Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 27 of 33
Found at i:4478717 original size:25 final size:25
Alignment explanation
Indices: 4478674--4478722 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4478664 AATATTAAAA
*
4478674 ATATTTTATATTAATATTTAAATAT
1 ATATTTTAAATTAATATTTAAATAT
4478699 ATATTTTAAAATTAA-ATTTAAATA
1 ATATTTT-AAATTAATATTTAAATA
4478723 AAATATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATTTTAAATTAATATTTAAATAT
Found at i:4478731 original size:25 final size:26
Alignment explanation
Indices: 4478671--4478731 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
4478661 TAAAATATTA
* *
4478671 AAAATATTTTATATTAATATTTAAAT
1 AAAATATTTAAAATTAATATTTAAAT
*
4478697 -ATATATTTTAAAATTAA-ATTTAAAT
1 AAAATA-TTTAAAATTAATATTTAAAT
4478722 AAAATATTTA
1 AAAATATTTA
4478732 TTATATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 16 0.55
26 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAATATTTAAAATTAATATTTAAAT
Found at i:4481921 original size:22 final size:19
Alignment explanation
Indices: 4481894--4481938 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
4481884 TAATATTTTA
4481894 AATACTATAATTAATTAAAAAT
1 AATACT-TAATTAA-T-AAAAT
*
4481916 AATACTTTATTAATAAAAT
1 AATACTTAATTAATAAAAT
4481935 AATA
1 AATA
4481939 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 1 0.05
21 6 0.27
22 6 0.27
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AATACTTAATTAATAAAAT
Found at i:4482837 original size:2 final size:2
Alignment explanation
Indices: 4482832--4482861 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4482822 TCTTTTTTAT
4482832 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
4482862 CACAAACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4483134 original size:23 final size:23
Alignment explanation
Indices: 4483101--4483144 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
4483091 GGTCGAAATA
4483101 AGATTGAAAATAATTATGATGATG
1 AGATTGAAAATAATT-TGATGATG
4483125 AGATT-AAAATAATTTGATGA
1 AGATTGAAAATAATTTGATGA
4483145 GATATGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 9 0.45
24 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (23 bp):
AGATTGAAAATAATTTGATGATG
Found at i:4483205 original size:16 final size:16
Alignment explanation
Indices: 4483180--4483226 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
4483170 TAATGAAAGT
4483180 AAAATAAATTATAATAA
1 AAAAT-AATTATAATAA
4483197 AAAATAATTAT--TAA
1 AAAATAATTATAATAA
4483211 ATAAATAGATTATAAT
1 A-AAATA-ATTATAAT
4483227 GAATTTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 5 0.19
16 11 0.42
17 5 0.19
18 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAATAATTATAATAA
Found at i:4496802 original size:46 final size:46
Alignment explanation
Indices: 4496749--4496842 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
4496739 CAAGACTTAA
4496749 TCACCACCCATAGTTTACCTTTTGATTTTTGATAATATTTGCCATT
1 TCACCACCCATAGTTTACCTTTTGATTTTTGATAATATTTGCCATT
4496795 TCACCACCCATAGTTTACCTTTTGATTTTTGATAATATTTGCCATT
1 TCACCACCCATAGTTTACCTTTTGATTTTTGATAATATTTGCCATT
4496841 TC
1 TC
4496843 TATGTATGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (46 bp):
TCACCACCCATAGTTTACCTTTTGATTTTTGATAATATTTGCCATT
Found at i:4497740 original size:29 final size:29
Alignment explanation
Indices: 4497698--4497757 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
4497688 ATATGATTAC
4497698 AAATATTAAATTTTAAATTAAAATT-TATT
1 AAATATTAAATTTTAAA-TAAAATTATATT
** *
4497727 AAATATTATTTTTTAAATATAATTATATT
1 AAATATTAAATTTTAAATAAAATTATATT
4497756 AA
1 AA
4497758 TCAACTGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
AAATATTAAATTTTAAATAAAATTATATT
Found at i:4498108 original size:11 final size:11
Alignment explanation
Indices: 4498057--4498152 Score: 85
Period size: 11 Copynumber: 8.7 Consensus size: 11
4498047 AAAAATATTA
4498057 TATATTATATATT
1 TATATT-TATA-T
4498070 TATCATGTTATA-
1 TAT-AT-TTATAT
* *
4498082 TAAATTT-TAA
1 TATATTTATAT
4498092 TATATTTATAT
1 TATATTTATAT
4498103 TATATTTATAT
1 TATATTTATAT
4498114 TATATTT-TAAT
1 TATATTTAT-AT
*
4498125 T-T-TTTATAA
1 TATATTTATAT
4498134 TATATTTATAT
1 TATATTTATAT
4498145 TATATTTA
1 TATATTTA
4498153 AAATTATTGA
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
9 7 0.10
10 12 0.17
11 39 0.56
12 2 0.03
13 3 0.04
14 6 0.09
15 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:4498636 original size:28 final size:28
Alignment explanation
Indices: 4498598--4498667 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
4498588 TAATCAATAA
* *
4498598 ATAGTCATTTTTGTATTTGTTAAATATG
1 ATAGTTATTTTTGTATTTGTCAAATATG
*
4498626 ATAGTTTTTTTTGTATTTGTCAAATATG
1 ATAGTTATTTTTGTATTTGTCAAATATG
* *
4498654 GTGGTTATTTTTGT
1 ATAGTTATTTTTGT
4498668 TTGTAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57
Consensus pattern (28 bp):
ATAGTTATTTTTGTATTTGTCAAATATG
Found at i:4498700 original size:24 final size:25
Alignment explanation
Indices: 4498641--4498700 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
4498631 TTTTTTTGTA
* *
4498641 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG-TATTGTTG
* *
4498667 TTTGTAAAAAATGGTGG-CTTGTTG
1 TTTGTCAAAAATGGTGGTATTGTTG
4498691 TTTGTCAAAA
1 TTTGTCAAAA
4498701 TTGATGGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 14 0.48
26 15 0.52
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (25 bp):
TTTGTCAAAAATGGTGGTATTGTTG
Found at i:4501265 original size:21 final size:22
Alignment explanation
Indices: 4501236--4501281 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
4501226 TGTTCAGACA
** *
4501236 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
4501258 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
4501279 AGT
1 AGT
4501282 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:4502710 original size:28 final size:28
Alignment explanation
Indices: 4502648--4502702 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
4502638 CAAATGCCAC
*
4502648 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGATGGTTT
4502676 CCTTTGTATTTGTCAAATATGATGGTT
1 CCTTTGTATTTGTCAAATATGATGGTT
4502703 ATTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGATGGTTT
Found at i:4503635 original size:16 final size:15
Alignment explanation
Indices: 4503607--4503658 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 15
4503597 TATTTAATTT
4503607 TTTTAAA-AATTATA
1 TTTTAAATAATTATA
4503621 TATTTAAATAATTATA
1 T-TTTAAATAATTATA
*
4503637 TTTT-TATAATTATA
1 TTTTAAATAATTATA
4503651 -TTTAAATA
1 TTTTAAATA
4503659 TATAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 3 0.09
14 13 0.39
15 9 0.27
16 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTAAATAATTATA
Found at i:4510536 original size:14 final size:14
Alignment explanation
Indices: 4510517--4510544 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4510507 GGTACGTGAT
4510517 CCAAAGATTTCCAA
1 CCAAAGATTTCCAA
4510531 CCAAAGATTTCCAA
1 CCAAAGATTTCCAA
4510545 GAACACCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
CCAAAGATTTCCAA
Found at i:4511210 original size:1 final size:1
Alignment explanation
Indices: 4511204--4511228 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4511194 ATCTCCCCTT
4511204 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
4511229 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:4513635 original size:21 final size:21
Alignment explanation
Indices: 4513609--4513657 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
4513599 AATATTAAAT
4513609 TTATTAAA-ATAATAATATTCA
1 TTATTAAAGA-AATAATATTCA
* *
4513630 TTATTAAAGAAATAATTTTTA
1 TTATTAAAGAAATAATATTCA
4513651 TTATTAA
1 TTATTAA
4513658 TTATTAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TTATTAAAGAAATAATATTCA
Found at i:4513651 original size:18 final size:19
Alignment explanation
Indices: 4513594--4513653 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 19
4513584 TTAATAAATG
*
4513594 ATTAAAATATTAA-A-TTT
1 ATTAAAATAATAATATTTT
4513611 ATTAAAATAATAATATTCATT
1 ATTAAAATAATAATATT--TT
4513632 ATTAAAGA-AATAAT-TTTT
1 ATTAAA-ATAATAATATTTT
4513650 ATTA
1 ATTA
4513654 TTAATTATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 12 0.32
18 7 0.19
19 1 0.03
20 2 0.05
21 14 0.38
22 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTAAAATAATAATATTTT
Found at i:4514054 original size:40 final size:42
Alignment explanation
Indices: 4514010--4514090 Score: 139
Period size: 43 Copynumber: 2.0 Consensus size: 42
4514000 TAATAACTCG
4514010 AATTTTATA-T-AAAAAAAAGTAAGAACTCAATAAAACAACA
1 AATTTTATATTAAAAAAAAAGTAAGAACTCAATAAAACAACA
4514050 AATTTTATATTAAAAAAAAAAGTAAGAACTCAATAAAACAA
1 AATTTTATATT-AAAAAAAAAGTAAGAACTCAATAAAACAA
4514091 AGGTCTAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
40 9 0.24
41 1 0.03
43 28 0.74
ACGTcount: A:0.63, C:0.09, G:0.05, T:0.23
Consensus pattern (42 bp):
AATTTTATATTAAAAAAAAAGTAAGAACTCAATAAAACAACA
Found at i:4514311 original size:3 final size:3
Alignment explanation
Indices: 4514303--4514327 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4514293 CAATGTTGAC
4514303 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
4514328 GAAGAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4515311 original size:30 final size:28
Alignment explanation
Indices: 4515277--4515378 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 28
4515267 AAAAATAATA
*
4515277 ATTTAAAAATAAGTATATTTTTAATCAAAT
1 ATTTAAAAATAAATATATTTTT-AT-AAAT
4515307 ATTTAAAAAATAAATAAATATTTTT-TAAAT
1 ATTT-AAAAATAAAT--ATATTTTTATAAAT
*
4515337 ATTAAAAAATAAATATATTTTTTATAAA-
1 ATTTAAAAATAAATATA-TTTTTATAAAT
4515365 ATTTTAAATAATAA
1 A-TTTAAA-AATAA
4515379 TAATAATAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
27 3 0.05
28 6 0.10
29 19 0.31
30 16 0.26
31 10 0.16
33 8 0.13
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (28 bp):
ATTTAAAAATAAATATATTTTTATAAAT
Found at i:4515379 original size:3 final size:3
Alignment explanation
Indices: 4515371--4515404 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4515361 TAAAATTTTA
4515371 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4515405 TAGGATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4515380 original size:29 final size:29
Alignment explanation
Indices: 4515281--4515378 Score: 108
Period size: 30 Copynumber: 3.3 Consensus size: 29
4515271 ATAATAATTT
* *
4515281 AAAAATAAGTATATTTTTAATCAAATATTTA
1 AAAAATAAATATATTTTTTAT-AAAT-TTTA
* *
4515312 AAAAATAAATAAATATTTTT-TAAATATTA
1 AAAAATAAATATAT-TTTTTATAAATTTTA
4515341 AAAAATAAATATATTTTTTATAAAATTTTA
1 AAAAATAAATATATTTTTTAT-AAATTTTA
*
4515371 AATAATAA
1 AAAAATAA
4515379 TAATAATAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
28 5 0.09
29 17 0.30
30 18 0.32
31 13 0.23
32 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (29 bp):
AAAAATAAATATATTTTTTATAAATTTTA
Found at i:4515727 original size:23 final size:24
Alignment explanation
Indices: 4515700--4515778 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 24
4515690 TTTATCGATT
4515700 TATTTTTTAAATATATTAT-TTTA
1 TATTTTTTAAATATATTATATTTA
*
4515723 TATTTATTAAATATATTTATATTTA
1 TATTTTTTAAATATA-TTATATTTA
* *
4515748 TATTATATTTAAATTTATTAAATTT-
1 TATT-T-TTTAAATATATTATATTTA
4515773 TATTTT
1 TATTTT
4515779 AATTCTAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
23 15 0.31
24 5 0.10
25 12 0.25
26 8 0.17
27 8 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTTTTAAATATATTATATTTA
Found at i:4515743 original size:6 final size:6
Alignment explanation
Indices: 4515710--4515765 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
4515700 TATTTTTTAA
**
4515710 ATATATT AT-TTT ATATTT ATTAAAT ATATTT ATATTT ATA-TT ATATTT
1 ATAT-TT ATATTT ATATTT A-TATTT ATATTT ATATTT ATATTT ATATTT
*
4515758 AAATTT AT
1 ATATTT AT
4515766 TAAATTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
5 9 0.22
6 25 0.62
7 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (6 bp):
ATATTT
Found at i:4515766 original size:27 final size:25
Alignment explanation
Indices: 4515700--4515779 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 25
4515690 TTTATCGATT
4515700 TATTT-TTTAAATATA-TTATTTTA
1 TATTTATTTAAATATATTTATTTTA
4515723 TATTTA-TTAAATATATTTATATTTA
1 TATTTATTTAAATATATTTAT-TTTA
* *
4515748 TATTATATTTAAATTTATTAAATTTTA
1 TATT-TATTTAAATATATT-TATTTTA
4515775 T-TTTA
1 TATTTA
4515780 ATTCTAAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
23 14 0.29
24 4 0.08
25 10 0.20
26 4 0.08
27 15 0.31
28 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTATTTAAATATATTTATTTTA
Found at i:4515779 original size:21 final size:20
Alignment explanation
Indices: 4515714--4515782 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 20
4515704 TTTTAAATAT
*
4515714 ATTAT-TTTATATTTATTAA
1 ATTATATTTAAATTTATTAA
*
4515733 A-TATATTTATATTTA-T--
1 ATTATATTTAAATTTATTAA
4515749 ATTATATTTAAATTTATTAA
1 ATTATATTTAAATTTATTAA
* *
4515769 ATTTTATTTTAATT
1 ATTATATTTAAATT
4515783 CTAAACTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
16 1 0.02
17 13 0.31
18 5 0.12
19 11 0.26
20 12 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATATTTAAATTTATTAA
Found at i:4515908 original size:2 final size:2
Alignment explanation
Indices: 4515901--4515926 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4515891 TGTAGGACAC
4515901 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
4515927 CATTATTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4516240 original size:21 final size:21
Alignment explanation
Indices: 4516190--4516230 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
4516180 CATATTAAAT
4516190 ATAATATAATTATAAAATATAA
1 ATAA-ATAATTATAAAATATAA
4516212 ATAAATAATTA-AAAATATA
1 ATAAATAATTATAAAATATA
4516231 TTAAAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAATAATTATAAAATATAA
Found at i:4517947 original size:24 final size:24
Alignment explanation
Indices: 4517894--4517949 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
4517884 CAAAAATTAT
4517894 AAAT-ATTAAAATTAAAATTTTAA
1 AAATAATTAAAATTAAAATTTTAA
** *
4517917 ATTTAATT-AAATATAATATTTTAA
1 AAATAATTAAAAT-TAAAATTTTAA
4517941 AAATAATTA
1 AAATAATTA
4517950 TATAAATCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATAATTAAAATTAAAATTTTAA
Found at i:4519385 original size:2 final size:2
Alignment explanation
Indices: 4519378--4519409 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4519368 TTAACCCAGC
*
4519378 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4519410 TTCATTCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:4523371 original size:2 final size:2
Alignment explanation
Indices: 4523364--4523409 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4523354 ACTCATTGGA
4523364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4523406 AT AT
1 AT AT
4523410 GGATGGATAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4523769 original size:2 final size:2
Alignment explanation
Indices: 4523762--4523803 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4523752 TATCCACCAC
4523762 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4523804 TTCATCTGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4523915 original size:17 final size:16
Alignment explanation
Indices: 4523887--4523959 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 16
4523877 GTTTTAGATT
*
4523887 TAATTATAAAAAATTA
1 TAATTTTAAAAAATTA
4523903 TAGATTTTAAAAAATTA
1 TA-ATTTTAAAAAATTA
* *
4523920 -AATATTAAATATAATAA
1 TAATTTTAAA-A-AATTA
* *
4523937 TAATTTTATAAATTTA
1 TAATTTTAAAAAATTA
4523953 TAGATTT
1 TA-ATTT
4523960 AATTTAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
15 7 0.16
16 9 0.20
17 22 0.49
18 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TAATTTTAAAAAATTA
Found at i:4523999 original size:21 final size:21
Alignment explanation
Indices: 4523957--4523999 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4523947 AATTTATAGA
* * *
4523957 TTTAATTTAAATATTATGATT
1 TTTAATATAAATATGATAATT
*
4523978 TTTAATATAAATCTGATAATT
1 TTTAATATAAATATGATAATT
4523999 T
1 T
4524000 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTAATATAAATATGATAATT
Found at i:4528146 original size:16 final size:16
Alignment explanation
Indices: 4528108--4528148 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
4528098 TTTATATAAA
*
4528108 TAATAAAATTTAAATT
1 TAATAATATTTAAATT
*
4528124 TAATAATATTTTAATT
1 TAATAATATTTAAATT
4528140 TAATAATAT
1 TAATAATAT
4528149 AATACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATAATATTTAAATT
Found at i:4528597 original size:20 final size:21
Alignment explanation
Indices: 4528571--4528627 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
4528561 ATTTATTTTT
4528571 TAATATTATAATTATAT-TTAA
1 TAATATTAT-ATTATATATTAA
4528592 -AATATT-TATATATATATTAA
1 TAATATTATAT-TATATATTAA
4528612 TAAT-TTATATTATATA
1 TAATATTATATTATATA
4528628 AAATTTAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.06
19 6 0.19
20 18 0.56
21 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATATTATATTATATATTAA
Found at i:4528617 original size:19 final size:18
Alignment explanation
Indices: 4528595--4528644 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
4528585 TATTTAAAAT
4528595 ATTTATATATATATTAATA
1 ATTTATATATATATTAA-A
4528614 ATTTATAT-TATA-TAAA
1 ATTTATATATATATTAAA
*
4528630 ATTTA-AGATATATTA
1 ATTTATATATATATTA
4528645 TTATATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 10 0.36
17 5 0.18
18 4 0.14
19 8 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTATATATATATTAAA
Found at i:4528665 original size:19 final size:19
Alignment explanation
Indices: 4528641--4528696 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
4528631 TTTAAGATAT
4528641 ATTATTATATTATATTTTA
1 ATTATTATATTATATTTTA
*
4528660 ATTATTATATATATTTTTTA
1 ATTATTATAT-TATATTTTA
*
4528680 TTTA-TATAATTATATTT
1 ATTATTAT-ATTATATTT
4528697 AATATTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTATTATATTATATTTTA
Found at i:4528680 original size:16 final size:17
Alignment explanation
Indices: 4528640--4528687 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
4528630 ATTTAAGATA
4528640 TATTATTATATTATATTT
1 TATTATTATA-TATATTT
4528658 TAATTATTATATATATTT
1 T-ATTATTATATATATTT
4528676 T-TTATT-TATATA
1 TATTATTATATATA
4528688 ATTATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.21
16 5 0.17
18 9 0.31
19 9 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATATATATTT
Found at i:4528702 original size:21 final size:21
Alignment explanation
Indices: 4528577--4528702 Score: 63
Period size: 19 Copynumber: 5.9 Consensus size: 21
4528567 TTTTTAATAT
4528577 TATAATTATATTTAAAATATTTA
1 TATAATTATATTT--AATATTTA
4528600 TAT-A-TATA-TTAATAATTTA
1 TATAATTATATTTAAT-ATTTA
* *
4528619 TATTATATAAAATTTAAGATATATTA
1 TA-TA-ATTATATTT-A-ATAT-TTA
4528645 T-TATATTATATTTTAAT-TATTA
1 TATA-ATTATA-TTTAATAT-TTA
*
4528667 TAT-A-TAT-TTT-TTATTTA
1 TATAATTATATTTAATATTTA
4528684 TATAATTATATTTAATATT
1 TATAATTATATTTAATATT
4528703 AAAAATTTTA
Statistics
Matches: 81, Mismatches: 6, Indels: 34
0.67 0.05 0.28
Matches are distributed among these distances:
17 7 0.09
18 8 0.10
19 10 0.12
20 9 0.11
21 9 0.11
22 8 0.10
23 8 0.10
24 10 0.12
25 6 0.07
26 6 0.07
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (21 bp):
TATAATTATATTTAATATTTA
Found at i:4534357 original size:18 final size:18
Alignment explanation
Indices: 4534334--4534414 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
4534324 AAAGGTTGAC
4534334 ATTAATTTAAAATTTAAA
1 ATTAATTTAAAATTTAAA
* **
4534352 ATTAATATATTATTTAAA
1 ATTAATTTAAAATTTAAA
*
4534370 ATT-ATTTAAAA-AT-AA
1 ATTAATTTAAAATTTAAA
* *
4534385 TTTATATTTTTAAATTTAAA
1 ATTA-A-TTTAAAATTTAAA
4534405 ATT-ATTTAAA
1 ATTAATTTAAA
4534415 TACTTAATTT
Statistics
Matches: 46, Mismatches: 12, Indels: 11
0.67 0.17 0.16
Matches are distributed among these distances:
15 4 0.09
16 1 0.02
17 11 0.24
18 25 0.54
19 1 0.02
20 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAATTTAAAATTTAAA
Found at i:4534372 original size:25 final size:26
Alignment explanation
Indices: 4534338--4534408 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 26
4534328 GTTGACATTA
4534338 ATTTAAAATTTAAAATTAA-TATATT
1 ATTTAAAATTTAAAATTAATTATATT
*
4534363 ATTTAAAATTATTTAAAAATAATTTATATT
1 ATTT-AAA--ATTTAAAATTAA-TTATATT
4534393 -TTT-AAATTTAAAATTA
1 ATTTAAAATTTAAAATTA
4534409 TTTAAATACT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
25 14 0.36
26 3 0.08
27 2 0.05
28 11 0.28
29 3 0.08
30 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAAAATTTAAAATTAATTATATT
Found at i:4534426 original size:13 final size:12
Alignment explanation
Indices: 4534334--4534438 Score: 62
Period size: 13 Copynumber: 8.8 Consensus size: 12
4534324 AAAGGTTGAC
4534334 ATTAATTTAAA-
1 ATTAATTTAAAT
*
4534345 ATTTAAAATTAATAT
1 A-TT-AATTTAA-AT
4534360 ATT-ATTTAAA-
1 ATTAATTTAAAT
4534370 ATT-ATTTAAA-
1 ATTAATTTAAAT
* *
4534380 AATAATTTATATT
1 ATTAATTTA-AAT
*
4534393 TTTAAATTTAAA-
1 ATT-AATTTAAAT
4534405 ATT-ATTTAAAT
1 ATTAATTTAAAT
4534416 ACTTAATTTAAAT
1 A-TTAATTTAAAT
4534429 ATTAAATTTA
1 ATT-AATTTA
4534439 TAAATAAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
10 19 0.26
11 8 0.11
12 14 0.19
13 23 0.31
14 9 0.12
15 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTAATTTAAAT
Found at i:4534469 original size:16 final size:15
Alignment explanation
Indices: 4534422--4534474 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
4534412 AAATACTTAA
*
4534422 TTTAAAT-ATTAAAT
1 TTTAAATAAATAAAT
*
4534436 TTATAAATAAAAATAAT
1 TT-TAAATAAATA-AAT
4534453 TTTAAATTAAATAAAT
1 TTTAAA-TAAATAAAT
4534469 TTTAAA
1 TTTAAA
4534475 AAAAGACATC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 2 0.06
15 5 0.16
16 15 0.47
17 10 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAAATAAATAAAT
Found at i:4535388 original size:14 final size:14
Alignment explanation
Indices: 4535371--4535400 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4535361 CAAAAAATTA
*
4535371 AAAAGACAAAAAAG
1 AAAAGAAAAAAAAG
4535385 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
4535399 AA
1 AA
4535401 GGTTCCAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:4538633 original size:16 final size:16
Alignment explanation
Indices: 4538614--4538655 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4538604 TAATTTTAAA
4538614 ATATTTATAT-ATATTT
1 ATATTTATATAATA-TT
*
4538630 ATATTTGTATAATATT
1 ATATTTATATAATATT
*
4538646 ATATATATAT
1 ATATTTATAT
4538656 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
ATATTTATATAATATT
Found at i:4539312 original size:2 final size:2
Alignment explanation
Indices: 4539305--4539341 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4539295 TGGATTTGTT
4539305 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4539342 TTTTAAGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4550467 original size:20 final size:21
Alignment explanation
Indices: 4550439--4550478 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4550429 TTAATTAATT
4550439 AATAATTTAT-TATATTTTAA
1 AATAATTTATATATATTTTAA
* *
4550459 AATATTTTATATTTATTTTA
1 AATAATTTATATATATTTTA
4550479 TTTATTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATAATTTATATATATTTTAA
Found at i:4550571 original size:27 final size:24
Alignment explanation
Indices: 4550540--4550604 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 24
4550530 TTATATTTGC
4550540 ATATATATATATATATATATAATGAA
1 ATATATAT-TATATATATATAAT-AA
* * *
4550566 AGTATATTTTCATATGTATATAATAT
1 A-TATATATT-ATATATATATAATAA
4550592 ATATATATTATAT
1 ATATATATTATAT
4550605 TGTTAAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 4 0.12
25 7 0.21
26 4 0.12
27 18 0.55
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (24 bp):
ATATATATTATATATATATAATAA
Found at i:4551160 original size:19 final size:17
Alignment explanation
Indices: 4551132--4551182 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 17
4551122 ATTGATTTTT
*
4551132 ATAATATGATATAATAA
1 ATAAAATGATATAATAA
4551149 ATATAAATTGATATAA-AA
1 ATA-AAA-TGATATAATAA
4551167 ATAAAATGATATAATA
1 ATAAAATGATATAATA
4551183 TTAATATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.27
17 7 0.23
18 7 0.23
19 8 0.27
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
ATAAAATGATATAATAA
Found at i:4556720 original size:23 final size:23
Alignment explanation
Indices: 4556689--4556759 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 23
4556679 TATATATATA
*
4556689 TATATATATATAAAT-TTTAAAAT
1 TATAAATAT-TAAATATTTAAAAT
*
4556712 TATAAATATTTAATATTTAAAATTT
1 TATAAATATTAAATATTTAAAA--T
* *
4556737 TTTAAATATTAAATATATAAAAT
1 TATAAATATTAAATATTTAAAAT
4556760 AAATATTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 4 0.10
23 16 0.40
25 20 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATAAATATTAAATATTTAAAAT
Found at i:4557137 original size:2 final size:2
Alignment explanation
Indices: 4557132--4557176 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4557122 ATATATCAAG
* *
4557132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4557174 AT A
1 AT A
4557177 AAGAACTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4557272 original size:2 final size:2
Alignment explanation
Indices: 4557265--4557297 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4557255 TATTAACATT
4557265 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4557298 GAACAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4558457 original size:3 final size:3
Alignment explanation
Indices: 4558449--4558473 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4558439 GATCATCGAG
4558449 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
4558474 AAGTTTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:4562367 original size:22 final size:22
Alignment explanation
Indices: 4562341--4562384 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4562331 ATATGTCCTT
4562341 TGATTATGTTAGAAATATGAAC
1 TGATTATGTTAGAAATATGAAC
*
4562363 TGATTATGTTAGGAATATGAAC
1 TGATTATGTTAGAAATATGAAC
4562385 AGAGTAGGCA
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:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (22 bp):
TGATTATGTTAGAAATATGAAC
Found at i:4566318 original size:13 final size:13
Alignment explanation
Indices: 4566296--4566338 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
4566286 AAACTCAGAT
4566296 GAAACAGAAGCTG
1 GAAACAGAAGCTG
* *
4566309 GAAACTGAAGCTAA
1 GAAACAGAAGCT-G
4566323 GAAACAGAAGCTG
1 GAAACAGAAGCTG
4566336 GAA
1 GAA
4566339 GCTGGAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.49, C:0.14, G:0.28, T:0.09
Consensus pattern (13 bp):
GAAACAGAAGCTG
Found at i:4571774 original size:32 final size:32
Alignment explanation
Indices: 4571733--4571807 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
4571723 CTTAAGATCA
* *
4571733 GGACCTTGGTGATGCATTGAAGGATTTGCTAG
1 GGACCTTGGTGACGCATTGAAGGATTTGATAG
*
4571765 GGACCTTGGTGACGCGTTGAAGGATTTGATAG
1 GGACCTTGGTGACGCATTGAAGGATTTGATAG
4571797 GGACCTTGGTG
1 GGACCTTGGTG
4571808 GTTGGAGGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.20, C:0.13, G:0.37, T:0.29
Consensus pattern (32 bp):
GGACCTTGGTGACGCATTGAAGGATTTGATAG
Found at i:4577049 original size:7 final size:7
Alignment explanation
Indices: 4577037--4577068 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
4577027 CCAATCTTTC
4577037 CTTTTTT
1 CTTTTTT
4577044 CTTTTTT
1 CTTTTTT
4577051 -TTTTTT
1 CTTTTTT
4577057 -TTTTTT
1 CTTTTTT
4577063 CTTTTT
1 CTTTTT
4577069 GTTACTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
CTTTTTT
Found at i:4583013 original size:2 final size:2
Alignment explanation
Indices: 4583008--4583047 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4582998 AAAAAACAGA
4583008 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4583048 TGTGGGGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4585440 original size:16 final size:16
Alignment explanation
Indices: 4585419--4585459 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
4585409 TTTAAAAAGT
*
4585419 AAAATATATATTTATA
1 AAAATATATATATATA
4585435 AAAATAT-TATATATA
1 AAAATATATATATATA
4585450 AAAA-ATATAT
1 AAAATATATAT
4585460 GATTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 2 0.09
15 14 0.61
16 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATATATATATATA
Found at i:4585446 original size:21 final size:20
Alignment explanation
Indices: 4585390--4585449 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
4585380 CTTAATTTAA
*
4585390 TTAAAAA-ATTATATAAAATT
1 TTAAAAATATTATAT-ATATT
**
4585410 TTAAAAAGTAAAATATATATT
1 TTAAAAA-TATTATATATATT
4585431 TATAAAAATATTATATATA
1 T-TAAAAATATTATATATA
4585450 AAAAATATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 7 0.22
21 14 0.44
22 11 0.34
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TTAAAAATATTATATATATT
Found at i:4585722 original size:25 final size:22
Alignment explanation
Indices: 4585693--4585749 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 22
4585683 AAATAATACC
4585693 TTTAATTTTATTTTATTATTATAA
1 TTTAATTTTATTTT-TTA-TATAA
*
4585717 TTTTAA-TTTAATTTTTATATAA
1 -TTTAATTTTATTTTTTATATAA
4585739 TTT-ATTTTATT
1 TTTAATTTTATT
4585750 AAATTTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 8 0.28
22 5 0.17
23 3 0.10
24 7 0.24
25 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTAATTTTATTTTTTATATAA
Found at i:4585745 original size:20 final size:19
Alignment explanation
Indices: 4585699--4585750 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
4585689 TACCTTTAAT
* *
4585699 TTTATTTTATTATTATAAT
1 TTTATTTAATTATTATAAA
*
4585718 TTTAATTTAATTTTTATATAA
1 TTT-ATTTAATTATTATA-AA
*
4585739 TTTATTTTATTA
1 TTTATTTAATTA
4585751 AATTTATGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTAATTATTATAAA
Found at i:4586986 original size:21 final size:21
Alignment explanation
Indices: 4586962--4587003 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4586952 TTCAGTTTCC
*
4586962 AAACATCGTTGAA-TAATGAGA
1 AAACATCATTGAACT-ATGAGA
4586983 AAACATCATTGAACTATGAGA
1 AAACATCATTGAACTATGAGA
4587004 TGGGACAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.24
Consensus pattern (21 bp):
AAACATCATTGAACTATGAGA
Found at i:4588165 original size:3 final size:3
Alignment explanation
Indices: 4588159--4588191 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4588149 TTATTGCCAT
4588159 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4588192 GTGTTAGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4589005 original size:2 final size:2
Alignment explanation
Indices: 4588936--4588986 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4588926 GAGCAAGAAC
4588936 TA TA TA TA 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 TA
4588978 TA TA TA TA T
1 TA TA TA TA T
4588987 GTGTGTGTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4589370 original size:27 final size:27
Alignment explanation
Indices: 4589322--4589427 Score: 81
Period size: 26 Copynumber: 3.7 Consensus size: 27
4589312 ATAAAATAAA
* *
4589322 TAAAATATTATATAATAAAAATATATTT
1 TAAAAT-TTATTTAATATAAATATATTT
4589350 TAAAATTTATTTAATATAAATTATCAATATAT
1 TAAAATTTATTTAATATAAA-TAT--AT-T-T
* *
4589382 TTAAATTTATATAAATATAAA-ATATTT
1 TAAAATTTAT-TTAATATAAATATATTT
*
4589409 T-AAATATATTATAATATAA
1 TAAAATTTATT-TAATATAA
4589428 TAAAATATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
25 1 0.02
26 14 0.22
27 14 0.22
28 10 0.15
29 2 0.03
30 2 0.03
31 3 0.05
32 10 0.15
33 9 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAAATTTATTTAATATAAATATATTT
Found at i:4589424 original size:26 final size:27
Alignment explanation
Indices: 4589375--4589437 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
4589365 ATAAATTATC
*
4589375 AATATATTTAAATTTATATAAATATAA
1 AATATATTTAAATATATATAAATATAA
4589402 AATAT-TTTAAATATATTATAATATAATAA
1 AATATATTTAAATATA-TATAA-AT-ATAA
4589431 AATATAT
1 AATATAT
4589438 ATCCCGATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 9 0.29
27 10 0.32
28 2 0.06
29 9 0.29
30 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATATATTTAAATATATATAAATATAA
Found at i:4591373 original size:2 final size:2
Alignment explanation
Indices: 4591366--4591393 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4591356 AATCACTAAT
4591366 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
4591394 CATACTTGAA
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):
TA
Found at i:4591625 original size:27 final size:28
Alignment explanation
Indices: 4591569--4591625 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
4591559 TGGATTTTAA
* * *
4591569 TATTATATATTTATATCAGATTTATATT
1 TATTATATATTTATATAAAATTAATATT
4591597 TATT-TATATTTATATAATAATTAAT-TT
1 TATTATATATTTATATAA-AATTAATATT
4591624 TA
1 TA
4591626 AATATGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTATATATTTATATAAAATTAATATT
Found at i:4591840 original size:59 final size:59
Alignment explanation
Indices: 4591757--4591904 Score: 197
Period size: 59 Copynumber: 2.5 Consensus size: 59
4591747 AATTTAAATA
* * *
4591757 AAATCAAATCAAGTTTAAAATAATTAAATATATGATTCCTTATAATCATTTTAAAATTT
1 AAATCAAATCAAATCTAAAATAATTAAATATATGATTCCTTATAATCATTTTAAAATTC
* * * * *
4591816 AAATCAAATCAAAACTAAAATAATTACATATGTGATTCTTTATAATTATTTTAAAATTC
1 AAATCAAATCAAATCTAAAATAATTAAATATATGATTCCTTATAATCATTTTAAAATTC
* * *
4591875 AAATTAAATTAAATCAAAAATAATTAAATA
1 AAATCAAATCAAATCTAAAATAATTAAATA
4591905 CATAATTTAT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 76 1.00
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (59 bp):
AAATCAAATCAAATCTAAAATAATTAAATATATGATTCCTTATAATCATTTTAAAATTC
Found at i:4591920 original size:59 final size:58
Alignment explanation
Indices: 4591773--4591925 Score: 171
Period size: 59 Copynumber: 2.6 Consensus size: 58
4591763 AATCAAGTTT
* * * *
4591773 AAAATAATTAAATATATGATTCCTTATAATCATTTTAAAATTTAAATCAAATCAAAACT
1 AAAATAATTAAATATATGATT-TTTATAATTATTTTAAAATTCAAATCAAATCAAAACA
* * * * *
4591832 AAAATAATTACATATGTGATTCTTTATAATTATTTTAAAATTCAAATTAAATTAAATCA
1 AAAATAATTAAATATATGATT-TTTATAATTATTTTAAAATTCAAATCAAATCAAAACA
* * *
4591891 AAAATAATTAAATACATAATTTATAATAATTATTT
1 AAAATAATTAAATATATGATTT-TTATAATTATTT
4591926 ACTGTAATTT
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 1 0.01
59 78 0.99
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (58 bp):
AAAATAATTAAATATATGATTTTTATAATTATTTTAAAATTCAAATCAAATCAAAACA
Found at i:4592226 original size:21 final size:21
Alignment explanation
Indices: 4592163--4592227 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
4592153 TTGTGACAAG
*
4592163 ATTTAAAAAGGTATATATT-AT
1 ATTTAAAAAGTTATAT-TTAAT
* *
4592184 -TTTAAAAA-TT-TTTTTATGT
1 ATTTAAAAAGTTATATTTA-AT
4592203 ATTTAAAAAGTTATATTTAAT
1 ATTTAAAAAGTTATATTTAAT
4592224 ATTT
1 ATTT
4592228 TATTTAGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 2 0.06
20 16 0.47
21 7 0.21
22 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
ATTTAAAAAGTTATATTTAAT
Found at i:4592297 original size:2 final size:2
Alignment explanation
Indices: 4592290--4592325 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4592280 AAGTTATCTC
4592290 TA 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
4592326 AAAGATTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4592807 original size:100 final size:98
Alignment explanation
Indices: 4592420--4592828 Score: 576
Period size: 96 Copynumber: 4.1 Consensus size: 98
4592410 CTATACAAAT
* * *
4592420 ATATATATATATATGAATTTCTTATTTATGAATGTTAAAAAAAAAATCTTCCGTAATGGATCGGG
1 ATATATATATATATGAATATCTTATTTATGAATGTTAAAAAAAAAATCCTCCGTAATGGATCGAG
*
4592485 ATTTTAAATACACTACATGGGTAATCAAGATAC
66 ATTTTAAATACACTACATGGATAATCAAGATAC
* * * *
4592518 --ATATATATATATGAATATCTTATTTATGAATGTTAAAACAAAACTCCTTCGTAATGAATCGAG
1 ATATATATATATATGAATATCTTATTTATGAATGTTAAAAAAAAAATCCTCCGTAATGGATCGAG
4592581 ATTTTAAATACACTACAT-GAGTAATCAAGATAC
66 ATTTTAAATACACTACATGGA-TAATCAAGATAC
*
4592614 ATATATATATATATATGTGAATATCTTATTTATGAATATT-AAAAAAAAATCCTCCGTAATGGAT
1 --ATATATATATATA--TGAATATCTTATTTATGAATGTTAAAAAAAAAATCCTCCGTAATGGAT
*
4592678 CGGGATTTTAAATACACTACATAGG-TAATCAAGATAC
62 CGAGATTTTAAATACACTACAT-GGATAATCAAGATAC
* * *
4592715 ATATATATATATATGAATATCTTATTTATGAATGTTAAAAAAAAAAAATCTTTCGTAATGGATCA
1 ATATATATATATATGAATATCTTATTTATGAATGTT--AAAAAAAAAATCCTCCGTAATGGATCG
* *
4592780 AGATTTTAAATATACTACATGGATAATCAAGATAT
64 AGATTTTAAATACACTACATGGATAATCAAGATAC
4592815 ATATATATATATAT
1 ATATATATATATAT
4592829 ATATATTATA
Statistics
Matches: 277, Mismatches: 21, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
95 1 0.00
96 86 0.31
97 22 0.08
99 15 0.05
100 77 0.28
101 53 0.19
102 22 0.08
103 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (98 bp):
ATATATATATATATGAATATCTTATTTATGAATGTTAAAAAAAAAATCCTCCGTAATGGATCGAG
ATTTTAAATACACTACATGGATAATCAAGATAC
Found at i:4593591 original size:2 final size:2
Alignment explanation
Indices: 4593584--4593611 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4593574 TAATGATGAA
4593584 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
4593612 GCAGTACTTC
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:4595269 original size:20 final size:20
Alignment explanation
Indices: 4595241--4595315 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
4595231 TTTTACCTTG
4595241 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
4595261 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
4595281 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
4595301 ATGTATCGATACATT
1 ATGTATCGATACATT
4595316 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:4595308 original size:40 final size:39
Alignment explanation
Indices: 4595241--4595318 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
4595231 TTTTACCTTG
* *
4595241 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
4595281 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
4595319 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:4602398 original size:15 final size:14
Alignment explanation
Indices: 4602380--4602413 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4602370 GCAAAAGCAC
4602380 AAAAAATGAAAAGA
1 AAAAAATGAAAAGA
* *
4602394 AAAAAGTGTAAAGA
1 AAAAAATGAAAAGA
4602408 AAAAAA
1 AAAAAA
4602414 GTGCAAAAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (14 bp):
AAAAAATGAAAAGA
Found at i:4602414 original size:15 final size:14
Alignment explanation
Indices: 4602380--4602422 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
4602370 GCAAAAGCAC
4602380 AAAAAA-TGAAAAG
1 AAAAAAGTGAAAAG
*
4602393 AAAAAAGTGTAAAG
1 AAAAAAGTGAAAAG
4602407 AAAAAAAGTGCAAAAG
1 -AAAAAAGTG-AAAAG
4602423 CACAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 9 0.36
16 4 0.16
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (14 bp):
AAAAAAGTGAAAAG
Found at i:4603810 original size:27 final size:27
Alignment explanation
Indices: 4603773--4604236 Score: 676
Period size: 27 Copynumber: 17.0 Consensus size: 27
4603763 GTGGCATTTT
* *
4603773 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
4603801 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
** **
4603828 CTTTTAAGTCCACAACTCTATGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
4603855 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4603882 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4603909 CTTTTAAGTCCACAACTCCGTGGGACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
4603936 CTTTTAAATCCACAACTTCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
4603964 CTTTTAAGACCACAATTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4603991 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
4604018 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
4604046 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4604073 CTTTTAAAGTCCACAACTCCGTAGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
4604101 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4604128 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4604155 CTTTTAAGTCCACAACACCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4604182 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
4604209 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4604236 C
1 C
4604237 ATTCCAAAGC
Statistics
Matches: 391, Mismatches: 42, Indels: 7
0.89 0.10 0.02
Matches are distributed among these distances:
27 316 0.81
28 75 0.19
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:4604274 original size:32 final size:31
Alignment explanation
Indices: 4604219--4604758 Score: 567
Period size: 32 Copynumber: 18.0 Consensus size: 31
4604209 CTTTTAAATC
* * *
4604219 CACAACTCTGTGGCACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* *
4604250 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
**
4604282 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
*
4604314 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
* *
4604346 CACAAGTCAGTGGCAACCCATTCCAAAGCTCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
* *
4604378 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
4604410 CACAAGTC-GATGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAG-TGGC-ACCCATTTCAAAGCCCA
4604442 CACAAGTCAGTGGCACCC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* *
4604470 CACAAGTTAGTGGCACCC-TTTCAGAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
*
4604498 CACAAGTCAGTGGCACCC-TTTCGAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* *
4604526 CACAAGTCAGTGGCA-CCATTGCGAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* * *
4604554 CATAATTCAGTGGCACTC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* *
4604582 CACAAGTCAGTGGCA-CCTTTTTAAAGCCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
*
4604612 CACAAGTTAGTGGCACCC-TTTCAAAGCCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
4604642 CACAAGTCAGTGGCACTCC-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAC-CCATTTCAAAGCCCA
* *
4604673 CGCAAGTCAGTGGCA-CCTTTTCAAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* * *
4604701 CACGAGTCAGTGGCACTC-TTTCAAA-ACC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
4604729 CACAAGTCAGTGGCACCC-TTTC-AAGCCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
4604758 C
1 C
4604759 GAGTCAGTGG
Statistics
Matches: 458, Mismatches: 36, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
27 5 0.01
28 160 0.35
29 11 0.02
30 56 0.12
31 47 0.10
32 178 0.39
33 1 0.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (31 bp):
CACAAGTCAGTGGCACCCATTTCAAAGCCCA
Found at i:4604482 original size:28 final size:29
Alignment explanation
Indices: 4604056--4604768 Score: 550
Period size: 28 Copynumber: 24.4 Consensus size: 29
4604046 CTTTTAAGTC
* * * *
4604056 CACAACTCTGTGGCACCCTTTTAAAGTC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* * * * *
4604084 CACAACTCCGTAGCACCCTTT-TAAGAC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* * * *
4604111 CACAACTCCGTGGCACCCTTT-TAAGTC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* * * *
4604138 CACAACTCCGTGGCACCCTTT-TAAGTC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
** * * *
4604165 CACAACACCGTGGCACCCTTT-TAAGTC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* * * * *
4604192 CACAACTCCGTGGCATCCTTTTAAA-TC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* * *
4604219 CACAACTCTGTGGCACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGCACCC-TTTCAAAG-CCA
* *
4604250 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGC-ACCC-TTTCAAAG-CCA
**
4604282 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGC-ACCC-TTTCAAAG-CCA
*
4604314 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGC-ACCC-TTTCAAAG-CCA
*
4604346 CACAAGTCAGTGGCAACCCATTCCAAAGCTCA
1 CACAAGTCAGTGGC-ACCC-TTTCAAAGC-CA
* *
4604378 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGC-ACCC-TTTCAAAG-CCA
4604410 CACAAGTC-GATGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAG-TGGC-ACCC-TTTCAAAG-CCA
4604442 CACAAGTCAGTGGCACCCTTTCAAAGCC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* *
4604470 CACAAGTTAGTGGCACCCTTTCAGAGCC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
*
4604498 CACAAGTCAGTGGCACCCTTTCGAAGCC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* * *
4604526 CACAAGTCAGTGGCACCATTGCGAAGCC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* * *
4604554 CATAATTCAGTGGCACTCTTTCAAAGCC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* *
4604582 CACAAGTCAGTGGCACCTTTTTAAAGCCCA
1 CACAAGTCAGTGGCACCCTTTCAAAG-CCA
*
4604612 CACAAGTTAGTGGCACCCTTTCAAAGCCCA
1 CACAAGTCAGTGGCACCCTTTCAAAG-CCA
4604642 CACAAGTCAGTGGCACTCCTTTCAAAGCCCA
1 CACAAGTCAGTGGCAC-CCTTTCAAAG-CCA
* *
4604673 CGCAAGTCAGTGGCACCTTTTCAAAGCC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
* * *
4604701 CACGAGTCAGTGGCACTCTTTCAAAACC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
4604729 CACAAGTCAGTGGCACCCTTTC-AAGCC-
1 CACAAGTCAGTGGCACCCTTTCAAAGCCA
*
4604756 CACGAGTCAGTGG
1 CACAAGTCAGTGG
4604769 TATCTTGTCA
Statistics
Matches: 615, Mismatches: 57, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
27 135 0.22
28 189 0.31
29 6 0.01
30 60 0.10
31 47 0.08
32 176 0.29
33 2 0.00
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.20
Consensus pattern (29 bp):
CACAAGTCAGTGGCACCCTTTCAAAGCCA
Found at i:4606243 original size:27 final size:26
Alignment explanation
Indices: 4606187--4606244 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
4606177 CATTATTAGT
*
4606187 CATTTTTTTAAATATAAAACTAATAG
1 CATTTTTTTAAATATAAAACTAATAA
4606213 CATTTATTTATAAA-ATAGAAAC-AATAA
1 CATTT-TTT-TAAATATA-AAACTAATAA
4606240 CATTT
1 CATTT
4606245 CTTACAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.18
27 15 0.54
28 8 0.29
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (26 bp):
CATTTTTTTAAATATAAAACTAATAA
Found at i:4606381 original size:2 final size:2
Alignment explanation
Indices: 4606374--4606426 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
4606364 ATTGGATTAA
4606374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4606416 AT AT AT AT AT A
1 AT AT AT AT AT A
4606427 AAGGAGAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4606386 original size:43 final size:41
Alignment explanation
Indices: 4606296--4606384 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 41
4606286 ATATAAAAAC
* *
4606296 ATATAAAAAACTTTTTATAAAACTAAAATTGAATTAAATAT
1 ATATATAAAACTTTTTATAAAACCAAAATTGAATTAAATAT
*
4606337 ATATATAAAACTTTTTATAAAACCAAAATTGGATTAAATAT
1 ATATATAAAACTTTTTATAAAACCAAAATTGAATTAAATAT
4606378 ATATATA
1 ATATATA
4606385 TATATATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (41 bp):
ATATATAAAACTTTTTATAAAACCAAAATTGAATTAAATAT
Found at i:4608114 original size:26 final size:26
Alignment explanation
Indices: 4608085--4608147 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
4608075 TAACCATAAC
*
4608085 ATTTAATAAATAATAAAAAATAATTT
1 ATTTAATAAATAATAAAAAATAAATT
* *
4608111 ATTTAATAAATTATTAAAAATAAATT
1 ATTTAATAAATAATAAAAAATAAATT
*
4608137 A-TTAAAAAATA
1 ATTTAATAAATA
4608148 TAACTTTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
ATTTAATAAATAATAAAAAATAAATT
Found at i:4608150 original size:17 final size:14
Alignment explanation
Indices: 4608089--4608144 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
4608079 CATAACATTT
* *
4608089 AATAAATAATAAAA
1 AATAAATTATTAAA
* *
4608103 AATAATTTATT--T
1 AATAAATTATTAAA
4608115 AATAAATTATTAAA
1 AATAAATTATTAAA
4608129 AATAAATTATTAAA
1 AATAAATTATTAAA
4608143 AA
1 AA
4608145 ATATAACTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 10 0.29
14 24 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAAATTATTAAA
Found at i:4614070 original size:23 final size:24
Alignment explanation
Indices: 4614041--4614086 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4614031 ATTTTATTTT
4614041 TTATTTT-CTTTTAATATTTTTAC
1 TTATTTTACTTTTAATATTTTTAC
* *
4614064 TTATTTTATTTTTAATGTTTTTA
1 TTATTTTACTTTTAATATTTTTA
4614087 TCATGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (24 bp):
TTATTTTACTTTTAATATTTTTAC
Found at i:4614218 original size:15 final size:15
Alignment explanation
Indices: 4614200--4614242 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
4614190 TTATTTAATT
*
4614200 TATTTAAATTTTAAA
1 TATTTAAATATTAAA
*
4614215 TATTTAGATATTAAA
1 TATTTAAATATTAAA
4614230 TATTTAAAATATT
1 TATTT-AAATATT
4614243 TAAAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TATTTAAATATTAAA
Found at i:4614219 original size:24 final size:23
Alignment explanation
Indices: 4614203--4614263 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
4614193 TTTAATTTAT
4614203 TTAAAT-TTT-AAATATTTAGATA
1 TTAAATATTTAAAATATTTA-ATA
*
4614225 TTAAATATTTAAAATATTTAAAA
1 TTAAATATTTAAAATATTTAATA
*
4614248 TT-CATATTTATAAATA
1 TTAAATATTTA-AAATA
4614264 AAAATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 13 0.38
23 12 0.35
24 9 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAAATATTTAAAATATTTAATA
Found at i:4614225 original size:8 final size:8
Alignment explanation
Indices: 4614200--4614246 Score: 62
Period size: 7 Copynumber: 6.0 Consensus size: 8
4614190 TTATTTAATT
4614200 TATTTAAA
1 TATTTAAA
4614208 T-TTTAAA
1 TATTTAAA
*
4614215 TATTTAGA
1 TATTTAAA
4614223 TA-TTAAA
1 TATTTAAA
4614230 TATTTAAAA
1 TATTT-AAA
4614239 TATTTAAA
1 TATTTAAA
4614247 ATTCATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 13 0.38
8 13 0.38
9 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (8 bp):
TATTTAAA
Found at i:4624145 original size:2 final size:2
Alignment explanation
Indices: 4624140--4624169 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4624130 GTGTGTGTGT
4624140 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4624170 AATGGATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4637676 original size:13 final size:13
Alignment explanation
Indices: 4637658--4637683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4637648 CAATTTTTTG
4637658 TGTATCGATACAT
1 TGTATCGATACAT
4637671 TGTATCGATACAT
1 TGTATCGATACAT
4637684 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4649569 original size:139 final size:139
Alignment explanation
Indices: 4649319--4649597 Score: 522
Period size: 139 Copynumber: 2.0 Consensus size: 139
4649309 CATAACCTGC
4649319 AAATTAAATGAGAATAACCATTGATCAATTCTTGATTATTGACTAAGAAGCAAGTTAGTTGCCAT
1 AAATTAAATGAGAATAACCATTGATCAATTCTTGATTATTGACTAAGAAGCAAGTTAGTTGCCAT
*
4649384 GTAAGTAAAGCACGAGAAAATAAACAAAGGAAATATATATGAAACCAGATGGCTTAACCTAAAGA
66 GTAACTAAAGCACGAGAAAATAAACAAAGGAAATATATATGAAACCAGATGGCTTAACCTAAAGA
4649449 TGAGTCATG
131 TGAGTCATG
**
4649458 AAATTAAATGAGAATAACCATTGATCAATTCTTGATTATTGACTAAGAAGCAAGTTAGTTGTTAT
1 AAATTAAATGAGAATAACCATTGATCAATTCTTGATTATTGACTAAGAAGCAAGTTAGTTGCCAT
*
4649523 GTAACTAAAGCACGAGAAAATAAACAAAGGAAATATATATGAAACCAGATGGCTTAACCTAGAGA
66 GTAACTAAAGCACGAGAAAATAAACAAAGGAAATATATATGAAACCAGATGGCTTAACCTAAAGA
4649588 TGAGTCATG
131 TGAGTCATG
4649597 A
1 A
4649598 GATTGAACAA
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (139 bp):
AAATTAAATGAGAATAACCATTGATCAATTCTTGATTATTGACTAAGAAGCAAGTTAGTTGCCAT
GTAACTAAAGCACGAGAAAATAAACAAAGGAAATATATATGAAACCAGATGGCTTAACCTAAAGA
TGAGTCATG
Found at i:4653565 original size:2 final size:2
Alignment explanation
Indices: 4653558--4653589 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4653548 TTCTTGTCAC
4653558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4653590 GCGCAAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4654653 original size:2 final size:2
Alignment explanation
Indices: 4654641--4654677 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4654631 GCACATGCTC
*
4654641 AT AT CT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4654678 TTGAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4655221 original size:2 final size:2
Alignment explanation
Indices: 4655214--4655263 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
4655204 CCAGAAATAA
*
4655214 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4655256 AT AT AT AT
1 AT AT AT AT
4655264 CGATTTAGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4658092 original size:4 final size:4
Alignment explanation
Indices: 4658083--4658107 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4658073 TAATAATTAA
4658083 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
4658108 TACAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:4659866 original size:21 final size:23
Alignment explanation
Indices: 4659837--4659882 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
4659827 ACATCAAATT
4659837 AAATACAAAG-AA-CAAATAAAA
1 AAATACAAAGCAAGCAAATAAAA
* *
4659858 AAATTCAAAGCAAGGAAATAAAA
1 AAATACAAAGCAAGCAAATAAAA
4659881 AA
1 AA
4659883 TAAAAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 2 0.10
23 10 0.48
ACGTcount: A:0.72, C:0.09, G:0.09, T:0.11
Consensus pattern (23 bp):
AAATACAAAGCAAGCAAATAAAA
Found at i:4668138 original size:2 final size:2
Alignment explanation
Indices: 4668133--4668159 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4668123 AAAAAAAAAA
4668133 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
4668160 CTTTAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4681390 original size:2 final size:2
Alignment explanation
Indices: 4681383--4681420 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4681373 CTACCCAGAA
4681383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4681421 TTAGCAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4681998 original size:14 final size:15
Alignment explanation
Indices: 4681981--4682009 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4681971 ATAAAAAAGG
4681981 AAATAA-AAAATTGA
1 AAATAATAAAATTGA
4681995 AAATAATAAAATTGA
1 AAATAATAAAATTGA
4682010 CCAAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (15 bp):
AAATAATAAAATTGA
Found at i:4683091 original size:35 final size:34
Alignment explanation
Indices: 4683029--4683095 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
4683019 ATCATAACGT
* *
4683029 TCACTTAATATTTTTTTATTAAATCTTTGACTAA
1 TCACTTAATATTTTTTGACTAAATCTTTGACTAA
**
4683063 TCACTTAATAATTTTTTGACTAGCTCTTTGACT
1 TCACTTAAT-ATTTTTTGACTAAATCTTTGACT
4683096 GACAATGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 9 0.32
35 19 0.68
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (34 bp):
TCACTTAATATTTTTTGACTAAATCTTTGACTAA
Found at i:4686118 original size:22 final size:22
Alignment explanation
Indices: 4686088--4686138 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 22
4686078 ACATCAAATT
*
4686088 AAATACAAAGAACAAGTAAA-AAA
1 AAATACAAAG--CAAGGAAATAAA
4686111 AAAT-CAAAGCAAGGAAATAAA
1 AAATACAAAGCAAGGAAATAAA
4686132 AAATACA
1 AAATACA
4686139 TAGATGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.28
21 7 0.28
22 7 0.28
23 4 0.16
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (22 bp):
AAATACAAAGCAAGGAAATAAA
Found at i:4687240 original size:56 final size:57
Alignment explanation
Indices: 4687152--4687261 Score: 204
Period size: 56 Copynumber: 1.9 Consensus size: 57
4687142 ATCATGATAA
*
4687152 ATTTTTTAACTCCACCTTGAATAATTGTCCATTGGAAATGTGTCGTTCACGCAATAT
1 ATTTTTTAACTCCACCTTGAATAATTGCCCATTGGAAATGTGTCGTTCACGCAATAT
4687209 ATTTTTTAACTCCACCTT-AATAATTGCCCATTGGAAATGTGTCGTTCACGCAA
1 ATTTTTTAACTCCACCTTGAATAATTGCCCATTGGAAATGTGTCGTTCACGCAA
4687262 ATCATAGTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
56 34 0.65
57 18 0.35
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (57 bp):
ATTTTTTAACTCCACCTTGAATAATTGCCCATTGGAAATGTGTCGTTCACGCAATAT
Found at i:4691195 original size:2 final size:2
Alignment explanation
Indices: 4691188--4691220 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4691178 AACCAATAAG
4691188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4691221 CTACAGTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4699763 original size:3 final size:3
Alignment explanation
Indices: 4699757--4699790 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4699747 GTGAAAGGAG
*
4699757 GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
4699791 TGGCTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4702158 original size:21 final size:21
Alignment explanation
Indices: 4702089--4702174 Score: 63
Period size: 21 Copynumber: 4.1 Consensus size: 21
4702079 ATTAATAGTA
*
4702089 TAATTATAAATATAATTTAATT
1 TAATTATAAATATAATAT-ATT
*
4702111 T-ATT-TAAATTTTAA-A-ATT
1 TAATTATAAA-TATAATATATT
*
4702129 TAAAATATAAATATAATATATT
1 T-AATTATAAATATAATATATT
* * *
4702151 TAATTATAACTATATTAAATT
1 TAATTATAAATATAATATATT
4702172 TAA
1 TAA
4702175 AAGTAATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
18 4 0.08
20 10 0.20
21 31 0.62
22 5 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTATAAATATAATATATT
Found at i:4703688 original size:15 final size:16
Alignment explanation
Indices: 4703663--4703694 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4703653 TCATAAAAAT
4703663 AAAATATTATATATAA
1 AAAATATTATATATAA
4703679 AAAATA-TATATATAA
1 AAAATATTATATATAA
4703694 A
1 A
4703695 CATAACTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATATTATATATAA
Found at i:4703959 original size:17 final size:16
Alignment explanation
Indices: 4703939--4703973 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4703929 TTATAAATAA
*
4703939 AAAATACTTATAATCTT
1 AAAATAATTATAAT-TT
4703956 AAAATAATTATAATTT
1 AAAATAATTATAATTT
4703972 AA
1 AA
4703974 TTAATAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATAATTATAATTT
Found at i:4707437 original size:13 final size:15
Alignment explanation
Indices: 4707419--4707450 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4707409 TAATTTTTAA
4707419 TATATTA-AT-AATT
1 TATATTATATAAATT
4707432 TATATTATATAAATT
1 TATATTATATAAATT
4707447 TATA
1 TATA
4707451 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:4707583 original size:23 final size:23
Alignment explanation
Indices: 4707526--4707576 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
4707516 TTTTTTTATG
*
4707526 TTAATAAAATCAT-AAT-TTAAAA
1 TTAA-AAAATTATAAATATTAAAA
*
4707548 ATAAAAAATTATAAATATTAAAA
1 TTAAAAAATTATAAATATTAAAA
4707571 TTAAAA
1 TTAAAA
4707577 TTTTATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 11 0.46
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TTAAAAAATTATAAATATTAAAA
Found at i:4712936 original size:15 final size:15
Alignment explanation
Indices: 4712916--4713010 Score: 56
Period size: 15 Copynumber: 6.3 Consensus size: 15
4712906 ACATATAAAA
4712916 ATAATTAAAAATAAT
1 ATAATTAAAAATAAT
*
4712931 ATAATTTTAAAA-AAT
1 ATAA-TTAAAAATAAT
* *
4712946 ATAAATAAATA-AAT
1 ATAATTAAAAATAAT
* *
4712960 AT-ATTAAAATTTAT
1 ATAATTAAAAATAAT
4712974 ATAATATAAATTAATAAT
1 ATAAT-TAAA--AATAAT
*
4712992 AT--TTAAATATAATT
1 ATAATTAAAAATAA-T
4713006 ATAAT
1 ATAAT
4713011 ACATAAATAT
Statistics
Matches: 60, Mismatches: 11, Indels: 17
0.68 0.12 0.19
Matches are distributed among these distances:
13 9 0.15
14 16 0.27
15 17 0.28
16 12 0.20
18 6 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTAAAAATAAT
Found at i:4712995 original size:24 final size:24
Alignment explanation
Indices: 4712941--4712996 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
4712931 ATAATTTTAA
* * *
4712941 AAAATATAAATAAATAAATATATT
1 AAAATTTATATAAATAAATATAAT
4712965 AAAATTTATATAATATAAAT-TAAT
1 AAAATTTATATAA-ATAAATATAAT
*
4712989 AATATTTA
1 AAAATTTA
4712997 AATATAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATTTATATAAATAAATATAAT
Found at i:4713011 original size:19 final size:19
Alignment explanation
Indices: 4712955--4713021 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
4712945 TATAAATAAA
*
4712955 TAAATAT-ATTAAAAT-TT
1 TAAATATAATTATAATATT
4712972 ATATAATATAAATTAATAATATT
1 -TA-AATAT-AATT-ATAATATT
**
4712995 TAAATATAATTATAATACA
1 TAAATATAATTATAATATT
4713014 TAAATATA
1 TAAATATA
4713022 TTAAATACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.05
19 19 0.46
20 4 0.10
21 8 0.20
22 6 0.15
23 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATATAATTATAATATT
Found at i:4714903 original size:2 final size:2
Alignment explanation
Indices: 4714896--4714947 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4714886 TTTTCAGAGC
4714896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4714938 AT AT AT AT AT
1 AT AT AT AT AT
4714948 GTTCTTAGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4715157 original size:19 final size:19
Alignment explanation
Indices: 4715129--4715167 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4715119 TTATTACTCA
*
4715129 AATTTGAATAAATATTTAT
1 AATTTGAATAAATATATAT
* *
4715148 AATTTTAATATATATATAT
1 AATTTGAATAAATATATAT
4715167 A
1 A
4715168 TTTATAACGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AATTTGAATAAATATATAT
Found at i:4715444 original size:11 final size:11
Alignment explanation
Indices: 4715412--4715449 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4715402 AATATGAAAA
4715412 GATTTAATTTT
1 GATTTAATTTT
* *
4715423 TATTGAA-TTT
1 GATTTAATTTT
4715433 GATTTAATTTT
1 GATTTAATTTT
4715444 GATTTA
1 GATTTA
4715450 GATTATAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (11 bp):
GATTTAATTTT
Done.