *
5438105 AATTATTGCATTATAATTAATCTATCACAATCTAA
1 AATTATTGAATTATAATTAATCGATCACAATCTAA
5438140 A
1 A
5438141 TTTGTGCGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.39
Consensus pattern (35 bp):
AATTATTGAATTATAATTAATCGATCACAATCTAA
Found at i:5441435 original size:10 final size:10
Alignment explanation
Indices: 5441422--5441447 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5441412 TTTTTTATTT
5441422 TATTTTTTTA
1 TATTTTTTTA
5441432 TATTTTTTTA
1 TATTTTTTTA
5441442 TATTTT
1 TATTTT
5441448 AAATAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TATTTTTTTA
Found at i:5441692 original size:18 final size:18
Alignment explanation
Indices: 5441666--5441700 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5441656 GTTTTTTTCC
*
5441666 TTTAATTTTTTTCTATTA
1 TTTAATTTTTTTATATTA
*
5441684 TTTATTTTTTTTATATT
1 TTTAATTTTTTTATATT
5441701 TAATAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTAATTTTTTTATATTA
Found at i:5441700 original size:15 final size:17
Alignment explanation
Indices: 5441670--5441702 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5441660 TTTTCCTTTA
5441670 ATTTTTTTCTATTATTT
1 ATTTTTTTCTATTATTT
5441687 ATTTTTTT-TA-TATTT
1 ATTTTTTTCTATTATTT
5441702 A
1 A
5441703 ATAAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTTTCTATTATTT
Found at i:5442194 original size:2 final size:2
Alignment explanation
Indices: 5442187--5442214 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5442177 TTCAAATTTG
5442187 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5442215 CAATCCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5443275 original size:36 final size:36
Alignment explanation
Indices: 5443235--5443347 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
5443225 TATATAAAAG
5443235 TATATATTTTATTATCTATTTAATTTTATATTTATA
1 TATATATTTTATTATCTATTTAATTTTATATTTATA
* * * * * *
5443271 TATATATTATA-CAT-AATAT-ATTTGTATA-TAAAA
1 TATATATTTTATTATCTATTTAATTT-TATATTTATA
* *
5443304 GTATATACTTTATTAGCTATTTAATTTTATATTTATA
1 -TATATATTTTATTATCTATTTAATTTTATATTTATA
5443341 TATATAT
1 TATATAT
5443348 ATATGTATTC
Statistics
Matches: 56, Mismatches: 15, Indels: 12
0.67 0.18 0.14
Matches are distributed among these distances:
33 7 0.12
34 16 0.29
35 3 0.05
36 23 0.41
37 7 0.12
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.56
Consensus pattern (36 bp):
TATATATTTTATTATCTATTTAATTTTATATTTATA
Found at i:5444805 original size:21 final size:21
Alignment explanation
Indices: 5444779--5444820 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5444769 CCTGTCAGCC
5444779 ACCCAACCAACTCCCC-GACCA
1 ACCCAACCAAC-CCCCTGACCA
5444800 ACCCAACCAACCCCCTGACCA
1 ACCCAACCAACCCCCTGACCA
5444821 GCTCTCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.33, C:0.57, G:0.05, T:0.05
Consensus pattern (21 bp):
ACCCAACCAACCCCCTGACCA
Found at i:5445043 original size:24 final size:24
Alignment explanation
Indices: 5445016--5445061 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
5445006 ACACCGAAAA
5445016 AAAAAAGCAAA-AAAAACAAAAACC
1 AAAAAAG-AAACAAAAACAAAAACC
* *
5445040 AAAACAGAAACAAAAATAAAAA
1 AAAAAAGAAACAAAAACAAAAA
5445062 AATACACGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.80, C:0.13, G:0.04, T:0.02
Consensus pattern (24 bp):
AAAAAAGAAACAAAAACAAAAACC
Found at i:5445050 original size:18 final size:18
Alignment explanation
Indices: 5444995--5445055 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
5444985 CAAAATACCC
* *
5444995 AAACAAAAACC-ACACCG
1 AAACAAAAACCAAAACAG
* *
5445012 AAAAAAAAAAGCAAAA-A-
1 -AAACAAAAACCAAAACAG
5445029 AAACAAAAACCAAAACAG
1 AAACAAAAACCAAAACAG
5445047 AAACAAAAA
1 AAACAAAAA
5445056 TAAAAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 13 0.38
17 1 0.03
18 18 0.53
19 2 0.06
ACGTcount: A:0.75, C:0.20, G:0.05, T:0.00
Consensus pattern (18 bp):
AAACAAAAACCAAAACAG
Found at i:5445359 original size:28 final size:29
Alignment explanation
Indices: 5445310--5445369 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
5445300 TTAATTAATG
* *
5445310 AATAAATAGCTAAATTTCATAAATACATA
1 AATAAATAGATAAATTTCATAAATAAATA
* *
5445339 AATAAATA-ATAAATTTTATAATTAAATA
1 AATAAATAGATAAATTTCATAAATAAATA
5445367 AAT
1 AAT
5445370 TATTAGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (29 bp):
AATAAATAGATAAATTTCATAAATAAATA
Found at i:5452207 original size:50 final size:50
Alignment explanation
Indices: 5452152--5452368 Score: 185
Period size: 50 Copynumber: 4.4 Consensus size: 50
5452142 AACAAATATT
* * * ** *
5452152 TTGAAACTTTAAAAATCTCATTTGAAAGGAGCACTTTTTAAACGGAGGCC
1 TTGAAACTTTAAAAATCTCATATAAAAAGAGCACTTTTTAAACAAAGGCA
* * * * * *
5452202 TTGAAACATTAAAAATCTCATTTGAAAAGA--ATTTTTCTTAAATAAAGGCC
1 TTGAAACTTTAAAAATCTCATATAAAAAGAGCA-CTTT-TTAAACAAAGGCA
* * *
5452252 TTGAAACTTTAAACAA-CTCATATAAAAAGAGCTA-TTCTTAATCAGAGGCA
1 TTGAAACTTTAAA-AATCTCATATAAAAAGAGC-ACTTTTTAAACAAAGGCA
* *
5452302 TTGGAAA-TTTAAAAATCTTATATAAAAAGAGCTCTTTTTAAA-AAAGGCA
1 TT-GAAACTTTAAAAATCTCATATAAAAAGAGCACTTTTTAAACAAAGGCA
*
5452351 TTAAAACTTTAAAAATCT
1 TTGAAACTTTAAAAATCT
5452369 TAAAGAATCT
Statistics
Matches: 137, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
48 4 0.03
49 24 0.18
50 100 0.73
51 8 0.06
53 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (50 bp):
TTGAAACTTTAAAAATCTCATATAAAAAGAGCACTTTTTAAACAAAGGCA
Found at i:5452300 original size:100 final size:99
Alignment explanation
Indices: 5452152--5452368 Score: 226
Period size: 100 Copynumber: 2.2 Consensus size: 99
5452142 AACAAATATT
* * * * * *
5452152 TTGAAACTTTAAAAATCTCATTTGAAAGGAGCACTTTTTAAACGGAGGCCTT-GAAACATTAAAA
1 TTGAAACTTTAAAAATCTCATATAAAAAGAGCACTTCTTAAACAGAGGCATTGGAAA-ATTAAAA
* * * *
5452216 ATCTCATTTGAAAAGA-ATTTTTCTTAAATAAAGGCC
65 ATCTCATATAAAAAGAGATCTTT-TTAAA-AAAGGCA
* *
5452252 TTGAAACTTTAAACAA-CTCATATAAAAAGAGCTA-TTCTTAATCAGAGGCATTGGAAATTTAAA
1 TTGAAACTTTAAA-AATCTCATATAAAAAGAGC-ACTTCTTAAACAGAGGCATTGGAAAATTAAA
* *
5452315 AATCTTATATAAAAAGAGCTCTTTTTAAAAAAGGCA
64 AATCTCATATAAAAAGAGATCTTTTTAAAAAAGGCA
*
5452351 TTAAAACTTTAAAAATCT
1 TTGAAACTTTAAAAATCT
5452369 TAAAGAATCT
Statistics
Matches: 97, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
98 2 0.02
99 20 0.21
100 64 0.66
101 11 0.11
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (99 bp):
TTGAAACTTTAAAAATCTCATATAAAAAGAGCACTTCTTAAACAGAGGCATTGGAAAATTAAAAA
TCTCATATAAAAAGAGATCTTTTTAAAAAAGGCA
Found at i:5461114 original size:9 final size:9
Alignment explanation
Indices: 5461088--5461139 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
5461078 TGTAAGTAAT
5461088 TAAAATATA
1 TAAAATATA
5461097 -AAAA-A-A
1 TAAAATATA
*
5461103 TAATATATA
1 TAAAATATA
5461112 TAAAATA-A
1 TAAAATATA
5461120 TAAAATAT-
1 TAAAATATA
5461128 TAAAAATATA
1 T-AAAATATA
5461138 TA
1 TA
5461140 GATAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
6 1 0.03
7 4 0.11
8 14 0.40
9 15 0.43
10 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAATATA
Found at i:5461133 original size:32 final size:33
Alignment explanation
Indices: 5461088--5461150 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
5461078 TGTAAGTAAT
*
5461088 TAAAATATAAAAAA-ATA-ATATATATAAAATAA
1 TAAAATATAAAAAATATATAGATA-ATAAAATAA
*
5461120 TAAAATATTAAAAATATATAGATAATAAAAT
1 TAAAATATAAAAAATATATAGATAATAAAAT
5461151 GATTTTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 13 0.48
33 10 0.37
34 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (33 bp):
TAAAATATAAAAAATATATAGATAATAAAATAA
Found at i:5461134 original size:17 final size:16
Alignment explanation
Indices: 5461088--5461135 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
5461078 TGTAAGTAAT
5461088 TAAAATATAAAAA-AA
1 TAAAATATAAAAATAA
*
5461103 TAATATATATAAAATAA
1 TAAAATATA-AAAATAA
5461120 TAAAATATTAAAAATA
1 TAAAATA-TAAAAATA
5461136 TATAGATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 14 0.50
18 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAATATAAAAATAA
Found at i:5463701 original size:13 final size:12
Alignment explanation
Indices: 5463682--5463713 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
5463672 TTTATTTTAT
5463682 ATTTATATGATA
1 ATTTATATGATA
5463694 ATTATATATGATA
1 ATT-TATATGATA
5463707 ATTTATA
1 ATTTATA
5463714 AAAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (12 bp):
ATTTATATGATA
Found at i:5464712 original size:29 final size:28
Alignment explanation
Indices: 5464677--5464739 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
5464667 AGTGTAATAT
* *
5464677 TTAATTTTATATTTAAATTTTAAAAATTA
1 TTAATTTAATATTTAAATTAT-AAAATTA
*
5464706 TTAATTTAATATTTAAATTATAAATTTA
1 TTAATTTAATATTTAAATTATAAAATTA
5464734 TTAATT
1 TTAATT
5464740 AATGTGATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTAATTTAATATTTAAATTATAAAATTA
Found at i:5464723 original size:20 final size:20
Alignment explanation
Indices: 5464671--5464733 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
5464661 AATTTTAGTG
5464671 TAATATTT-AATT-TTATATT
1 TAATATTTAAATTATTA-ATT
5464690 TAA-ATTTTAAAAATTATTAATT
1 TAATA-TTT--AAATTATTAATT
*
5464712 TAATATTTAAATTATAAATT
1 TAATATTTAAATTATTAATT
5464732 TA
1 TA
5464734 TTAATTAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
18 1 0.03
19 6 0.16
20 13 0.35
22 13 0.35
23 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATATTTAAATTATTAATT
Found at i:5464741 original size:20 final size:20
Alignment explanation
Indices: 5464700--5464741 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5464690 TAAATTTTAA
* *
5464700 AAATTATTAATTTAATATTT
1 AAATTATAAATTTAATAATT
*
5464720 AAATTATAAATTTATTAATT
1 AAATTATAAATTTAATAATT
5464740 AA
1 AA
5464742 TGTGATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATTATAAATTTAATAATT
Found at i:5464869 original size:28 final size:28
Alignment explanation
Indices: 5464819--5464878 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
5464809 AATCAATATA
* *
5464819 TTTATAATTTAAATATAGCATTAAAAAT
1 TTTATAATTCAAATATAACATTAAAAAT
* *
5464847 GTTTA-AATTCAAATATAATATTATAAAT
1 -TTTATAATTCAAATATAACATTAAAAAT
5464875 TTTA
1 TTTA
5464879 CTATAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.15
28 19 0.70
29 4 0.15
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (28 bp):
TTTATAATTCAAATATAACATTAAAAAT
Found at i:5464883 original size:20 final size:20
Alignment explanation
Indices: 5464860--5464908 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
5464850 TAAATTCAAA
*
5464860 TATAATATTATAAATT-TTAC
1 TATAATATTAAAAATTATT-C
5464880 TATAAT-TTAAAAATTATTC
1 TATAATATTAAAAATTATTC
5464899 -ATAATATTAA
1 TATAATATTAA
5464909 TCCATATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 13 0.50
20 8 0.31
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
TATAATATTAAAAATTATTC
Found at i:5471055 original size:19 final size:17
Alignment explanation
Indices: 5471014--5471054 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5471004 ATAATTTATT
5471014 ATAAT-ATATTTTTTTA
1 ATAATAATATTTTTTTA
*
5471030 ATTATAATATTTTTTTA
1 ATAATAATATTTTTTTA
5471047 ATAA-AATA
1 ATAATAATA
5471055 ACATATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAATAATATTTTTTTA
Found at i:5472466 original size:29 final size:28
Alignment explanation
Indices: 5472426--5472487 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
5472416 AACTAATAAA
*
5472426 TTTATAATTTAAATATTACATTAAAAATAT
1 TTTATAATTTAAATATCACATT--AAATAT
*
5472456 TTTA-AATTTAAATATCATATTAAATAT
1 TTTATAATTTAAATATCACATTAAATAT
5472483 TTTAT
1 TTTAT
5472488 TGTAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 10 0.34
29 15 0.52
30 4 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTATAATTTAAATATCACATTAAATAT
Found at i:5477506 original size:28 final size:28
Alignment explanation
Indices: 5477474--5477543 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
5477464 GATGAAACTT
*
5477474 GAAAGGAAGGAAAGGAGAAGCCAAGAAG
1 GAAAGGAAGGAAAGCAGAAGCCAAGAAG
* *
5477502 GAAAGGAAGAAAAGCAGAAGCCGAGAAG
1 GAAAGGAAGGAAAGCAGAAGCCAAGAAG
*
5477530 GAAAGGGAGGAAAG
1 GAAAGGAAGGAAAG
5477544 ATTGTTTGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.53, C:0.07, G:0.40, T:0.00
Consensus pattern (28 bp):
GAAAGGAAGGAAAGCAGAAGCCAAGAAG
Found at i:5478057 original size:27 final size:31
Alignment explanation
Indices: 5478021--5478089 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 31
5478011 ATTAATAAAT
5478021 TTATAATTTATATATCACAT-TAA-ATTTT-
1 TTATAATTTATATATCACATGTAATATTTTA
*
5478049 TT-TAATTTAAATATCACATGTAATATTTTA
1 TTATAATTTATATATCACATGTAATATTTTA
5478079 TTATAATTTAT
1 TTATAATTTAT
5478090 GAGCCATCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 16 0.46
28 5 0.14
29 5 0.14
30 2 0.06
31 7 0.20
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (31 bp):
TTATAATTTATATATCACATGTAATATTTTA
Found at i:5478573 original size:20 final size:19
Alignment explanation
Indices: 5478518--5478578 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
5478508 ACTAATATTC
*
5478518 TTACTTTTAATAAA-TAAA
1 TTACTATTAATAAATTAAA
* *
5478536 TTACTATAAAATACATTAAA
1 TTACTAT-TAATAAATTAAA
5478556 TTACTATTAATCAAATTAAA
1 TTACTATTAAT-AAATTAAA
5478576 TTA
1 TTA
5478579 AATGAATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 6 0.17
19 8 0.23
20 21 0.60
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
TTACTATTAATAAATTAAA
Found at i:5480269 original size:10 final size:10
Alignment explanation
Indices: 5480256--5480298 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
5480246 GAAAGAAAAC
*
5480256 AAAGGAAAGG
1 AAAGTAAAGG
* *
5480266 AAAGAAAAGT
1 AAAGTAAAGG
5480276 AAAGTAAAGG
1 AAAGTAAAGG
*
5480286 AATGTAAAGG
1 AAAGTAAAGG
5480296 AAA
1 AAA
5480299 CAAAATCCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.28, T:0.09
Consensus pattern (10 bp):
AAAGTAAAGG
Found at i:5480274 original size:15 final size:15
Alignment explanation
Indices: 5480256--5480303 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
5480246 GAAAGAAAAC
*
5480256 AAAGGAAAGGAAAGA
1 AAAGTAAAGGAAAGA
* *
5480271 AAAGTAAAGTAAAGG
1 AAAGTAAAGGAAAGA
* *
5480286 AATGTAAAGGAAACA
1 AAAGTAAAGGAAAGA
5480301 AAA
1 AAA
5480304 TCCCAATTCC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (15 bp):
AAAGTAAAGGAAAGA
Found at i:5483858 original size:7 final size:7
Alignment explanation
Indices: 5483846--5484038 Score: 214
Period size: 7 Copynumber: 29.3 Consensus size: 7
5483836 ATAAGAAAAA
5483846 AATATTT
1 AATATTT
5483853 AATATTT
1 AATATTT
5483860 AAT-TTT
1 AATATTT
5483866 AATATTT
1 AATATTT
5483873 AATATTT
1 AATATTT
5483880 AATA-TT
1 AATATTT
5483886 AATATTT
1 AATATTT
5483893 AATATTT
1 AATATTT
*
5483900 GATATTT
1 AATATTT
5483907 AATATTT
1 AATATTT
5483914 AATATTT
1 AATATTT
5483921 AAT-TTT
1 AATATTT
5483927 AATA-TT
1 AATATTT
*
5483933 AAAATTT
1 AATATTT
*
5483940 AAAATTT
1 AATATTT
* *
5483947 AAAATGT
1 AATATTT
5483954 AATA-TT
1 AATATTT
5483960 AATA-TT
1 AATATTT
5483966 AATA-TT
1 AATATTT
5483972 AATA-TT
1 AATATTT
5483978 AATATTT
1 AATATTT
5483985 AATATTT
1 AATATTT
5483992 AAT-TTT
1 AATATTT
5483998 AAT-TTT
1 AATATTT
5484004 AATA-TT
1 AATATTT
5484010 AA-AGTTT
1 AATA-TTT
*
5484017 TAT-TTT
1 AATATTT
*
5484023 AATTTTT
1 AATATTT
*
5484030 AATTTTT
1 AATATTT
5484037 AA
1 AA
5484039 AAAATTTAAT
Statistics
Matches: 168, Mismatches: 8, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
5 1 0.01
6 67 0.40
7 100 0.60
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (7 bp):
AATATTT
Found at i:5483871 original size:20 final size:20
Alignment explanation
Indices: 5483846--5484038 Score: 211
Period size: 20 Copynumber: 9.8 Consensus size: 20
5483836 ATAAGAAAAA
5483846 AATATTTAATATTTAATTTT
1 AATATTTAATATTTAATTTT
*
5483866 AATATTTAATATTTAATATT
1 AATATTTAATATTTAATTTT
*
5483886 AATATTTAATATTTGATATTT
1 AATATTTAATATTTAAT-TTT
5483907 AATATTTAATATTTAATTTT
1 AATATTTAATATTTAATTTT
* *
5483927 AATA-TTAAAATTTAAAATTT
1 AATATTTAATATTT-AATTTT
* * *
5483947 AAAATGTAATA-TTAATATT
1 AATATTTAATATTTAATTTT
5483966 AATA-TTAATA-TTAATATTT
1 AATATTTAATATTTAAT-TTT
5483985 AATATTTAAT-TTTAATTTT
1 AATATTTAATATTTAATTTT
*
5484004 AATA-TTAA-AGTTTTATTTT
1 AATATTTAATA-TTTAATTTT
* *
5484023 AATTTTTAATTTTTAA
1 AATATTTAATATTTAA
5484039 AAAATTTAAT
Statistics
Matches: 145, Mismatches: 18, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
18 14 0.10
19 39 0.27
20 70 0.48
21 22 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AATATTTAATATTTAATTTT
Found at i:5484029 original size:26 final size:26
Alignment explanation
Indices: 5483846--5484038 Score: 191
Period size: 27 Copynumber: 7.3 Consensus size: 26
5483836 ATAAGAAAAA
5483846 AATATTTAATATTTAATTTTAATATTT
1 AATATTTAATATTTAATTTTAAT-TTT
5483873 AATATTTAATA-TTAATATTTAATATTT
1 AATATTTAATATTTAAT-TTTAAT-TTT
*
5483900 GATATTTAATATTTAATATTTAATTTT
1 AATATTTAATATTTAAT-TTTAATTTT
* * * *
5483927 AATA-TTAAAATTTAAAATTTAAAATGT
1 AATATTTAATATTT--AATTTTAATTTT
* *
5483954 AATA-TTAATA-TTAATATTAATATT
1 AATATTTAATATTTAATTTTAATTTT
5483978 AATATTTAATATTTAATTTTAATTTT
1 AATATTTAATATTTAATTTTAATTTT
*
5484004 AATA-TTAA-AGTTTTATTTTAATTTTT
1 AATATTTAATA-TTTAATTTTAA-TTTT
*
5484030 AATTTTTAA
1 AATATTTAA
5484039 AAAATTTAAT
Statistics
Matches: 141, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
24 12 0.09
25 20 0.14
26 38 0.27
27 56 0.40
28 15 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
AATATTTAATATTTAATTTTAATTTT
Found at i:5484525 original size:16 final size:16
Alignment explanation
Indices: 5484506--5484536 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5484496 GATATATTAA
*
5484506 TCTATTGATAATTTTT
1 TCTATTGAAAATTTTT
5484522 TCTATTGAAAATTTT
1 TCTATTGAAAATTTT
5484537 ATTTTGAATC
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:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TCTATTGAAAATTTTT
Found at i:5484881 original size:14 final size:14
Alignment explanation
Indices: 5484864--5484905 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
5484854 TAGGGTTTAG
5484864 ATTTTAAATTTAAT
1 ATTTTAAATTTAAT
*
5484878 ATTTTATAAATT-AT
1 ATTTTA-AATTTAAT
5484892 ATTTTAAATATTAA
1 ATTTTAAAT-TTAA
5484906 AAATAAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 2 0.09
14 16 0.70
15 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTAAATTTAAT
Found at i:5486196 original size:17 final size:18
Alignment explanation
Indices: 5486176--5486212 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5486166 AGGATGCTAC
*
5486176 TATTTCAAAT-TTTTTTA
1 TATTTCAAATATATTTTA
5486193 TATTTCAAATATATTTTA
1 TATTTCAAATATATTTTA
5486211 TA
1 TA
5486213 AAATATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTCAAATATATTTTA
Found at i:5487472 original size:17 final size:17
Alignment explanation
Indices: 5487440--5487487 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
5487430 TGGAAGGATT
*
5487440 AAATTAAAATAATTTTGAG
1 AAATT-AAA-AATTTTGAA
* *
5487459 TAATTAAAAATTTTTAA
1 AAATTAAAAATTTTGAA
5487476 AAATTAAAAATT
1 AAATTAAAAATT
5487488 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 18 0.72
18 3 0.12
19 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
AAATTAAAAATTTTGAA
Found at i:5491427 original size:5 final size:6
Alignment explanation
Indices: 5491412--5491436 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5491402 CTACTCTTCC
5491412 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
5491437 GTACAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:5491828 original size:2 final size:2
Alignment explanation
Indices: 5491815--5491854 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5491805 GTTGTCTCCT
*
5491815 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5491855 AAAGAGGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5492419 original size:11 final size:13
Alignment explanation
Indices: 5492395--5492426 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5492385 CTTCAACAAC
5492395 CCCAAACACCATA
1 CCCAAACACCATA
5492408 -CCAAAC-CCATA
1 CCCAAACACCATA
5492419 CCCAAACA
1 CCCAAACA
5492427 AAAACGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.47, C:0.47, G:0.00, T:0.06
Consensus pattern (13 bp):
CCCAAACACCATA
Found at i:5493230 original size:22 final size:23
Alignment explanation
Indices: 5493188--5493236 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
5493178 TTGATGCATC
*
5493188 ATAAATTTTTAAATTTGTTAA-A
1 ATAAATATTTAAATTTGTTAATA
*
5493210 ATAAATATTT-AATTGTTTTAATA
1 ATAAATATTTAAATT-TGTTAATA
5493233 ATAA
1 ATAA
5493237 TAAAATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
22 14 0.61
23 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
ATAAATATTTAAATTTGTTAATA
Found at i:5493596 original size:15 final size:15
Alignment explanation
Indices: 5493576--5493631 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
5493566 AAAACTCCTT
5493576 AAATCCAAATCCCTA
1 AAATCCAAATCCCTA
5493591 AAATCCAAAAT-CCTA
1 AAATCC-AAATCCCTA
* *
5493606 AAATCCAAAACTCTA
1 AAATCCAAATCCCTA
*
5493621 AAATCCGAATC
1 AAATCCAAATC
5493632 TTCAAAATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
14 3 0.09
15 28 0.80
16 4 0.11
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATCCAAATCCCTA
Found at i:5493610 original size:8 final size:8
Alignment explanation
Indices: 5493565--5493626 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
5493555 CCTAGGTTTT
5493565 TAAAACTCC
1 TAAAA-TCC
*
5493574 TTAAATCC
1 TAAAATCC
5493582 --AAATCCC
1 TAAAAT-CC
5493589 TAAAATCC
1 TAAAATCC
5493597 -AAAATCC
1 TAAAATCC
5493604 TAAAATCC
1 TAAAATCC
5493612 -AAAA-CTC
1 TAAAATC-C
5493619 TAAAATCC
1 TAAAATCC
5493627 GAATCTTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
6 5 0.11
7 14 0.31
8 17 0.38
9 9 0.20
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (8 bp):
TAAAATCC
Found at i:5493611 original size:30 final size:31
Alignment explanation
Indices: 5493566--5493626 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
5493556 CTAGGTTTTT
* *
5493566 AAAACTCCTTAAATCCAAATCCCTAAAATCC
1 AAAACTCCTAAAATCCAAAACCCTAAAATCC
*
5493597 AAAA-TCCTAAAATCCAAAACTCTAAAATCC
1 AAAACTCCTAAAATCCAAAACCCTAAAATCC
5493627 GAATCTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (31 bp):
AAAACTCCTAAAATCCAAAACCCTAAAATCC
Found at i:5498311 original size:10 final size:9
Alignment explanation
Indices: 5498294--5498335 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
5498284 TCAAGATTTC
5498294 AAAAAACAA
1 AAAAAACAA
5498303 AACAAAAC-A
1 AA-AAAACAA
5498312 AAAAAACAA
1 AAAAAACAA
*
5498321 AAAAAAGAA
1 AAAAAACAA
5498330 AAAAAA
1 AAAAAA
5498336 GTTTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 5 0.17
9 20 0.67
10 5 0.17
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:5498317 original size:18 final size:17
Alignment explanation
Indices: 5498294--5498334 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
5498284 TCAAGATTTC
5498294 AAAAAACAAAACAAAACA
1 AAAAAACAAAA-AAAACA
*
5498312 AAAAAACAAAAAAAAGA
1 AAAAAACAAAAAAAACA
5498329 AAAAAA
1 AAAAAA
5498335 AGTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAAACAAAAAAAACA
Found at i:5500742 original size:41 final size:42
Alignment explanation
Indices: 5500654--5500742 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 42
5500644 AGATGAATTG
* *
5500654 TTCTT-AATCAAGATTTCAAAGCCTCTGTTTAAAATGAACCA
1 TTCTTCAATCAAGATTTCAAAGCCTCTATTTAAAAGGAACCA
* * *
5500695 AT-TTCAATCAAGATTTCAAAGCCTCTATTTAGAGGGAACC-
1 TTCTTCAATCAAGATTTCAAAGCCTCTATTTAAAAGGAACCA
5500735 TTCTTCAA
1 TTCTTCAA
5500743 AAAAGACCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 3 0.08
41 37 0.93
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (42 bp):
TTCTTCAATCAAGATTTCAAAGCCTCTATTTAAAAGGAACCA
Found at i:5500978 original size:23 final size:23
Alignment explanation
Indices: 5500946--5501013 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
5500936 TATCTTAGTC
* *
5500946 GATTCAGTAAGACCTCCAGGCAT
1 GATTCTGTAAGACCTTCAGGCAT
*
5500969 GATTCTGTAAGACCTTCAGACAT
1 GATTCTGTAAGACCTTCAGGCAT
* *
5500992 GATT-TCTAAGATCTTCAGGCAT
1 GATTCTGTAAGACCTTCAGGCAT
5501014 AATTTTGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 15 0.38
23 24 0.62
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (23 bp):
GATTCTGTAAGACCTTCAGGCAT
Found at i:5501007 original size:22 final size:22
Alignment explanation
Indices: 5500953--5501018 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
5500943 GTCGATTCAG
* * *
5500953 TAAGACCTCCAGGCATGATTCTG
1 TAAGACCTTCAGACATGATT-TC
5500976 TAAGACCTTCAGACATGATTTC
1 TAAGACCTTCAGACATGATTTC
* * *
5500998 TAAGATCTTCAGGCATAATTT
1 TAAGACCTTCAGACATGATTT
5501019 TGATTCGTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (22 bp):
TAAGACCTTCAGACATGATTTC
Found at i:5501504 original size:22 final size:22
Alignment explanation
Indices: 5501477--5501529 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
5501467 GTTGATTCTA
* *
5501477 TAAGACCTCCAGGTATGA-TTCC
1 TAAGACCTCCAAGCATGACTT-C
5501499 TAAGACCTCCAAGCATGACTTC
1 TAAGACCTCCAAGCATGACTTC
5501521 TAAGACCTC
1 TAAGACCTC
5501530 TGGGCATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (22 bp):
TAAGACCTCCAAGCATGACTTC
Found at i:5502132 original size:101 final size:102
Alignment explanation
Indices: 5502012--5502203 Score: 242
Period size: 101 Copynumber: 1.9 Consensus size: 102
5502002 TGATTTACGA
* * * *
5502012 TTCAATCTCGATCTCTTTAATTTAAAATCATAATTTAATCTCAATTATTGTTATCCTCTGACTCG
1 TTCAATCCCGATCTCTTTAATTCAAAATCACAATTTAATCTCAATTATTGTTAGCCTCTGACTCG
5502077 CGATTTAATCTCGATC-TTTTATTTTTCGATTCGCGG
66 CGATTTAATCTCGATCTTTTTATTTTTCGATTCGCGG
* ** * * * *
5502113 TTCAATCCCGATCTCTTTAATTCAAAGTTGCAGTTTAATTTCGATTGTTGTTAGCCTCTGACTCG
1 TTCAATCCCGATCTCTTTAATTCAAAATCACAATTTAATCTCAATTATTGTTAGCCTCTGACTCG
* * * *
5502178 TGATTTATTCTTGGTCTTTTTATTTT
66 CGATTTAATCTCGATCTTTTTATTTT
5502204 CTGACTTGTG
Statistics
Matches: 75, Mismatches: 15, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
101 66 0.88
102 9 0.12
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (102 bp):
TTCAATCCCGATCTCTTTAATTCAAAATCACAATTTAATCTCAATTATTGTTAGCCTCTGACTCG
CGATTTAATCTCGATCTTTTTATTTTTCGATTCGCGG
Found at i:5502386 original size:169 final size:170
Alignment explanation
Indices: 5502068--5502391 Score: 399
Period size: 169 Copynumber: 1.9 Consensus size: 170
5502058 ATTGTTATCC
* * **
5502068 TCTGACTCGCGATTTAATCTCGATCTTTTATTTTTCGATTCGCGGTTCAATCCCGATCTCTTTAA
1 TCTGACTCGCGATTTAATCTCGATCTTTTATTCTCCGATTCGAAGTTCAATCCCGATCTCTTTAA
* * * * *
5502133 TTCAAAGTTGCAGTTTAATTTCGATTGTTGTTAGCCTCTGACTCGTGATTTATTCTTGGTCTTTT
66 TTCAAAGATGCAGTTTAATTTCGATTGTTGTTAGCCTCTGACTCGCGATTTAATCTTGATCTCTT
5502198 TATTTTCTGACTTGTGATTCAATCCAAGTTAATGTCATTT
131 TATTTTCTGACTTGTGATTCAATCCAAGTTAATGTCATTT
* * *
5502238 TCTGACTCGC-AGTTTAATTTCGGTCTCTTTATTCTCCGATTC-AAGTTCAATCCTGATCTCTTT
1 TCTGACTCGCGA-TTTAATCTCGATCT-TTTATTCTCCGATTCGAAGTTCAATCCCGATCTCTTT
* * *** *
5502301 AATTTAAA-ATGTAGTTTAATCTT-GATTGTTGTTATTTTTTGACTCGCGATTTAATCTTGATCT
64 AATTCAAAGATGCAGTTTAAT-TTCGATTGTTGTTAGCCTCTGACTCGCGATTTAATCTTGATCT
5502364 CTTTATTCTTC-GA-TTCGTGATTCAATCC
128 CTTTATT-TTCTGACTT-GTGATTCAATCC
5502392 CGATCTCTTT
Statistics
Matches: 131, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
168 2 0.02
169 64 0.49
170 52 0.40
171 13 0.10
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (170 bp):
TCTGACTCGCGATTTAATCTCGATCTTTTATTCTCCGATTCGAAGTTCAATCCCGATCTCTTTAA
TTCAAAGATGCAGTTTAATTTCGATTGTTGTTAGCCTCTGACTCGCGATTTAATCTTGATCTCTT
TATTTTCTGACTTGTGATTCAATCCAAGTTAATGTCATTT
Found at i:5502462 original size:105 final size:104
Alignment explanation
Indices: 5502237--5502709 Score: 507
Period size: 105 Copynumber: 4.6 Consensus size: 104
5502227 TAATGTCATT
** * * * ** *
5502237 TTCTGACTCGCAGTTTAATTTCGGTCTCTTTATTCTCCGATTCAAGTTCAATCCTGATCTCTTTA
1 TTCTGACTCGTGGTTTAATCTCGATCTCTTTATTCTTCGATTCGTGTTCAATCCCGATCTCTTTA
* *
5502302 ATTTAAAAT-GTAGTTTAATCTTGATTGTTGTTATT-T-
66 ATTTAAAATCGTAGTTTAATCTCGATTGTTGTTGTTATC
* * *
5502338 TT-TGACTCGCGATTTAATCTTGATCTCTTTATTCTTCGATTCGTGATTCAATCCCGATCTCTTT
1 TTCTGACTCGTGGTTTAATCTCGATCTCTTTATTCTTCGATTCGTG-TTCAATCCCGATCTCTTT
* *
5502402 AATTTAAATTCGTAGTTTAATCTTGATTGTTGTTGTTATC
65 AATTTAAAATCGTAGTTTAATCTCGATTGTTGTTGTTATC
* * * *
5502442 TTCTGACTCGTGGTTTAATCTCAATATTTTTATTCTTCGATTTACG-GTTGAATCCCGATCTCTT
1 TTCTGACTCGTGGTTTAATCTCGATCTCTTTATTCTTCGA-TT-CGTGTTCAATCCCGATCTCTT
* *
5502506 TAATTTAAAATCGTAATTTAATCTCAATTGTTGTTGTTATC
64 TAATTTAAAATCGTAGTTTAATCTCGATTGTTGTTGTTATC
* * * **
5502547 TTCTGACTCATGATTTAATCTCGATCTTTTTATTC-TCTGATTCACG-GTTCAATTTCGATCTCT
1 TTCTGACTCGTGGTTTAATCTCGATCTCTTTATTCTTC-GATT--CGTGTTCAATCCCGATCTCT
** *
5502610 TTAATTTAAAATCACAGTTTTAATCTCGA---TTGTTGTTATT
63 TTAATTTAAAATCGTAG-TTTAATCTCGATTGTTGTTGTTATC
* * * *
5502650 TTCTGACTCGTGGTTTAATCCCGATCTCTTTATTCTTTGATTCGTGATTTAATCCTGATC
1 TTCTGACTCGTGGTTTAATCTCGATCTCTTTATTCTTCGATTCGTG-TTCAATCCCGATC
5502710 CTTAGCATTT
Statistics
Matches: 316, Mismatches: 43, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
100 35 0.11
101 30 0.09
102 26 0.08
103 55 0.17
104 7 0.02
105 148 0.47
106 13 0.04
107 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.48
Consensus pattern (104 bp):
TTCTGACTCGTGGTTTAATCTCGATCTCTTTATTCTTCGATTCGTGTTCAATCCCGATCTCTTTA
ATTTAAAATCGTAGTTTAATCTCGATTGTTGTTGTTATC
Found at i:5503047 original size:3 final size:3
Alignment explanation
Indices: 5503041--5503081 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
5503031 TGTCTACTAT
*
5503041 TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5503082 ATATATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:5503128 original size:8 final size:8
Alignment explanation
Indices: 5503115--5503145 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5503105 TAATTTTATA
5503115 AAAAAAAT
1 AAAAAAAT
5503123 AAAAAAAT
1 AAAAAAAT
*
5503131 AAAAAAAC
1 AAAAAAAT
5503139 AAAAAAA
1 AAAAAAA
5503146 GAGAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.06
Consensus pattern (8 bp):
AAAAAAAT
Found at i:5503248 original size:11 final size:11
Alignment explanation
Indices: 5503191--5503254 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
5503181 TGCCTGGCAC
5503191 CAGCCACCCTA
1 CAGCCACCCTA
*
5503202 CAACCACCACTA
1 CAGCCACC-CTA
* *
5503214 GCTGCCCACGCT-
1 -CAG-CCACCCTA
*
5503226 CA-CCAGCCTA
1 CAGCCACCCTA
5503236 CAGCCACCCTA
1 CAGCCACCCTA
5503247 CAGCCACC
1 CAGCCACC
5503255 AATTGTTCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
9 5 0.12
10 2 0.05
11 23 0.57
12 3 0.08
13 3 0.08
14 4 0.10
ACGTcount: A:0.27, C:0.53, G:0.11, T:0.09
Consensus pattern (11 bp):
CAGCCACCCTA
Found at i:5504651 original size:31 final size:31
Alignment explanation
Indices: 5504608--5504756 Score: 103
Period size: 31 Copynumber: 4.9 Consensus size: 31
5504598 CTAAGTTTCT
* *
5504608 AAAACTCCTTAAATGCAAACCTCTAAAATCC
1 AAAACTCCTTAAATCCAAACCCCTAAAATCC
* *
5504639 AAAA-TCCTTTAAATCCAAGCCCCTAAAATCT
1 AAAACTCC-TTAAATCCAAACCCCTAAAATCC
* * * *
5504670 AAAACCCCCTAAAATCCAAAACCATAAAATCTC
1 AAAA-CTCCTTAAATCCAAACCCCTAAAATC-C
* * *
5504703 --AAC-CTTTAAATCCAGACGCC-AAAA-CTC
1 AAAACTCCTTAAATCCAAACCCCTAAAATC-C
* *
5504730 AAAACTCCTAAAATCCAAAACCCTAAA
1 AAAACTCCTTAAATCCAAACCCCTAAA
5504757 TTCTGAATTT
Statistics
Matches: 89, Mismatches: 21, Indels: 16
0.71 0.17 0.13
Matches are distributed among these distances:
27 3 0.03
28 4 0.04
29 14 0.16
30 16 0.18
31 32 0.36
32 18 0.20
33 2 0.02
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (31 bp):
AAAACTCCTTAAATCCAAACCCCTAAAATCC
Found at i:5504680 original size:17 final size:17
Alignment explanation
Indices: 5504658--5504692 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5504648 TAAATCCAAG
*
5504658 CCCCTAAAATCTAAAAC
1 CCCCTAAAATCCAAAAC
5504675 CCCCTAAAATCCAAAAC
1 CCCCTAAAATCCAAAAC
5504692 C
1 C
5504693 ATAAAATCTC
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:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (17 bp):
CCCCTAAAATCCAAAAC
Found at i:5504756 original size:15 final size:15
Alignment explanation
Indices: 5504624--5504756 Score: 78
Period size: 15 Copynumber: 8.7 Consensus size: 15
5504614 CCTTAAATGC
5504624 AAACCTCTAAAATCCA
1 AAACC-CTAAAATCCA
* *
5504640 AAATCCTTTAAATCCA
1 AAA-CCCTAAAATCCA
** *
5504656 AGCCCCTAAAATCTA
1 AAACCCTAAAATCCA
5504671 AAACCCCCTAAAATCCA
1 AAA--CCCTAAAATCCA
*
5504688 AAACCATAAAATCTC-
1 AAACCCTAAAATC-CA
* *
5504703 -AACCTTTAAATCC-
1 AAACCCTAAAATCCA
*
5504716 AGACGCC-AAAA-CTCA
1 AAAC-CCTAAAATC-CA
5504731 AAACTCCTAAAATCCA
1 AAAC-CCTAAAATCCA
5504747 AAACCCTAAA
1 AAACCCTAAA
5504757 TTCTGAATTT
Statistics
Matches: 89, Mismatches: 18, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
13 2 0.02
14 16 0.18
15 31 0.35
16 23 0.26
17 17 0.19
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.19
Consensus pattern (15 bp):
AAACCCTAAAATCCA
Found at i:5507762 original size:14 final size:15
Alignment explanation
Indices: 5507745--5507773 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5507735 TTTAAAAATT
5507745 TATTTTATTT-TTAA
1 TATTTTATTTGTTAA
5507759 TATTTTATTTGTTAA
1 TATTTTATTTGTTAA
5507774 GTTATCTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTTTATTTGTTAA
Found at i:5507872 original size:30 final size:30
Alignment explanation
Indices: 5507809--5507877 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
5507799 CTTAAAAATA
**
5507809 AAAAATAAATATATGTTAAAAAAAAGTGCT
1 AAAAATAAATATATGTTAAAAAAAAAAGCT
* *
5507839 AAAAATATATATAT-TTAAAAATAAAAAGGT
1 AAAAATAAATATATGTTAAAAA-AAAAAGCT
*
5507869 AAAATTAAA
1 AAAAATAAA
5507878 ATTTTTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (30 bp):
AAAAATAAATATATGTTAAAAAAAAAAGCT
Found at i:5508836 original size:3 final size:3
Alignment explanation
Indices: 5508828--5508856 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5508818 TGTTTCTTTA
5508828 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5508857 AAGGAAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5515128 original size:73 final size:72
Alignment explanation
Indices: 5514992--5515142 Score: 207
Period size: 73 Copynumber: 2.1 Consensus size: 72
5514982 TGAGTTCCTT
* * *
5514992 TTAGTAGTGATATCAAAAATCATTTGCATCTTTACTCGATGATGATATCCAAGCATTCGTGTTTA
1 TTAGAAGTGATATCAAAAATCATTTGCATCTTTACTAGATGATGATATCCAAGCATTCATGTTTA
5515057 CATATCA
66 CATATCA
* * *
5515064 TTAGAAGTCGATAT-AAGAAATCATTTGCATCTTTACTTAG-TGGTGATATCCGAGTATTCATGT
1 TTAGAAGT-GATATCAA-AAATCATTTGCATCTTTAC-TAGATGATGATATCCAAGCATTCATGT
5515127 TTACATATCA
63 TTACATATCA
5515137 TTAGAA
1 TTAGAA
5515143 TTTTCTTGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
72 9 0.13
73 59 0.84
74 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (72 bp):
TTAGAAGTGATATCAAAAATCATTTGCATCTTTACTAGATGATGATATCCAAGCATTCATGTTTA
CATATCA
Found at i:5517937 original size:17 final size:17
Alignment explanation
Indices: 5517917--5517950 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5517907 AATTAGCTTT
5517917 TTATAA-ATTTTAATTAA
1 TTATAAGATTTT-ATTAA
5517934 TTATAAGATTTTATTAA
1 TTATAAGATTTTATTAA
5517951 AAAGGTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTATAAGATTTTATTAA
Found at i:5520403 original size:16 final size:17
Alignment explanation
Indices: 5520382--5520428 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
5520372 GAGGAGGCTT
*
5520382 TTAGAG-CTGAGCAAGC
1 TTAGAGTCTAAGCAAGC
5520398 TTAGAGTTCTAAGCAAGC
1 TTAGAG-TCTAAGCAAGC
*
5520416 TTAAAGTTCTAAG
1 TTAGAG-TCTAAG
5520429 TAGGATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 6 0.22
18 21 0.78
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (17 bp):
TTAGAGTCTAAGCAAGC
Found at i:5520412 original size:18 final size:18
Alignment explanation
Indices: 5520391--5520428 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5520381 TTTAGAGCTG
*
5520391 AGCAAGCTTAGAGTTCTA
1 AGCAAGCTTAAAGTTCTA
5520409 AGCAAGCTTAAAGTTCTA
1 AGCAAGCTTAAAGTTCTA
5520427 AG
1 AG
5520429 TAGGATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (18 bp):
AGCAAGCTTAAAGTTCTA
Found at i:5523931 original size:6 final size:6
Alignment explanation
Indices: 5523914--5524012 Score: 90
Period size: 6 Copynumber: 16.2 Consensus size: 6
5523904 ATTTTTAATC
* * * * *
5523914 TGATTT TAATTT TGATTT TGATTT TGCTTT TGCTTT TGCTTT TAATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
* * * * *
5523962 TAATTT TGATTT TGATTTT TAATTT TGATTTT TGTTTT TAATTT TAATTT
1 TGATTT TGATTT TGA-TTT TGATTT TGA-TTT TGATTT TGATTT TGATTT
5524012 T
1 T
5524013 AGTAAAAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
6 70 0.88
7 10 0.12
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (6 bp):
TGATTT
Found at i:5524054 original size:22 final size:20
Alignment explanation
Indices: 5524016--5524059 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
5524006 TAATTTTAGT
5524016 AAAAAAAATGTAGAAAATCTA
1 AAAAAAAATGTAGAAAAT-TA
5524037 AAAAAGAAATGT-GAAAAATTA
1 AAAAA-AAATGTAG-AAAATTA
5524058 AA
1 AA
5524060 GATCACGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAAAAAATGTAGAAAATTA
Found at i:5525748 original size:20 final size:20
Alignment explanation
Indices: 5525697--5525747 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5525687 TAAGGGACCC
*
5525697 GATCGATCCCCTATCTAGGT
1 GATCGATCCCCTATCTAGGG
* *
5525717 GATCAATCCCCTATGTAGGGG
1 GATCGATCCCCTATCTA-GGG
5525738 GATCGATCCC
1 GATCGATCCC
5525748 TTCTAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (20 bp):
GATCGATCCCCTATCTAGGG
Found at i:5526865 original size:17 final size:17
Alignment explanation
Indices: 5526817--5526869 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5526807 TTTTTGTTTG
* *
5526817 GTTTAATTTTATCTTCTT
1 GTTTGATTTTAT-TTTTT
* * *
5526835 ATTTGGTTTGATTTTTT
1 GTTTGATTTTATTTTTT
5526852 GTTTGATTTTATTTTTT
1 GTTTGATTTTATTTTTT
5526869 G
1 G
5526870 ATCATTTGGA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.13, C:0.04, G:0.13, T:0.70
Consensus pattern (17 bp):
GTTTGATTTTATTTTTT
Done.