Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold293
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: 1704560
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 12
Found at i:489854 original size:27 final size:30
Alignment explanation
Indices: 489788--489856 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
489778 ACTTAACATC
*
489788 ATTAATTATATAATAATTATCAAAAATAAT
1 ATTAAATATATAATAATTATCAAAAATAAT
*
489818 ATGTATATATA-AATAATTAAT-AAAAAT-A-
1 AT-TAAATATATAATAATT-ATCAAAAATAAT
489846 ATTAAATATAT
1 ATTAAATATAT
489857 CATTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
27 7 0.21
28 2 0.06
29 1 0.03
30 15 0.45
31 8 0.24
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (30 bp):
ATTAAATATATAATAATTATCAAAAATAAT
Found at i:489995 original size:11 final size:11
Alignment explanation
Indices: 489981--490009 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
489971 AAAAATAATT
489981 AAAAAAAGAGA
1 AAAAAAAGAGA
489992 AAAAAAAGAGA
1 AAAAAAAGAGA
490003 AAAAAAA
1 AAAAAAA
490010 AAGGAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:490024 original size:13 final size:13
Alignment explanation
Indices: 489981--490017 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
489971 AAAAATAATT
489981 AAAAAAAGAG--A
1 AAAAAAAGAGAAA
489992 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
490005 AAAAAAAG-GAAA
1 AAAAAAAGAGAAA
490017 A
1 A
490018 TACAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.42
12 5 0.21
13 9 0.38
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:490110 original size:2 final size:2
Alignment explanation
Indices: 490099--490134 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
490089 AAAATAATGG
490099 TA TA TA -A 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
490135 CCTTACTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:491804 original size:24 final size:25
Alignment explanation
Indices: 491758--491808 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
491748 ACATAATTAA
*
491758 AAGCATTAAACATAGTTACAAACAC
1 AAGCATTAAACATAATTACAAACAC
* *
491783 AAGCA-TAAGCATAATTATAAACAC
1 AAGCATTAAACATAATTACAAACAC
491807 AA
1 AA
491809 CGGTGGGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.55, C:0.18, G:0.08, T:0.20
Consensus pattern (25 bp):
AAGCATTAAACATAATTACAAACAC
Found at i:494159 original size:21 final size:22
Alignment explanation
Indices: 494126--494169 Score: 56
Period size: 20 Copynumber: 2.0 Consensus size: 22
494116 ATTAATTATA
494126 AAATATAATAATCAAATTAAAAT
1 AAATATAATAATC-AATTAAAAT
*
494149 AAATAT-A-AATCATTTAAAAT
1 AAATATAATAATCAATTAAAAT
494169 A
1 A
494170 TTTTAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 4 0.20
22 1 0.05
23 6 0.30
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATAATAATCAATTAAAAT
Found at i:494206 original size:19 final size:20
Alignment explanation
Indices: 494182--494220 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
494172 TTAAAAACAA
494182 GTAAAATTA-ATTTTTCATT
1 GTAAAATTATATTTTTCATT
*
494201 GTAAAATTATCTTTTTCATT
1 GTAAAATTATATTTTTCATT
494221 AATTAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (20 bp):
GTAAAATTATATTTTTCATT
Found at i:494254 original size:15 final size:14
Alignment explanation
Indices: 494218--494264 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
494208 TATCTTTTTC
*
494218 ATTAATTAATGTTT
1 ATTAATTAATGTTA
*
494232 GTTAAATTAAATGTTA
1 ATT-AATT-AATGTTA
494248 ATTAATT-ATGTTA
1 ATTAATTAATGTTA
494261 ATTA
1 ATTA
494265 TAACTACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.36
14 2 0.07
15 8 0.29
16 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (14 bp):
ATTAATTAATGTTA
Found at i:495355 original size:3 final size:3
Alignment explanation
Indices: 495347--495389 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
495337 CTGCTTCTAA
* * *
495347 TTG TTG TTG TTG TTG CTG TTG TCG ATTG TTG TTG TTG CTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG -TTG TTG TTG TTG TTG TTG
495390 CCAATCTGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.02, C:0.07, G:0.33, T:0.58
Consensus pattern (3 bp):
TTG
Found at i:495434 original size:58 final size:54
Alignment explanation
Indices: 495316--495434 Score: 139
Period size: 58 Copynumber: 2.1 Consensus size: 54
495306 TCTATTTTTA
* *
495316 GTTGTTGTTGCTGCTGTTGATCTGCTTCTAATTGTTGTTGTTGTTGCTGTTGTC
1 GTTGTTGTTGCTGCTGTTGATCTGCTTCTAATTGATGTTGCTGTTGCTGTTGTC
* * * *
495370 GATTGTTGTTGTTGCTGTTGCCAATCTGCTTCTAGTTGATGTTGCTGTTGTTGATTGTT
1 G-TTGTTGTTGCTGCTGTTG---ATCTGCTTCTAATTGATGTTGCTGTTGCTG-TTGTC
495429 GTTGTT
1 GTTGTT
495435 AGGTTTAGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
54 1 0.02
55 17 0.31
58 31 0.57
59 5 0.09
ACGTcount: A:0.08, C:0.12, G:0.28, T:0.53
Consensus pattern (54 bp):
GTTGTTGTTGCTGCTGTTGATCTGCTTCTAATTGATGTTGCTGTTGCTGTTGTC
Found at i:495537 original size:18 final size:18
Alignment explanation
Indices: 495514--495561 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
495504 TGAATTGTGA
**
495514 TTTTTTTATTTCGCTTTG
1 TTTTTTTATTAAGCTTTG
495532 TTTTTTTATTAAGCTTTG
1 TTTTTTTATTAAGCTTTG
495550 TTATTTTT-TTAA
1 TT-TTTTTATTAA
495562 TTGGATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.71
Consensus pattern (18 bp):
TTTTTTTATTAAGCTTTG
Found at i:495556 original size:21 final size:20
Alignment explanation
Indices: 495508--495560 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
495498 TGTTTGTGAA
**
495508 TTGTGATTTTTTTATTTCGCT
1 TTGT-ATTTTTTTATTAAGCT
495529 TTG--TTTTTTTATTAAGCT
1 TTGTATTTTTTTATTAAGCT
495547 TTGTTATTTTTTTA
1 TTG-TATTTTTTTA
495561 ATTGGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 16 0.59
21 11 0.41
ACGTcount: A:0.13, C:0.06, G:0.11, T:0.70
Consensus pattern (20 bp):
TTGTATTTTTTTATTAAGCT
Found at i:495604 original size:45 final size:45
Alignment explanation
Indices: 495555--495664 Score: 170
Period size: 45 Copynumber: 2.4 Consensus size: 45
495545 CTTTGTTATT
*
495555 TTTTTAATTGGATTTTAATTGGGTTTGGGTTTAAGTTTATATAGA
1 TTTTTAATTGGATTTTAATTGGATTTGGGTTTAAGTTTATATAGA
495600 TTTTTAATTAGG-TTTTAATTGGATTTGGGTTTAAGTTTATATAGA
1 TTTTTAATT-GGATTTTAATTGGATTTGGGTTTAAGTTTATATAGA
*
495645 TTTTTAGTT-GAGTTTTAATT
1 TTTTTAATTGGA-TTTTAATT
495665 AGGTCTGAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
43 1 0.02
45 57 0.95
46 2 0.03
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (45 bp):
TTTTTAATTGGATTTTAATTGGATTTGGGTTTAAGTTTATATAGA
Found at i:495637 original size:23 final size:23
Alignment explanation
Indices: 495567--495637 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 23
495557 TTTAATTGGA
*
495567 TTTTAATTGGGTTTGGGTTTAAG
1 TTTTAATTGGATTTGGGTTTAAG
* **** *
495590 -TTT-ATATAGATTTTTAATTAGG
1 TTTTAAT-TGGATTTGGGTTTAAG
495612 TTTTAATTGGATTTGGGTTTAAG
1 TTTTAATTGGATTTGGGTTTAAG
495635 TTT
1 TTT
495638 ATATAGATTT
Statistics
Matches: 32, Mismatches: 13, Indels: 6
0.63 0.25 0.12
Matches are distributed among these distances:
21 2 0.06
22 12 0.38
23 16 0.50
24 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (23 bp):
TTTTAATTGGATTTGGGTTTAAG
Found at i:495646 original size:22 final size:22
Alignment explanation
Indices: 495578--495647 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
495568 TTTAATTGGG
495578 TTTGGGTTTAAGTTTATATAGA
1 TTTGGGTTTAAGTTTATATAGA
**** * *
495600 TTTTTAATTAGGTTT-TAATTGGA
1 TTTGGGTTTAAGTTTAT-A-TAGA
495623 TTTGGGTTTAAGTTTATATAGA
1 TTTGGGTTTAAGTTTATATAGA
495645 TTT
1 TTT
495648 TTAGTTGAGT
Statistics
Matches: 33, Mismatches: 12, Indels: 6
0.65 0.24 0.12
Matches are distributed among these distances:
21 1 0.03
22 17 0.52
23 14 0.42
24 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.54
Consensus pattern (22 bp):
TTTGGGTTTAAGTTTATATAGA
Found at i:495721 original size:10 final size:10
Alignment explanation
Indices: 495695--495732 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
495685 TTATATTTTA
495695 TTAAATATATT
1 TTAAATAT-TT
495706 TT-AATATTT
1 TTAAATATTT
495715 TTAAATA-TT
1 TTAAATATTT
495724 TTAAATATT
1 TTAAATATT
495733 AAATTCAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 13 0.52
10 10 0.40
11 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTAAATATTT
Found at i:502386 original size:25 final size:25
Alignment explanation
Indices: 502332--502383 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
502322 TTCAATTTAA
502332 ATTT-AATGTACTTAGTTATCATAT
1 ATTTAAATGTACTTAGTTATCATAT
502356 ATTTAAATGTACTTAGTTATC-TAT
1 ATTTAAATGTACTTAGTTATCATAT
502380 ATTT
1 ATTT
502384 TAATATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.52
Consensus pattern (25 bp):
ATTTAAATGTACTTAGTTATCATAT
Found at i:502556 original size:18 final size:18
Alignment explanation
Indices: 502533--502587 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
502523 TATTTACATT
502533 ATATTTTTATATTAAATA
1 ATATTTTTATATTAAATA
* *
502551 ATA-TTTGATTTTAAATA
1 ATATTTTTATATTAAATA
502568 A-ATTTTAATATATT-AATA
1 ATATTTT--TATATTAAATA
502586 AT
1 AT
502588 TATATTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 1 0.03
17 16 0.55
18 8 0.28
19 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATATTTTTATATTAAATA
Found at i:502648 original size:52 final size:51
Alignment explanation
Indices: 502560--502665 Score: 122
Period size: 52 Copynumber: 2.1 Consensus size: 51
502550 AATATTTGAT
502560 TTTAAATAAATTTTAATATATTAATAATTATATTATATATATATATTAATAA
1 TTTAAATAAATTTTAATATATTAATAATTATATTATAT-TATATATTAATAA
* * * * ** * * *
502612 TTTAAATAATTTTTATTGTATTTATTTTTATGTTATATTATATTTTAATTA
1 TTTAAATAAATTTTAATATATTAATAATTATATTATATTATATATTAATAA
502663 TTT
1 TTT
502666 TTCGAATCTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
51 14 0.31
52 31 0.69
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (51 bp):
TTTAAATAAATTTTAATATATTAATAATTATATTATATTATATATTAATAA
Found at i:510747 original size:3 final size:3
Alignment explanation
Indices: 510739--510776 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
510729 AAAGAGATTA
510739 GAT GAT GAT GAT GAT -AT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
510777 TATTATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
GAT
Found at i:511066 original size:16 final size:16
Alignment explanation
Indices: 511047--511089 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
511037 ATTTATTATT
511047 ATAATAATTATAAATA
1 ATAATAATTATAAATA
511063 ATAATAATTATAAATA
1 ATAATAATTATAAATA
511079 ATAATAATTAT
1 ATAATAATTAT
511090 TGAAGGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATAATTATAAATA
Found at i:511346 original size:9 final size:9
Alignment explanation
Indices: 511334--511418 Score: 56
Period size: 9 Copynumber: 9.8 Consensus size: 9
511324 ATATTTTTTA
511334 AAATTAAAT
1 AAATTAAAT
* *
511343 AAATTTATT
1 AAATTAAAT
511352 AAA-TAAAT
1 AAATTAAAT
511360 AAA-TAAAT
1 AAATTAAAT
*
511368 --ATTATA-
1 AAATTAAAT
511374 AAATTAAA-
1 AAATTAAAT
511382 ATAATTAAATT
1 A-AATTAAA-T
511393 AAATTTAAAT
1 AAA-TTAAAT
*
511403 AAAATAAAT
1 AAATTAAAT
*
511412 TAATTAA
1 AAATTAA
511419 TTTTAAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
6 1 0.02
7 3 0.05
8 17 0.28
9 27 0.45
10 6 0.10
11 6 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATTAAAT
Found at i:511353 original size:19 final size:19
Alignment explanation
Indices: 511326--511405 Score: 65
Period size: 19 Copynumber: 4.1 Consensus size: 19
511316 TTGGTTTTAT
*
511326 ATTTTTTAAAATTAAATAA
1 ATTTATTAAAATTAAATAA
*
511345 ATTTATTAAATAAATAAATAA
1 ATTTATT-AA-AATTAAATAA
511366 ATATTA-TAAAATTAAA-ATA
1 AT-TTATTAAAATTAAATA-A
* *
511385 ATTAAATTAAATTTAAATAA
1 ATT-TATTAAAATTAAATAA
511405 A
1 A
511406 ATAAATTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
18 2 0.04
19 16 0.33
20 15 0.31
21 13 0.27
22 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTTATTAAAATTAAATAA
Found at i:511395 original size:20 final size:21
Alignment explanation
Indices: 511372--511414 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
511362 ATAAATATTA
*
511372 TAAAATTAAAAT-AATTAAAT
1 TAAAATTAAAATAAAATAAAT
*
511392 T-AAATTTAAATAAAATAAAT
1 TAAAATTAAAATAAAATAAAT
511412 TAA
1 TAA
511415 TTAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 9 0.47
20 9 0.47
21 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATTAAAATAAAATAAAT
Found at i:511405 original size:24 final size:24
Alignment explanation
Indices: 511335--511425 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 24
511325 TATTTTTTAA
*
511335 AATTAAA-TAAATTT--ATTAAAT
1 AATTAAATTAAATTTAAATAAAAT
* *
511356 AAATAAATAAATATTATAAAATTAAAAT
1 AATTAAATTAA-ATT-T-AAA-TAAAAT
511384 AATTAAATTAAATTTAAATAAAAT
1 AATTAAATTAAATTTAAATAAAAT
*
511408 AAATT-AATTAATTTTAAA
1 -AATTAAATTAAATTTAAA
511426 AAATAAAGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
21 6 0.11
22 2 0.04
23 3 0.05
24 19 0.34
25 7 0.12
26 1 0.02
27 4 0.07
28 14 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATTAAATTAAATTTAAATAAAAT
Found at i:512022 original size:13 final size:12
Alignment explanation
Indices: 511997--512026 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
511987 TAAGTAACGT
511997 AAATTAGTTAAA
1 AAATTAGTTAAA
*
512009 AAATTAGTTTAA
1 AAATTAGTTAAA
512021 AAATTA
1 AAATTA
512027 TATTGAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTAGTTAAA
Found at i:512202 original size:18 final size:19
Alignment explanation
Indices: 512179--512219 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
512169 ATTTTAATTA
512179 TTTTATTG-TGATAAAAAT
1 TTTTATTGTTGATAAAAAT
*
512197 TTTTATTGTTGATATAAAT
1 TTTTATTGTTGATAAAAAT
512216 TTTT
1 TTTT
512220 TTTATGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
TTTTATTGTTGATAAAAAT
Found at i:512220 original size:21 final size:19
Alignment explanation
Indices: 512174--512221 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
512164 AAAAAATTTT
*
512174 AATTATTTTATTGTGATAA
1 AATTTTTTTATTGTGATAA
*
512193 AA-ATTTTTATTGTTGATATA
1 AATTTTTTTATTG-TGATA-A
512213 AATTTTTTT
1 AATTTTTTT
512222 TATGATTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
20 3 0.13
21 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
AATTTTTTTATTGTGATAA
Found at i:512715 original size:12 final size:12
Alignment explanation
Indices: 512698--512731 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
512688 AAATAAAAAG
512698 AAATAAATAAAC
1 AAATAAATAAAC
512710 AAATAAATAAAC
1 AAATAAATAAAC
*
512722 AAACAAATAA
1 AAATAAATAA
512732 GCTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAATAAAC
Found at i:512719 original size:16 final size:16
Alignment explanation
Indices: 512698--512731 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
512688 AAATAAAAAG
*
512698 AAATAAATAAACAAAT
1 AAATAAACAAACAAAT
512714 AAATAAACAAACAAAT
1 AAATAAACAAACAAAT
512730 AA
1 AA
512732 GCTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATAAACAAACAAAT
Found at i:513106 original size:2 final size:2
Alignment explanation
Indices: 513099--513125 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
513089 GTACATTATT
513099 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 T
513126 GTATGTATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:513434 original size:17 final size:16
Alignment explanation
Indices: 513397--513433 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
513387 AATTAAATAT
513397 AAAAATTATTATTTTA
1 AAAAATTATTATTTTA
513413 AAAAATTAATT-TTTTA
1 AAAAATT-ATTATTTTA
513429 AAAAA
1 AAAAA
513434 AATTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAAATTATTATTTTA
Found at i:513509 original size:23 final size:21
Alignment explanation
Indices: 513468--513510 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
513458 CGATTATATC
*
513468 AAATTTAAATTTATTTAATTA
1 AAATTTAAATTTATCTAATTA
513489 AAATTTAATTATTTATCTAATT
1 AAATTTAA--ATTTATCTAATT
513511 TTAAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATTTAAATTTATCTAATTA
Found at i:513628 original size:24 final size:22
Alignment explanation
Indices: 513593--513638 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
513583 TATGATTAAA
*
513593 AATATATAAAATATAAATTATT
1 AATATATAAAATATAAAATATT
513615 AATATATTATAAATATAAAATATT
1 AATATA-TA-AAATATAAAATATT
513639 TTAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 2 0.10
24 13 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATATAAAATATAAAATATT
Found at i:513629 original size:33 final size:33
Alignment explanation
Indices: 513587--513656 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
513577 ACTATTTATG
*
513587 ATTAAAAATATATAAA-A-TATAAATTATTAATAT
1 ATTAAAAATATA-AAATATTATAAA-TATAAATAT
* *
513620 ATTATAAATATAAAATATTTTAAATATAAATAT
1 ATTAAAAATATAAAATATTATAAATATAAATAT
513653 ATTA
1 ATTA
513657 CACTAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 3 0.09
33 24 0.75
34 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
ATTAAAAATATAAAATATTATAAATATAAATAT
Found at i:513643 original size:16 final size:16
Alignment explanation
Indices: 513618--513681 Score: 62
Period size: 15 Copynumber: 4.2 Consensus size: 16
513608 AATTATTAAT
*
513618 ATATTATAAATATAAA
1 ATATTTTAAATATAAA
513634 ATATTTTAAATAT-AA
1 ATATTTTAAATATAAA
* * *
513649 ATATATTACA-CTAAA
1 ATATTTTAAATATAAA
*
513664 ATA-TTTAAGTATAAA
1 ATATTTTAAATATAAA
513679 ATA
1 ATA
513682 AATTATCGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 4 0.11
15 22 0.58
16 12 0.32
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (16 bp):
ATATTTTAAATATAAA
Found at i:513652 original size:15 final size:15
Alignment explanation
Indices: 513618--513678 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 15
513608 AATTATTAAT
*
513618 ATATTATAAATATAAA
1 ATATTTTAAATAT-AA
513634 ATATTTTAAATATAA
1 ATATTTTAAATATAA
* *
513649 ATATATTACACTA-AA
1 ATATTTTA-AATATAA
*
513664 ATA-TTTAAGTATAA
1 ATATTTTAAATATAA
513678 A
1 A
513679 ATAAATTATC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 3 0.08
14 6 0.16
15 14 0.37
16 15 0.39
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (15 bp):
ATATTTTAAATATAA
Found at i:513681 original size:30 final size:30
Alignment explanation
Indices: 513630--513686 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
513620 ATTATAAATA
*
513630 TAAAATATTTTAAATATAAATATATTACAC
1 TAAAATATTTTAAATATAAATAAATTACAC
*
513660 TAAAATA-TTTAAGTATAAAATAAATTA
1 TAAAATATTTTAAATAT-AAATAAATTA
513687 TCGTAGCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAAATATTTTAAATATAAATAAATTACAC
Found at i:521975 original size:23 final size:21
Alignment explanation
Indices: 521905--521977 Score: 58
Period size: 24 Copynumber: 3.2 Consensus size: 21
521895 AGTTTTAGGC
*
521905 TTTTTTTTATTAGAATATTAATT
1 TTTTTTTTTTTA-AATATT-ATT
521928 TTTTTTATTTTGTAAATAGGTT-TT
1 TTTTTT-TTTT-TAAATA--TTATT
*
521952 TAATTTTTTTTTAAATATTATT
1 T-TTTTTTTTTTAAATATTATT
521974 TTTT
1 TTTT
521978 AAATTCGTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
21 4 0.10
22 3 0.07
23 12 0.29
24 14 0.34
25 6 0.15
26 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTTTTTTTTAAATATTATT
Found at i:522219 original size:113 final size:112
Alignment explanation
Indices: 522095--522430 Score: 312
Period size: 113 Copynumber: 2.9 Consensus size: 112
522085 TAATTAAATT
* * * *
522095 TAAAAAATTTAATAAATAATAATATATTAATTATGATTTTTAATAAAAAATAATATTTAATTAAG
1 TAAAAAATTTAAAAAATAATAAAATATTTATTAT-ATTTTTAATAAAAAATAATATTTAATTAAA
*
522160 TTTAAAAATTTACATTAATAAATTAAAATATTAATTACTT-T-TTTAAAA
65 TTTAAAAATTTACATTAACAAATTAAAATATTAATTA-TTATATTT-AAA
* ** *
522208 TAAAAAATTTAAACAAAAAATGAAAAGGGTTTATTGATATTATTT--T---TAATAATATTTAAT
1 TAAAAAATTTAAA-AAATAAT-AAAA-TATTTATT-ATATT-TTTAATAAAAAATAATATTTAAT
* **
522268 TAAATTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTATATTTTTA
61 TAAA-TTTAAAAATTTACATTAACAAATTAAAATATTAATTATTATATTTAAA
* ** *
522321 T-AAAAA-TAAAAAAATAAATAAGGTTTTTATTATAATTTTTAATAAAATAAAAAATAATATTTA
1 TAAAAAATTTAAAAAAT-AATAAAATATTTATTAT-A-TTTT--T--AATAAAAAATAATATTTA
*
522384 ATTAAATTTAAAAATTTATATTAACAAATTAAAATATTAATTATTAT
59 ATTAAATTTAAAAATTTACATTAACAAATTAAAATATTAATTATTAT
522431 GTTTTTTTTA
Statistics
Matches: 182, Mismatches: 21, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
108 2 0.01
109 9 0.05
110 7 0.04
111 8 0.04
112 23 0.13
113 50 0.27
114 9 0.05
115 5 0.03
116 8 0.04
117 44 0.24
118 17 0.09
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (112 bp):
TAAAAAATTTAAAAAATAATAAAATATTTATTATATTTTTAATAAAAAATAATATTTAATTAAAT
TTAAAAATTTACATTAACAAATTAAAATATTAATTATTATATTTAAA
Found at i:522462 original size:16 final size:17
Alignment explanation
Indices: 522432--522474 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
522422 AATTATTATG
522432 TTTTTTTTAAAATAA-A
1 TTTTTTTTAAAATAATA
**
522448 TTTTTTTTATTATAATA
1 TTTTTTTTAAAATAATA
*
522465 ATTTTTTTAA
1 TTTTTTTTAA
522475 TTCTTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTTTAAAATAATA
Found at i:523372 original size:90 final size:88
Alignment explanation
Indices: 523168--523614 Score: 415
Period size: 90 Copynumber: 5.0 Consensus size: 88
523158 TAATGCATGA
* * *
523168 ATTGTAAATGTCAGACTATAAAGATTAAACTAATGCATGAATTATATTTGAGAATCGAATTCTTT
1 ATTGTAAATGTCAGACTACAAAGATTAGACTAATGCATGAATTATATTTGAGAATCAAATT-TTT
*
523233 TTTACAGAAACAAAGAAAAGTTGATTG
65 TTTA-A-AAATAAA-AAAAGTTGATTG
* * * *
523260 ATTATAAATGTCAGACTACAAGGATTAGACTAATGCATTAATTATATTTGAGAATCAAATTCTGT
1 ATTGTAAATGTCAGACTACAAAGATTAGACTAATGCATGAATTATATTTGAGAATCAAATT-TTT
**
523325 CATAAAAATAAAGAAAAGTTGATTG
65 TTTAAAAATAAA-AAAAGTTGATTG
* *** *
523350 ATTGTAAATGTCAGACTACAAGGATTAGACTAATGCATGAATTATATCAAAGAATCAGATTTTTT
1 ATTGTAAATGTCAGACTACAAAGATTAGACTAATGCATGAATTATATTTGAGAATCAAATTTTTT
** * *
523415 TTTTATAGAAAAAAAGTTGATTG
66 TTAAAAATAAAAAAAGTTGATTG
* * * * * * * * **
523438 AGTATAAATGTTAGACTGCAAAGATTAAACTAATGCATAAATTATATCTAAGAAT-TGA-TTTTT
1 ATTGTAAATGTCAGACTACAAAGATTAGACTAATGCATGAATTATATTTGAGAATCAAATTTTTT
523501 TT---AATAAAAAAA-TTGATTG
66 TTAAAAATAAAAAAAGTTGATTG
** * * *
523520 ATTGTAAATGTCAGACTGTAAAAATTAGATTAATGCAT-AGATTATATTTGAGAATCAGATTTCT
1 ATTGTAAATGTCAGACTACAAAGATTAGACTAATGCATGA-ATTATATTTGAGAATCAAATTT-T
*
523584 TTTTATAGAAA-AGCAGAAAAGTTGATTG
64 TTTTA-A-AAATA--AAAAAAGTTGATTG
523612 ATT
1 ATT
523615 TTACATGTTA
Statistics
Matches: 298, Mismatches: 45, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
81 1 0.00
82 51 0.17
83 10 0.03
84 2 0.01
85 5 0.02
86 7 0.02
87 2 0.01
88 59 0.20
89 9 0.03
90 76 0.26
91 6 0.02
92 70 0.23
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (88 bp):
ATTGTAAATGTCAGACTACAAAGATTAGACTAATGCATGAATTATATTTGAGAATCAAATTTTTT
TTAAAAATAAAAAAAGTTGATTG
Found at i:523483 original size:178 final size:169
Alignment explanation
Indices: 523168--523595 Score: 482
Period size: 178 Copynumber: 2.4 Consensus size: 169
523158 TAATGCATGA
* *
523168 ATTGTAAATGTCAGACTATAAAGATTAAACTAATGCATGAATTATATTTGAGAATC-GAATTCTT
1 ATTGTAAATGTCAGACTATAAAGATTAGACTAATGCATGAATTATATTTGAGAATCAG-ATTTTT
* * * *
523232 TTTTACAGAAACAAAGAAAAGTTGATTGATTATAAATGTCAGACTACAAGGATTAGACTAATGCA
65 TTTTATAG----AAA-AAAAGTTGATTGAGTATAAATGTCAGACTACAAAGATTAAACTAATGCA
* * *
523297 TTAATTATATTTGAGAATCAAATTCTGTCATAAAAATAAAGAAAAGTTGATTG
125 TAAATTATATCTAAGAAT-AAATT-T-T--T-AAAATAAA-AAAA-TTGATTG
* * ***
523350 ATTGTAAATGTCAGACTACAAGGATTAGACTAATGCATGAATTATATCAAAGAATCAGATTTTTT
1 ATTGTAAATGTCAGACTATAAAGATTAGACTAATGCATGAATTATATTTGAGAATCAGA-TTTTT
* *
523415 TTTTATAGAAAAAAAGTTGATTGAGTATAAATGTTAGACTGCAAAGATTAAACTAATGCATAAAT
65 TTTTATAGAAAAAAAGTTGATTGAGTATAAATGTCAGACTACAAAGATTAAACTAATGCATAAAT
** **
523480 TATATCTAAGAATTGATTTTTTTAATAAAAAAATTGATTG
130 TATATCTAAGAATAAATTTTTAAAATAAAAAAATTGATTG
* * * *
523520 ATTGTAAATGTCAGACTGTAAAAATTAGATTAATGCAT-AGATTATATTTGAGAATCAGATTTCT
1 ATTGTAAATGTCAGACTATAAAGATTAGACTAATGCATGA-ATTATATTTGAGAATCAGATTTTT
523584 TTTTATAGAAAA
65 TTTTATAGAAAA
523596 GCAGAAAAGT
Statistics
Matches: 214, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
169 17 0.08
170 56 0.26
171 4 0.02
172 6 0.03
173 1 0.00
175 1 0.00
176 1 0.00
177 3 0.01
178 59 0.28
179 3 0.01
182 51 0.24
183 12 0.06
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (169 bp):
ATTGTAAATGTCAGACTATAAAGATTAGACTAATGCATGAATTATATTTGAGAATCAGATTTTTT
TTTATAGAAAAAAAGTTGATTGAGTATAAATGTCAGACTACAAAGATTAAACTAATGCATAAATT
ATATCTAAGAATAAATTTTTAAAATAAAAAAATTGATTG
Found at i:525676 original size:14 final size:15
Alignment explanation
Indices: 525654--525683 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
525644 TTTTAATATT
525654 TTAATATTAAATAAA
1 TTAATATTAAATAAA
525669 TTAA-ATTAAATAAA
1 TTAATATTAAATAAA
525683 T
1 T
525684 AATGTGGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAATATTAAATAAA
Found at i:526302 original size:23 final size:23
Alignment explanation
Indices: 526276--526364 Score: 85
Period size: 23 Copynumber: 3.8 Consensus size: 23
526266 TAATGATAAA
526276 ATTTTTTAAATTCT-TTAAATATT
1 ATTTTTTAAATT-TATTAAATATT
* *
526299 ATTTTTTTAATTTGTTAATATAATT
1 ATTTTTTAAATTTATTAA-AT-ATT
*
526324 -TTTTTAAAATTTAATTAAATATT
1 ATTTTTTAAATTT-ATTAAATATT
*
526347 ATTTTTT-ATTTTATTAAA
1 ATTTTTTAAATTTATTAAA
526365 AAAATAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
22 7 0.13
23 22 0.40
24 19 0.35
25 7 0.13
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (23 bp):
ATTTTTTAAATTTATTAAATATT
Found at i:526304 original size:24 final size:24
Alignment explanation
Indices: 526277--526353 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 24
526267 AATGATAAAA
526277 TTTTTTAAATTCT-TTAAATATTAT
1 TTTTTTAAATT-TATTAAATATTAT
* *
526301 TTTTTT-AATTTGTT-AATATAAT
1 TTTTTTAAATTTATTAAATATTAT
526323 TTTTTTAAAATTTAATTAAATATTAT
1 TTTTTT-AAATTT-ATTAAATATTAT
526349 TTTTT
1 TTTTT
526354 ATTTTATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
22 14 0.31
23 6 0.13
24 11 0.24
25 2 0.04
26 12 0.27
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (24 bp):
TTTTTTAAATTTATTAAATATTAT
Found at i:526383 original size:30 final size:31
Alignment explanation
Indices: 526349--526424 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
526339 TAAATATTAT
*
526349 TTTTTATTTTATTAAAAAA-ATAATAAATAC
1 TTTTTATTTTATTAAAAAACATAATAAATAA
* *
526379 TTTTTATTTTA-AAAAAAACATAATAATTAA
1 TTTTTATTTTATTAAAAAACATAATAAATAA
*
526409 TATTTTAATTTATTAA
1 T-TTTTATTTTATTAA
526425 TTTAAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 6 0.16
30 21 0.55
31 9 0.24
32 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
TTTTTATTTTATTAAAAAACATAATAAATAA
Found at i:526513 original size:117 final size:115
Alignment explanation
Indices: 526379--526680 Score: 408
Period size: 117 Copynumber: 2.7 Consensus size: 115
526369 TAATAAATAC
* * * *
526379 TTTTTATTTTAAAAAAAACATAATAATTAATATTTTAATTTATTAATTTAAATTTTATAACCTTA
1 TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTATTAATTTAAATTTTTTAAACTTA
* *
526444 CTTAAATATTATTTTTATTTTATT-AAAAATTATAATAAAAAAC-CTTTTTTAT
66 ATTAAATATT-TTTTTATTTTATTAAAAAATAATAATAAAAAACAC---TTTAT
*
526496 TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTATTAATTTAATTTTTTTAAACTTA
1 TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTATTAATTTAAATTTTTTAAACTTA
*
526561 ATTAAATA-TTTTTTATTTTATTAAAAAATAATAATAATAAACACTTTAT
66 ATTAAATATTTTTTTATTTTATTAAAAAATAATAATAAAAAACACTTTAT
* *
526610 TTTTTA--TTT-T--AAA-A-AATAATTAATATTTTAATTTGTTAATATAAATTTTTTAAACTTA
1 TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTATTAATTTAAATTTTTTAAACTTA
526668 ATTAAATATTTTT
66 ATTAAATATTTTT
526681 ATTAAAATAA
Statistics
Matches: 171, Mismatches: 11, Indels: 15
0.87 0.06 0.08
Matches are distributed among these distances:
107 49 0.29
108 5 0.03
109 3 0.02
111 1 0.01
112 3 0.02
114 11 0.06
115 13 0.08
116 18 0.11
117 68 0.40
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (115 bp):
TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTATTAATTTAAATTTTTTAAACTTA
ATTAAATATTTTTTTATTTTATTAAAAAATAATAATAAAAAACACTTTAT
Found at i:526866 original size:15 final size:14
Alignment explanation
Indices: 526846--526896 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
526836 TTCTTAACGA
526846 ATTTTAAAAAAATAT
1 ATTTT-AAAAAATAT
526861 ATTTT-AAAAATAT
1 ATTTTAAAAAATAT
*
526874 -TTTTAAAAAATTT
1 ATTTTAAAAAATAT
526887 ATTTATAAAA
1 ATTT-TAAAA
526897 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 4 0.12
13 15 0.47
14 3 0.09
15 10 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAAAAATAT
Found at i:526897 original size:26 final size:26
Alignment explanation
Indices: 526846--526896 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
526836 TTCTTAACGA
526846 ATTTTAAAAAAATATATTTTAAAAAT
1 ATTTTAAAAAAATATATTTTAAAAAT
* *
526872 ATTTTTAAAAAATTTATTTATAAAA
1 ATTTTAAAAAAATATATTT-TAAAA
526897 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTTAAAAAAATATATTTTAAAAAT
Found at i:527468 original size:6 final size:6
Alignment explanation
Indices: 527460--527500 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
527450 TCAGGCGTCA
*
527460 CACTCA CACTCG CACTCG CACTCG CACTCG CACTCG CACTC
1 CACTCG CACTCG CACTCG CACTCG CACTCG CACTCG CACTC
527501 ACCGTATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.20, C:0.51, G:0.12, T:0.17
Consensus pattern (6 bp):
CACTCG
Found at i:527582 original size:3 final size:3
Alignment explanation
Indices: 527574--527606 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
527564 ATCGCATCCA
527574 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
527607 ATGTTTAATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:536269 original size:3 final size:3
Alignment explanation
Indices: 536261--536301 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
536251 ACTAAAGCTT
536261 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
536302 TTCTTCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:540751 original size:27 final size:27
Alignment explanation
Indices: 540711--540771 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
540701 AACTATCACA
*
540711 GGAGAGGGCCCGCTTCGAAACGAAAGT
1 GGAGAGGGCCCGCTTCAAAACGAAAGT
* *
540738 GGAGAGGGCTCGCTTCAAAACGGAAGT
1 GGAGAGGGCCCGCTTCAAAACGAAAGT
540765 GGAGAGG
1 GGAGAGG
540772 CATGAGGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.41, T:0.11
Consensus pattern (27 bp):
GGAGAGGGCCCGCTTCAAAACGAAAGT
Found at i:541061 original size:18 final size:18
Alignment explanation
Indices: 541040--541074 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
541030 TGACTGGTGG
* *
541040 GGTCGAGGCAATCGAGGA
1 GGTCGAGACAACCGAGGA
541058 GGTCGAGACAACCGAGG
1 GGTCGAGACAACCGAGG
541075 GAGTTGGTCG
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:0.29, C:0.20, G:0.43, T:0.09
Consensus pattern (18 bp):
GGTCGAGACAACCGAGGA
Found at i:541763 original size:26 final size:25
Alignment explanation
Indices: 541719--541771 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
541709 ATAGTATTGA
*
541719 TGCCATGAGGCGATTAGGATCGAAG
1 TGCCATGAGGCGATCAGGATCGAAG
541744 TGCCATGATGGCGATCAGGATCGAAG
1 TGCCATGA-GGCGATCAGGATCGAAG
541770 TG
1 TG
541772 ACTCGGCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (25 bp):
TGCCATGAGGCGATCAGGATCGAAG
Found at i:541879 original size:59 final size:59
Alignment explanation
Indices: 541800--541926 Score: 191
Period size: 59 Copynumber: 2.2 Consensus size: 59
541790 TCTGGGATTG
*
541800 CCTTGGTGGCGATCTGAGTTTGAGTGACGAGGCATCACTTAGTGTTTGAATTTAGGTCA
1 CCTTGGTGGCGATCTAAGTTTGAGTGACGAGGCATCACTTAGTGTTTGAATTTAGGTCA
* ** * *
541859 CCTTGGTGGCGATCTAAGTTTGAGTGACTAGGTGTCACTTAGTGTTTGAATTTGGGTCG
1 CCTTGGTGGCGATCTAAGTTTGAGTGACGAGGCATCACTTAGTGTTTGAATTTAGGTCA
*
541918 CCTCGGTGG
1 CCTTGGTGG
541927 TGATTACAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.17, C:0.16, G:0.32, T:0.35
Consensus pattern (59 bp):
CCTTGGTGGCGATCTAAGTTTGAGTGACGAGGCATCACTTAGTGTTTGAATTTAGGTCA
Found at i:548819 original size:28 final size:28
Alignment explanation
Indices: 548779--548850 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
548769 AAAAAAAAAT
* ** *
548779 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* *
548807 CGGGGTTGGAGTATCTCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
548835 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
548851 TCGATTGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:548908 original size:52 final size:52
Alignment explanation
Indices: 548843--548967 Score: 155
Period size: 51 Copynumber: 2.4 Consensus size: 52
548833 AACGAGGTTG
* *
548843 GAGTATCCTCGATTGTGA-AAAATTGGTATTTTTAGAAATAAAATCGGAGTTA
1 GAGTATCCTCGATTGTGAGAAAATTAGTATTTTGA-AAATAAAATCGGAGTTA
* * * *
548895 GAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCTCGATTGTGAGAAAATTAGTATTTTGAAAATAAAATCGGAGTTA
*
548946 GAATATCCTCGATTGTGGAGAA
1 GAGTATCCTCGATTGT-GAGAA
548968 TTGAGAAACT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
51 30 0.49
52 27 0.44
53 4 0.07
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (52 bp):
GAGTATCCTCGATTGTGAGAAAATTAGTATTTTGAAAATAAAATCGGAGTTA
Found at i:551347 original size:13 final size:13
Alignment explanation
Indices: 551329--551354 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
551319 ACAAAGATCC
551329 ATGTATCGATACA
1 ATGTATCGATACA
551342 ATGTATCGATACA
1 ATGTATCGATACA
551355 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:551350 original size:33 final size:33
Alignment explanation
Indices: 551308--551374 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
551298 AAAATTTCCA
***
551308 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
551341 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
551374 A
1 A
551375 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:551418 original size:19 final size:18
Alignment explanation
Indices: 551394--551461 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
551384 CAGTAGCTAA
551394 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
551413 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
551428 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
551445 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
551462 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:551434 original size:13 final size:13
Alignment explanation
Indices: 551416--551440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
551406 ACAATACTTA
551416 TGTATCGATACAT
1 TGTATCGATACAT
551429 TGTATCGATACA
1 TGTATCGATACA
551441 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:551438 original size:32 final size:32
Alignment explanation
Indices: 551397--551459 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
551387 TAGCTAATTA
*
551397 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
551429 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
551460 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:551744 original size:19 final size:19
Alignment explanation
Indices: 551720--551787 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
551710 AATTCAACAA
551720 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
551739 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
551754 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
551771 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
551788 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:551759 original size:13 final size:13
Alignment explanation
Indices: 551741--551765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
551731 ACATAAGTTT
551741 TGTATCGATACAA
1 TGTATCGATACAA
551754 TGTATCGATACA
1 TGTATCGATACA
551766 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:551763 original size:32 final size:32
Alignment explanation
Indices: 551722--551784 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
551712 TTCAACAATT
*
551722 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
551754 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
551785 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:551845 original size:13 final size:13
Alignment explanation
Indices: 551827--551852 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
551817 CATTTTTCTG
551827 TGTATCGATACAT
1 TGTATCGATACAT
551840 TGTATCGATACAT
1 TGTATCGATACAT
551853 GGATCTTTGT
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:551864 original size:33 final size:33
Alignment explanation
Indices: 551807--551869 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
551797 GCCAAGGAAA
***
551807 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
551840 TGTATCGATACATGGATCTTTGTATCGATA
1 TGTATCGATACATGGATCTGTGTATCGATA
551870 ATTTGGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:554333 original size:52 final size:50
Alignment explanation
Indices: 554217--554340 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 50
554207 CTCAATTCTC
* * *
554217 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT
1 CACAATCGAGGATACTCCAACTCCGATTTTATTTTAAAAACACCAATTTT
* * * *
554267 CTATAATCGGGGATACTCTAACTCCGATTTTATTTCTAAAAATACCAATTTTT
1 C-ACAATCGAGGATACTCCAACTCCGATTTTATTT-TAAAAACACCAA-TTTT
554320 CACAATCGAGGATACTCCAAC
1 CACAATCGAGGATACTCCAAC
554341 CTCGTTATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
50 1 0.02
51 29 0.48
52 26 0.43
53 5 0.08
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.34
Consensus pattern (50 bp):
CACAATCGAGGATACTCCAACTCCGATTTTATTTTAAAAACACCAATTTT
Found at i:554389 original size:28 final size:28
Alignment explanation
Indices: 554329--554400 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
554319 TCACAATCGA
* * **
554329 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
* *
554357 AGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
554385 GGATACTCCAATCCCG
1 GGATACTCCAACCCCG
554401 ATTTTTTTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:557441 original size:20 final size:20
Alignment explanation
Indices: 557399--557437 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
557389 AATGAATAAT
*
557399 TTTTTAAGAATAAATATGTA
1 TTTTTAAGAATAAATATGAA
*
557419 TTTTTAA-AATATATATGAA
1 TTTTTAAGAATAAATATGAA
557438 ATTTGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTTTAAGAATAAATATGAA
Found at i:560060 original size:2 final size:2
Alignment explanation
Indices: 560048--560094 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
560038 GAAGACGAAG
*
560048 AT AT AT GT 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
560090 AT AT A
1 AT AT A
560095 GCTTCAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:560369 original size:2 final size:2
Alignment explanation
Indices: 560357--560391 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
560347 TGTATGTGTC
*
560357 TA TA CA 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 T
560392 GTCTTTTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:562463 original size:2 final size:2
Alignment explanation
Indices: 562456--562491 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
562446 TTCCAAACAT
562456 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
562492 ATTGTAGAAG
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:565598 original size:2 final size:2
Alignment explanation
Indices: 565591--565626 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
565581 GGAATGCTAA
565591 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
565627 TTTACATTTG
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):
AT
Found at i:570781 original size:75 final size:75
Alignment explanation
Indices: 570676--570909 Score: 303
Period size: 75 Copynumber: 3.1 Consensus size: 75
570666 TCAATTTCAC
* * * * *
570676 CTCTCTCCCGCACCCTGTCGTGCTCGCGATCACCCTCGTGCCTCCTCGACCTACTACTGCTTCTT
1 CTCTCTCCCGCTCCCTCTCCTGCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTT
570741 TCTCTCTCAT
66 TCTCTCTCAT
* * *
570751 CTCTCTCCCGCTCCCTCTCCTGCTCACGATCAATCTCGTGTCTCCTTGACCTACTACTGCTTCTT
1 CTCTCTCCCGCTCCCTCTCCTGCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTT
570816 TCTCTCGT-AT
66 TCTCTC-TCAT
** *
570826 CTCTCTCCCGCTCCCTCT-CTCGCTCACGATCACTCTCGCACCTCCTCGACCTACTACTACTTCT
1 CTCTCTCCCGCTCCCTCTCCT-GCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTTCT
*
570890 CTCTCTC-CTAT
65 TTCTCTCTC-AT
*
570901 CACTCTCCC
1 CTCTCTCCC
570910 TTTCTTTCTC
Statistics
Matches: 139, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
74 2 0.01
75 136 0.98
76 1 0.01
ACGTcount: A:0.11, C:0.46, G:0.10, T:0.33
Consensus pattern (75 bp):
CTCTCTCCCGCTCCCTCTCCTGCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTT
TCTCTCTCAT
Found at i:570957 original size:21 final size:20
Alignment explanation
Indices: 570928--571039 Score: 80
Period size: 21 Copynumber: 6.0 Consensus size: 20
570918 TCCTTTTCCT
*
570928 TCTCGTTTTCCCTCCTCTCTC
1 TCTCCTTTTCCCT-CTCTCTC
570949 TCTCCTTTTCCCTCTCTCTCC
1 TCTCCTTTTCCCTCTCTCT-C
* *
570970 TATCCTTATCCCTCTCT-T-
1 TCTCCTTTTCCCTCTCTCTC
* *
570988 TCTCCTTAT--CTCTGTCTC
1 TCTCCTTTTCCCTCTCTCTC
*
571006 T-T-C-TTT--CTCTCTCCC
1 TCTCCTTTTCCCTCTCTCTC
*
571021 TTTCCTTTTCCCTCTCTCT
1 TCTCCTTTTCCCTCTCTCT
571040 ACTACTCCTC
Statistics
Matches: 74, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
15 10 0.14
16 7 0.09
17 3 0.04
18 12 0.16
20 14 0.19
21 28 0.38
ACGTcount: A:0.03, C:0.45, G:0.02, T:0.51
Consensus pattern (20 bp):
TCTCCTTTTCCCTCTCTCTC
Found at i:570965 original size:72 final size:72
Alignment explanation
Indices: 570888--571048 Score: 186
Period size: 72 Copynumber: 2.2 Consensus size: 72
570878 ACTACTACTT
* * * *
570888 CTCTCTCTCCTATCAC-TCTCCCTTTCTTTCTCCTTTTC-CT-TCTCGTT-TTCCCTCCTCTCTC
1 CTCTCTCTCCTATC-CTTATCCCTCTCTTTCTCCTTATCTCTGTCTC-TTCTT-CCT-CTCTCCC
570949 TCTCCTTTTCC
62 TCTCCTTTTCC
* *
570960 CTCTCTCTCCTATCCTTATCCCTCTCTTTCTCCTTATCTCTGTCTCTTCTTTCTCTCTCCCTTTC
1 CTCTCTCTCCTATCCTTATCCCTCTCTTTCTCCTTATCTCTGTCTCTTCTTCCTCTCTCCCTCTC
571025 CTTTTCC
66 CTTTTCC
*
571032 CTCTCTCTACTACTCCT
1 CTCTCTCTCCTA-TCCT
571049 CTCTAAATCC
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
71 1 0.01
72 60 0.78
73 10 0.13
74 6 0.08
ACGTcount: A:0.04, C:0.45, G:0.01, T:0.50
Consensus pattern (72 bp):
CTCTCTCTCCTATCCTTATCCCTCTCTTTCTCCTTATCTCTGTCTCTTCTTCCTCTCTCCCTCTC
CTTTTCC
Found at i:570984 original size:39 final size:37
Alignment explanation
Indices: 570941--571048 Score: 98
Period size: 39 Copynumber: 2.9 Consensus size: 37
570931 CGTTTTCCCT
570941 CCTCTCTCTCTCCTTTTCCCTCTCTCTCCTATCCTTATC
1 CCTCTCTCTCTCCTTTTCCCTCTCTCT-CTATCCTT-TC
* * *
570980 CCTCTCTTTCTCCTTAT--CTCTGTCTCT-T-CTTTC
1 CCTCTCTCTCTCCTTTTCCCTCTCTCTCTATCCTTTC
* * *
571013 TCTCTCCCTTTCCTTTTCCCTCTCTCTACTACTCCT
1 CCTCTCTCTCTCCTTTTCCCTCTCTCT-CTA-TCCT
571049 CTCTAAATCC
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
33 14 0.26
34 3 0.06
35 8 0.15
36 4 0.07
37 7 0.13
38 1 0.02
39 17 0.31
ACGTcount: A:0.05, C:0.45, G:0.01, T:0.49
Consensus pattern (37 bp):
CCTCTCTCTCTCCTTTTCCCTCTCTCTCTATCCTTTC
Found at i:571901 original size:24 final size:24
Alignment explanation
Indices: 571874--571920 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
571864 ATTTTTATAC
571874 AAAATAAAT-AAATATAATTTATTT
1 AAAA-AAATAAAATATAATTTATTT
**
571898 AAAAATTTAAAATATAATTTATT
1 AAAAAAATAAAATATAATTTATT
571921 ATAATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAAATAAAATATAATTTATTT
Found at i:571931 original size:24 final size:24
Alignment explanation
Indices: 571883--571934 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
571873 CAAAATAAAT
571883 AAATATAATTTATTTAAAAATTTA
1 AAATATAATTTATTTAAAAATTTA
* *
571907 AAATATAATTTATTATAATAATTAA
1 AAATATAATTTATT-TAAAAATTTA
571932 AAA
1 AAA
571935 ATTGTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATAATTTATTTAAAAATTTA
Found at i:572467 original size:12 final size:11
Alignment explanation
Indices: 572442--572476 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
572432 GGGTGACAAT
572442 TAATTTATTAAA
1 TAATTTATT-AA
572454 TAATTATATTAA
1 TAATT-TATTAA
572466 TAATTTATTAA
1 TAATTTATTAA
572477 AAATAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 12 0.55
13 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TAATTTATTAA
Found at i:572471 original size:24 final size:25
Alignment explanation
Indices: 572442--572495 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
572432 GGGTGACAAT
*
572442 TAATTTATT-AAATAATTATATTAA
1 TAATTTATTAAAATAATTATAATAA
572466 TAATTTATTAAAAATAATTATAATAA
1 TAATTTATT-AAAATAATTATAATAA
572492 -AATT
1 TAATT
572496 ATGTGATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.33
25 4 0.15
26 14 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATTTATTAAAATAATTATAATAA
Found at i:572974 original size:15 final size:15
Alignment explanation
Indices: 572951--572991 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
572941 TTAAATATAA
572951 TTTTA-ATTTATATT
1 TTTTATATTTATATT
572965 TTTTATATTT-TATT
1 TTTTATATTTATATT
572979 TATTTATTATTTA
1 T-TTTA-TATTTA
572992 CACAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 10 0.43
15 8 0.35
16 5 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATATTTATATT
Found at i:573289 original size:20 final size:21
Alignment explanation
Indices: 573228--573293 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 21
573218 GCATATTTAC
*
573228 ATTAAATAATTATCAAAATTAT
1 ATTAAATAAATAT-AAAATTAT
*
573250 ATTTATATTAAATA-ATAAATTA-
1 A-TTA-AATAAATATA-AAATTAT
573272 ATTAAATAAATATAAAATTAT
1 ATTAAATAAATATAAAATTAT
573293 A
1 A
573294 AAAAAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
20 13 0.36
21 5 0.14
22 3 0.08
23 9 0.25
24 6 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAAATAAATATAAAATTAT
Found at i:574424 original size:22 final size:22
Alignment explanation
Indices: 574399--574442 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
574389 ACAACTAACA
574399 ATATTGAAGAACTCTCTAATCT
1 ATATTGAAGAACTCTCTAATCT
574421 ATATTGAAGAACTCTCTAATCT
1 ATATTGAAGAACTCTCTAATCT
574443 CTTACTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
ATATTGAAGAACTCTCTAATCT
Found at i:578470 original size:23 final size:21
Alignment explanation
Indices: 578444--578495 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
578434 AATATATATT
*
578444 TTTTATATATAATAAAATAATAA
1 TTTTATATAAAAT-AAATAAT-A
* *
578467 TTTTATAAAAAATAAATTATA
1 TTTTATATAAAATAAATAATA
578488 TTTTATAT
1 TTTTATAT
578496 TTATAACTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 6 0.24
23 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTATATAAAATAAATAATA
Found at i:578956 original size:15 final size:16
Alignment explanation
Indices: 578931--578961 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
578921 ATTATTATAT
578931 AATTATATCATATTTA
1 AATTATATCATATTTA
578947 AATT-TATCATATTTA
1 AATTATATCATATTTA
578962 TAAATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTATATCATATTTA
Found at i:578965 original size:17 final size:17
Alignment explanation
Indices: 578923--578969 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
578913 AATGTGTCAT
578923 TATTATATAATTATATCA
1 TATTATA-AATTATATCA
578941 TATT-TAAATT-TATCA
1 TATTATAAATTATATCA
578956 TATTTATAAATTAT
1 TA-TTATAAATTAT
578970 TTATCATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.27
16 6 0.23
17 8 0.31
18 5 0.19
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTATAAATTATATCA
Found at i:578969 original size:16 final size:15
Alignment explanation
Indices: 578936--578969 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
578926 TATATAATTA
*
578936 TATCATATTTAAATT
1 TATCATATTTAAAAT
578951 TATCATATTTATAAAT
1 TATCATATTTA-AAAT
578967 TAT
1 TAT
578970 TTATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TATCATATTTAAAAT
Found at i:585645 original size:13 final size:13
Alignment explanation
Indices: 585606--585648 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
585596 ATAGAATATG
*
585606 TATAAAGTTATAAA
1 TATAAA-TTATTAA
*
585620 AATAAATTA-TAA
1 TATAAATTATTAA
585632 TATAAATTATTAA
1 TATAAATTATTAA
585645 TATA
1 TATA
585649 TTAAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 10 0.40
13 10 0.40
14 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
TATAAATTATTAA
Found at i:585699 original size:10 final size:10
Alignment explanation
Indices: 585643--585710 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 10
585633 ATAAATTATT
*
585643 AATATATTAA
1 AATATAATAA
*
585653 AATTTATATAA
1 AATATA-ATAA
* *
585664 AATAT-TTTA
1 AATATAATAA
*
585673 AATATAATTAT
1 AATATAA-TAA
585684 AATATAATAA
1 AATATAATAA
585694 AATAT-AT-A
1 AATATAATAA
585702 AATATAATA
1 AATATAATA
585711 GGAATATATA
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
8 6 0.14
9 11 0.25
10 12 0.27
11 15 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATAATAA
Found at i:585716 original size:29 final size:27
Alignment explanation
Indices: 585631--585731 Score: 82
Period size: 29 Copynumber: 3.6 Consensus size: 27
585621 ATAAATTATA
* *
585631 ATATAAATTATT-AATAT-ATTAAAATTT
1 ATATAAAATATTAAATATAATTAGAA--T
*
585658 ATATAAAATATTTTAAATATAATTATAAT
1 ATATAAAATA--TTAAATATAATTAGAAT
585687 ATAATAAAATATATAAATATAA-TAGGAAT
1 AT-ATAAAATAT-TAAATATAATTA-GAAT
*
585716 ATATAAATTATTAAAT
1 ATATAAAATATTAAAT
585732 TTTTATATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
27 14 0.22
28 11 0.17
29 19 0.30
30 13 0.21
31 6 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATAAAATATTAAATATAATTAGAAT
Found at i:585718 original size:19 final size:18
Alignment explanation
Indices: 585621--585723 Score: 66
Period size: 19 Copynumber: 5.3 Consensus size: 18
585611 AGTTATAAAA
585621 ATAAATTATAATATAAAT-T
1 ATAAA-TATAATA-AAATAT
* *
585640 ATTAATATATTAAAATTTAT
1 ATAAATATAATAAAA--TAT
* *
585660 ATAAA-ATATTTTAAATAT
1 ATAAATATA-ATAAAATAT
585678 AATTATAATATAATAAAATAT
1 -A-TA-AATATAATAAAATAT
*
585699 ATAAATATAATAGGAATAT
1 ATAAATATAATA-AAATAT
585718 ATAAAT
1 ATAAAT
585724 TATTAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
17 3 0.04
18 18 0.26
19 22 0.32
20 13 0.19
21 9 0.13
22 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
ATAAATATAATAAAATAT
Found at i:586300 original size:2 final size:2
Alignment explanation
Indices: 586293--586317 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
586283 AGAGCCTTTT
586293 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 G
586318 GCGAATCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:587248 original size:2 final size:2
Alignment explanation
Indices: 587241--587274 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
587231 AGCTTTTATT
587241 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
587275 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:587279 original size:2 final size:2
Alignment explanation
Indices: 587274--587308 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
587264 ATATATATAT
587274 AG AG AG AG 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 AG AG AG AG A
587309 TGATAGATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:588713 original size:15 final size:15
Alignment explanation
Indices: 588693--588740 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
588683 AGTTAAGGTG
588693 TATTTAATTATTATA
1 TATTTAATTATTATA
588708 TATTT-ATT-TTATA
1 TATTTAATTATTATA
* *
588721 -ATTTCATAATT-TA
1 TATTTAATTATTATA
588734 TATTTAA
1 TATTTAA
588741 ATTTTGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 4 0.14
13 9 0.32
14 10 0.36
15 5 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTAATTATTATA
Found at i:596951 original size:24 final size:24
Alignment explanation
Indices: 596919--596967 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
596909 GGATATCCAA
596919 GTCACTTCAAAAACCCAATCTCCT
1 GTCACTTCAAAAACCCAATCTCCT
596943 GTCACTTCAAAAACCCAATCTCCT
1 GTCACTTCAAAAACCCAATCTCCT
596967 G
1 G
596968 ACTAAGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.06, T:0.24
Consensus pattern (24 bp):
GTCACTTCAAAAACCCAATCTCCT
Found at i:608653 original size:16 final size:15
Alignment explanation
Indices: 608610--608657 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
608600 TGATCTTATA
* *
608610 TAAATTTAATAAATT
1 TAAATATAATATATT
608625 TAAATATAATATATT
1 TAAATATAATATATT
*
608640 TAATATATATTATATT
1 TAA-ATATAATATATT
608656 TA
1 TA
608658 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATAATATATT
Found at i:609464 original size:16 final size:15
Alignment explanation
Indices: 609408--609466 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
609398 TTATTTTAAT
*
609408 TTTAAATAATTTTGAG
1 TTTAAATTA-TTTGAG
*
609424 TTTAAATTAATTGAG
1 TTTAAATTATTTGAG
609439 TTTAAATTATTTGAG
1 TTTAAATTATTTGAG
*
609454 ATTTAAGTTATTT
1 -TTTAAATTATTT
609467 TGGATTAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
15 19 0.50
16 19 0.50
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTAAATTATTTGAG
Found at i:609871 original size:27 final size:27
Alignment explanation
Indices: 609820--609871 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
609810 AAATAAATAT
*
609820 TTTAAAGATTAGAATTCAAGGTTTTAA
1 TTTAAAGATTAGAATTCAAGATTTTAA
*
609847 TTTAAAGAATTAGACTTCAA-ATTTT
1 TTTAAAG-ATTAGAATTCAAGATTTT
609872 GAAATAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (27 bp):
TTTAAAGATTAGAATTCAAGATTTTAA
Found at i:611124 original size:25 final size:26
Alignment explanation
Indices: 611061--611129 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
611051 AAAATATTAT
* *
611061 ATTAAAATATTTATATATAATAAATA
1 ATTAAAATATATATTTATAATAAATA
*
611087 ATTAAAAGT-TATATTTATATTAAATA
1 ATTAAAA-TATATATTTATAATAAATA
611113 A-TAAAATATATATTTAT
1 ATTAAAATATATATTTAT
611130 TAAAATTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 1 0.03
25 14 0.37
26 22 0.58
27 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
ATTAAAATATATATTTATAATAAATA
Found at i:611130 original size:23 final size:24
Alignment explanation
Indices: 611080--611180 Score: 69
Period size: 23 Copynumber: 4.5 Consensus size: 24
611070 TTTATATATA
611080 ATAAATAATTAAAAGTTATA-TTTAT
1 ATAAATAA-TAAAA-TTATATTTTAT
*
611105 ATTAAATAATAAAA-TATATATT-T
1 A-TAAATAATAAAATTATATTTTAT
611128 AT---T-A-AAA-TTATATTTTA-
1 ATAAATAATAAAATTATATTTTAT
* *
611145 ATATATATTAAAATTATATTTTAT
1 ATAAATAATAAAATTATATTTTAT
611169 GATAAATAATAA
1 -ATAAATAATAA
611181 TTAAGATATA
Statistics
Matches: 59, Mismatches: 5, Indels: 24
0.67 0.06 0.27
Matches are distributed among these distances:
17 12 0.20
18 1 0.02
19 1 0.02
20 1 0.02
22 4 0.07
23 16 0.27
24 2 0.03
25 15 0.25
26 7 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
ATAAATAATAAAATTATATTTTAT
Found at i:611163 original size:40 final size:40
Alignment explanation
Indices: 611087--611168 Score: 105
Period size: 39 Copynumber: 2.0 Consensus size: 40
611077 ATAATAAATA
*
611087 ATTAAAAGTTATATTTATATTAAATAATAAAATATATATTT
1 ATTAAAAGTTATATTTATAATAAATAATAAAATATAT-TTT
* *
611128 ATTAAAA-TTATATTT-TAATATATATTAAAATTATATTTT
1 ATTAAAAGTTATATTTATAATAAATAATAAAA-TATATTTT
611167 AT
1 AT
611169 GATAAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 17 0.46
40 13 0.35
41 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (40 bp):
ATTAAAAGTTATATTTATAATAAATAATAAAATATATTTT
Found at i:611176 original size:29 final size:27
Alignment explanation
Indices: 611144--611211 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 27
611134 ATTATATTTT
611144 AATATATATTAAAATTATATTTTATGAT-A
1 AATATATATTAAAA-TATA-TTTAT-ATCA
*
611173 AATA-ATAATTAAGATATATTTATATCA
1 AATATAT-ATTAAAATATATTTATATCA
*
611200 AAAATATATTAA
1 AATATATATTAA
611212 TAAAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
26 2 0.06
27 14 0.41
28 8 0.24
29 10 0.29
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (27 bp):
AATATATATTAAAATATATTTATATCA
Found at i:611221 original size:64 final size:63
Alignment explanation
Indices: 611054--611221 Score: 157
Period size: 66 Copynumber: 2.6 Consensus size: 63
611044 ATCATTAAAA
*
611054 ATATTATATTAAAATATTTATATATAATAAATAATTAAAAGTTATATTTATATTAAATAATAAAA
1 ATATT-TATTAAAATA--TATAT-TAATATATAA-TAAAAGTTATATTTATATTAAATAATAAAA
*
611119 TAT
61 GAT
* *
611122 ATATTTATTAAAATTATATTTTAATATATATTAAAA-TTATATTT-TATGATAAATAATAATTAA
1 ATATTTATTAAAA-TATATATTAATATATAATAAAAGTTATATTTATAT--TAAATAATAA--AA
611185 GAT
61 GAT
611188 ATATTTATATCAAAA-ATATATTAATA-A-AATAAAA
1 ATATTTAT-T-AAAATATATATTAATATATAATAAAA
611222 ACTAAAAGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
62 3 0.03
63 8 0.09
64 21 0.24
65 9 0.10
66 26 0.30
67 9 0.10
68 11 0.13
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (63 bp):
ATATTTATTAAAATATATATTAATATATAATAAAAGTTATATTTATATTAAATAATAAAAGAT
Found at i:612585 original size:20 final size:22
Alignment explanation
Indices: 612542--612589 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
612532 TAATTTATTA
612542 TATTATAATGATAGGTTAATTTT
1 TATTATAATGATA-GTTAATTTT
*
612565 TATTATAATGGTA-TTAATTTT
1 TATTATAATGATAGTTAATTTT
612586 TATT
1 TATT
612590 TGAGTTACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.50
23 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (22 bp):
TATTATAATGATAGTTAATTTT
Found at i:612646 original size:19 final size:20
Alignment explanation
Indices: 612609--612651 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
612599 TGGATCAGGG
612609 TTAATATTTATTATGATATTA
1 TTAATATTTATTA-GATATTA
*
612630 TTAATTTTTATTA-ATATTA
1 TTAATATTTATTAGATATTA
612649 TTA
1 TTA
612652 TAATATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
21 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAATATTTATTAGATATTA
Found at i:612649 original size:27 final size:30
Alignment explanation
Indices: 612617--612679 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 30
612607 GGTTAATATT
*
612617 TATTATGATATTATT-A-ATTTTTAT-TAA
1 TATTATGATAATATTAACATTTTTATGTAA
* *
612644 TATTATTATAATATTAACATTTTTATGTAC
1 TATTATGATAATATTAACATTTTTATGTAA
612674 TATTAT
1 TATTAT
612680 TGTTAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 13 0.43
28 1 0.03
29 8 0.27
30 8 0.27
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (30 bp):
TATTATGATAATATTAACATTTTTATGTAA
Found at i:612652 original size:30 final size:29
Alignment explanation
Indices: 612609--612680 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
612599 TGGATCAGGG
*
612609 TTAATATTTATTATGATATTATTA-ATTTTTA
1 TTAATA-TTATTATAATATTA--ACATTTTTA
612640 TTAATATTATTATAATATTAACATTTTTA
1 TTAATATTATTATAATATTAACATTTTTA
*
612669 TGTACTATTATT
1 T-TAATATTATT
612681 GTTAATAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 8 0.22
30 22 0.59
31 6 0.16
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (29 bp):
TTAATATTATTATAATATTAACATTTTTA
Found at i:613084 original size:18 final size:18
Alignment explanation
Indices: 613058--613092 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
613048 CGTTGATGAT
*
613058 AAATTTATATAAATATAA
1 AAATATATATAAATATAA
*
613076 AAATATATATATATATA
1 AAATATATATAAATATA
613093 TAACATTTTG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATATATAAATATAA
Found at i:614356 original size:2 final size:2
Alignment explanation
Indices: 614349--614377 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
614339 CTAGCATTTA
614349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
614378 GTTCCACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:619015 original size:2 final size:2
Alignment explanation
Indices: 619008--619044 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
618998 CTTTTTCGCT
* *
619008 AC AC AC AC AC AC AC AC AA AC AC AC AA AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
619045 AAAGCATGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:622057 original size:5 final size:5
Alignment explanation
Indices: 622047--622075 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
622037 GTGTGACCTG
622047 CCCTT CCCTT CCCTT CCCTT CCCTT CCCT
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCT
622076 ACCATAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (5 bp):
CCCTT
Found at i:623289 original size:17 final size:17
Alignment explanation
Indices: 623269--623316 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
623259 TATGAATATT
623269 TTAAATATAATT-TTTAA
1 TTAAA-ATAATTATTTAA
*
623286 TTAAACTAATTATTTAA
1 TTAAAATAATTATTTAA
623303 TTAAAA-AATTATTT
1 TTAAAATAATTATTT
623317 TCACAAGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAATAATTATTTAA
Found at i:623312 original size:16 final size:17
Alignment explanation
Indices: 623277--623316 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
623267 TTTTAAATAT
*
623277 AATT-TTTAATTAAACT
1 AATTATTTAATTAAACA
623293 AATTATTTAATTAAA-A
1 AATTATTTAATTAAACA
623309 AATTATTT
1 AATTATTT
623317 TCACAAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTATTTAATTAAACA
Found at i:625275 original size:16 final size:17
Alignment explanation
Indices: 625256--625298 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
625246 TTTTTGTTTA
625256 TAAATTTTTATT-ATTT
1 TAAATTTTTATTAATTT
625272 TAAATATTTT-TTAATTT
1 TAAAT-TTTTATTAATTT
*
625289 TTAATTTTTA
1 TAAATTTTTA
625299 AAAATATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAAATTTTTATTAATTT
Found at i:625638 original size:21 final size:22
Alignment explanation
Indices: 625614--625672 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
625604 ATTTAAAAAA
625614 TAAATTTAATATTAA-ATATAT
1 TAAATTTAATATTAATATATAT
*
625635 TAAATAATTAATA-AAATATATAT
1 TAAAT--TTAATATTAATATATAT
*
625658 TTAATTTAATTATTA
1 TAAATTTAA-TATTA
625673 TCTTTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 9 0.30
22 4 0.13
23 17 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATTTAATATTAATATATAT
Done.