Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 160 of 279
Found at i:52859556 original size:22 final size:24
Alignment explanation
Indices: 52859457--52859595 Score: 89
Period size: 22 Copynumber: 5.8 Consensus size: 24
52859447 ACGTATGTAT
*
52859457 ATATATAA-ATAATAATGGTATTAGAA
1 ATATATAACATAATAAT-ATA-TA-AA
* * *
52859483 ATATACAAAAT-ATAGTAT-TAGAA
1 ATATATAACATAATAATATATA-AA
52859506 ATATAT-ACATAA-AATAGTATAAAAA
1 ATATATAACATAATAATA-TAT--AAA
*
52859531 ATATATAAC-TAATGATAT-TAAA
1 ATATATAACATAATAATATATAAA
52859553 ATATAT-ACATAATAATATATAAA
1 ATATATAACATAATAATATATAAA
*
52859576 AAATATATACATAAT-ATATA
1 ATATATA-ACATAATAATATA
52859596 CATATTAGAA
Statistics
Matches: 92, Mismatches: 9, Indels: 26
0.72 0.07 0.20
Matches are distributed among these distances:
21 2 0.02
22 23 0.25
23 21 0.23
24 7 0.08
25 20 0.22
26 17 0.18
27 2 0.02
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (24 bp):
ATATATAACATAATAATATATAAA
Found at i:52859596 original size:11 final size:11
Alignment explanation
Indices: 52859564--52859599 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
52859554 TATATACATA
*
52859564 ATAATATATAA
1 ATAATATATAC
*
52859575 AAAATATATAC
1 ATAATATATAC
52859586 ATAATATATAC
1 ATAATATATAC
52859597 ATA
1 ATA
52859600 TTAGAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATATATAC
Found at i:52859663 original size:21 final size:20
Alignment explanation
Indices: 52859634--52859687 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
52859624 TAATACTACA
*
52859634 TAAATATATACATATATATAT
1 TAAACATATACATATATA-AT
*
52859655 TAAAGATATATACATATATAAT
1 T-AA-ACATATACATATATAAT
*
52859677 AAAACATATAC
1 TAAACATATAC
52859688 TAGCATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 3 0.10
22 4 0.14
23 15 0.52
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAACATATACATATATAAT
Found at i:52860111 original size:36 final size:36
Alignment explanation
Indices: 52860064--52860155 Score: 166
Period size: 36 Copynumber: 2.6 Consensus size: 36
52860054 CCGGGTCAAG
52860064 TAAAACGACGTCGTTTTGGGTTTAAAAGGCAGCCCC
1 TAAAACGACGTCGTTTTGGGTTTAAAAGGCAGCCCC
*
52860100 TAAAACGACGTCGTTTTGGGTTTAAAAGGCAGCCCT
1 TAAAACGACGTCGTTTTGGGTTTAAAAGGCAGCCCC
*
52860136 TAAAACGATGTCGTTTTGGG
1 TAAAACGACGTCGTTTTGGG
52860156 AGGCTATAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (36 bp):
TAAAACGACGTCGTTTTGGGTTTAAAAGGCAGCCCC
Found at i:52864500 original size:15 final size:16
Alignment explanation
Indices: 52864480--52864510 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
52864470 TTGACTACCG
52864480 CACAAATC-ATAATTT
1 CACAAATCAATAATTT
52864495 CACAAATCAATAATTT
1 CACAAATCAATAATTT
52864511 TTTTTCCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (16 bp):
CACAAATCAATAATTT
Found at i:52875005 original size:19 final size:19
Alignment explanation
Indices: 52874981--52875017 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52874971 GTTATAAATT
*
52874981 TAATTATGTTAAATTATAA
1 TAATTATATTAAATTATAA
*
52875000 TAATTATATTATATTATA
1 TAATTATATTAAATTATA
52875018 TTATGAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TAATTATATTAAATTATAA
Found at i:52880531 original size:23 final size:23
Alignment explanation
Indices: 52880481--52880525 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
52880471 ATTCCAACCT
* *
52880481 GTTCAAGCAATTTAACTTTTACA
1 GTTCAAACAATTTAACTTATACA
52880504 GTTCAAACAATTTAACTTATAC
1 GTTCAAACAATTTAACTTATAC
52880526 GTTTCATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (23 bp):
GTTCAAACAATTTAACTTATACA
Found at i:52886759 original size:9 final size:9
Alignment explanation
Indices: 52886747--52886773 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
52886737 ACTTTTTACT
52886747 TTTTTAAAA
1 TTTTTAAAA
52886756 TTTTTAAAA
1 TTTTTAAAA
52886765 TTTTTAAAA
1 TTTTTAAAA
52886774 ATTAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:52887589 original size:30 final size:30
Alignment explanation
Indices: 52887546--52887607 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
52887536 CTTAACAAGT
*
52887546 AAATGACTCTAAAATAATAATAAAAATAAC
1 AAATGACTCTAAAATAATAACAAAAATAAC
* * *
52887576 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGACTCTAAAATAATAACAAAAATAAC
52887606 AA
1 AA
52887608 GAAATAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.24
Consensus pattern (30 bp):
AAATGACTCTAAAATAATAACAAAAATAAC
Found at i:52889872 original size:26 final size:26
Alignment explanation
Indices: 52889849--52889899 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52889839 GTTTTTTTCT
52889849 AGAT-TATATATATTTTGA-ATTTTTA
1 AGATATATATATATTTT-ATATTTTTA
*
52889874 ATATATATATATATTTTATATTTTTA
1 AGATATATATATATTTTATATTTTTA
52889900 CATAGAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
AGATATATATATATTTTATATTTTTA
Found at i:52901561 original size:26 final size:26
Alignment explanation
Indices: 52901511--52901562 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
52901501 AAAAATGTAA
* *
52901511 TTTTATAATTTTTAAAATATTAAAAT
1 TTTTATAATTTTTAAAAGATCAAAAT
* *
52901537 TTTTATTATTTTTAAGAGATCAAAAT
1 TTTTATAATTTTTAAAAGATCAAAAT
52901563 ATAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (26 bp):
TTTTATAATTTTTAAAAGATCAAAAT
Found at i:52901599 original size:16 final size:16
Alignment explanation
Indices: 52901575--52901624 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
52901565 AAATTTATTA
*
52901575 TTATTAATTTAAAATT
1 TTATAAATTTAAAATT
**
52901591 TTATAAATTATAAAAAA
1 TTATAAATT-TAAAATT
52901608 TTA-AAA-TTAAAATT
1 TTATAAATTTAAAATT
52901622 TTA
1 TTA
52901625 CCGGTCATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 8 0.29
15 1 0.04
16 11 0.39
17 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTATAAATTTAAAATT
Found at i:52903357 original size:17 final size:17
Alignment explanation
Indices: 52903335--52903395 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
52903325 ACATTCTCTT
52903335 TTTCTTTTATTTTCATA
1 TTTCTTTTATTTTCATA
*
52903352 TTTCTTTTGTTTT--T-
1 TTTCTTTTATTTTCATA
*
52903366 TTCCTTTTATTTTCATA
1 TTTCTTTTATTTTCATA
52903383 TTTCTTTTATTTT
1 TTTCTTTTATTTT
52903396 ACTTTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
16 1 0.03
17 24 0.65
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTCTTTTATTTTCATA
Found at i:52903374 original size:31 final size:30
Alignment explanation
Indices: 52903333--52903408 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 30
52903323 ACACATTCTC
*
52903333 TTTTTCTTTTATTTTCATATTTCTTTTGTT
1 TTTTTCTTTTATTTTCATATTTCTTTTATT
52903363 TTTTTCCTTTTATTTTCATATTTCTTTTATT
1 TTTTT-CTTTTATTTTCATATTTCTTTTATT
*
52903394 TTACTT-TTTTATTTT
1 TT-TTTCTTTTATTTT
52903409 GTTCCTTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 14 0.33
31 26 0.62
32 2 0.05
ACGTcount: A:0.12, C:0.11, G:0.01, T:0.76
Consensus pattern (30 bp):
TTTTTCTTTTATTTTCATATTTCTTTTATT
Found at i:52903440 original size:9 final size:9
Alignment explanation
Indices: 52903426--52903502 Score: 66
Period size: 10 Copynumber: 8.2 Consensus size: 9
52903416 AATAAATTGT
52903426 TTTTTTTTA
1 TTTTTTTTA
52903435 TTTTTTTTTA
1 -TTTTTTTTA
*
52903445 CTTTTTTTGA
1 -TTTTTTTTA
52903455 TTTTTTTT-
1 TTTTTTTTA
* * *
52903463 CTTATTTCA
1 TTTTTTTTA
*
52903472 TTTTGTTTA
1 TTTTTTTTA
52903481 TTTTGTTTTA
1 TTTT-TTTTA
52903491 TTTTTTATTA
1 TTTTTT-TTA
52903501 TT
1 TT
52903503 AACTTTAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
8 5 0.09
9 18 0.34
10 30 0.57
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:52903557 original size:23 final size:22
Alignment explanation
Indices: 52903492--52903585 Score: 59
Period size: 22 Copynumber: 4.2 Consensus size: 22
52903482 TTTGTTTTAT
* **
52903492 TTTTTATTATTAACTTTAAAAA
1 TTTTTATAATTATTTTTAAAAA
* * *
52903514 -ATTTGTAATGTATATTT-AAAA
1 TTTTTATAAT-TATTTTTAAAAA
52903535 TGTTTTATAA-TATTTTTTAAAAA
1 T-TTTTATAATTA-TTTTTAAAAA
* *
52903558 TTTTAATTATTATTTTTAAAAA
1 TTTTTATAATTATTTTTAAAAA
52903580 TATTTT
1 T-TTTT
52903586 TTTTAACTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
21 12 0.22
22 26 0.48
23 16 0.30
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTTTATAATTATTTTTAAAAA
Found at i:52903676 original size:14 final size:14
Alignment explanation
Indices: 52903659--52903685 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52903649 TTTTTGAAAA
52903659 TTTTAAATATTAAT
1 TTTTAAATATTAAT
52903673 TTTTAAATATTAA
1 TTTTAAATATTAA
52903686 CCATATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAATATTAAT
Found at i:52903685 original size:37 final size:37
Alignment explanation
Indices: 52903605--52903685 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
52903595 TAGATATGTG
* * *
52903605 AAATTAATTTTTTATATATTTTAAAAATGTATTTTTC
1 AAATTAATTTTTGATAAATTTTAAAAATGTATTTTTA
*
52903642 AAATTAATTTTTGA-AAATTTTAAATAT-TAATTTTTA
1 AAATTAATTTTTGATAAATTTTAAAAATGT-ATTTTTA
52903678 AATATTAA
1 AA-ATTAA
52903686 CCATATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 1 0.03
36 19 0.50
37 18 0.47
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (37 bp):
AAATTAATTTTTGATAAATTTTAAAAATGTATTTTTA
Found at i:52903692 original size:23 final size:22
Alignment explanation
Indices: 52903644--52903685 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
52903634 TATTTTTCAA
*
52903644 ATTAATTTTTGAAAATTTTAAAT
1 ATTAATTTTT-AAAATATTAAAT
52903667 ATTAATTTTT-AAATATTAA
1 ATTAATTTTTAAAATATTAA
52903686 CCATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTAATTTTTAAAATATTAAAT
Found at i:52903880 original size:18 final size:19
Alignment explanation
Indices: 52903865--52903956 Score: 58
Period size: 18 Copynumber: 5.2 Consensus size: 19
52903855 TATTATTTTT
52903865 TTTTA-CTTTTTTATTTAA
1 TTTTATCTTTTTTATTTAA
*
52903883 TTTTATC-TTTTT-CTTAA
1 TTTTATCTTTTTTATTTAA
*
52903900 TTTT-T-TTCTTT-TTTAA
1 TTTTATCTTTTTTATTTAA
* *
52903916 GTTTTATATTATTTT-CTT-A
1 -TTTTATCTT-TTTTATTTAA
52903935 TTTTAT-TTTGTTTATTTAA
1 TTTTATCTTT-TTTATTTAA
52903954 TTT
1 TTT
52903957 ATATTATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
16 10 0.17
17 17 0.29
18 19 0.32
19 8 0.14
20 5 0.08
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTATCTTTTTTATTTAA
Found at i:52903931 original size:36 final size:36
Alignment explanation
Indices: 52903855--52903964 Score: 110
Period size: 36 Copynumber: 3.2 Consensus size: 36
52903845 CTACAACCAT
*
52903855 TATTATTTT-TT--TTTACTTT-TTTATTTAATTT-
1 TATTATTTTCTTAATTTATTTTCTTTATTTAATTTA
52903886 TATCT-TTTTCTTAATTT-TTTTCTTT-TTTAAGTTTTA
1 TAT-TATTTTCTTAATTTATTTTCTTTATTTAA--TTTA
* *
52903922 TATTATTTTCTTATTTTATTTTGTTTATTTAATTTA
1 TATTATTTTCTTAATTTATTTTCTTTATTTAATTTA
52903958 TATTATT
1 TATTATT
52903965 AATTTTAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
31 7 0.11
32 3 0.05
33 8 0.12
34 6 0.09
35 4 0.06
36 25 0.38
37 7 0.11
38 5 0.08
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.74
Consensus pattern (36 bp):
TATTATTTTCTTAATTTATTTTCTTTATTTAATTTA
Found at i:52904033 original size:147 final size:145
Alignment explanation
Indices: 52903953--52904263 Score: 536
Period size: 147 Copynumber: 2.1 Consensus size: 145
52903943 TGTTTATTTA
52903953 ATTTAT-ATTATTAATTTTAAAAAATTTGTAATGTATATTTAAAATGTTTTACAATTTTTTATAA
1 ATTTATCATTATTAATTTTAAAAAATTTGTAATGTATATTTAAAATGTTTTACAATTTTTTATAA
52904017 ATTTAAATTATTATTTTTAAAATTATTTTTTTAACTTTAGATATATATTTGTGAAATTATTTTTT
66 ATTTAAATTATTATTTTTAAAATTATTTTTTTAACTTT--ATATATATTTGTGAAATTATTTTTT
52904082 TATAAATTTAAATATAT
129 TATAAATTTAAATATAT
* *
52904099 ATTTTTCCTTATTAATTTTAAAAAATTTGTAATGTATATTTAAAATGTTTTACAATTTTTTATAA
1 ATTTATCATTATTAATTTTAAAAAATTTGTAATGTATATTTAAAATGTTTTACAATTTTTTATAA
52904164 ATTTAAATTATTATTTTTAAAATTATTTTTTTAACTTTAGATATATATTTGTGAAATTATTTTTT
66 ATTTAAATTATTATTTTTAAAATTATTTTTTTAACTTT--ATATATATTTGTGAAATTATTTTTT
52904229 TATAAATTTAAATATAT
129 TATAAATTTAAATATAT
* *
52904246 ATTTTTCA-AATTAATTTT
1 ATTTATCATTATTAATTTT
52904264 GAAATTATTA
Statistics
Matches: 160, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
146 14 0.09
147 146 0.91
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (145 bp):
ATTTATCATTATTAATTTTAAAAAATTTGTAATGTATATTTAAAATGTTTTACAATTTTTTATAA
ATTTAAATTATTATTTTTAAAATTATTTTTTTAACTTTATATATATTTGTGAAATTATTTTTTTA
TAAATTTAAATATAT
Found at i:52904041 original size:15 final size:14
Alignment explanation
Indices: 52904021--52904050 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
52904011 TTATAAATTT
52904021 AAATTATTATTTTTA
1 AAATTATT-TTTTTA
52904036 AAATTATTTTTTTA
1 AAATTATTTTTTTA
52904050 A
1 A
52904051 CTTTAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AAATTATTTTTTTA
Found at i:52904093 original size:70 final size:70
Alignment explanation
Indices: 52904007--52904263 Score: 263
Period size: 70 Copynumber: 3.6 Consensus size: 70
52903997 TGTTTTACAA
52904007 TTTTTTATAAATTTAAAT-TATTATTTTTAAAATTATTTTTTTAACTTTAGATATATATTTGTGA
1 TTTTTTATAAATTTAAATATA-TATTTTTAAAATTATTTTTTTAACTTTAGATATATATTTGTGA
52904071 AATTAT
65 AATTAT
*** *** * *
52904077 TTTTTTATAAATTTAAATATATATTTTTCCTTATTAATTTTAAAAAATTT-G-TAATGTATATT-
1 TTTTTTATAAATTTAAATATATATTTTT-AAAATT-ATTTTTTTAACTTTAGAT-ATATAT-TTG
* *
52904139 TAAAATGTTTTACAA
62 TGAAA----TT--AT
52904154 TTTTTTATAAATTTAAAT-TATTATTTTTAAAATTATTTTTTTAACTTTAGATATATATTTGTGA
1 TTTTTTATAAATTTAAATATA-TATTTTTAAAATTATTTTTTTAACTTTAGATATATATTTGTGA
52904218 AATTAT
65 AATTAT
* *
52904224 TTTTTTATAAATTTAAATATATATTTTTCAAATTAATTTT
1 TTTTTTATAAATTTAAATATATATTTTTAAAATTATTTTT
52904264 GAAATTATTA
Statistics
Matches: 149, Mismatches: 22, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
70 62 0.42
71 17 0.11
72 14 0.09
75 14 0.09
76 15 0.10
77 27 0.18
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (70 bp):
TTTTTTATAAATTTAAATATATATTTTTAAAATTATTTTTTTAACTTTAGATATATATTTGTGAA
ATTAT
Found at i:52904188 original size:15 final size:14
Alignment explanation
Indices: 52904168--52904197 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
52904158 TTATAAATTT
52904168 AAATTATTATTTTTA
1 AAATTATT-TTTTTA
52904183 AAATTATTTTTTTA
1 AAATTATTTTTTTA
52904197 A
1 A
52904198 CTTTAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AAATTATTTTTTTA
Found at i:52904229 original size:36 final size:36
Alignment explanation
Indices: 52904005--52904263 Score: 176
Period size: 36 Copynumber: 7.2 Consensus size: 36
52903995 AATGTTTTAC
* *
52904005 AATTTTTTATAAATTTAAAT-TATTATTTTTAAAATT
1 AATTTTTTATAAATTTAAATATA-TATTTGTCAAATT
* * *
52904041 -ATTTTTT-TAACTTTAGATATATATTTGTGAAATT
1 AATTTTTTATAAATTTAAATATATATTTGTCAAATT
* * **
52904075 ATTTTTTTATAAATTTAAATATATATTTTTCCTTATT
1 AATTTTTTATAAATTTAAATATATATTTGT-CAAATT
* * * * *
52904112 AA-TTTTAAAAAATTTGTAATGTATA-TT-TAAAATGTTTT
1 AATTTTTTATAAATTT-AAATATATATTTGTCAAA----TT
* *
52904150 ACAATTTTTTATAAATTTAAAT-TATTATTTTTAAAATT
1 --AATTTTTTATAAATTTAAATATA-TATTTGTCAAATT
* * *
52904188 -ATTTTTT-TAACTTTAGATATATATTTGTGAAATT
1 AATTTTTTATAAATTTAAATATATATTTGTCAAATT
* *
52904222 ATTTTTTTATAAATTTAAATATATATTTTTCAAATT
1 AATTTTTTATAAATTTAAATATATATTTGTCAAATT
52904258 AATTTT
1 AATTTT
52904264 GAAATTATTA
Statistics
Matches: 173, Mismatches: 32, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
34 41 0.24
35 31 0.18
36 59 0.34
37 11 0.06
38 4 0.02
39 2 0.01
40 7 0.04
41 13 0.08
42 5 0.03
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.57
Consensus pattern (36 bp):
AATTTTTTATAAATTTAAATATATATTTGTCAAATT
Found at i:52904344 original size:147 final size:146
Alignment explanation
Indices: 52903962--52904344 Score: 468
Period size: 147 Copynumber: 2.6 Consensus size: 146
52903952 AATTTATATT
* * *
52903962 ATTAATTTTAAAAAATTTGTAATGTATATTTAAAATGTTTTACAATTTTTTATAAATTTAAATTA
1 ATTAATTTTAAAAAATTAGTAATATATATTTAAAATGTTTTACAATATTTTATAAATTTAAATTA
** *
52904027 TTATTTTTAAAATTATTTTTTTAACTTTAGATATATATTTGTGAAATTATTTTTTTATAAATTTA
66 CAATTTTTAAAATTA-TTGTTTAACTTTAGATATATATTTGTGAAATTATTTTTTTATAAATTTA
**
52904092 AATATATATTTTTCCTT
130 AATATATATTTTTCCAA
* * *
52904109 ATTAATTTTAAAAAATTTGTAATGTATATTTAAAATGTTTTACAATTTTTTATAAATTTAAATTA
1 ATTAATTTTAAAAAATTAGTAATATATATTTAAAATGTTTTACAATATTTTATAAATTTAAATTA
** *
52904174 TTATTTTTAAAATTATTTTTTTAACTTTAGATATATATTTGTGAAATTATTTTTTTATAAATTTA
66 CAATTTTTAAAATTA-TTGTTTAACTTTAGATATATATTTGTGAAATTATTTTTTTATAAATTTA
52904239 AATATATATTTTT-CAA
130 AATATATATTTTTCCAA
** ** * * *
52904255 ATTAATTTTGAAATTATTAGTTTTATAATATTTGAAATGTATGTT-TAATATTTTATTAATTTTA
1 ATTAATTTT-AAAAAATTAGTAATAT-ATATTTAAAATGT-T-TTACAATATTTTA-TAAATTTA
* *
52904319 CA-TACAATTTTTTAAATTA-TGTTTAA
61 AATTACAATTTTTAAAATTATTGTTTAA
52904345 AATTTACTTT
Statistics
Matches: 214, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
146 10 0.05
147 159 0.74
148 12 0.06
149 23 0.11
150 10 0.05
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (146 bp):
ATTAATTTTAAAAAATTAGTAATATATATTTAAAATGTTTTACAATATTTTATAAATTTAAATTA
CAATTTTTAAAATTATTGTTTAACTTTAGATATATATTTGTGAAATTATTTTTTTATAAATTTAA
ATATATATTTTTCCAA
Found at i:52904356 original size:18 final size:19
Alignment explanation
Indices: 52904335--52904373 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
52904325 ATTTTTTAAA
52904335 TTATG-TTTAAAATTTACT
1 TTATGTTTTAAAATTTACT
52904353 TTATGTTTTTAAAATTTACT
1 TTATG-TTTTAAAATTTACT
52904373 T
1 T
52904374 CAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
20 14 0.74
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATGTTTTAAAATTTACT
Found at i:52904401 original size:7 final size:8
Alignment explanation
Indices: 52904375--52904400 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
52904365 AATTTACTTC
52904375 AAATAAAA
1 AAATAAAA
52904383 AAATAAAA
1 AAATAAAA
52904391 AAATAAAA
1 AAATAAAA
52904399 AA
1 AA
52904401 TCCTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:52904525 original size:37 final size:36
Alignment explanation
Indices: 52904478--52904588 Score: 129
Period size: 34 Copynumber: 3.1 Consensus size: 36
52904468 TAATAATTTC
* *
52904478 AAAACTAATTTGAAAAATATATATTTAAAATTTATAA
1 AAAAATAATTTCAAAAATATATATTT-AAATTTATAA
* * *
52904515 AAAAATAATTTCACAAATATATATCTAAA-GT-TAA
1 AAAAATAATTTCAAAAATATATATTTAAATTTATAA
*
52904549 AAAAATAATTTTAAAAATA-ATAATTTAAATTTATAA
1 AAAAATAATTTCAAAAATATAT-ATTTAAATTTATAA
52904585 AAAA
1 AAAA
52904589 TTGTAAAACA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
33 2 0.03
34 26 0.42
35 2 0.03
36 10 0.16
37 22 0.35
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (36 bp):
AAAAATAATTTCAAAAATATATATTTAAATTTATAA
Found at i:52904564 original size:14 final size:15
Alignment explanation
Indices: 52904545--52904574 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52904535 ATATCTAAAG
52904545 TTAAAAA-AATAATT
1 TTAAAAATAATAATT
52904559 TTAAAAATAATAATT
1 TTAAAAATAATAATT
52904574 T
1 T
52904575 AAATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAATAATAATT
Found at i:52904848 original size:20 final size:20
Alignment explanation
Indices: 52904820--52904866 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
52904810 CCAACTTTTT
52904820 AAAAA-TTAAAAA-AAATTTA
1 AAAAATTTAAAAAGAAA-TTA
52904839 AAAAATTTAAAAAGAAATTA
1 AAAAATTTAAAAAGAAATTA
52904859 AAGAAATT
1 AA-AAATT
52904867 GTATTTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 8 0.32
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (20 bp):
AAAAATTTAAAAAGAAATTA
Found at i:52904859 original size:11 final size:10
Alignment explanation
Indices: 52904820--52904860 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
52904810 CCAACTTTTT
52904820 AAAAATTAAA
1 AAAAATTAAA
*
52904830 AAAAATTTAA
1 AAAAATTAAA
*
52904840 AAAATTTAAA
1 AAAAATTAAA
52904850 AAGAAATTAAA
1 AA-AAATTAAA
52904861 GAAATTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:52904938 original size:23 final size:25
Alignment explanation
Indices: 52904911--52904969 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 25
52904901 TATTATTAAA
52904911 AATATGATAAATA-TTT-AAAAATT
1 AATATGATAAATATTTTCAAAAATT
*
52904934 AATAT-TTAAA-ATTTTCAAAAATT
1 AATATGATAAATATTTTCAAAAATT
* *
52904957 AATTTGAAAAATA
1 AATATGATAAATA
52904970 CATTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 1 0.04
22 7 0.25
23 16 0.57
24 3 0.11
25 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (25 bp):
AATATGATAAATATTTTCAAAAATT
Found at i:52904968 original size:36 final size:36
Alignment explanation
Indices: 52904923--52905062 Score: 103
Period size: 37 Copynumber: 3.9 Consensus size: 36
52904913 TATGATAAAT
* *
52904923 ATTTAAAAATTA-ATATTTAAAAT-TTTCAAAAATTA
1 ATTTAAAAA-TACATATTTAAAATATATAAAAAATTA
*
52904958 ATTTGAAAAATACATTTTTAAAATATATAAAAAATTA
1 ATTT-AAAAATACATATTTAAAATATATAAAAAATTA
* * * *
52904995 ATTTCACAAATATATATCTAAAGT-TA-AAAAAA-TA
1 ATTT-AAAAATACATATTTAAAATATATAAAAAATTA
* * * *
52905029 TTTTTAAAAATA-ATAATTAAAATTTAAAAAAAAT
1 -ATTTAAAAATACATATTTAAAATATATAAAAAAT
52905063 ATTATAAAAC
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
33 8 0.10
34 10 0.12
35 21 0.25
36 17 0.20
37 28 0.33
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (36 bp):
ATTTAAAAATACATATTTAAAATATATAAAAAATTA
Found at i:52905127 original size:10 final size:9
Alignment explanation
Indices: 52905106--52905176 Score: 56
Period size: 9 Copynumber: 7.9 Consensus size: 9
52905096 TTTTAAAGTT
52905106 AATAATAAAA
1 AATAA-AAAA
52905116 AATAAAACAA
1 AATAAAA-AA
52905126 AATAAAAAA
1 AATAAAAAA
* *
52905135 AAT-GAAAT
1 AATAAAAAA
*
52905143 AAGAAAAAA
1 AATAAAAAA
*
52905152 AAT-CAAAA
1 AATAAAAAA
**
52905160 AGGAAAAAA
1 AATAAAAAA
52905169 AATAAAAA
1 AATAAAAA
52905177 GACAATTTAT
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
8 10 0.22
9 22 0.48
10 14 0.30
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (9 bp):
AATAAAAAA
Found at i:52905175 original size:16 final size:17
Alignment explanation
Indices: 52905129--52905177 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
52905119 AAAACAAAAT
*
52905129 AAAAAAAATGAAATAA-G
1 AAAAAAAATCAAA-AAGG
52905146 AAAAAAAATCAAAAAGG
1 AAAAAAAATCAAAAAGG
52905163 AAAAAAAAT-AAAAAG
1 AAAAAAAATCAAAAAG
52905178 ACAATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 8 0.27
17 22 0.73
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (17 bp):
AAAAAAAATCAAAAAGG
Found at i:52905220 original size:21 final size:20
Alignment explanation
Indices: 52905195--52905245 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
52905185 ATTAAGGAAC
52905195 AAAATAAAAAAGTAAAA-AAA
1 AAAATAAAAAA-TAAAAGAAA
52905215 AGAAATAAGAAAATAAAAGAAA
1 A-AAATAA-AAAATAAAAGAAA
*
52905237 AAAACAAAA
1 AAAATAAAA
52905246 GAAATATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 16 0.59
22 8 0.30
ACGTcount: A:0.82, C:0.02, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAATAAAAAATAAAAGAAA
Found at i:52905232 original size:17 final size:16
Alignment explanation
Indices: 52905201--52905270 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 16
52905191 GAACAAAATA
52905201 AAAAAGTAAAA-AAAAG
1 AAAAAG-AAAATAAAAG
52905217 AAATAAGAAAATAAAAG
1 AAA-AAGAAAATAAAAG
*
52905234 --AAA-AAAACAAAAG
1 AAAAAGAAAATAAAAG
*
52905247 AAATATGAAAATAAAAG
1 AAA-AAGAAAATAAAAG
52905264 AAAAAGA
1 AAAAAGA
52905271 GAATGTGTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
13 9 0.20
14 2 0.05
15 2 0.05
16 11 0.25
17 20 0.45
ACGTcount: A:0.79, C:0.01, G:0.11, T:0.09
Consensus pattern (16 bp):
AAAAAGAAAATAAAAG
Found at i:52905248 original size:30 final size:29
Alignment explanation
Indices: 52905195--52905268 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 29
52905185 ATTAAGGAAC
*
52905195 AAAATAAAA-AAGTAAAAAAAAGAAATAAG
1 AAAATAAAAGAA-AAAAAAAAAGAAATAAG
*
52905224 AAAATAAAAGAAAAAAACAAAAGAAATATG
1 AAAATAAAAGAAAAAAA-AAAAGAAATAAG
52905254 AAAATAAAAGAAAAA
1 AAAATAAAAGAAAAA
52905269 GAGAATGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 13 0.32
30 28 0.68
ACGTcount: A:0.80, C:0.01, G:0.09, T:0.09
Consensus pattern (29 bp):
AAAATAAAAGAAAAAAAAAAAGAAATAAG
Found at i:52914627 original size:11 final size:11
Alignment explanation
Indices: 52914613--52914680 Score: 55
Period size: 11 Copynumber: 6.2 Consensus size: 11
52914603 TTTTTTACTG
52914613 TTTTGTTATTA
1 TTTTGTTATTA
*
52914624 TTTTCTTATTA
1 TTTTGTTATTA
* **
52914635 TTTTGCTACAA
1 TTTTGTTATTA
** *
52914646 TTTTACTAATA
1 TTTTGTTATTA
* *
52914657 TGTTGTTACTA
1 TTTTGTTATTA
52914668 TTTTGTTATTA
1 TTTTGTTATTA
52914679 TT
1 TT
52914681 GTTTGAATAT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:52914638 original size:22 final size:22
Alignment explanation
Indices: 52914613--52914680 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
52914603 TTTTTTACTG
*
52914613 TTTTGTTATTATTTTCTTATTA
1 TTTTGTTACTATTTTCTTATTA
* * *
52914635 TTTTGCTACAATTTTAC-TAATA
1 TTTTGTTACTATTTT-CTTATTA
* *
52914657 TGTTGTTACTATTTTGTTATTA
1 TTTTGTTACTATTTTCTTATTA
52914679 TT
1 TT
52914681 GTTTGAATAT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTTGTTACTATTTTCTTATTA
Found at i:52928217 original size:18 final size:18
Alignment explanation
Indices: 52928196--52928235 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52928186 GAAATATTTA
*
52928196 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
52928214 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
52928232 TTTT
1 TTTT
52928236 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:52928317 original size:31 final size:31
Alignment explanation
Indices: 52928279--52928347 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
52928269 ACGGGCAGGT
** *
52928279 CAGGTCGGACTCGGATTTTAGCATTTTTATC
1 CAGGTCGGACTCAAAATTTAGCATTTTTATC
52928310 CAGGTCGGACTCAAAATTTAGCATTTTTATC
1 CAGGTCGGACTCAAAATTTAGCATTTTTATC
*
52928341 CGGGTCG
1 CAGGTCG
52928348 AGTTTAGGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (31 bp):
CAGGTCGGACTCAAAATTTAGCATTTTTATC
Found at i:52928496 original size:24 final size:24
Alignment explanation
Indices: 52928465--52928512 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
52928455 GCAGCATATC
52928465 TCATCATATAATTGCAAAAAGAAA
1 TCATCATATAATTGCAAAAAGAAA
52928489 TCATCATATAATTGCAAAAAGAAA
1 TCATCATATAATTGCAAAAAGAAA
52928513 GATAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.25
Consensus pattern (24 bp):
TCATCATATAATTGCAAAAAGAAA
Found at i:52928808 original size:9 final size:9
Alignment explanation
Indices: 52928794--52928897 Score: 147
Period size: 9 Copynumber: 11.6 Consensus size: 9
52928784 ACAAGTATAA
52928794 AATTAACCG
1 AATTAACCG
52928803 AATTAACCG
1 AATTAACCG
*
52928812 AATTAATCG
1 AATTAACCG
52928821 AATTAACCG
1 AATTAACCG
52928830 AATT-ACCTG
1 AATTAACC-G
*
52928839 AATTAATCG
1 AATTAACCG
52928848 AATTAACCG
1 AATTAACCG
*
52928857 AATTACCCG
1 AATTAACCG
* *
52928866 AATTACCCA
1 AATTAACCG
52928875 AATTAACCG
1 AATTAACCG
52928884 AATTAACCG
1 AATTAACCG
52928893 AATTA
1 AATTA
52928898 TTTTTATAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
8 3 0.04
9 80 0.94
10 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:52928927 original size:6 final size:6
Alignment explanation
Indices: 52928916--52928950 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
52928906 AAATTATATG
52928916 TTTTTA TTTTTA GTTTTATA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
52928951 ATTAAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 17 0.63
7 8 0.30
8 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:52928939 original size:14 final size:14
Alignment explanation
Indices: 52928915--52928948 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
52928905 AAAATTATAT
52928915 GTTTT-TATTTTTA
1 GTTTTATATTTTTA
52928928 GTTTTATATTTTTA
1 GTTTTATATTTTTA
*
52928942 TTTTTAT
1 GTTTTAT
52928949 TTATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (14 bp):
GTTTTATATTTTTA
Found at i:52932787 original size:62 final size:62
Alignment explanation
Indices: 52932690--52932813 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
52932680 CCAAATTTCC
52932690 TATAGTTTCATTTCCCTCCATGTTCCATGAACAATGCACAATCTTCATTTTTTGCTTAGCTG
1 TATAGTTTCATTTCCCTCCATGTTCCATGAACAATGCACAATCTTCATTTTTTGCTTAGCTG
52932752 TATAGTTTCATTTCCCTCCATGTTCCATGAACAATGCACAATCTTCATTTTTTGCTTAGCTG
1 TATAGTTTCATTTCCCTCCATGTTCCATGAACAATGCACAATCTTCATTTTTTGCTTAGCTG
52932814 ATGCCTTCCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (62 bp):
TATAGTTTCATTTCCCTCCATGTTCCATGAACAATGCACAATCTTCATTTTTTGCTTAGCTG
Found at i:52941007 original size:17 final size:17
Alignment explanation
Indices: 52940985--52941019 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
52940975 AAAATATTAT
*
52940985 TAATTTTTTTAATAAAA
1 TAATTTTTTTAAAAAAA
52941002 TAATTTTTTTAAAAAAA
1 TAATTTTTTTAAAAAAA
52941019 T
1 T
52941020 TGATTCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTTTTTTAAAAAAA
Found at i:52945902 original size:16 final size:16
Alignment explanation
Indices: 52945881--52945915 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52945871 GTCCTACTAA
*
52945881 AGAAAAAAATGAAGAG
1 AGAAAAAAAGGAAGAG
*
52945897 AGAAAAATAGGAAGAG
1 AGAAAAAAAGGAAGAG
52945913 AGA
1 AGA
52945916 GAGAGAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.06
Consensus pattern (16 bp):
AGAAAAAAAGGAAGAG
Found at i:52948740 original size:15 final size:16
Alignment explanation
Indices: 52948717--52948749 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52948707 AGGAGTATAG
52948717 TAAAAA-TTTAAAAAA
1 TAAAAATTTTAAAAAA
*
52948732 TAAATATTTTAAAAAA
1 TAAAAATTTTAAAAAA
52948748 TA
1 TA
52948750 CACATTGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAATTTTAAAAAA
Found at i:52955257 original size:16 final size:16
Alignment explanation
Indices: 52955215--52955267 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
52955205 ATTCAACCAA
52955215 ACAGTTCTATTCAATT
1 ACAGTTCTATTCAATT
* * *
52955231 AAAATTTTATTCAATT
1 ACAGTTCTATTCAATT
*
52955247 ACAGCTCTATTCAATT
1 ACAGTTCTATTCAATT
52955263 ACAGT
1 ACAGT
52955268 GAAACAAACA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (16 bp):
ACAGTTCTATTCAATT
Found at i:52955668 original size:33 final size:33
Alignment explanation
Indices: 52955627--52955707 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 33
52955617 TTAGGGTAAT
* *
52955627 TATATATATATGAAATTTTAATTGTGATTCAAG
1 TATATATATATAAAATTTTAATTGTAATTCAAG
* * * *
52955660 TATATATATTTAAAATTTTGATTTTAATTCAAT
1 TATATATATATAAAATTTTAATTGTAATTCAAG
* *
52955693 TATACATATTTAAAA
1 TATATATATATAAAA
52955708 AATATATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (33 bp):
TATATATATATAAAATTTTAATTGTAATTCAAG
Found at i:52960837 original size:24 final size:26
Alignment explanation
Indices: 52960805--52960854 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
52960795 ATAGTAAAAA
*
52960805 TATAATTTTATCA-TTTT-AATAGTT
1 TATAATTTTATAATTTTTAAATAGTT
*
52960829 TATATTTTTATAATTTTTAAATAGTT
1 TATAATTTTATAATTTTTAAATAGTT
52960855 AAATCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 4 0.18
26 7 0.32
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (26 bp):
TATAATTTTATAATTTTTAAATAGTT
Found at i:52961552 original size:24 final size:22
Alignment explanation
Indices: 52961517--52961562 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
52961507 ATTTAATTTC
52961517 GACCAAAAAAAATTATATGATTAT
1 GACCAAAAAAAA-TATAT-ATTAT
*
52961541 GACCAAAGAAAATATATATTAT
1 GACCAAAAAAAATATATATTAT
52961563 ATATAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 5 0.24
24 11 0.52
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (22 bp):
GACCAAAAAAAATATATATTAT
Found at i:52965302 original size:15 final size:15
Alignment explanation
Indices: 52965282--52965315 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
52965272 AGGAGGAGTG
*
52965282 CAACAACATCAACAT
1 CAACAACAACAACAT
52965297 CAACAACAACAACAT
1 CAACAACAACAACAT
52965312 CAAC
1 CAAC
52965316 TCTTCCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.35, G:0.00, T:0.09
Consensus pattern (15 bp):
CAACAACAACAACAT
Found at i:52966652 original size:18 final size:18
Alignment explanation
Indices: 52966625--52966717 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
52966615 TACGACCGTT
52966625 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
52966643 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
52966661 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
52966679 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
52966697 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
52966715 TAC
1 TAC
52966718 AGTAGTTGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:52966672 original size:36 final size:36
Alignment explanation
Indices: 52966625--52966717 Score: 177
Period size: 36 Copynumber: 2.6 Consensus size: 36
52966615 TACGACCGTT
52966625 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
52966661 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
52966697 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
52966718 AGTAGTTGGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTCACGTA
Found at i:52979856 original size:40 final size:39
Alignment explanation
Indices: 52979792--52979870 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
52979782 TAGTAAAATG
*
52979792 CATATAATATCGACTAAGAACAATAGCCAACCTCAAACT
1 CATATAATATCGACTAAGAACAATAACCAACCTCAAACT
52979831 CATATAATATCGAACTAAGAACAATAACCAACCTCAAACT
1 CATATAATATCG-ACTAAGAACAATAACCAACCTCAAACT
52979871 TCTTTTCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 12 0.32
40 26 0.68
ACGTcount: A:0.48, C:0.25, G:0.06, T:0.20
Consensus pattern (39 bp):
CATATAATATCGACTAAGAACAATAACCAACCTCAAACT
Found at i:52983628 original size:17 final size:17
Alignment explanation
Indices: 52983601--52983634 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
52983591 ATCATGGGGA
52983601 AAAACTGACCTGCAACGT
1 AAAACTGACCTG-AACGT
52983619 AAAA-TGACCTGAACGT
1 AAAACTGACCTGAACGT
52983635 TAACGCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAACTGACCTGAACGT
Found at i:52985750 original size:28 final size:28
Alignment explanation
Indices: 52985719--52985772 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
52985709 AAAAGAAAAA
52985719 AAAAATACAT-AAATCATCATTAAATTTT
1 AAAAAT-CATAAAATCATCATTAAATTTT
* *
52985747 AAAAATTATAAAATTATCATTAAATT
1 AAAAATCATAAAATCATCATTAAATT
52985773 ATTTGAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAAATCATAAAATCATCATTAAATTTT
Found at i:52986785 original size:17 final size:17
Alignment explanation
Indices: 52986765--52986798 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52986755 AGGTTTAAGT
*
52986765 TTAAAAATTTTAATTAA
1 TTAAAAATTTCAATTAA
52986782 TTAAAAATTTCAATTAA
1 TTAAAAATTTCAATTAA
52986799 AATTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAAATTTCAATTAA
Found at i:53001693 original size:40 final size:37
Alignment explanation
Indices: 53001629--53001719 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 37
53001619 CAGTTTGGCA
*
53001629 CCAGTGCCTCATCGGATAATCTGAAGTAGTAAATTGACAC
1 CCAGTGCCTCATCGGATAAACTG-A--AGTAAATTGACAC
* * * *
53001669 CCAGTGTCTCATCTGTTAAACTGAAGTAAATTGGCAC
1 CCAGTGCCTCATCGGATAAACTGAAGTAAATTGACAC
*
53001706 CCAGTGCATCATCG
1 CCAGTGCCTCATCG
53001720 ACTCGAATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
37 23 0.53
39 1 0.02
40 19 0.44
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (37 bp):
CCAGTGCCTCATCGGATAAACTGAAGTAAATTGACAC
Found at i:53002613 original size:9 final size:9
Alignment explanation
Indices: 53002590--53002644 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
53002580 ATCTTTCTCC
53002590 TTTCTTT-T
1 TTTCTTTCT
53002598 TTT-TTTCT
1 TTTCTTTCT
53002606 TTTCTTTCT
1 TTTCTTTCT
*
53002615 TTCCTTTCT
1 TTTCTTTCT
*
53002624 GTTCGTTT-T
1 TTTC-TTTCT
53002633 GTTTCTTTCT
1 -TTTCTTTCT
53002643 TT
1 TT
53002645 GTTTATTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
7 3 0.08
8 7 0.18
9 21 0.55
10 7 0.18
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.76
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:53002705 original size:26 final size:26
Alignment explanation
Indices: 53002672--53002730 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
53002662 TTTGTCCTGT
* * *
53002672 TTAT-TATATTTACTTTATTATTATA
1 TTATATATATTTACTTAAATATTAAA
53002697 TTATATATATTTACTTAAATATTAAA
1 TTATATATATTTACTTAAATATTAAA
*
53002723 TAATATAT
1 TTATATAT
53002731 TATTATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATATATATTTACTTAAATATTAAA
Found at i:53005327 original size:35 final size:35
Alignment explanation
Indices: 53005204--53005334 Score: 120
Period size: 35 Copynumber: 3.6 Consensus size: 35
53005194 CCTCATTAAA
* * *
53005204 ATACCATACCTACATTTTACAACTCGGTATGGGA-A
1 ATACCATACCTACATTTCACAACTCAGTAT-GGATG
** * **
53005239 ATGTCATACCTACGTTTCTTAACTCAGTATGGATTTG
1 ATACCATACCTACATTTCACAACTCAGTATGGA--TG
*
53005276 ATAATACCATATCTACATTTCACAACTCAGTATGGATG
1 ---ATACCATACCTACATTTCACAACTCAGTATGGATG
53005314 ATACCATACCTACATTTCACA
1 ATACCATACCTACATTTCACA
53005335 CTTTGCCATG
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
34 3 0.04
35 43 0.57
38 2 0.03
40 27 0.36
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (35 bp):
ATACCATACCTACATTTCACAACTCAGTATGGATG
Found at i:53008426 original size:12 final size:12
Alignment explanation
Indices: 53008404--53008429 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53008394 CACAGCAGCG
53008404 GCAGCAGCAGTA
1 GCAGCAGCAGTA
53008416 GCAGCAGCAGTA
1 GCAGCAGCAGTA
53008428 GC
1 GC
53008430 GGGAGTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.35, T:0.08
Consensus pattern (12 bp):
GCAGCAGCAGTA
Found at i:53029074 original size:21 final size:21
Alignment explanation
Indices: 53029048--53029090 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
53029038 AAGGTGCACA
53029048 GATATTCTGTGACGTGGTTCT
1 GATATTCTGTGACGTGGTTCT
53029069 GATATTCTGTGACGTGGTTCT
1 GATATTCTGTGACGTGGTTCT
53029090 G
1 G
53029091 CTTTAATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.42
Consensus pattern (21 bp):
GATATTCTGTGACGTGGTTCT
Found at i:53035094 original size:21 final size:22
Alignment explanation
Indices: 53035057--53035099 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
53035047 AGAGAACGAC
53035057 TAAAATATTTAATTTTA-AAAA
1 TAAAATATTTAATTTTAGAAAA
*
53035078 TAAAATAATTTGA-TTTAGAAAA
1 TAAAAT-ATTTAATTTTAGAAAA
53035100 ACATTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
TAAAATATTTAATTTTAGAAAA
Found at i:53047736 original size:9 final size:9
Alignment explanation
Indices: 53047720--53047780 Score: 95
Period size: 9 Copynumber: 6.8 Consensus size: 9
53047710 GGTATTTTTC
53047720 GGTAATTCG
1 GGTAATTCG
*
53047729 GTTAATTCG
1 GGTAATTCG
*
53047738 GTTAATTCG
1 GGTAATTCG
53047747 GGTAATTCG
1 GGTAATTCG
53047756 GGTAATTCG
1 GGTAATTCG
*
53047765 GATAATTCG
1 GGTAATTCG
53047774 GGTAATT
1 GGTAATT
53047781 TTAACCAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.38
Consensus pattern (9 bp):
GGTAATTCG
Found at i:53048765 original size:15 final size:15
Alignment explanation
Indices: 53048727--53048765 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
53048717 TTTTTTGAAA
*
53048727 TTTTAA-AAAATATT
1 TTTTAATAAAATAGT
53048741 TTTATAATAAAATAGT
1 TTT-TAATAAAATAGT
53048757 TTTTAATAA
1 TTTTAATAA
53048766 TTTTAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.41
16 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
TTTTAATAAAATAGT
Found at i:53048771 original size:9 final size:9
Alignment explanation
Indices: 53048757--53048806 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
53048747 ATAAAATAGT
53048757 TTTTAATAA
1 TTTTAATAA
*
53048766 TTTTAATGAT
1 TTTTAAT-AA
*
53048776 TTTTAATAT
1 TTTTAATAA
*
53048785 TTTTTAT-A
1 TTTTAATAA
53048793 TTTTAA-AA
1 TTTTAATAA
53048801 TTTTAA
1 TTTTAA
53048807 AAAATTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 12 0.34
9 15 0.43
10 8 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTAATAA
Found at i:53048780 original size:19 final size:18
Alignment explanation
Indices: 53048751--53048806 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
53048741 TTTATAATAA
53048751 AATAGTTTTTAATAATTTT
1 AATA-TTTTTAATAATTTT
*
53048770 AATGATTTTTAATATTTTT
1 AAT-ATTTTTAATAATTTT
*
53048789 TATA-TTTTAA-AATTTT
1 AATATTTTTAATAATTTT
53048805 AA
1 AA
53048807 AAAATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.19
17 6 0.19
18 1 0.03
19 18 0.56
20 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
AATATTTTTAATAATTTT
Found at i:53049316 original size:25 final size:24
Alignment explanation
Indices: 53049270--53049335 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
53049260 TTCTCTACAA
**
53049270 TAAAAATATTTTTA-TTTAATTA-
1 TAAAAATATTTAAATTTTAATTAT
* *
53049292 TAATATTATTTTAAATTTTACATTAT
1 TAAAAATA-TTTAAATTTTA-ATTAT
53049318 TAAAAATATTTAAATTTT
1 TAAAAATATTTAAATTTT
53049336 TCTACAAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 6 0.18
23 4 0.12
24 4 0.12
25 14 0.41
26 6 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TAAAAATATTTAAATTTTAATTAT
Found at i:53049389 original size:20 final size:20
Alignment explanation
Indices: 53049364--53049411 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
53049354 TGTATATTGC
53049364 TATTTTTATATTTT-TAA-TA
1 TATTTTTAT-TTTTATAATTA
*
53049383 TTATTTTTCTTTTTATAATTA
1 -TATTTTTATTTTTATAATTA
53049404 TATTTTTA
1 TATTTTTA
53049412 ATTCAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 18 0.75
21 2 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTTATTTTTATAATTA
Found at i:53051812 original size:21 final size:21
Alignment explanation
Indices: 53051787--53051844 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
53051777 AATTAATTAT
*
53051787 AAAAGTATTGATACATTTTCA
1 AAAAGTATCGATACATTTTCA
*
53051808 AAAAGTATCGATACCTTTT-A
1 AAAAGTATCGATACATTTTCA
**
53051828 TCAAGTATCGATA-ATTT
1 AAAAGTATCGATACATTT
53051845 GTGTTTAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 17 0.53
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAAGTATCGATACATTTTCA
Found at i:53059375 original size:53 final size:53
Alignment explanation
Indices: 53059294--53059444 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
53059284 CTTACACGGT
* *
53059294 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
53059349 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
53059402 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
53059445 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:53066893 original size:53 final size:53
Alignment explanation
Indices: 53066812--53066962 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
53066802 CTTACACGGT
* *
53066812 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
53066867 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
53066920 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
53066963 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:53068206 original size:10 final size:10
Alignment explanation
Indices: 53068191--53068218 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
53068181 ACAATTTCAC
53068191 AAATTCTTCT
1 AAATTCTTCT
53068201 AAATTCTTCT
1 AAATTCTTCT
53068211 AAATTCTT
1 AAATTCTT
53068219 ACTTGACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATTCTTCT
Found at i:53071743 original size:35 final size:35
Alignment explanation
Indices: 53071690--53072162 Score: 506
Period size: 35 Copynumber: 13.6 Consensus size: 35
53071680 CCTCATTGAA
* **
53071690 ATACCATACCTACGTTTCACAACTCGGTATGGAAA
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
* * ** * **
53071725 ACACCATACCTACTTTTCA-TGCTCGGTATGGAAA
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
** * *
53071759 ATACCATACCTATATTTCATAACTCAGTATGGACG
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
* * * * *
53071794 ATGCCATACCTACGTATCATAGCTCAGTATGGACG
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
* * * * *
53071829 ATGCCATACCTACGTATCATAGCTCAGTATGGACG
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
* * *
53071864 ACT-CCATATCTACGTTTCACAGCTCAGTATGGA-A
1 A-TACCATACCTACGTTTCACAACTCAGTATGGATG
* * *
53071898 ATACCATACTTACGTTTCACAGCTCAGTATGGA-A
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
* * * *
53071932 ATACCATACCTACATTTCACAGCTCAGTATGGTTA
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
* *
53071967 ATACCATACCTATGTTTCACAACTCGGTATGGATG
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
* *
53072002 ATACCATACCTACGTATT-ACAACTCGGTAAGGATG
1 ATACCATACCTACGT-TTCACAACTCAGTATGGATG
* * *
53072037 ATACCATACCTACATTTCACAACTCAGTATGGTTA
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
*
53072072 ATACCATACCTACGTTTCACAACTCGGTATGGATG
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
53072107 ATACCATACCTACGTTTCACAACTCAGTATGGATG
1 ATACCATACCTACGTTTCACAACTCAGTATGGATG
*
53072142 ATACCATACCTACATTTCACA
1 ATACCATACCTACGTTTCACA
53072163 CTTTACCATG
Statistics
Matches: 387, Mismatches: 45, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
33 1 0.00
34 91 0.24
35 292 0.75
36 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (35 bp):
ATACCATACCTACGTTTCACAACTCAGTATGGATG
Found at i:53072066 original size:105 final size:105
Alignment explanation
Indices: 53071690--53072162 Score: 560
Period size: 105 Copynumber: 4.5 Consensus size: 105
53071680 CCTCATTGAA
* ** * * * *
53071690 ATACCATACCTACGTTTCACAACTCGGTATGGAAAACACCATACCTACTTTTCA-TGCTCGGTAT
1 ATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATACCTACATTTCACAGCTCAGTAT
** ** * *
53071754 GGAAAATACCATACCTATATTTCATAACTCAGTATGGACG
66 GGTTAATACCATACCTACGTTTCACAACTCAGTATGGATG
* * * * * * * * *
53071794 ATGCCATACCTACGTATCATAGCTCAGTATGGACGATGCCATACCTACGTATCATAGCTCAGTAT
1 ATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATACCTACATTTCACAGCTCAGTAT
** * * * *
53071859 GGACGACT-CCATATCTACGTTTCACAGCTCAGTATGGA-A
66 GG-TTAATACCATACCTACGTTTCACAACTCAGTATGGATG
* * *
53071898 ATACCATACTTACGTTTCACAGCTCAGTATGGA-AATACCATACCTACATTTCACAGCTCAGTAT
1 ATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATACCTACATTTCACAGCTCAGTAT
* *
53071962 GGTTAATACCATACCTATGTTTCACAACTCGGTATGGATG
66 GGTTAATACCATACCTACGTTTCACAACTCAGTATGGATG
* * *
53072002 ATACCATACCTACGTATT-ACAACTCGGTAAGGATGATACCATACCTACATTTCACAACTCAGTA
1 ATACCATACCTACGT-TTCACAACTCAGTATGGATGATACCATACCTACATTTCACAGCTCAGTA
*
53072066 TGGTTAATACCATACCTACGTTTCACAACTCGGTATGGATG
65 TGGTTAATACCATACCTACGTTTCACAACTCAGTATGGATG
53072107 ATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATACCTACATTTCACA
1 ATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATACCTACATTTCACA
53072163 CTTTACCATG
Statistics
Matches: 314, Mismatches: 48, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
102 2 0.01
103 54 0.17
104 100 0.32
105 156 0.50
106 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (105 bp):
ATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATACCTACATTTCACAGCTCAGTAT
GGTTAATACCATACCTACGTTTCACAACTCAGTATGGATG
Found at i:53074413 original size:22 final size:22
Alignment explanation
Indices: 53074385--53074452 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
53074375 CTCCGATTAC
*
53074385 TAGCACATTAATGCTCTTTGTT
1 TAGCACATTAATGCTCTCTGTT
* *
53074407 TAGCACATTCATGCTCTCTGTA
1 TAGCACATTAATGCTCTCTGTT
* *
53074429 TAGCACTTTAGTGCTCTCTGTT
1 TAGCACATTAATGCTCTCTGTT
53074451 TA
1 TA
53074453 ATAGTGCATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.43
Consensus pattern (22 bp):
TAGCACATTAATGCTCTCTGTT
Found at i:53079229 original size:46 final size:46
Alignment explanation
Indices: 53079177--53079312 Score: 202
Period size: 46 Copynumber: 3.0 Consensus size: 46
53079167 GCTTTCTGAA
*
53079177 ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACATGAC
*
53079223 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACATGAC
* * * *
53079269 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACATG
53079313 TCAAAGATAA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 1 0.01
46 81 0.99
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACATGAC
Found at i:53079614 original size:16 final size:17
Alignment explanation
Indices: 53079593--53079625 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53079583 ATGATGGAGC
53079593 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
53079609 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
53079626 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:53082092 original size:18 final size:19
Alignment explanation
Indices: 53082048--53082094 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
53082038 ACGATTGAAC
*
53082048 TGATTTTTTATTTTTTAAA
1 TGATTTATTATTTTTTAAA
53082067 T-ATTTTTATTATTTTTT-AA
1 TGA--TTTATTATTTTTTAAA
53082086 TGATTTATT
1 TGATTTATT
53082095 CAATTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
18 7 0.29
19 4 0.17
20 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (19 bp):
TGATTTATTATTTTTTAAA
Found at i:53092756 original size:92 final size:93
Alignment explanation
Indices: 53092585--53092771 Score: 231
Period size: 93 Copynumber: 2.0 Consensus size: 93
53092575 ACAGTAGTAG
*
53092585 AACCTTTTAAATTTAAGGCACCCCAAATTTGGAAAAAAATAACTTATATAAAACAAAAGACAATT
1 AACCTTTTAAATTTAAAGCACCCCAAATTTGGAAAAAAATAACTTATATAAAACAAAAGACAATT
53092650 TTATTTTTAAATTTTGTTG-AAAAAATC
66 TTATTTTTAAATTTTGTTGAAAAAAATC
* * * * *
53092677 AACCTTTTTAAATTTAAAG-TCCTCAAATTTGG-AATAAATAACTTATATCAAA-GAAAGACAAA
1 AACC-TTTTAAATTTAAAGCACCCCAAATTTGGAAAAAAATAACTTATATAAAACAAAAGAC-AA
* *
53092739 TCTGTTCTTTTT-TATTTTGTTGAAAAAAATC
64 T-T-TTATTTTTAAATTTTGTTGAAAAAAATC
53092770 AA
1 AA
53092772 ATTGAAGGTA
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
90 6 0.07
91 21 0.26
92 25 0.30
93 30 0.37
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (93 bp):
AACCTTTTAAATTTAAAGCACCCCAAATTTGGAAAAAAATAACTTATATAAAACAAAAGACAATT
TTATTTTTAAATTTTGTTGAAAAAAATC
Found at i:53096251 original size:17 final size:17
Alignment explanation
Indices: 53096214--53096267 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
53096204 ATAATTATTC
*
53096214 TTATTTTAAATTAATTAAA
1 TTATTTTAAAAT-ATT-AA
*
53096233 TTTTTTTAAAATATTAA
1 TTATTTTAAAATATTAA
* *
53096250 TTAATTTAAAATAGTAA
1 TTATTTTAAAATATTAA
53096267 T
1 T
53096268 AATCCACAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 17 0.57
18 3 0.10
19 10 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTATTTTAAAATATTAA
Found at i:53097247 original size:17 final size:16
Alignment explanation
Indices: 53097214--53097257 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
53097204 TATACACCAT
53097214 AAAGTACCTAACATTA
1 AAAGTACCTAACATTA
53097230 AAAGATACCTGAAC-TTA
1 AAAG-TACCT-AACATTA
*
53097247 AAAGTAACTAA
1 AAAGTACCTAA
53097258 AATTTGACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 8 0.32
17 12 0.48
18 3 0.12
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.23
Consensus pattern (16 bp):
AAAGTACCTAACATTA
Found at i:53101690 original size:12 final size:12
Alignment explanation
Indices: 53101661--53101701 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
53101651 TCTTGACAAA
53101661 GATAGAGAAGGT
1 GATAGAGAAGGT
*
53101673 -ATAGAGAAAGT
1 GATAGAGAAGGT
53101684 GATAGAGAAGGT
1 GATAGAGAAGGT
53101696 GATAGA
1 GATAGA
53101702 TTCAGCGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (12 bp):
GATAGAGAAGGT
Found at i:53112596 original size:3 final size:3
Alignment explanation
Indices: 53112588--53112634 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
53112578 TCTTTTATTT
* *
53112588 AAG AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
53112635 CCTGTAAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:53117449 original size:31 final size:31
Alignment explanation
Indices: 53117414--53117472 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
53117404 AGAAAAATGC
53117414 ACTTTTATATAAATCCGTAAAATTAAAATTA
1 ACTTTTATATAAATCCGTAAAATTAAAATTA
53117445 ACTTTTATATAAATCCGTAAAATTAAAA
1 ACTTTTATATAAATCCGTAAAATTAAAA
53117473 ATAAATTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.37
Consensus pattern (31 bp):
ACTTTTATATAAATCCGTAAAATTAAAATTA
Found at i:53121629 original size:21 final size:21
Alignment explanation
Indices: 53121583--53121629 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
53121573 AAAAAATTGC
* *
53121583 ATTTTTTAGTATTTTCTTGCT
1 ATTTTTTACTATTTTCTTACT
*
53121604 TTTTTTTACTATTTTAC-TACT
1 ATTTTTTACTATTTT-CTTACT
53121625 ATTTT
1 ATTTT
53121630 ACTATTATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.68
Consensus pattern (21 bp):
ATTTTTTACTATTTTCTTACT
Found at i:53143155 original size:17 final size:18
Alignment explanation
Indices: 53143122--53143172 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
53143112 AAAAAAATCA
53143122 TTTTAATCTTTTATTTA-AT
1 TTTTAAT-TTTT-TTTATAT
* *
53143141 TTTTCATTTTTTTTATCT
1 TTTTAATTTTTTTTATAT
53143159 TTTTAATTTTTTTT
1 TTTTAATTTTTTTT
53143173 TGTAAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 18 0.64
19 6 0.21
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTAATTTTTTTTATAT
Found at i:53143322 original size:23 final size:22
Alignment explanation
Indices: 53143269--53143322 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
53143259 TTAATTAATT
*
53143269 TTTAATATATATTTTTATAAAAA
1 TTTAA-ATATATTTTTAAAAAAA
*
53143292 -TTATAATATCTTTTTACAAAAAA
1 TTTA-AATATATTTTTA-AAAAAA
53143315 TTTAAATA
1 TTTAAATA
53143323 GTTTTAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 13 0.50
23 10 0.38
24 3 0.12
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATATATTTTTAAAAAAA
Found at i:53147370 original size:50 final size:50
Alignment explanation
Indices: 53147314--53147412 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
53147304 TTCTTTTGCT
* * *
53147314 GTTTTCTTTTCTTCATTTTTCTAGGAAGATTGTTTTTCTCC-CTTTTCAAC
1 GTTTTCTTTTCTTCATTATCCTAGGAAGATTGTGTTTC-CCTCTTTTCAAC
53147364 GTTTTCTTTTCTTCATTATCCTAGGAAGATTGTGTTTCCCTCTTTTCAA
1 GTTTTCTTTTCTTCATTATCCTAGGAAGATTGTGTTTCCCTCTTTTCAA
53147413 TAAGTGTGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 2 0.04
50 43 0.96
ACGTcount: A:0.15, C:0.20, G:0.11, T:0.54
Consensus pattern (50 bp):
GTTTTCTTTTCTTCATTATCCTAGGAAGATTGTGTTTCCCTCTTTTCAAC
Found at i:53156062 original size:24 final size:25
Alignment explanation
Indices: 53156029--53156090 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
53156019 AATAAAACAC
*
53156029 TACATAAATATATATTGAAAA-TAGA
1 TACAT-AATATATATTGAAAAGCAGA
* * *
53156054 TATATAATA-ATATTTAAAAGCATA
1 TACATAATATATATTGAAAAGCAGA
53156078 TACATAATATATA
1 TACATAATATATA
53156091 CATAACATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 9 0.30
24 14 0.47
25 7 0.23
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (25 bp):
TACATAATATATATTGAAAAGCAGA
Found at i:53156158 original size:15 final size:15
Alignment explanation
Indices: 53156115--53156158 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
53156105 CAAAATATAC
53156115 ACATAATAT-ATTAAA
1 ACATAATATGA-TAAA
*
53156130 ACATATACATGATAAA
1 ACATA-ATATGATAAA
53156146 ACATAATATGATA
1 ACATAATATGATA
53156159 TTTACAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
16 12 0.48
17 1 0.04
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.30
Consensus pattern (15 bp):
ACATAATATGATAAA
Found at i:53159760 original size:37 final size:38
Alignment explanation
Indices: 53159710--53159830 Score: 127
Period size: 46 Copynumber: 3.0 Consensus size: 38
53159700 AGTGTGCTCT
*
53159710 CTGATATGAAATGTGTAAGA-CATAGTTGATAGATACC
1 CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACC
*
53159747 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATAGTTGAAAGAT---A---C--C
* *
53159793 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACC
1 CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACC
53159831 ATGGCAACGT
Statistics
Matches: 72, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
37 20 0.28
38 13 0.18
40 1 0.01
41 1 0.01
43 1 0.01
44 1 0.01
46 35 0.49
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.26
Consensus pattern (38 bp):
CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACC
Found at i:53159813 original size:46 final size:46
Alignment explanation
Indices: 53159746--53159928 Score: 242
Period size: 46 Copynumber: 4.0 Consensus size: 46
53159736 TGATAGATAC
* *
53159746 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
* * *
53159792 CCTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
* * *
53159838 CGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
* * * *
53159884 CATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CCTGACATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
53159929 TCACGTCAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 122 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CCTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
Found at i:53160234 original size:23 final size:25
Alignment explanation
Indices: 53160189--53160235 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
53160179 AATAAATATA
*
53160189 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
53160214 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
53160236 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:53161298 original size:43 final size:41
Alignment explanation
Indices: 53161161--53161310 Score: 122
Period size: 43 Copynumber: 3.5 Consensus size: 41
53161151 ATTTTCAGCC
* * ** *
53161161 TGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCATTGAT
1 TGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAAT--TTGCT
* * * ** *
53161204 CTGTTTCCCTACTGCTTAGGGGTTT-AGATCTGTAAATTCAACC
1 -TGTTACCCTACTGCTTAGGGGTTTAAGGTTTG-AAATT-TGCT
53161247 TGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAAATTTGGCT
1 TGTTACCCTACTGCTTAGGGGTTTAAGGTTTG-AAATTT-GCT
*
53161290 TGTTACCCTATTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGG
53161311 GTTGAAGCTC
Statistics
Matches: 83, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
42 24 0.29
43 35 0.42
44 24 0.29
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
TGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAATTTGCT
Found at i:53161313 original size:86 final size:85
Alignment explanation
Indices: 53161154--53161310 Score: 201
Period size: 86 Copynumber: 1.8 Consensus size: 85
53161144 ACATTTGATT
* ** *
53161154 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCATTGATCTGTTTCCCTACTGC
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAAAT-ATTGATCTGTTACCCTACTGC
53161219 TTAGGGGTTTAGATCTGTAAA
65 TTAGGGGTTTAGATCTGTAAA
* * * *
53161240 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAA-ATTTG-GCTTGTTACCCTATTG
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATA-TTGATC-TGTTACCCTACTG
53161303 CTTAGGGG
64 CTTAGGGG
53161311 GTTGAAGCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
84 2 0.03
85 22 0.36
86 37 0.61
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.38
Consensus pattern (85 bp):
TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATATTGATCTGTTACCCTACTGCT
TAGGGGTTTAGATCTGTAAA
Found at i:53161745 original size:44 final size:43
Alignment explanation
Indices: 53161695--53161839 Score: 141
Period size: 44 Copynumber: 3.3 Consensus size: 43
53161685 TGATCTGCTT
53161695 CCCTACTGCTTAGGGTGATAAGATCTATAAACTTCAGCTTGTTA
1 CCCTACTGCTTAGGGTGATAAGATCTAT-AACTTCAGCTTGTTA
* * * ** * * *
53161739 CCCTACTGCTTAGGGGGTTAAAGCTCGT-TGCCTT-TGATCTGTTT
1 CCCTACTGCTTAGGGTGAT-AAGATC-TATAACTTCAGCT-TGTTA
* * *
53161783 CCCTAATGCTTAGGGTGATAAGATCTATATCTTCAGCCTGTTA
1 CCCTACTGCTTAGGGTGATAAGATCTATAACTTCAGCTTGTTA
53161826 CCCTACTGCTTAGG
1 CCCTACTGCTTAGG
53161840 TGGTTAAAGT
Statistics
Matches: 77, Mismatches: 19, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
42 1 0.01
43 28 0.36
44 41 0.53
45 6 0.08
46 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (43 bp):
CCCTACTGCTTAGGGTGATAAGATCTATAACTTCAGCTTGTTA
Found at i:53161787 original size:88 final size:87
Alignment explanation
Indices: 53161683--53161848 Score: 278
Period size: 88 Copynumber: 1.9 Consensus size: 87
53161673 TTCGCCGTCT
* *
53161683 TTTGATCTGCTTCCCTACTGCTTAGGGTGATAAGATCTATAAACTTCAGCTTGTTACCCTACTGC
1 TTTGATCTGCTTCCCTAATGCTTAGGGTGATAAGATCTAT-AACTTCAGCCTGTTACCCTACTGC
53161748 TTAGGGGGTTAAAGCTCGTTGCC
65 TTAGGGGGTTAAAGCTCGTTGCC
* *
53161771 TTTGATCTGTTTCCCTAATGCTTAGGGTGATAAGATCTATATCTTCAGCCTGTTACCCTACTGCT
1 TTTGATCTGCTTCCCTAATGCTTAGGGTGATAAGATCTATAACTTCAGCCTGTTACCCTACTGCT
*
53161836 TAGGTGGTTAAAG
66 TAGGGGGTTAAAG
53161849 TCTGGTGAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
87 35 0.48
88 38 0.52
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (87 bp):
TTTGATCTGCTTCCCTAATGCTTAGGGTGATAAGATCTATAACTTCAGCCTGTTACCCTACTGCT
TAGGGGGTTAAAGCTCGTTGCC
Found at i:53162418 original size:55 final size:55
Alignment explanation
Indices: 53162348--53162467 Score: 231
Period size: 55 Copynumber: 2.2 Consensus size: 55
53162338 ACAAAATTTG
53162348 AAGGGAATAGATTAATCACAGTCAACAAACATTACTGGAATACAAAATGAATAAA
1 AAGGGAATAGATTAATCACAGTCAACAAACATTACTGGAATACAAAATGAATAAA
*
53162403 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
1 AAGGGAATAGATTAATCACAGTCAACAAACATTACTGGAATACAAAATGAATAAA
53162458 AAGGGAATAG
1 AAGGGAATAG
53162468 GTGCCCCAGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (55 bp):
AAGGGAATAGATTAATCACAGTCAACAAACATTACTGGAATACAAAATGAATAAA
Found at i:53176067 original size:23 final size:20
Alignment explanation
Indices: 53176040--53176097 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
53176030 TTATAGAATG
53176040 TATAAAAATATATACATGTTA
1 TATAAAAATATATACAT-TTA
*
53176061 TAGATAAAAATTATATATATTTA
1 T--ATAAAAA-TATATACATTTA
*
53176084 TATAAAATTATATA
1 TATAAAAATATATA
53176098 TATTCTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 6 0.19
21 7 0.22
23 11 0.34
24 8 0.25
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (20 bp):
TATAAAAATATATACATTTA
Found at i:53176100 original size:22 final size:23
Alignment explanation
Indices: 53176040--53176100 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
53176030 TTATAGAATG
* *
53176040 TATAAAAATATATACATGTTATA
1 TATAAAAATATATATATATTATA
*
53176063 GATAAAAAT-TATATATATT-TA
1 TATAAAAATATATATATATTATA
*
53176084 TATAAAATTATATATAT
1 TATAAAAATATATATAT
53176101 TCTTCGATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 9 0.28
22 15 0.47
23 8 0.25
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (23 bp):
TATAAAAATATATATATATTATA
Found at i:53178089 original size:20 final size:20
Alignment explanation
Indices: 53178064--53178104 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
53178054 ATTAATTATT
53178064 TGTAAAATATAATTTAAATA
1 TGTAAAATATAATTTAAATA
* *
53178084 TGTAAATTATATTTTAAATA
1 TGTAAAATATAATTTAAATA
53178104 T
1 T
53178105 TAATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TGTAAAATATAATTTAAATA
Found at i:53178156 original size:22 final size:21
Alignment explanation
Indices: 53178109--53178156 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
53178099 AAATATTAAT
*
53178109 TATTAAAATATAAACTTTACA
1 TATTTAAATATAAACTTTACA
* * *
53178130 AATTTAAATATATAATTTTATA
1 TATTTAAATATA-AACTTTACA
53178152 TATTT
1 TATTT
53178157 GAAAAAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTTAAATATAAACTTTACA
Found at i:53183491 original size:24 final size:23
Alignment explanation
Indices: 53183445--53183491 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
53183435 ATTAAAAATT
*
53183445 TAATTAAATATATGATATTTAAA
1 TAATTAAATATATGATATATAAA
* *
53183468 TAATTTAATATAATTATATATAAA
1 TAATTAAATAT-ATGATATATAAA
53183492 ATATAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATTAAATATATGATATATAAA
Found at i:53183584 original size:22 final size:21
Alignment explanation
Indices: 53183566--53183606 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
53183556 AACATAATAC
53183566 TAAATAAAATTTAATATAATGA
1 TAAATAAAATTTAA-ATAATGA
* *
53183588 TAAATGATATTTAAATAAT
1 TAAATAAAATTTAAATAAT
53183607 TTAATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
TAAATAAAATTTAAATAATGA
Found at i:53183634 original size:31 final size:32
Alignment explanation
Indices: 53183573--53183643 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
53183563 TACTAAATAA
* * *
53183573 AATTTAATATAATGATAAATGATATTTAAA-T
1 AATTTAATATAATGATAAATAAAATATAAATT
53183604 AATTTAATATAATGATAAATAAAATATAAATT
1 AATTTAATATAATGATAAATAAAATATAAATT
*
53183636 AATCTAAT
1 AATTTAAT
53183644 TATTTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 27 0.77
32 8 0.23
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (32 bp):
AATTTAATATAATGATAAATAAAATATAAATT
Found at i:53183959 original size:15 final size:16
Alignment explanation
Indices: 53183941--53183975 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
53183931 AAAATTTTTA
53183941 AAATTA-TTCTAATAT
1 AAATTATTTCTAATAT
53183956 AAATTATTTCTAATAT
1 AAATTATTTCTAATAT
53183972 AAAT
1 AAAT
53183976 AATGATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTATTTCTAATAT
Found at i:53185675 original size:24 final size:23
Alignment explanation
Indices: 53185619--53185687 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 23
53185609 CAAATCTAAT
*
53185619 TTTAAAAAAATTACTTTTATATA
1 TTTAAAAAAATTACTTTTATAAA
*
53185642 TGTCAAAAAAATTACTTTTATACAA
1 T-TTAAAAAAATTACTTTTATA-AA
* *
53185667 TTTATAAAAATTA-TATTATAA
1 TTTAAAAAAATTACTTTTATAA
53185688 GCATAAACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 7 0.18
24 29 0.74
25 2 0.05
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (23 bp):
TTTAAAAAAATTACTTTTATAAA
Found at i:53186094 original size:16 final size:16
Alignment explanation
Indices: 53186073--53186103 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53186063 GTAAAATTTT
*
53186073 TTATAAATGTTATATA
1 TTATAAATATTATATA
53186089 TTATAAATATTATAT
1 TTATAAATATTATAT
53186104 TATATTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TTATAAATATTATATA
Found at i:53186845 original size:17 final size:18
Alignment explanation
Indices: 53186805--53186845 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
53186795 ATTGTTTAGA
* *
53186805 AATTATTTTTATCATATT
1 AATTAATTTTATCATAAT
53186823 AA-TAATTTTAT-ATAAT
1 AATTAATTTTATCATAAT
53186839 AATTAAT
1 AATTAAT
53186846 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.30
17 12 0.60
18 2 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTAATTTTATCATAAT
Found at i:53186858 original size:19 final size:20
Alignment explanation
Indices: 53186820--53186858 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
53186810 TTTTTATCAT
*
53186820 ATTAATAATTTTATATAATA
1 ATTAATAATTTTATAAAATA
*
53186840 ATTAAT-ATTTTTTAAAATA
1 ATTAATAATTTTATAAAATA
53186859 TAAATTATAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAATAATTTTATAAAATA
Found at i:53189149 original size:39 final size:39
Alignment explanation
Indices: 53189042--53189176 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
53189032 GACCTCGAGT
* * *
53189042 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
53189083 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
53189121 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
53189160 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
53189177 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:53193509 original size:136 final size:136
Alignment explanation
Indices: 53193349--53193612 Score: 501
Period size: 136 Copynumber: 1.9 Consensus size: 136
53193339 AACTCTGTTA
53193349 TACATGCAATTTGTATCTTCTTGAAAGTGATAAAAAAATATGGCAAGTTCAAGAAGGTTGTAATA
1 TACATGCAATTTGTATCTTCTTGAAAGTGATAAAAAAATATGGCAAGTTCAAGAAGGTTGTAATA
* * *
53193414 CTAGTCCACTATCTACTCTACTTTGCATTGGGATTAGTACACATCACAATCATGTACTCTTTTGA
66 CTAGTCCACTATCTACTCTACTTTGCAGTGGGATCAATACACATCACAATCATGTACTCTTTTGA
53193479 AAACTC
131 AAACTC
53193485 TACATGCAATTTGTATCTTCTTGAAAGTGATAAAAAAATATGGCAAGTTCAAGAAGGTTGTAATA
1 TACATGCAATTTGTATCTTCTTGAAAGTGATAAAAAAATATGGCAAGTTCAAGAAGGTTGTAATA
53193550 CTAGTCCACTATCTACTCTACTTTGCAGTGGGATCAATACACATCACAATCATGTACTCTTTT
66 CTAGTCCACTATCTACTCTACTTTGCAGTGGGATCAATACACATCACAATCATGTACTCTTTT
53193613 TCAATAGAAA
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 125 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (136 bp):
TACATGCAATTTGTATCTTCTTGAAAGTGATAAAAAAATATGGCAAGTTCAAGAAGGTTGTAATA
CTAGTCCACTATCTACTCTACTTTGCAGTGGGATCAATACACATCACAATCATGTACTCTTTTGA
AAACTC
Done.