Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 23 of 31
Found at i:4825741 original size:21 final size:20
Alignment explanation
Indices: 4825711--4825750 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
4825701 AATTTTTTAA
*
4825711 TTTATTAAATAATATATTAT
1 TTTATTAAATAATAAATTAT
4825731 TTTATATAAATAATAAATTA
1 TTTAT-TAAATAATAAATTA
4825751 ATTGATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATTAAATAATAAATTAT
Found at i:4826663 original size:21 final size:20
Alignment explanation
Indices: 4826638--4826701 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
4826628 AAAAAGTAGA
4826638 TTAAATTATGATTTAAAAATT
1 TTAAATTAT-ATTTAAAAATT
* *
4826659 TTAAATTATTTTTAAAAATAAA
1 TTAAATTATATTTAAAAAT--T
4826681 TTAAATTA-ATTT-AAAATT
1 TTAAATTATATTTAAAAATT
4826699 TTA
1 TTA
4826702 TTTCATTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 3 0.08
20 14 0.38
21 12 0.32
22 8 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATTATATTTAAAAATT
Found at i:4826749 original size:19 final size:22
Alignment explanation
Indices: 4826727--4826780 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
4826717 TATTATTAAA
4826727 ATATTAAAATTT-TA-T-TTTT
1 ATATTAAAATTTATATTATTTT
*
4826746 ATATTAATATTTATATTATTTT
1 ATATTAAAATTTATATTATTTT
4826768 ATAATT-AAATTTA
1 AT-ATTAAAATTTA
4826781 AATAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 1 0.03
22 12 0.41
23 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATTAAAATTTATATTATTTT
Found at i:4830294 original size:11 final size:11
Alignment explanation
Indices: 4830278--4830443 Score: 96
Period size: 11 Copynumber: 16.5 Consensus size: 11
4830268 TTGATAACTT
4830278 TAAATATAATA
1 TAAATATAATA
4830289 TAAATATAATA
1 TAAATATAATA
4830300 TAAGA-ATAAT-
1 TAA-ATATAATA
4830310 TAAAATATAATA
1 T-AAATATAATA
* *
4830322 AAAATAAAAT-
1 TAAATATAATA
*
4830332 TTAATATAA-A
1 TAAATATAATA
4830342 -AAAT-TAATA
1 TAAATATAATA
* *
4830351 CAAAAATAATA
1 TAAATATAATA
*
4830362 TAAATATATTA
1 TAAATATAATA
*
4830373 -AAAT-TTATA
1 TAAATATAATA
4830382 T-AA-AT-ATA
1 TAAATATAATA
4830390 T-AATAT-AT-
1 TAAATATAATA
*
4830398 TAAATATAATT
1 TAAATATAATA
*
4830409 TTAATAT-ATA
1 TAAATATAATA
4830419 -AAA-ATAATA
1 TAAATATAATA
**
4830428 TAAATACGATA
1 TAAATATAATA
4830439 TAAAT
1 TAAAT
4830444 TTACAAATGA
Statistics
Matches: 121, Mismatches: 17, Indels: 34
0.70 0.10 0.20
Matches are distributed among these distances:
8 12 0.10
9 24 0.20
10 22 0.18
11 62 0.51
12 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (11 bp):
TAAATATAATA
Found at i:4830327 original size:20 final size:20
Alignment explanation
Indices: 4830290--4830431 Score: 73
Period size: 20 Copynumber: 7.1 Consensus size: 20
4830280 AATATAATAT
4830290 AAATATAATATAAGAATAATTA
1 AAATATAATA-AA-AATAATTA
4830312 AAATATAATAAAAATAAAATT-
1 AAATATAATAAAAAT--AATTA
* *
4830333 TAATATAA-AAAATTAA-TA
1 AAATATAATAAAAATAATTA
* *
4830351 CAAAAATAATATAAATATATTA
1 -AAATATAATAAAAATA-ATTA
* *
4830373 AAAT-TTATATAAAT-A-TA
1 AAATATAATAAAAATAATTA
* * * *
4830390 TAATATATTAAATATAATTT
1 AAATATAATAAAAATAATTA
*
4830410 TAATAT-ATAAAAATAATATA
1 AAATATAATAAAAATAAT-TA
4830430 AA
1 AA
4830432 TACGATATAA
Statistics
Matches: 91, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
17 6 0.07
18 9 0.10
19 16 0.18
20 31 0.34
21 13 0.14
22 16 0.18
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
AAATATAATAAAAATAATTA
Found at i:4830386 original size:10 final size:10
Alignment explanation
Indices: 4830354--4830443 Score: 59
Period size: 9 Copynumber: 9.4 Consensus size: 10
4830344 ATTAATACAA
4830354 AAATA-ATAT
1 AAATATATAT
4830363 AAATATAT-T
1 AAATATATAT
*
4830372 AAA-ATTTAT
1 AAATATATAT
4830381 ATAA-ATATAT
1 A-AATATATAT
4830391 -AATATAT-T
1 AAATATATAT
*
4830399 AAATATAATTT
1 AAATAT-ATAT
* *
4830410 TAATATATAA
1 AAATATATAT
4830420 AAATA-ATAT
1 AAATATATAT
*
4830429 AAATACGATAT
1 AAATA-TATAT
4830440 AAAT
1 AAAT
4830444 TTACAAATGA
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
8 6 0.09
9 28 0.43
10 17 0.26
11 14 0.22
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (10 bp):
AAATATATAT
Found at i:4830414 original size:27 final size:27
Alignment explanation
Indices: 4830357--4830419 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
4830347 AATACAAAAA
*
4830357 TAATATA-AATATATTAAAATTTATAT
1 TAATATATAATATATTAAAATTAATAT
* *
4830383 AAATATATAATATATT-AAATATAATTT
1 TAATATATAATATATTAAAAT-TAATAT
4830410 TAATATATAA
1 TAATATATAA
4830420 AAATAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAATATATAATATATTAAAATTAATAT
Found at i:4832927 original size:6 final size:6
Alignment explanation
Indices: 4832916--4833008 Score: 61
Period size: 6 Copynumber: 15.5 Consensus size: 6
4832906 CAATAATAAA
* * *
4832916 AAATTT AAATTT AAATTT -GATTT AAAATTT ACATTTT AAAATTT -TATTT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT A-AATTT -AAATTT AAATTT
* *
4832965 AAATTT -AA-TT AAATTTT ATATTT AAAATTT -AATTT TAATTT AAA
1 AAATTT AAATTT AAA-TTT AAATTT -AAATTT AAATTT AAATTT AAA
4833009 ATAAAGATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
4 2 0.03
5 17 0.25
6 27 0.40
7 21 0.31
8 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:4832933 original size:12 final size:11
Alignment explanation
Indices: 4832916--4833007 Score: 78
Period size: 11 Copynumber: 7.7 Consensus size: 11
4832906 CAATAATAAA
4832916 AAATTTAAATTT
1 AAATTT-AATTT
*
4832928 AAATTTGATTT
1 AAATTTAATTT
4832939 AAAATTTACATTTT
1 -AAATTTA-A-TTT
*
4832953 AAAATTTTATTT
1 -AAATTTAATTT
4832965 AAATTTAA-TT
1 AAATTTAATTT
4832975 AAATTTTATATTT
1 AAA-TTTA-ATTT
4832988 AAAATTTAATTT
1 -AAATTTAATTT
*
4833000 TAATTTAA
1 AAATTTAA
4833008 AATAAAGATT
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
10 5 0.07
11 22 0.32
12 20 0.29
13 8 0.12
14 13 0.19
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:4833006 original size:24 final size:23
Alignment explanation
Indices: 4832915--4833005 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 23
4832905 GCAATAATAA
*
4832915 AAAATTTAAATTTAAATTTGATTT
1 AAAATTT-AATTTAAATTTTATTT
4832939 AAAATTTACATTTTAAAATTTTATTT
1 AAAATTTA-A-TTT-AAATTTTATTT
4832965 -AAATTTAA-TTAAATTTTATATTT
1 AAAATTTAATTTAAA-TTT-TATTT
*
4832988 AAAATTTAATTTTAATTT
1 AAAATTTAATTTAAATTT
4833006 AAAATAAAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
21 3 0.05
22 5 0.09
23 6 0.10
24 20 0.34
25 14 0.24
26 10 0.17
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
AAAATTTAATTTAAATTTTATTT
Found at i:4833090 original size:24 final size:24
Alignment explanation
Indices: 4833063--4833111 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4833053 TTAATAAAAA
*
4833063 TTAAATATAATT-TTATGTTTAATT
1 TTAAATATAATTATTAT-TTAAATT
*
4833087 TTAAATTTAATTATTATTTAAATT
1 TTAAATATAATTATTATTTAAATT
4833111 T
1 T
4833112 GAATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTAAATATAATTATTATTTAAATT
Found at i:4833129 original size:24 final size:23
Alignment explanation
Indices: 4833080--4833129 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
4833070 TAATTTTATG
* **
4833080 TTTAATTTTAAATTTAATTATTA
1 TTTAAATTTAAATTTAATTAAAA
*
4833103 TTTAAATTTGAATTTAAATTAAAA
1 TTTAAATTTAAATTT-AATTAAAA
4833127 TTT
1 TTT
4833130 TTTAATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATTAAAA
Found at i:4834384 original size:13 final size:13
Alignment explanation
Indices: 4834366--4834398 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
4834356 TATTTTTTTA
4834366 AATATTTATATTT
1 AATATTTATATTT
4834379 AATATTTATATTT
1 AATATTTATATTT
4834392 AATATTT
1 AATATTT
4834399 TTAAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:4834385 original size:7 final size:7
Alignment explanation
Indices: 4834366--4834398 Score: 52
Period size: 6 Copynumber: 5.0 Consensus size: 7
4834356 TATTTTTTTA
4834366 AATATTT
1 AATATTT
4834373 -ATATTT
1 AATATTT
4834379 AATATTT
1 AATATTT
4834386 -ATATTT
1 AATATTT
4834392 AATATTT
1 AATATTT
4834399 TTAAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
AATATTT
Found at i:4835527 original size:30 final size:29
Alignment explanation
Indices: 4835493--4835558 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
4835483 TTTGCACATG
* *
4835493 AATAAGCTTTTTATCTTTAATTTTTATCTA
1 AATAAACTTTTTATCTTTAATTTATA-CTA
*
4835523 AATAAATTTTTTATCTTTAATTTATACTA
1 AATAAACTTTTTATCTTTAATTTATACTA
4835552 AATAAAC
1 AATAAAC
4835559 ACTTGAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.52
Consensus pattern (29 bp):
AATAAACTTTTTATCTTTAATTTATACTA
Found at i:4835552 original size:29 final size:30
Alignment explanation
Indices: 4835500--4835557 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
4835490 ATGAATAAGC
*
4835500 TTTTTATCTTTAATTTTTATCTAAATAAAT
1 TTTTTATCTTTAATTTATATCTAAATAAAT
4835530 TTTTTATCTTTAATTTATA-CTAAATAAA
1 TTTTTATCTTTAATTTATATCTAAATAAA
4835558 CACTTGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTTATCTTTAATTTATATCTAAATAAAT
Found at i:4837041 original size:23 final size:24
Alignment explanation
Indices: 4837005--4837050 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
4836995 ATATAATAAA
4837005 TATATTAAACTTAT-TTTATTAAT
1 TATATTAAACTTATATTTATTAAT
** *
4837028 TATATTAATTTTATATTTGTTAA
1 TATATTAAACTTATATTTATTAA
4837051 ACTTTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
TATATTAAACTTATATTTATTAAT
Found at i:4837057 original size:18 final size:18
Alignment explanation
Indices: 4837036--4837080 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
4837026 ATTATATTAA
4837036 TTTTATATT-TGTTAAACT
1 TTTTATATTATGTTAAA-T
* *
4837054 TTTTATTTTATGTTATAT
1 TTTTATATTATGTTAAAT
4837072 TTTTATATT
1 TTTTATATT
4837081 GTATCTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTATATTATGTTAAAT
Found at i:4844463 original size:2 final size:2
Alignment explanation
Indices: 4844456--4844488 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4844446 GGATCTGCAT
4844456 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4844489 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4844728 original size:25 final size:25
Alignment explanation
Indices: 4844696--4844750 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
4844686 ATTAATTTTT
*
4844696 TTAT-TTTTTATATATATTAAAAAA
1 TTATATTTTAATATATATTAAAAAA
* *
4844720 TTATATTTTAATTTATATTTAAAAA
1 TTATATTTTAATATATATTAAAAAA
4844745 -TATATT
1 TTATATT
4844751 AAATACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATATTTTAATATATATTAAAAAA
Found at i:4846279 original size:12 final size:12
Alignment explanation
Indices: 4846247--4846285 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4846237 TATTAAGTAA
* *
4846247 AAATATTAATTC
1 AAATATCAATTT
4846259 AAATAATCAATTT
1 AAAT-ATCAATTT
4846272 AAATATCAATTT
1 AAATATCAATTT
4846284 AA
1 AA
4846286 TAAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATCAATTT
Found at i:4846637 original size:13 final size:13
Alignment explanation
Indices: 4846607--4846654 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
4846597 TAAAATTTTT
*
4846607 AAATATATATATA
1 AAATTTATATATA
* *
4846620 TAATTTATATTTA
1 AAATTTATATATA
*
4846633 AAATTTTTA-ATA
1 AAATTTATATATA
4846645 AAATTTATAT
1 AAATTTATAT
4846655 TATTTATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATTTATATATA
Found at i:4846654 original size:34 final size:34
Alignment explanation
Indices: 4846593--4846663 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
4846583 TTTGATATAT
*
4846593 TATTTAAAATTTTTAAATATATATATATAATTTA
1 TATTTAAAATTTTTAAATAAATATATATAATTTA
* *
4846627 TATTTAAAATTTTT-AATAAAATTTATATTATTTA
1 TATTTAAAATTTTTAAAT-AAATATATATAATTTA
4846661 TAT
1 TAT
4846664 ATGTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 3 0.09
34 30 0.91
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
TATTTAAAATTTTTAAATAAATATATATAATTTA
Found at i:4846754 original size:27 final size:26
Alignment explanation
Indices: 4846724--4846780 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
4846714 AGATTATAAT
**
4846724 TTATAAATATTTAATAAAAAATTAAAA
1 TTATAAATAAATAATAAAAAA-TAAAA
* *
4846751 TTATTAATAAATAATAAAATATAAAA
1 TTATAAATAAATAATAAAAAATAAAA
4846777 TTAT
1 TTAT
4846781 TTTAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TTATAAATAAATAATAAAAAATAAAA
Found at i:4846797 original size:20 final size:19
Alignment explanation
Indices: 4846765--4846806 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
4846755 TAATAAATAA
4846765 TAAAATATAAAATTATT-T
1 TAAAATATAAAATTATTAT
4846783 TAAAATATATTAAATTATTAT
1 TAAAATATA--AAATTATTAT
4846804 TAA
1 TAA
4846807 TTAGATGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
20 8 0.38
21 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAATATAAAATTATTAT
Found at i:4846997 original size:19 final size:19
Alignment explanation
Indices: 4846962--4847003 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4846952 TATATTAATC
*
4846962 AATATAACTTGATTAAAAT
1 AATATAACTTAATTAAAAT
*
4846981 AATATAA-TTAATATAAATT
1 AATATAACTTAAT-TAAAAT
4847000 AATA
1 AATA
4847004 CATAAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AATATAACTTAATTAAAAT
Found at i:4847223 original size:16 final size:16
Alignment explanation
Indices: 4847202--4847256 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
4847192 TTATTATATT
*
4847202 TTTTTTATAATTTTAA
1 TTTTTTATAATATTAA
*
4847218 TTTTTTTTAATATTAA
1 TTTTTTATAATATTAA
*
4847234 ---ATT-TAATATTAA
1 TTTTTTATAATATTAA
4847246 TTTTTTATAAT
1 TTTTTTATAAT
4847257 CGATTTTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
12 9 0.29
13 2 0.06
15 2 0.06
16 18 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTTATAATATTAA
Found at i:4848188 original size:24 final size:23
Alignment explanation
Indices: 4848151--4848211 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 23
4848141 GACAACTTTG
*
4848151 TATATAATACAAAAAAATAATTAAAA
1 TATAT-ATA-AAATAAAT-ATTAAAA
4848177 TATGATATAAAATAAATATTAAAA
1 TAT-ATATAAAATAAATATTAAAA
4848201 TATAT-TAAAAT
1 TATATATAAAAT
4848212 TTTTATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.18
23 2 0.06
24 10 0.30
25 7 0.21
26 6 0.18
27 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
TATATATAAAATAAATATTAAAA
Found at i:4848207 original size:10 final size:10
Alignment explanation
Indices: 4848164--4848211 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 10
4848154 ATAATACAAA
4848164 AAAATA-ATT
1 AAAATATATT
4848173 AAAATATGATAT
1 AAAATAT-AT-T
4848185 AAAATAAATATT
1 AAAAT--ATATT
4848197 AAAATATATT
1 AAAATATATT
4848207 AAAAT
1 AAAAT
4848212 TTTTATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 6 0.18
10 10 0.29
11 2 0.06
12 12 0.35
13 2 0.06
14 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAATATATT
Found at i:4848522 original size:22 final size:21
Alignment explanation
Indices: 4848494--4848535 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4848484 TATTAAAAAA
4848494 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
4848514 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
4848535 A
1 A
4848536 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:4848614 original size:17 final size:16
Alignment explanation
Indices: 4848592--4848649 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 16
4848582 TTGATCAAGA
4848592 AAATAAAATTTAAATCT
1 AAAT-AAATTTAAATCT
4848609 AAATAAA-TTAAA--T
1 AAATAAATTTAAATCT
*
4848622 AAAT-AATTTAACTCAT
1 AAATAAATTTAAATC-T
4848638 AAATAAATTTAA
1 AAATAAATTTAA
4848650 TTATACGACA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 9 0.26
15 5 0.14
16 8 0.23
17 11 0.31
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAAATTTAAATCT
Found at i:4849238 original size:2 final size:2
Alignment explanation
Indices: 4849231--4849260 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4849221 GATTTCATGA
*
4849231 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4849261 TGCTAGAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4849508 original size:21 final size:21
Alignment explanation
Indices: 4849484--4849527 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4849474 ATTTGATTAA
*
4849484 TTAATTAATTTAAACAA-AATT
1 TTAAATAATTTAAA-AATAATT
*
4849505 TTAAATATTTTAAAAATAATT
1 TTAAATAATTTAAAAATAATT
4849526 TT
1 TT
4849528 CAAGTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATAATTTAAAAATAATT
Found at i:4849662 original size:2 final size:2
Alignment explanation
Indices: 4849657--4849694 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4849647 ATGTGTGATT
4849657 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
4849695 GAGAGAGAGA
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):
TA
Found at i:4849699 original size:2 final size:2
Alignment explanation
Indices: 4849694--4849740 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4849684 ATATATATAT
4849694 AG AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG AG
4849736 AG AG A
1 AG AG A
4849741 TTATGATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4850551 original size:21 final size:20
Alignment explanation
Indices: 4850511--4850555 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
4850501 TTTTCGTATA
*
4850511 AAAAAATAAATTATATATATT
1 AAAAAATAAATTATAAATA-T
* *
4850532 AAAAATTAAATTTTAAATAT
1 AAAAAATAAATTATAAATAT
4850552 AAAA
1 AAAA
4850556 GATATTATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATAAATTATAAATAT
Found at i:4850953 original size:26 final size:28
Alignment explanation
Indices: 4850924--4850980 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 28
4850914 AATTTAATCT
4850924 TATTTGAA-TTATTATTT-ATTA-AAAAA
1 TATTTGAATTTA-TATTTAATTATAAAAA
**
4850950 TATTTTTATTTATATTTAATTATAAAAA
1 TATTTGAATTTATATTTAATTATAAAAA
4850978 TAT
1 TAT
4850981 ATATAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 11 0.42
27 7 0.27
28 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TATTTGAATTTATATTTAATTATAAAAA
Found at i:4852184 original size:41 final size:41
Alignment explanation
Indices: 4852127--4852214 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
4852117 TTATATATAT
4852127 TAAATTAATGATCAAGCATATATAAATATATGGGGAGAAAA
1 TAAATTAATGATCAAGCATATATAAATATATGGGGAGAAAA
*
4852168 TAAATTTATGATCAAGCATATATAAATATATGGGGAGAAAA
1 TAAATTAATGATCAAGCATATATAAATATATGGGGAGAAAA
4852209 TAAATT
1 TAAATT
4852215 GAGAACCACT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.30
Consensus pattern (41 bp):
TAAATTAATGATCAAGCATATATAAATATATGGGGAGAAAA
Found at i:4858574 original size:17 final size:17
Alignment explanation
Indices: 4858549--4858589 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4858539 TTTTAAGAAG
4858549 TTTAA-TTAA-ATTTCTT
1 TTTAATTTAATATTT-TT
4858565 TTTAATTTAATATTTTT
1 TTTAATTTAATATTTTT
*
4858582 ATTAATTT
1 TTTAATTT
4858590 TACCCCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 13 0.59
18 4 0.18
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAATTTAATATTTTT
Found at i:4858969 original size:2 final size:2
Alignment explanation
Indices: 4858958--4859007 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
4858948 ATTGTTTAGG
4858958 AT AT -T AT AT AT 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 AT AT AT AT AT AT AT
4858998 AT AT A- AT AT A
1 AT AT AT AT AT A
4859008 AAAGCATTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4859599 original size:2 final size:2
Alignment explanation
Indices: 4859592--4859622 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4859582 AGATTGTATC
4859592 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4859623 ATAGTATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4859779 original size:25 final size:24
Alignment explanation
Indices: 4859751--4859797 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
4859741 AATTTTGATA
*
4859751 TATTATTTTTATTATGTTATAATTT
1 TATTATTTTTA-TATCTTATAATTT
4859776 TATTATTTTTATATCTTATAAT
1 TATTATTTTTATATCTTATAAT
4859798 CATACCATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTATTTTTATATCTTATAATTT
Found at i:4870854 original size:3 final size:3
Alignment explanation
Indices: 4870846--4870874 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4870836 ACAAATTCCA
4870846 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4870875 CTCTGCCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4874042 original size:24 final size:24
Alignment explanation
Indices: 4873998--4874043 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4873988 TTCTGGTGTT
*
4873998 CGATAAATTTAATAATTTTAAATA
1 CGATAAATTTAATAATATTAAATA
*
4874022 CGATATATTATAA-AATATTAAA
1 CGATAAATT-TAATAATATTAAA
4874044 AAATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
CGATAAATTTAATAATATTAAATA
Found at i:4874078 original size:19 final size:19
Alignment explanation
Indices: 4874034--4874080 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
4874024 ATATATTATA
*
4874034 AAATATTAAAAAATAAAAT
1 AAATATAAAAAAATAAAAT
* *
4874053 ATCATATAAAAAAATAATAT
1 A-AATATAAAAAAATAAAAT
4874073 AAATATAA
1 AAATATAA
4874081 TATATCAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATATAAAAAAATAAAAT
Found at i:4874083 original size:24 final size:25
Alignment explanation
Indices: 4874041--4874099 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
4874031 ATAAAATATT
*
4874041 AAAA-AATA-AAATATCATATA-AA
1 AAAATAATATAAATATAATATATAA
*
4874063 AAAATAATATAAATATAATATATCA
1 AAAATAATATAAATATAATATATAA
*
4874088 AAATTAATATAA
1 AAAATAATATAA
4874100 TACGAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.13
23 4 0.13
24 11 0.35
25 12 0.39
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAATAATATAAATATAATATATAA
Found at i:4874488 original size:2 final size:2
Alignment explanation
Indices: 4874481--4874509 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4874471 ACAGAAATCA
4874481 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
4874510 CACATTTATA
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:4875155 original size:170 final size:168
Alignment explanation
Indices: 4874852--4875162 Score: 407
Period size: 170 Copynumber: 1.8 Consensus size: 168
4874842 GACTTATAAT
*
4874852 GACATGAAGGATTCTTACTTAACTTTTAAATTATAAAAAATAAAATAAAATTAAGCATTCAGCAC
1 GACATGAAGGATTCTTACCTAACTTTTAAATTAT-AAAAATAAAATAAAATTAAGCATTCAGCAC
* * * *
4874917 TTTTTTTTTAATAAAATTTTAAATTCGAATTTTATGAAAAGAAAAAATAAGCATTTAGAGAGCTT
65 TTTTTTTTTAATAAAATTTTAAATTCGAACTTTATGAAAAGAAAAAATAAG-ATTTACAAAACTT
4874982 TATCTCATAATGGATCAGTTTGATTTGAATTAAATTAGTC
129 TATCTCATAATGGATCAGTTTGATTTGAATTAAATTAGTC
* * *
4875022 GACATGAAGGGTT-TGTACCTAATTTTTAAATTAT-AAAA-AAAATATAATTAAGCATTCAGCAC
1 GACATGAAGGATTCT-TACCTAACTTTTAAATTATAAAAATAAAATAAAATTAAGCATTCAGCAC
* * *
4875084 TTATTTTTCTTTAGTAAAATTTTAAATTTGGACTTTATG-AAAGAAAAAAATCAATG-TTTACAA
65 -T-TTTTT-TTTAATAAAATTTTAAATTCGAACTTTATGAAAAG-AAAAAAT-AA-GATTTACAA
4875147 AACTTTATCTCATAAT
124 AACTTTATCTCATAAT
4875163 AAGCTGACCT
Statistics
Matches: 123, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
167 23 0.19
168 5 0.04
169 10 0.08
170 82 0.67
171 2 0.02
172 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (168 bp):
GACATGAAGGATTCTTACCTAACTTTTAAATTATAAAAATAAAATAAAATTAAGCATTCAGCACT
TTTTTTTTAATAAAATTTTAAATTCGAACTTTATGAAAAGAAAAAATAAGATTTACAAAACTTTA
TCTCATAATGGATCAGTTTGATTTGAATTAAATTAGTC
Found at i:4875892 original size:18 final size:17
Alignment explanation
Indices: 4875841--4875893 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
4875831 TATTAAATTA
*
4875841 TTTTAA-AAAATTAAAA
1 TTTTAATAAAATTAAAC
* * *
4875857 ATATAATATAATTAAAC
1 TTTTAATAAAATTAAAC
4875874 TTTTAATAAAATATAAAC
1 TTTTAATAAAAT-TAAAC
4875892 TT
1 TT
4875894 AGACAAAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 4 0.14
17 17 0.61
18 7 0.25
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTTAATAAAATTAAAC
Found at i:4876203 original size:17 final size:17
Alignment explanation
Indices: 4876178--4876210 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4876168 ACTTTGTTAT
*
4876178 TTTATATTTAATAATAA
1 TTTAAATTTAATAATAA
4876195 TTTAAATTTAATAATA
1 TTTAAATTTAATAATA
4876211 TTTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAATAATAA
Found at i:4877775 original size:32 final size:33
Alignment explanation
Indices: 4877739--4877802 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
4877729 TATTTTATAT
*
4877739 TTATATAAATTTTGATACATTAATA-ATTCATA
1 TTATATAAATTTTGAAACATTAATATATTCATA
* *
4877771 TTATATAGATTTTGAAACATTCATATATTCAT
1 TTATATAAATTTTGAAACATTAATATATTCAT
4877803 GTCTGTGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (33 bp):
TTATATAAATTTTGAAACATTAATATATTCATA
Found at i:4879691 original size:19 final size:19
Alignment explanation
Indices: 4879667--4879708 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
4879657 ATAGATACAT
*
4879667 AATTTAAAAAGATTATCCA
1 AATTTAAAAAGATGATCCA
4879686 AATTTAAAAAGATGATCCA
1 AATTTAAAAAGATGATCCA
4879705 AATT
1 AATT
4879709 GGCAGAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (19 bp):
AATTTAAAAAGATGATCCA
Found at i:4884184 original size:55 final size:57
Alignment explanation
Indices: 4884120--4884244 Score: 125
Period size: 55 Copynumber: 2.3 Consensus size: 57
4884110 TATAGGGTAA
* * * *
4884120 AAAAAAAAAATAATAAAAAAAT-AAAAATTAAAA-TATTAATT-ATTATATTTTTTAT
1 AAAATAAAAATAATAAAAAAATAAAAAATAAAAAGAATT-ATTAATTATATTTTTAAT
*** * *
4884175 AAAAT-AAAA-AATGTTAAATTAAAAAATAAAAAGAATTTTTAATTATATTTTTAAT
1 AAAATAAAAATAATAAAAAAATAAAAAATAAAAAGAATTATTAATTATATTTTTAAT
4884230 AAAATAAAAATAATA
1 AAAATAAAAATAATA
4884245 TTTAATTAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
53 7 0.13
54 16 0.29
55 25 0.45
56 4 0.07
57 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (57 bp):
AAAATAAAAATAATAAAAAAATAAAAAATAAAAAGAATTATTAATTATATTTTTAAT
Found at i:4884238 original size:33 final size:32
Alignment explanation
Indices: 4884193--4884265 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 32
4884183 AAATGTTAAA
* *
4884193 TTAAAAAATAAAAAGAATTTTTAATTATATTT
1 TTAAAAAATAAAAAGAATATTTAATTAAATTT
*
4884225 TTAATAAAATAAAAATAATATTTAATTAAA-TT
1 TTAA-AAAATAAAAAGAATATTTAATTAAATTT
*
4884257 TAAAAAAAT
1 TTAAAAAAT
4884266 TACATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 5 0.14
32 9 0.25
33 22 0.61
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (32 bp):
TTAAAAAATAAAAAGAATATTTAATTAAATTT
Found at i:4884304 original size:45 final size:44
Alignment explanation
Indices: 4884255--4884429 Score: 119
Period size: 43 Copynumber: 4.2 Consensus size: 44
4884245 TTTAATTAAA
4884255 TTTAAAAAAATTACATTAATAAATTAAAATTATTATTATTATATT
1 TTTAAAAAAATTACATTAATAAATTAAAA-TATTATTATTATATT
** **
4884300 TTTAAAATAAAAAAC-TT--TAAATTAAAA-AAAATTATTATAATT
1 TTTAAAA-AAATTACATTAATAAATTAAAATATTATTATTAT-ATT
* * *
4884342 TTTAAGAAAA-T--A--AA-AAA-T--AATATT-TAATTA-AGT
1 TTTAAAAAAATTACATTAATAAATTAAAATATTATTATTATATT
* *
4884375 TTTAAAAAAATTTACATTAACAACTTAAAATATTAATTATTATATT
1 TTTAAAAAAA-TTACATTAATAAATTAAAATATT-ATTATTATATT
4884421 TTTAAAAAA
1 TTTAAAAAA
4884430 TAAAAATTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 37
0.66 0.09 0.25
Matches are distributed among these distances:
33 11 0.11
35 8 0.08
36 1 0.01
37 2 0.02
38 3 0.03
39 2 0.02
40 2 0.02
41 13 0.13
42 9 0.09
43 16 0.16
45 14 0.14
46 16 0.16
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (44 bp):
TTTAAAAAAATTACATTAATAAATTAAAATATTATTATTATATT
Found at i:4884566 original size:13 final size:13
Alignment explanation
Indices: 4884548--4884573 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4884538 TATTACTATT
4884548 TTAAAAATTAAAA
1 TTAAAAATTAAAA
4884561 TTAAAAATTAAAA
1 TTAAAAATTAAAA
4884574 AGTTTTTATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAAATTAAAA
Found at i:4885394 original size:13 final size:13
Alignment explanation
Indices: 4885378--4885402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4885368 TTGATAAAAC
4885378 TTTTTTTATATTA
1 TTTTTTTATATTA
4885391 TTTTTTTATATT
1 TTTTTTTATATT
4885403 TTAAAAAACT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTATATTA
Found at i:4886572 original size:34 final size:32
Alignment explanation
Indices: 4886506--4886592 Score: 95
Period size: 34 Copynumber: 2.7 Consensus size: 32
4886496 GTATATATTT
* *
4886506 TTATATAAAATTTTAATATATTAATAATTTATA
1 TTATAT-AAATTTTAAAATATTAATAAATTATA
*
4886539 TTATATAAATTTTAAAATATATATTTAAATTATA
1 TTATATAAATTTTAAAATAT-TA-ATAAATTATA
* *
4886573 TTATTTATATTTT-AAATATT
1 TTATATAAATTTTAAAATATT
4886593 TTATTCATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
32 14 0.30
33 14 0.30
34 19 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TTATATAAATTTTAAAATATTAATAAATTATA
Found at i:4886596 original size:20 final size:22
Alignment explanation
Indices: 4886556--4886597 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
4886546 AATTTTAAAA
4886556 TATATATTTAAATTATATTATT
1 TATATATTTAAATTATATTATT
*
4886578 TATAT-TTTAAA-TATTTTATT
1 TATATATTTAAATTATATTATT
4886598 CATAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATATATTTAAATTATATTATT
Found at i:4886607 original size:34 final size:34
Alignment explanation
Indices: 4886506--4886613 Score: 89
Period size: 34 Copynumber: 3.2 Consensus size: 34
4886496 GTATATATTT
* * *
4886506 TTATATAAAATTTTAATATAT-TAAT-AATTTATA
1 TTATAT-AAATTTTAAAATATATATTCAAATTATA
*
4886539 TTATATAAATTTTAAAATATATATTTAAATTATA
1 TTATATAAATTTTAAAATATATATTCAAATTATA
* * *
4886573 TTATTTATATTTT-AAATATTTTATTCATAA-TATA
1 TTATATAAATTTTAAAATA-TATATTCA-AATTATA
4886607 TTTATAT
1 -TTATAT
4886614 GATTATATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
32 13 0.21
33 14 0.23
34 28 0.45
35 7 0.11
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (34 bp):
TTATATAAATTTTAAAATATATATTCAAATTATA
Found at i:4886621 original size:16 final size:15
Alignment explanation
Indices: 4886470--4886623 Score: 69
Period size: 15 Copynumber: 10.5 Consensus size: 15
4886460 ACTCATTCAA
*
4886470 TATAAATTTAT-TAAT
1 TATATATTTATAT-AT
*
4886485 TATATATTTATGTA-
1 TATATATTTATATAT
4886499 TATAT-TTT-TATAT
1 TATATATTTATATAT
* *
4886512 AAAAT-TTTAATATAT
1 TATATATTT-ATATAT
4886527 TA-ATAATTTATAT-T
1 TATAT-ATTTATATAT
* * *
4886541 ATATAAATTT-TAAAA
1 -TATATATTTATATAT
4886556 TATATATTTA-A-AT
1 TATATATTTATATAT
*
4886569 TATATTATTTATATTT
1 TATA-TATTTATATAT
*
4886585 TAAATATTT-TATTCAT
1 TATATATTTATA-T-AT
*
4886601 AATATATTTATATGAT
1 TATATATTTATAT-AT
4886617 TATATAT
1 TATATAT
4886624 AATATTATAA
Statistics
Matches: 106, Mismatches: 17, Indels: 31
0.69 0.11 0.20
Matches are distributed among these distances:
12 3 0.03
13 14 0.13
14 27 0.25
15 34 0.32
16 26 0.25
17 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (15 bp):
TATATATTTATATAT
Found at i:4887055 original size:23 final size:20
Alignment explanation
Indices: 4887024--4887064 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
4887014 TTAGATGATT
4887024 ATTTAGTTTTAATATTTTTTTA
1 ATTTAGTTTT-AT-TTTTTTTA
4887046 ATTTAAGTTTTATTTTTTT
1 ATTT-AGTTTTATTTTTTT
4887065 ACAGAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 6 0.33
23 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
ATTTAGTTTTATTTTTTTTA
Found at i:4887231 original size:4 final size:4
Alignment explanation
Indices: 4887218--4887271 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
4887208 AAATTTTTAA
** *
4887218 AAAT -AAT AAAT AAAT ATTT AAAT ATAA- AAAT ATA- AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT
4887264 AAAT AAAT
1 AAAT AAAT
4887272 CCGATTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
3 7 0.17
4 31 0.77
5 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:4887237 original size:21 final size:20
Alignment explanation
Indices: 4887208--4887249 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4887198 TATTTAATTA
*
4887208 AAATTTTTAAAAATAATAAAT
1 AAATATTTAAAAATAA-AAAT
*
4887229 AAATATTTAAATATAAAAAT
1 AAATATTTAAAAATAAAAAT
4887249 A
1 A
4887250 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATATTTAAAAATAAAAAT
Found at i:4887266 original size:27 final size:27
Alignment explanation
Indices: 4887215--4887268 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
4887205 TTAAAATTTT
**
4887215 TAAAAATAATAAATAAATATTTAAATA
1 TAAAAATAATAAATAAATAAATAAATA
4887242 TAAAAAT-ATAAAATAAATAAATAAATA
1 TAAAAATAAT-AAATAAATAAATAAATA
4887269 AATCCGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
TAAAAATAATAAATAAATAAATAAATA
Found at i:4888087 original size:27 final size:26
Alignment explanation
Indices: 4888022--4888167 Score: 84
Period size: 26 Copynumber: 5.4 Consensus size: 26
4888012 AGTTTGTTGA
* *
4888022 TATAA-TATATTAATTTTTTTAGATT
1 TATAATTATATTAATTTTATTATATT
4888047 TAATAGTTATTATATTTATATTTTATTATA-T
1 T-ATA---ATTATA-TTA-ATTTTATTATATT
*
4888078 TATAATTATATTAATTTTTTTATATT
1 TATAATTATATTAATTTTATTATATT
** * *
4888104 TATAAAAATTTTAATATTT-TAATAATT
1 TATAATTATATTAAT-TTTATTAT-ATT
* **
4888131 TAT-ATTATATAAATTTTAAAATATTT
1 TATAATTATATTAATTTTATTATA-TT
*
4888157 TATATTTATAT
1 TATAATTATAT
4888168 CATATTTATA
Statistics
Matches: 95, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
25 15 0.16
26 37 0.39
27 21 0.22
29 1 0.01
30 7 0.07
31 5 0.05
32 9 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (26 bp):
TATAATTATATTAATTTTATTATATT
Found at i:4888106 original size:26 final size:26
Alignment explanation
Indices: 4888022--4888147 Score: 96
Period size: 26 Copynumber: 4.7 Consensus size: 26
4888012 AGTTTGTTGA
*
4888022 TATAA-TATATTAATTTTTTTAGATT
1 TATAATTATATTAATTTTTTTATATT
*
4888047 TAATAGTTATTATATTTATATTTTATTATA-T
1 T-ATA---ATTATA-TTA-ATTTTTTTATATT
4888078 TATAATTATATTAATTTTTTTATATT
1 TATAATTATATTAATTTTTTTATATT
** * * *
4888104 TATAAAAATTTTAATATTTTAATAATT
1 TATAATTATATTAATTTTTTTAT-ATT
*
4888131 TAT-ATTATATAAATTTT
1 TATAATTATATTAATTTT
4888148 AAAATATTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
25 11 0.14
26 34 0.43
27 12 0.15
29 1 0.01
30 7 0.09
31 5 0.06
32 9 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TATAATTATATTAATTTTTTTATATT
Found at i:4888126 original size:34 final size:35
Alignment explanation
Indices: 4888088--4888177 Score: 87
Period size: 34 Copynumber: 2.6 Consensus size: 35
4888078 TATAATTATA
4888088 TTAATTTTTTTATATTTATAAAAATTTT-AATATT
1 TTAATTTTTTTATATTTATAAAAATTTTAAATATT
** *
4888122 TTAA-TAATTTATA-TTATATAAATTTTAAAATATT
1 TTAATTTTTTTATATTTATAAAAATTTT-AAATATT
* *
4888156 TTATATTTATATCATATTTATA
1 TTA-ATTT-TTTTATATTTATA
4888178 TTTTTTTATA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
32 12 0.28
33 7 0.16
34 13 0.30
35 1 0.02
36 1 0.02
37 4 0.09
38 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (35 bp):
TTAATTTTTTTATATTTATAAAAATTTTAAATATT
Found at i:4888130 original size:17 final size:18
Alignment explanation
Indices: 4888094--4888149 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
4888084 TATATTAATT
*
4888094 TTTTTATATTTATAAAAA
1 TTTTAATATTTATAAAAA
*
4888112 TTTTAATATTT-TAATAA
1 TTTTAATATTTATAAAAA
*
4888129 -TTT-ATA-TTATATAAA
1 TTTTAATATTTATAAAAA
4888144 TTTTAA
1 TTTTAA
4888150 AATATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 2 0.06
15 7 0.23
16 6 0.19
17 6 0.19
18 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATATTTATAAAAA
Found at i:4888140 original size:20 final size:19
Alignment explanation
Indices: 4888075--4888140 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
4888065 TATTTTATTA
* *
4888075 TATTATAATTATATTAATTT
1 TATTAT-ATTTTAATAATTT
* *
4888095 TTTTATATTTATAAAAATTT
1 TATTATATTT-TAATAATTT
4888115 TA--ATATTTTAATAATTT
1 TATTATATTTTAATAATTT
4888132 ATATTATAT
1 -TATTATAT
4888141 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
17 8 0.22
18 8 0.22
19 3 0.08
20 17 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATATTTTAATAATTT
Found at i:4888161 original size:7 final size:7
Alignment explanation
Indices: 4888151--4888211 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
4888141 AAATTTTAAA
4888151 ATATTTT
1 ATATTTT
4888158 ATATTTAT
1 ATATTT-T
4888166 ATCATATTT
1 AT-AT-TTT
4888175 ATATTTTT
1 ATA-TTTT
* * *
4888183 TTATATC
1 ATATTTT
4888190 ATATTTT
1 ATATTTT
4888197 ATATTTT
1 ATATTTT
*
4888204 ATAATTT
1 ATATTTT
4888211 A
1 A
4888212 ACAAAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
7 26 0.60
8 9 0.21
9 6 0.14
10 2 0.05
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (7 bp):
ATATTTT
Found at i:4888174 original size:11 final size:11
Alignment explanation
Indices: 4888158--4888200 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
4888148 AAAATATTTT
4888158 ATATTTATATC
1 ATATTTATATC
4888169 ATATTTATAT-
1 ATATTTATATC
* *
4888179 TTTTTTATATC
1 ATATTTATATC
4888190 ATATTTTATAT
1 ATA-TTTATAT
4888201 TTTATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.31
11 11 0.42
12 7 0.27
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTTATATC
Found at i:4888181 original size:34 final size:34
Alignment explanation
Indices: 4888096--4888172 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 34
4888086 TATTAATTTT
*
4888096 TTTATATTTATAAAAATTTT--AATATTTTAATAA
1 TTTATA-TTATATAAATTTTAAAATATTTTAATAA
4888129 TTTATATTATATAAATTTTAAAATATTTT-AT-A
1 TTTATATTATATAAATTTTAAAATATTTTAATAA
*
4888161 TTTATATCATAT
1 TTTATATTATAT
4888173 TTATATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 24 0.60
33 8 0.20
34 8 0.20
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (34 bp):
TTTATATTATATAAATTTTAAAATATTTTAATAA
Found at i:4888200 original size:22 final size:21
Alignment explanation
Indices: 4888161--4888203 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4888151 ATATTTTATA
4888161 TTTATATCATATTTATATTTT
1 TTTATATCATATTTATATTTT
4888182 TTTATATCATATTTTATATTTT
1 TTTATATCATA-TTTATATTTT
4888204 ATAATTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATATCATATTTATATTTT
Found at i:4888555 original size:13 final size:13
Alignment explanation
Indices: 4888537--4888570 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4888527 AAAATATAAT
4888537 AAAAAATTCATTA
1 AAAAAATTCATTA
* *
4888550 ACAAAATTTATTA
1 AAAAAATTCATTA
4888563 AAAAAATT
1 AAAAAATT
4888571 ATAATTTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATTCATTA
Found at i:4902985 original size:2 final size:2
Alignment explanation
Indices: 4902978--4903006 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4902968 TGAAATTGGG
4902978 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
4903007 ATTAAAGCGA
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:4906116 original size:23 final size:24
Alignment explanation
Indices: 4906041--4906116 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
4906031 AATCTGTTAA
* *
4906041 TAATAAAAATTTAATAATATAATT
1 TAATAAAAAATTAATATTATAATT
* *
4906065 TGAT--AAAATTAAAAATTTATAATT
1 TAATAAAAAATT-AATA-TTATAATT
4906089 T-ATAAAAAATTAATATTA-AATT
1 TAATAAAAAATTAATATTATAATT
4906111 TAATAA
1 TAATAA
4906117 TTTAAAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
22 10 0.24
23 12 0.29
24 14 0.33
25 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
TAATAAAAAATTAATATTATAATT
Found at i:4907248 original size:21 final size:24
Alignment explanation
Indices: 4907224--4907283 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
4907214 ATTTTAAAAA
*
4907224 TAAATATAATA-ATTCATT-TA-T
1 TAAATATAATATATTAATTATATT
*
4907245 TAAATATATTATATTAATTATATT
1 TAAATATAATATATTAATTATATT
4907269 TAAATATATATATAT
1 TAAATATA-ATATAT
4907284 ATATAACTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 10 0.31
22 6 0.19
23 2 0.06
24 9 0.28
25 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATATAATATATTAATTATATT
Found at i:4907263 original size:26 final size:25
Alignment explanation
Indices: 4907204--4907283 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 25
4907194 AAATTATTAA
* * *
4907204 ATATATTAA-AAT-TTTAAAAATAA
1 ATATATTAATTATATTTAAATATAT
* *
4907227 ATATAATAATTCATTTATTAAATATAT
1 ATATATTAATT-ATAT-TTAAATATAT
4907254 -TATATTAATTATATTTAAATATAT
1 ATATATTAATTATATTTAAATATAT
4907278 ATATAT
1 ATATAT
4907284 ATATAACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 8 0.17
24 10 0.22
25 10 0.22
26 10 0.22
27 8 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATATTAATTATATTTAAATATAT
Found at i:4907559 original size:6 final size:6
Alignment explanation
Indices: 4907548--4907594 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
4907538 TGTAATTAGA
*
4907548 AAATTT AAATTT AAATTT -AATTT -AATTT -AATTT AATAATT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AA-ATTT AAATTT
4907594 A
1 A
4907595 TTATTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 15 0.41
6 17 0.46
7 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:4907592 original size:5 final size:5
Alignment explanation
Indices: 4907549--4907583 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
4907539 GTAATTAGAA
4907549 AATTT AAATTT AAATTT AATTT AATTT AATTT AAT
1 AATTT -AATTT -AATTT AATTT AATTT AATTT AAT
4907584 AATTAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
AATTT
Found at i:4907627 original size:8 final size:10
Alignment explanation
Indices: 4907596--4907658 Score: 63
Period size: 10 Copynumber: 6.0 Consensus size: 10
4907586 TTAAATTTAT
4907596 TATTTAAAATA
1 TATTT-AAATA
4907607 TATTTAAATA
1 TATTTAAATA
4907617 TATTTAAATA
1 TATTTAAATA
* * *
4907627 TTTTTATATTT
1 TATTTA-AATA
*
4907638 TATTATAATTA
1 TATT-TAAATA
4907649 TATTTAAATA
1 TATTTAAATA
4907659 AAAATATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 25 0.57
11 17 0.39
12 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATTTAAATA
Found at i:4907635 original size:18 final size:19
Alignment explanation
Indices: 4907591--4907639 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
4907581 AATAATTAAA
4907591 TTTAT-TATTTAAAATATAT
1 TTTATATATTT-AAATATAT
*
4907610 TTAAATATATTTAAATAT-T
1 TT-TATATATTTAAATATAT
4907629 TTTATAT-TTTA
1 TTTATATATTTA
4907640 TTATAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 4 0.15
18 4 0.15
19 5 0.19
20 8 0.31
21 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATATTTAAATATAT
Found at i:4907636 original size:16 final size:16
Alignment explanation
Indices: 4907615--4907658 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
4907605 TATATTTAAA
**
4907615 TATATTTAAATATTTT
1 TATATTTAAATATAAT
* *
4907631 TATATTTTATTATAAT
1 TATATTTAAATATAAT
4907647 TATATTTAAATA
1 TATATTTAAATA
4907659 AAAATATTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTTAAATATAAT
Found at i:4907883 original size:28 final size:30
Alignment explanation
Indices: 4907852--4907916 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
4907842 TTTGTAATTT
* *
4907852 TTATATA-ATTTATA-TTTATTTAATTTAA
1 TTATATATATTTATATTTTATTTAAATAAA
4907880 TTAT-TATATTTATATTTTATTTAAATAAA
1 TTATATATATTTATATTTTATTTAAATAAA
4907909 TTATATAT
1 TTATATAT
4907917 TAAATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.06
28 11 0.34
29 16 0.50
30 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTATATATATTTATATTTTATTTAAATAAA
Found at i:4908895 original size:20 final size:20
Alignment explanation
Indices: 4908780--4908897 Score: 68
Period size: 20 Copynumber: 5.8 Consensus size: 20
4908770 TATTAGATAT
* *
4908780 AATATAAATATAA-AATTTA
1 AATATAATTATAATATTTTA
*
4908799 AATATAA-TATAATA--TAA
1 AATATAATTATAATATTTTA
* * *
4908816 AATTATAA-AATAATATATAA
1 AA-TATAATTATAATATTTTA
4908836 AATA-AATTATTAATATTTTA
1 AATATAATTA-TAATATTTTA
4908856 AATTTTTATAAATATATAATATTTTA
1 AA----TAT-AAT-TATAATATTTTA
4908882 AATATAATTATAATAT
1 AATATAATTATAATAT
4908898 AAATATAATA
Statistics
Matches: 81, Mismatches: 5, Indels: 25
0.73 0.05 0.23
Matches are distributed among these distances:
17 4 0.05
18 18 0.22
19 11 0.14
20 23 0.28
21 3 0.04
22 3 0.04
24 2 0.02
26 15 0.19
27 2 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATATAATTATAATATTTTA
Found at i:4908898 original size:11 final size:11
Alignment explanation
Indices: 4908777--4908907 Score: 54
Period size: 11 Copynumber: 12.6 Consensus size: 11
4908767 TAATATTAGA
*
4908777 TATAATATAAA
1 TATAATATAAT
*
4908788 TATAA-A-ATT
1 TATAATATAAT
4908797 TA-AATATAA-
1 TATAATATAAT
4908806 TATAATATAAAAT
1 TATAATAT--AAT
*
4908819 TATAAAATAAT
1 TATAATATAAT
*
4908830 ATATAAAATAAAT
1 -TATAATAT-AAT
4908843 TATTAATAT--T
1 TA-TAATATAAT
**
4908853 T-TAA-ATTTT
1 TATAATATAAT
4908862 TATAA-AT-A-
1 TATAATATAAT
*
4908870 TATAATAT-TT
1 TATAATATAAT
4908880 TA-AATATAAT
1 TATAATATAAT
*
4908890 TATAATATAAA
1 TATAATATAAT
4908901 TATAATA
1 TATAATA
4908908 AACTTATTGT
Statistics
Matches: 95, Mismatches: 9, Indels: 32
0.70 0.07 0.24
Matches are distributed among these distances:
7 2 0.02
8 10 0.11
9 15 0.16
10 19 0.20
11 22 0.23
12 12 0.13
13 15 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATAATATAAT
Found at i:4908901 original size:43 final size:42
Alignment explanation
Indices: 4908782--4908909 Score: 112
Period size: 46 Copynumber: 3.1 Consensus size: 42
4908772 TTAGATATAA
4908782 TATAAATATA-AA-A-TTTAAATATAA-TATAATATAAA-AT
1 TATAAATATATAATATTTTAAATATAATTATAATATAAATAT
* * *
4908819 TAT-AA-A-ATAATATATAAAATA-AATTATTAATATTTTAAATTTT
1 TATAAATATATAATATTTTAAATATAATTA-TAATA---TAAA-TAT
4908862 TATAAATATATAATATTTTAAATATAATTATAATATAAATAT
1 TATAAATATATAATATTTTAAATATAATTATAATATAAATAT
*
4908904 AATAAA
1 TATAAA
4908910 CTTATTGTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
34 1 0.01
35 3 0.04
36 5 0.07
37 11 0.16
38 5 0.07
41 4 0.06
42 7 0.10
43 8 0.11
44 2 0.03
45 1 0.01
46 18 0.26
47 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (42 bp):
TATAAATATATAATATTTTAAATATAATTATAATATAAATAT
Found at i:4908902 original size:26 final size:26
Alignment explanation
Indices: 4908837--4908903 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
4908827 AATATATAAA
*
4908837 ATAAAT-TATTAATATTTTAAATTTTT
1 ATAAATATA-TAATATTTTAAATTATT
4908863 ATAAATATATAATATTTTAAATATAATT
1 ATAAATATATAATATTTTAAAT-T-ATT
4908891 AT-AATATA-AATAT
1 ATAAATATATAATAT
4908904 AATAAACTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 24 0.65
27 9 0.24
28 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAAATATATAATATTTTAAATTATT
Found at i:4909548 original size:6 final size:6
Alignment explanation
Indices: 4909531--4909596 Score: 59
Period size: 6 Copynumber: 11.0 Consensus size: 6
4909521 ATATTTTTGA
*
4909531 TATATAT TATATT TATATT TAAAATT T-TATT T-TATT TAATAATT T-TA-T
1 TATAT-T TATATT TATATT T-ATATT TATATT TATATT T-AT-ATT TATATT
4909579 TATATT TATATT TATATT
1 TATATT TATATT TATATT
4909597 ATTAATAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
4 2 0.04
5 12 0.24
6 22 0.43
7 11 0.22
8 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:4909561 original size:18 final size:19
Alignment explanation
Indices: 4909540--4909586 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
4909530 ATATATATTA
4909540 TATTTATATTTAA-AATTT
1 TATTTATATTTAATAATTT
4909558 TATTT-TATTTAATAATTT
1 TATTTATATTTAATAATTT
4909576 TA-TTATATTTA
1 TATTTATATTTA
4909587 TATTTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTATATTTAATAATTT
Found at i:4910676 original size:18 final size:18
Alignment explanation
Indices: 4910636--4910687 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
4910626 AAACTTTACA
*
4910636 ATAATAGTTAAAAAATAT
1 ATAAAAGTTAAAAAATAT
* **
4910654 GTAAAAGTTAAAACTTAT
1 ATAAAAGTTAAAAAATAT
* *
4910672 ATAAAAATTTAAAAAT
1 ATAAAAGTTAAAAAAT
4910688 CACATCTACC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (18 bp):
ATAAAAGTTAAAAAATAT
Found at i:4910894 original size:9 final size:9
Alignment explanation
Indices: 4910880--4910957 Score: 54
Period size: 9 Copynumber: 8.8 Consensus size: 9
4910870 TAAAAATTGT
4910880 ATTTTTAAA
1 ATTTTTAAA
**
4910889 ATTTTTTTA
1 ATTTTTAAA
* *
4910898 ATCATTTGAA
1 AT-TTTTAAA
4910908 ATTTTT--A
1 ATTTTTAAA
*
4910915 ATTTTTTAA
1 ATTTTTAAA
4910924 ATTTTT-AA
1 ATTTTTAAA
4910932 ATTTTTAAA
1 ATTTTTAAA
* *
4910941 AATTTTATGA
1 ATTTTTA-AA
4910951 ATTTTTA
1 ATTTTTA
4910958 TTATTTTACA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
7 7 0.13
8 8 0.15
9 27 0.49
10 13 0.24
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:4910922 original size:8 final size:8
Alignment explanation
Indices: 4910906--4910940 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
4910896 TAATCATTTG
4910906 AAATTTTT
1 AAATTTTT
*
4910914 AATTTTTT
1 AAATTTTT
4910922 AAATTTTT
1 AAATTTTT
4910930 AAATTTTT
1 AAATTTTT
4910938 AAA
1 AAA
4910941 AATTTTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AAATTTTT
Found at i:4910925 original size:16 final size:16
Alignment explanation
Indices: 4910892--4910940 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
4910882 TTTTAAAATT
* *
4910892 TTTTTAATCATTTGAAA
1 TTTTTAAT-TTTTTAAA
4910909 TTTTTAATTTTTTAAA
1 TTTTTAATTTTTTAAA
*
4910925 TTTTTAAATTTTTAAA
1 TTTTTAATTTTTTAAA
4910941 AATTTTATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTTAATTTTTTAAA
Found at i:4911452 original size:23 final size:22
Alignment explanation
Indices: 4911397--4911453 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
4911387 GATTAAATTA
*
4911397 AAAATTAA-AAATTTATTTTTT
1 AAAATTAATAAATTAATTTTTT
4911418 AATATATT-ATAAATTAATTTTTTT
1 AA-A-ATTAATAAATTAA-TTTTTT
4911442 AAAATTAATAAA
1 AAAATTAATAAA
4911454 ATTTAGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 2 0.07
22 5 0.17
23 15 0.50
24 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAATTAATAAATTAATTTTTT
Found at i:4911497 original size:8 final size:8
Alignment explanation
Indices: 4911486--4911553 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 8
4911476 AAAATTTTAA
4911486 TTTTAAAT
1 TTTTAAAT
4911494 TTTTAAAT
1 TTTTAAAT
4911502 TTTTAAAAAGT
1 TTTT--AAA-T
4911513 TTTTATAA-
1 TTTTA-AAT
**
4911521 TAATAAA-
1 TTTTAAAT
*
4911528 ATTTAAAT
1 TTTTAAAT
*
4911536 TTTTAATT
1 TTTTAAAT
4911544 TTTTAAAT
1 TTTTAAAT
4911552 TT
1 TT
4911554 ATATAAAAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
7 6 0.13
8 30 0.64
9 1 0.02
10 5 0.11
11 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (8 bp):
TTTTAAAT
Found at i:4911639 original size:21 final size:21
Alignment explanation
Indices: 4911600--4911641 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
4911590 ATTAAATTAT
*
4911600 TTAATATATTTAATATTAAAA
1 TTAATATAATTAATATTAAAA
*
4911621 TTAAT-TAATTAATATTTAAA
1 TTAATATAATTAATATTAAAA
4911641 T
1 T
4911642 GTTTTCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATATAATTAATATTAAAA
Found at i:4911880 original size:20 final size:21
Alignment explanation
Indices: 4911833--4911880 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
4911823 TTTTTACATT
*
4911833 ATATTTATATTTAAAATATTAT
1 ATATTTATATTT-AAATATTAA
4911855 ATATTTATATATT-AAT-TTAA
1 ATATTTATAT-TTAAATATTAA
4911875 ATATTT
1 ATATTT
4911881 TAATAATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 10 0.42
23 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTTATATTTAAATATTAA
Found at i:4911904 original size:32 final size:33
Alignment explanation
Indices: 4911862--4911929 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
4911852 TATATATTTA
* ** *
4911862 TATATTAATTTAAATATTTTAATA-ATTCATAT
1 TATATAAATTTAAATAAATTAACATATTCATAT
*
4911894 TATATAAATTTTAATAAATTAACATATTCATAT
1 TATATAAATTTAAATAAATTAACATATTCATAT
4911927 TAT
1 TAT
4911930 TTTTATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (33 bp):
TATATAAATTTAAATAAATTAACATATTCATAT
Found at i:4914112 original size:20 final size:19
Alignment explanation
Indices: 4914076--4914114 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4914066 AGTTTTTGTT
* *
4914076 GTAAAATTGATTATTTTAC
1 GTAAAAATGATAATTTTAC
4914095 GTAAAAATGATAACTTTTAC
1 GTAAAAATGATAA-TTTTAC
4914115 AAAAGGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (19 bp):
GTAAAAATGATAATTTTAC
Found at i:4914159 original size:17 final size:17
Alignment explanation
Indices: 4914137--4914171 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4914127 TATCACATTT
*
4914137 TTTATTTATTATATTAA
1 TTTATTAATTATATTAA
*
4914154 TTTATTAATTATTTTAA
1 TTTATTAATTATATTAA
4914171 T
1 T
4914172 AATCTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATTAATTATATTAA
Found at i:4915457 original size:21 final size:22
Alignment explanation
Indices: 4915431--4915471 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4915421 ACACACAAAA
* *
4915431 AACATATAATTAAAT-AAATTT
1 AACATAAAACTAAATCAAATTT
4915452 AACATAAAACTAAATCAAAT
1 AACATAAAACTAAATCAAAT
4915472 GCACGAGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (22 bp):
AACATAAAACTAAATCAAATTT
Found at i:4915967 original size:5 final size:5
Alignment explanation
Indices: 4915959--4916036 Score: 52
Period size: 5 Copynumber: 15.4 Consensus size: 5
4915949 TTTAATTTTA
* * * * * *
4915959 AATAT AATAT AAT-T -ATTT AACAT AATTAT AATAT AAAAT ATTAA AATAA
1 AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AATAT
*
4916008 AATAT AAAAT ATATAT AATATT AATAT AA
1 AATAT AATAT A-ATAT AATA-T AATAT AA
4916037 AAATATTTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 40 0.70
6 13 0.23
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:4916002 original size:24 final size:24
Alignment explanation
Indices: 4915961--4916065 Score: 62
Period size: 24 Copynumber: 4.5 Consensus size: 24
4915951 TAATTTTAAA
* *
4915961 TATAATATAATTATTTAACATAAT
1 TATAATATAAATATTTAAAATAAT
4915985 TATAATATAAA-ATATTAAAATAA-
1 TATAATATAAATAT-TTAAAATAAT
* * *
4916008 AAT-ATA-AAATATATATAAT-AT
1 TATAATATAAATATTTAAAATAAT
* *
4916029 TA-ATATAAAAATATTTTTAAATTAA-
1 TATA-ATATAAATA--TTTAAAATAAT
4916054 TATAATATAAAT
1 TATAATATAAAT
4916066 TATTAATATA
Statistics
Matches: 61, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
20 1 0.02
21 9 0.15
22 8 0.13
23 9 0.15
24 18 0.30
25 14 0.23
26 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
TATAATATAAATATTTAAAATAAT
Found at i:4916009 original size:13 final size:13
Alignment explanation
Indices: 4915991--4916043 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
4915981 TAATTATAAT
4915991 ATAAAATATTAAA
1 ATAAAATATTAAA
*
4916004 ATAAAATATAAAA
1 ATAAAATATTAAA
*
4916017 TATATATAATATTAAT
1 -ATA-A-AATATTAAA
4916033 ATAAAAATATT
1 AT-AAAATATT
4916044 TTTAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 12 0.36
14 9 0.27
15 4 0.12
16 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAAAATATTAAA
Found at i:4916014 original size:7 final size:7
Alignment explanation
Indices: 4915988--4916038 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
4915978 ACATAATTAT
4915988 AATATAA
1 AATATAA
*
4915995 AATATTA
1 AATATAA
4916002 AA-ATAA
1 AATATAA
4916008 AATATAA
1 AATATAA
4916015 AATATATA
1 AATATA-A
*
4916023 TAATAT-T
1 -AATATAA
4916030 AATATAA
1 AATATAA
4916037 AA
1 AA
4916039 ATATTTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
6 10 0.28
7 20 0.56
8 1 0.03
9 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
AATATAA
Found at i:4916033 original size:22 final size:21
Alignment explanation
Indices: 4915987--4916100 Score: 82
Period size: 20 Copynumber: 5.6 Consensus size: 21
4915977 AACATAATTA
*
4915987 TAATATAAAATATTAAAATA-
1 TAATATAAAATATTATAATAT
*
4916007 AAATATAAAATATATATAATAT
1 TAATATAAAATAT-TATAATAT
*
4916029 TAATATAAAAATATTTTTAA-AT
1 TAATAT-AAAATA-TTATAATAT
4916051 TAATAT--AATA-TA-AATTAT
1 TAATATAAAATATTATAA-TAT
*
4916069 TAATATATAAAAATT-T-ATAT
1 TAATATA-AAATATTATAATAT
*
4916089 AAATATAAAATA
1 TAATATAAAATA
4916101 ATTTGGTAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 23
0.71 0.08 0.22
Matches are distributed among these distances:
16 2 0.03
17 1 0.01
18 8 0.11
19 8 0.11
20 21 0.28
21 10 0.13
22 14 0.19
23 10 0.13
24 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATATAAAATATTATAATAT
Found at i:4916073 original size:40 final size:41
Alignment explanation
Indices: 4915989--4916102 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 41
4915979 CATAATTATA
* * *
4915989 ATATAAAATATTAAAATAAAATATAAAATATATATAATATTAAT
1 ATATAAAA-ATTTATAT-AAATATAATATA-ATATAATATTAAT
4916033 ATA-AAAATATTT-T-TAAAT-TAATATAATATAAATTATTAAT
1 ATATAAAA-ATTTATATAAATATAATATAATAT-AA-TATTAAT
*
4916073 ATATAAAAATTTATATAAATATAAAATAAT
1 ATATAAAAATTTATATAAATATAATATAAT
4916103 TTGGTAAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
38 4 0.07
39 8 0.13
40 18 0.30
41 6 0.10
42 5 0.08
43 16 0.27
44 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (41 bp):
ATATAAAAATTTATATAAATATAATATAATATAATATTAAT
Found at i:4916074 original size:13 final size:13
Alignment explanation
Indices: 4915987--4916091 Score: 70
Period size: 14 Copynumber: 7.7 Consensus size: 13
4915977 AACATAATTA
4915987 TAATATAAAATAT
1 TAATATAAAATAT
*
4916000 TAAAATAAAATAT
1 TAATATAAAATAT
*
4916013 AAAATATATATAATAT
1 -TAATATA-A-AATAT
4916029 TAATATAAAAATAT
1 TAATAT-AAAATAT
* *
4916043 T--TTTAAATTAAT
1 TAATATAAAAT-AT
*
4916055 ATAATATAAATTAT
1 -TAATATAAAATAT
*
4916069 TAATATATAAAAAT
1 TAATATA-AAATAT
*
4916083 TTATATAAA
1 TAATATAAA
4916092 TATAAAATAA
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
11 4 0.05
12 4 0.05
13 22 0.30
14 23 0.32
15 14 0.19
16 6 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATATAAAATAT
Found at i:4916086 original size:18 final size:17
Alignment explanation
Indices: 4916049--4916098 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
4916039 ATATTTTTAA
*
4916049 ATTAATATAATATAAATT
1 ATTAATAT-ATAAAAATT
4916067 ATTAATATATAAAAATTT
1 ATTAATATATAAAAA-TT
4916085 ATATAA-ATATAAAA
1 AT-TAATATATAAAA
4916099 TAATTTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 6 0.21
18 20 0.69
19 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAATATATAAAAATT
Found at i:4921894 original size:14 final size:15
Alignment explanation
Indices: 4921805--4921898 Score: 70
Period size: 14 Copynumber: 6.1 Consensus size: 15
4921795 ATACAATAAT
*
4921805 TTTTATTATA-TAAA
1 TTTTATTATATTATA
*
4921819 TTTTGATATATTTATATA
1 TTTT-AT-TATAT-TATA
*
4921837 TTTGTAGTATATTAATA
1 TTT-TATTATATT-ATA
*
4921854 TTTT-TTATATCATA
1 TTTTATTATATTATA
4921868 TTTTATT-TAATTAT-
1 TTTTATTAT-ATTATA
4921882 TTTTATTATATTATA
1 TTTTATTATATTATA
4921897 TT
1 TT
4921899 CATATTTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
14 24 0.38
15 16 0.25
16 5 0.08
17 10 0.16
18 7 0.11
19 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTTATTATATTATA
Found at i:4921898 original size:24 final size:22
Alignment explanation
Indices: 4921844--4921929 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 22
4921834 ATATTTGTAG
4921844 TATATTAATATTTTTTATATCATAT
1 TATATTAATA-TTTTTAT-T-ATAT
*
4921869 TTTATTTAATTATTTTTATTATAT
1 TATA-TTAA-TATTTTTATTATAT
*
4921893 TATATTCATATTTTATAATTATAT
1 TATATTAATATTTT-T-ATTATAT
* *
4921917 TATACTAAAATTT
1 TATATTAATATTT
4921930 AATAATATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 6 0.12
23 4 0.08
24 24 0.47
25 4 0.08
26 11 0.22
27 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTAATATTTTTATTATAT
Found at i:4921934 original size:24 final size:24
Alignment explanation
Indices: 4921886--4921935 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
4921876 AATTATTTTT
* * * *
4921886 ATTATATTATATTCATATTTTATA
1 ATTATATTATACTAAAATTTAATA
4921910 ATTATATTATACTAAAATTTAATA
1 ATTATATTATACTAAAATTTAATA
4921934 AT
1 AT
4921936 ATTACTGTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATATTATACTAAAATTTAATA
Found at i:4923379 original size:21 final size:20
Alignment explanation
Indices: 4923337--4923380 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4923327 TTTAAAATCA
* *
4923337 AAATTAAATTTTTATTTATT
1 AAATAAAATTTTAATTTATT
*
4923357 AAATAAAATTTTAAATTTTTT
1 AAATAAAATTTT-AATTTATT
4923378 AAA
1 AAA
4923381 ATTTATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATAAAATTTTAATTTATT
Found at i:4923864 original size:3 final size:3
Alignment explanation
Indices: 4923858--4923883 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4923848 CCACGGCCAC
4923858 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
4923884 ACACCACACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:4923939 original size:15 final size:15
Alignment explanation
Indices: 4923919--4923957 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4923909 GTCCCTTTCT
*
4923919 CTCCTCCTCGGCCTC
1 CTCCTCCTCGCCCTC
*
4923934 CTCCTCTTCGCCCTC
1 CTCCTCCTCGCCCTC
*
4923949 CTCCGCCTC
1 CTCCTCCTC
4923958 CCTCTCAGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.62, G:0.10, T:0.28
Consensus pattern (15 bp):
CTCCTCCTCGCCCTC
Found at i:4933467 original size:3 final size:3
Alignment explanation
Indices: 4933459--4933498 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4933449 AGCATTCACT
4933459 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
4933499 AATAATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:4934711 original size:23 final size:21
Alignment explanation
Indices: 4934654--4934711 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
4934644 ATTAATTTAT
4934654 ATATTT-ATTTTTAAAATATA
1 ATATTTAATTTTTAAAATATA
* *
4934674 ATATTTAATAATTTTAAATTTTA
1 ATATTTAAT--TTTTAAAATATA
4934697 ATATCTGTAATTTTT
1 ATAT-T-TAATTTTT
4934712 TTTATCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 6 0.19
21 2 0.06
23 18 0.58
24 1 0.03
25 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATTTAATTTTTAAAATATA
Found at i:4935252 original size:148 final size:145
Alignment explanation
Indices: 4935047--4935388 Score: 386
Period size: 148 Copynumber: 2.3 Consensus size: 145
4935037 TTCTTTTATG
* *
4935047 TTTTTCAATAAGAGATTCTATC-AAGTATTCTTTTTTTAATATGAAATTTTATATAATACTTACT
1 TTTTTCAATAAGAGATTCTATCTAA-T-TT-TTTTTTTAATGTGAGATTTTATATAATACTTACT
* * * *
4935111 TTAAAAATAATCAATAATTACGATATATATATACAAATTATCAAATTAATTATTAAAAATATTAA
63 TTAAAAATAATAAATAACTACGATATATATATACAAATCATCAAATCAATTATTAAAAATATTAA
4935176 AATCA-TTTTCTTTACTT-T
128 AAT-AGTTTTCTTT-CTTCT
* *
4935194 TTTTTCAATAAGAGATTCTATACTACATTTATATTTTTAATGTGAGATTTTATATAATACTTATT
1 TTTTTCAATAAGAGATTCTAT-CTA-ATTT-TTTTTTTAATGTGAGATTTTATATAATACTTACT
* * * * * *
4935259 TTAAAAATAGTAAATAACTATGATATGTATGTATAAATCATCAAATCAATTATTAAAGATATTAA
63 TTAAAAATAATAAATAACTACGATATATATATACAAATCATCAAATCAATTATTAAAAATATTAA
* *
4935324 CATAGTTTTCTTTGTTCT
128 AATAGTTTTCTTTCTTCT
* * *
4935342 TTTTTCAGTGAGCGATTCTATTCTAAATTTTTTTTTTAA-GTTGAGAT
1 TTTTTCAATAAGAGATTCTA-TCT-AATTTTTTTTTTAATG-TGAGAT
4935389 GCTCTATCAA
Statistics
Matches: 166, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
146 1 0.01
147 38 0.23
148 122 0.73
149 4 0.02
150 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.46
Consensus pattern (145 bp):
TTTTTCAATAAGAGATTCTATCTAATTTTTTTTTTAATGTGAGATTTTATATAATACTTACTTTA
AAAATAATAAATAACTACGATATATATATACAAATCATCAAATCAATTATTAAAAATATTAAAAT
AGTTTTCTTTCTTCT
Done.