Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold284
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: 702692
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
File 3 of 5
Found at i:259719 original size:18 final size:18
Alignment explanation
Indices: 259680--259759 Score: 51
Period size: 18 Copynumber: 4.4 Consensus size: 18
259670 TGATATAAAT
* *
259680 ATATAA-ATTAATTAATTT
1 ATATAATATAAATT-ATTA
259698 ATATAATATAAATTATTA
1 ATATAATATAAATTATTA
* *
259716 ATATATAAAAAAATTATATA
1 ATATA-ATATAAATTAT-TA
259736 A-AT-ATATAATATT-TTAA
1 ATATAATATAA-ATTATT-A
259753 ATATAAT
1 ATATAAT
259760 TTTAAGATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
16 1 0.02
17 7 0.14
18 19 0.39
19 19 0.39
20 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATATAAATTATTA
Found at i:260289 original size:16 final size:16
Alignment explanation
Indices: 260233--260288 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
260223 CAGACGAAAT
*
260233 ATAAAAGATAAT-TAAA
1 ATAAAATATAATAT-AA
*
260249 ATAAAATATAATATGA
1 ATAAAATATAATATAA
*
260265 ATATAATATAA-ATAA
1 ATAAAATATAATATAA
260280 AT-AAATATA
1 ATAAAATATA
260289 TTAAAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 6 0.18
15 5 0.15
16 22 0.65
17 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (16 bp):
ATAAAATATAATATAA
Found at i:260782 original size:32 final size:32
Alignment explanation
Indices: 260722--260791 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
260712 TTTAAATGTA
260722 ATATGAAAAAATAATATAATTATATATTAAAAT
1 ATAT-AAAAAATAATATAATTATATATTAAAAT
* *
260755 ATATAAAAAATAA-ATTATTAATTTATTAAAAT
1 ATATAAAAAATAATATAATT-ATATATTAAAAT
*
260787 TTATA
1 ATATA
260792 TAAATATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 5 0.15
32 24 0.73
33 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (32 bp):
ATATAAAAAATAATATAATTATATATTAAAAT
Found at i:260811 original size:27 final size:26
Alignment explanation
Indices: 260764--260815 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
260754 TATATAAAAA
* *
260764 ATAAATTATTAATTTATTAAAATTTAT
1 ATAAATTATTAATATAAT-AAATTTAT
260791 ATAAA-TATTTAATATAATAAATTTA
1 ATAAATTA-TTAATATAATAAATTTA
260816 ATTATAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATAAATTATTAATATAATAAATTTAT
Found at i:260821 original size:15 final size:14
Alignment explanation
Indices: 260783--260824 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
260773 TAATTTATTA
260783 AAATTT-ATATAA-
1 AAATTTAATATAAT
*
260795 ATATTTAATATAAT
1 AAATTTAATATAAT
260809 AAATTTAATTATAAT
1 AAATTTAA-TATAAT
260824 A
1 A
260825 CAAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.20
13 6 0.24
14 7 0.28
15 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATTTAATATAAT
Found at i:261408 original size:30 final size:28
Alignment explanation
Indices: 261350--261404 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
261340 AAAATTTTAA
261350 ATTTTTTTTACTAATTTAAAAATAAAAT
1 ATTTTTTTTACTAATTTAAAAATAAAAT
261378 ATTTATTTTTA-T-ATTATAAAAATAAAA
1 ATTT-TTTTTACTAATT-TAAAAATAAAA
261405 AATAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 3 0.12
28 16 0.64
29 6 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTTTTTTTACTAATTTAAAAATAAAAT
Found at i:262147 original size:3 final size:3
Alignment explanation
Indices: 262139--262168 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
262129 TTCCATAAAG
262139 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
262169 AACACTCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:263840 original size:2 final size:2
Alignment explanation
Indices: 263835--263872 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
263825 TATATATATA
263835 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
263873 ACTCTAACTC
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:264699 original size:2 final size:2
Alignment explanation
Indices: 264692--264717 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
264682 ATAATACTGA
264692 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
264718 AGAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:268514 original size:15 final size:15
Alignment explanation
Indices: 268489--268525 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
268479 GTTGTCACGA
*
268489 AAAAATTAAAATAAT
1 AAAAATAAAAATAAT
*
268504 TAAAATAAAAATAAT
1 AAAAATAAAAATAAT
268519 AAAAATA
1 AAAAATA
268526 TTTTATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAAAATAAT
Found at i:269283 original size:29 final size:29
Alignment explanation
Indices: 269232--269287 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
269222 GACAAAATTG
* *
269232 AATAAAAATAAAATTTATTAATTTAATCA
1 AATAAAAATAAAATATATAAATTTAATCA
269261 AATAAAAATAAAATGATA-AAATTTAAT
1 AATAAAAATAAAAT-ATATAAATTTAAT
269288 ATTTGCGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
AATAAAAATAAAATATATAAATTTAATCA
Found at i:272994 original size:30 final size:30
Alignment explanation
Indices: 272955--273023 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
272945 GAAAAATAAT
*
272955 GGTTCAATTAAACAAAAATAGTAACTTAAG
1 GGTTTAATTAAACAAAAATAGTAACTTAAG
* * * **
272985 GGTTTAATTAGATAAAAGTAGTATTTTAAG
1 GGTTTAATTAAACAAAAATAGTAACTTAAG
273015 GGTTTAATT
1 GGTTTAATT
273024 GGGAATAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.36
Consensus pattern (30 bp):
GGTTTAATTAAACAAAAATAGTAACTTAAG
Found at i:280578 original size:3 final size:3
Alignment explanation
Indices: 280570--280623 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
280560 GTATGTGTGT
280570 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
280618 TAA TAA
1 TAA TAA
280624 GCTTAAGATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:283377 original size:31 final size:31
Alignment explanation
Indices: 283342--283406 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
283332 TCAGAATTTC
283342 TAAATTATGGGATTCCTAGATTTAAGGAGAT
1 TAAATTATGGGATTCCTAGATTTAAGGAGAT
* * *
283373 TAAATTATGGGTTTCCTTGATTTAGGGAGAT
1 TAAATTATGGGATTCCTAGATTTAAGGAGAT
283404 TAA
1 TAA
283407 CCTTCCTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (31 bp):
TAAATTATGGGATTCCTAGATTTAAGGAGAT
Found at i:283714 original size:24 final size:24
Alignment explanation
Indices: 283636--283714 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 24
283626 TTTTTTTTTC
*
283636 TTGTTCAGCCTTCATTGCTGAAATT
1 TTGTTCAACCTTCATTGCTG-AATT
* * **
283661 TTTTTCTAATAGCCTTAATTGCTGTTTT
1 TTGTTC--A-A-CCTTCATTGCTGAATT
283689 TTGTTCAACCTTCATTGCTGAATT
1 TTGTTCAACCTTCATTGCTGAATT
283713 TT
1 TT
283715 TTTTTTTCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
24 15 0.37
25 6 0.15
26 1 0.02
27 1 0.02
28 7 0.17
29 11 0.27
ACGTcount: A:0.19, C:0.18, G:0.13, T:0.51
Consensus pattern (24 bp):
TTGTTCAACCTTCATTGCTGAATT
Found at i:286939 original size:31 final size:31
Alignment explanation
Indices: 286901--286996 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
286891 TTCAGAATTT
286901 TTAAATTATGGGATTCCTTGATTTAAGGAGA
1 TTAAATTATGGGATTCCTTGATTTAAGGAGA
* *
286932 TTAAATTATGGGTTTCCTTGATTTAGGGAGA
1 TTAAATTATGGGATTCCTTGATTTAAGGAGA
*
286963 TTAAATCATGGGATTCCTTGATTTAAGGAGA
1 TTAAATTATGGGATTCCTTGATTTAAGGAGA
286994 TTA
1 TTA
286997 GCCTTCCTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (31 bp):
TTAAATTATGGGATTCCTTGATTTAAGGAGA
Found at i:287197 original size:2 final size:2
Alignment explanation
Indices: 287185--287218 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
287175 ACATACATAA
*
287185 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
287219 GATTTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:305386 original size:10 final size:10
Alignment explanation
Indices: 305365--305393 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
305355 TTCCACAGCA
305365 TAGAAA-AAT
1 TAGAAAGAAT
305374 TAGAAAGAAT
1 TAGAAAGAAT
305384 TAGAAAGAAT
1 TAGAAAGAAT
305394 CACAGCCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (10 bp):
TAGAAAGAAT
Found at i:308113 original size:7 final size:7
Alignment explanation
Indices: 308101--308130 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
308091 TCCATAGCTA
308101 TTGAGAT
1 TTGAGAT
308108 TTGAGAT
1 TTGAGAT
308115 TTGAGAT
1 TTGAGAT
308122 TTGAGAT
1 TTGAGAT
308129 TT
1 TT
308131 TCAAGGTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (7 bp):
TTGAGAT
Found at i:310612 original size:20 final size:20
Alignment explanation
Indices: 310549--310614 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
310539 GATATTATTT
310549 TTTATTATAAAATT-ATATAA
1 TTTA-TATAAAATTAATATAA
* **
310569 -TTATATAAATTTTAATATTT
1 TTTATATAAA-ATTAATATAA
310589 TTTA-ATAAAATTAAATATAA
1 TTTATATAAAATT-AATATAA
310609 TTTATA
1 TTTATA
310615 ATTTACACAT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
18 6 0.17
19 7 0.20
20 18 0.51
21 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTATATAAAATTAATATAA
Found at i:310800 original size:13 final size:13
Alignment explanation
Indices: 310784--310813 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
310774 TATTTATAAA
310784 ATTTTATTTAAGC
1 ATTTTATTTAAGC
*
310797 ATTTTATTTAAGT
1 ATTTTATTTAAGC
310810 ATTT
1 ATTT
310814 AAACTCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (13 bp):
ATTTTATTTAAGC
Found at i:311363 original size:18 final size:19
Alignment explanation
Indices: 311324--311365 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
311314 TTTTACTCTC
* *
311324 TTTATAACTTTTTTTTTAA
1 TTTATAAATTTTTTTATAA
311343 TTTATAAATTTTTTTAT-A
1 TTTATAAATTTTTTTATAA
311361 TTTAT
1 TTTAT
311366 TATTTGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATAAATTTTTTTATAA
Found at i:316585 original size:2 final size:2
Alignment explanation
Indices: 316580--316608 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
316570 GAGAAAAAGA
316580 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
316609 ACCCGAAGGG
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:317824 original size:20 final size:22
Alignment explanation
Indices: 317787--317827 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
317777 TTGTTCAGCT
317787 GAAAAATGAAAGAAAGAAAAAG
1 GAAAAATGAAAGAAAGAAAAAG
317809 GAAAAAT-AAA-AAAGAAAAA
1 GAAAAATGAAAGAAAGAAAAA
317828 AAGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 3 0.16
22 7 0.37
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (22 bp):
GAAAAATGAAAGAAAGAAAAAG
Found at i:317881 original size:23 final size:24
Alignment explanation
Indices: 317854--317918 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
317844 GATCCGTATT
317854 TTTATTATTTTTATAT-TTAA-AA
1 TTTATTATTTTTATATATTAATAA
317876 TATTA-TATTTTTATATATTAATAA
1 T-TTATTATTTTTATATATTAATAA
*
317900 TTTATTTTATTTTATATAT
1 TTTATTAT-TTTTATATAT
317919 AGTTATATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 12 0.32
23 10 0.27
24 5 0.14
25 10 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTATTATTTTTATATATTAATAA
Found at i:317997 original size:16 final size:17
Alignment explanation
Indices: 317967--318024 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 17
317957 ATTATTGTTT
317967 TTTATTATC--TATTTA
1 TTTATTATCTATATTTA
317982 TTTA-TATCTATATTTA
1 TTTATTATCTATATTTA
317998 -TTATTAT-TATTATTT-
1 TTTATTATCTA-TATTTA
318013 TTTATTATCTAT
1 TTTATTATCTAT
318025 CTATCTATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.11
15 9 0.24
16 22 0.59
17 2 0.05
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTATCTATATTTA
Found at i:317999 original size:46 final size:46
Alignment explanation
Indices: 317949--318038 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
317939 GTATTATGTG
* * * *
317949 TTATTATTATTATTGTTTTTTATTATCTATTTATTTATATCTATAT
1 TTATTATTATTATTATTTTTTATTATCTATCTATCTATACCTATAT
317995 TTATTATTATTATTATTTTTTATTATCTATCTATCTATACCTAT
1 TTATTATTATTATTATTTTTTATTATCTATCTATCTATACCTAT
318039 CTAACATGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.64
Consensus pattern (46 bp):
TTATTATTATTATTATTTTTTATTATCTATCTATCTATACCTATAT
Found at i:318491 original size:2 final size:2
Alignment explanation
Indices: 318484--318516 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
318474 CATATAGATT
318484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
318517 GCAAAAAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:319114 original size:23 final size:23
Alignment explanation
Indices: 319087--319131 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
319077 AAAATTTACA
**
319087 TATTTATGTTTTTTATTATTTAT
1 TATTTATAATTTTTATTATTTAT
319110 TATTTATAATTTTTATTATTTA
1 TATTTATAATTTTTATTATTTA
319132 AAATATTATA
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:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TATTTATAATTTTTATTATTTAT
Found at i:319248 original size:27 final size:28
Alignment explanation
Indices: 319218--319287 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 28
319208 TATATATGTT
319218 ATTTTTTATATATTTA-AAATATTAAAA
1 ATTTTTTATATATTTATAAATATTAAAA
* * * **
319245 A-TTTATATAAATTTATACATATTAATT
1 ATTTTTTATATATTTATAAATATTAAAA
319272 ATTTATTTATATATTT
1 ATTT-TTTATATATTT
319288 TTTAATATAG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
26 12 0.36
27 10 0.30
28 2 0.06
29 9 0.27
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTTTATATATTTATAAATATTAAAA
Found at i:320281 original size:13 final size:12
Alignment explanation
Indices: 320263--320308 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
320253 AAAAACTTCA
320263 TATTTTTTATTT
1 TATTTTTTATTT
320275 GTATTTTTTATTT
1 -TATTTTTTATTT
*
320288 TTTTATTTTAATTT
1 TATT-TTTT-ATTT
320302 TATTTTT
1 TATTTTT
320309 AAATTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 3 0.10
13 19 0.66
14 7 0.24
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:320291 original size:21 final size:19
Alignment explanation
Indices: 320265--320308 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
320255 AAACTTCATA
*
320265 TTTTTTATTTGTATTTTTTAT
1 TTTTTTATTT-TA-ATTTTAT
320286 TTTTTTATTTTAATTTTAT
1 TTTTTTATTTTAATTTTAT
320305 TTTT
1 TTTT
320309 AAATTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 2 0.09
21 10 0.45
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (19 bp):
TTTTTTATTTTAATTTTAT
Found at i:322757 original size:27 final size:28
Alignment explanation
Indices: 322720--322783 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
322710 TTTGTTATGG
*
322720 ATAT-TTTAAAATTTTTAAAATTT-T-TT
1 ATATATTTAAAA-TATTAAAATTTATATT
*
322746 ATATATTTAAAATATTATAATTTATATT
1 ATATATTTAAAATATTAAAATTTATATT
322774 -TATATTTAAA
1 ATATATTTAAA
322784 TATGTATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 13 0.39
27 18 0.55
28 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATATTTAAAATATTAAAATTTATATT
Found at i:323161 original size:3 final size:3
Alignment explanation
Indices: 323153--323180 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
323143 CTTTCTATAC
323153 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
323181 CATCATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:323881 original size:38 final size:38
Alignment explanation
Indices: 323833--323942 Score: 125
Period size: 38 Copynumber: 2.9 Consensus size: 38
323823 ATTGAATTGG
* *
323833 CTGACAGTTAGAGAATTCAATTTGAAATTGACTGACGA
1 CTGACGGTTAGAGAATTCAATTTGAAATTGACCGACGA
* * *
323871 CTGACGGTTAGAGAATTCAATTT-AGCATT-AGCCGGCGG
1 CTGACGGTTAGAGAATTCAATTTGA-AATTGA-CCGACGA
**
323909 CTGACGACTAGAGAATTCAATTTGAAATTGACCG
1 CTGACGGTTAGAGAATTCAATTTGAAATTGACCG
323943 GTGGTTAGCG
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
37 2 0.03
38 56 0.93
39 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (38 bp):
CTGACGGTTAGAGAATTCAATTTGAAATTGACCGACGA
Found at i:328568 original size:40 final size:39
Alignment explanation
Indices: 328477--328616 Score: 167
Period size: 38 Copynumber: 3.6 Consensus size: 39
328467 TGGCCGACTG
** * *
328477 TTAGAGAATTCAATTTAAAATTGGCTGGCGACTG-ACGG
1 TTAGAGAATTCAATTTGGAATTGGCTGGCGGCTGAACGA
*
328515 TTAGAGAATTCAATTTGGAATTGGCTGGCGGGTGACACGA
1 TTAGAGAATTCAATTTGGAATTGGCTGGCGGCTGA-ACGA
** * *
328555 TTAGAGAATTCAATTTGGAATTGGCCAGTGGCT-AGCGA
1 TTAGAGAATTCAATTTGGAATTGGCTGGCGGCTGAACGA
*
328593 CTAGAGAATTCAATTTGGAATTGG
1 TTAGAGAATTCAATTTGGAATTGG
328617 TTGGTGACTG
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
38 56 0.63
39 1 0.01
40 32 0.36
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.29
Consensus pattern (39 bp):
TTAGAGAATTCAATTTGGAATTGGCTGGCGGCTGAACGA
Found at i:328640 original size:38 final size:38
Alignment explanation
Indices: 328478--328641 Score: 150
Period size: 38 Copynumber: 4.3 Consensus size: 38
328468 GGCCGACTGT
** *
328478 TAGAGAATTCAATTTAAAATTGGCTGGCGACTGACGGT
1 TAGAGAATTCAATTTGGAATTGGCTGGCGACTGACGGC
** **
328516 TAGAGAATTCAATTTGGAATTGGCTGGCGGGTGACACGAT
1 TAGAGAATTCAATTTGGAATTGGCTGGCGACTG--ACGGC
** * * *
328556 TAGAGAATTCAATTTGGAATTGGCCAGTGGCT-AGCGAC
1 TAGAGAATTCAATTTGGAATTGGCTGGCGACTGA-CGGC
* * *
328594 TAGAGAATTCAATTTGGAATTGGTTGGTGACTGATGGC
1 TAGAGAATTCAATTTGGAATTGGCTGGCGACTGACGGC
*
328632 TAGGGAATTC
1 TAGAGAATTC
328642 TAACGTGAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
37 1 0.01
38 71 0.68
39 1 0.01
40 32 0.30
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.29
Consensus pattern (38 bp):
TAGAGAATTCAATTTGGAATTGGCTGGCGACTGACGGC
Found at i:329277 original size:110 final size:110
Alignment explanation
Indices: 329084--329650 Score: 658
Period size: 110 Copynumber: 5.2 Consensus size: 110
329074 GGGTATCGGC
* * * * * *
329084 GGATTGGTCCCGAAATAAATCATCGTTTAGAGTTGTAAAGCGATGTACGAACGCCCTTTGCT-TT
1 GGATTGGCCCCGAAATAAATCATCGTCTAGAGTCGTAAAGCGACGTACGAACGCCCTTT-ATATA
*
329148 GGATAATTCATTTTTTACATTAATTACATAATATTCAGGCACCAAG
65 GGATAATTCATTTTTTACATTAATTACATAATATTCTGGCACCAAG
* * * *
329194 GGATTGGCCCCGAAATAAATTATCGTCTAGAGTCGTAAAGTGACGTACGAATGCCCTTTACATAG
1 GGATTGGCCCCGAAATAAATCATCGTCTAGAGTCGTAAAGCGACGTACGAACGCCCTTTATATAG
* *
329259 GATAATTCATTTTTTACATTAATTACGTAATATTCTGGCACTAAG
66 GATAATTCATTTTTTACATTAATTACATAATATTCTGGCACCAAG
* * * **
329304 GGATTGGCCTCGAAATAAATCATCGTCAAGAGTCGTAAAGCGACATACGAATACCCTTTATATAG
1 GGATTGGCCCCGAAATAAATCATCGTCTAGAGTCGTAAAGCGACGTACGAACGCCCTTTATATAG
* * *
329369 GATAATTCATTTTTTACATAAATTGCGTAATATTCTGGCACCAAG
66 GATAATTCATTTTTTACATTAATTACATAATATTCTGGCACCAAG
* * * *
329414 GGATTGGCCCTGAAACAAATCATCGTCAAGAGTCGT-AAGCGACATACGAACGCCCTTTATATAG
1 GGATTGGCCCCGAAATAAATCATCGTCTAGAGTCGTAAAGCGACGTACGAACGCCCTTTATATAG
* * * *
329478 GATAATTCTATTTTTTGCATTAATTACATAA-ATTCGGGCACTAAA
66 GATAATTC-ATTTTTTACATTAATTACATAATATTCTGGCACCAAG
* *** * ** * * *
329523 AGATTGGCCCCGAAATAGGCCATCGTCTAGAGTCATAAA-ATAGCGTACGAACACCCTCTATGTA
1 GGATTGGCCCCGAAATAAATCATCGTCTAGAGTCGTAAAGCGA-CGTACGAACGCCCTTTATAT-
** * * *
329587 AGG-TAATTCATTTTTTATGTAAATTACATAATATTTTGACACCAAG
64 AGGATAATTCATTTTTTACATTAATTACATAATATTCTGGCACCAAG
*
329633 GGATTGGCTCCGAAATAA
1 GGATTGGCCCCGAAATAA
329651 GTCTCTCTAA
Statistics
Matches: 390, Mismatches: 61, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
109 92 0.24
110 295 0.76
111 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (110 bp):
GGATTGGCCCCGAAATAAATCATCGTCTAGAGTCGTAAAGCGACGTACGAACGCCCTTTATATAG
GATAATTCATTTTTTACATTAATTACATAATATTCTGGCACCAAG
Found at i:329621 original size:219 final size:220
Alignment explanation
Indices: 329148--329647 Score: 639
Period size: 219 Copynumber: 2.3 Consensus size: 220
329138 CCTTTGCTTT
* * *
329148 GGATAATTCATTTTTTACATTAATTACATAATATTCAGGCACCAAGGGATTGGCCCCGAAATAAA
1 GGATAATTCATTTTTTACATAAATTACATAATATTCTGGCACCAAGGGATTGGCCCCGAAACAAA
* * * * *
329213 TTATCGTCTAGAGTCGTAAAGTGACGTACGAATGCCCTTTACATAGGATAATTCATTTTTTACAT
66 TCATCGTCAAGAGTCGTAAAGCGACATACGAACGCCCTTTACATAGGATAATTCATTTTTTACAT
* * ** * * *
329278 TAATTACGTAATATTCTGGCACTAAGGGATTGGCCTCGAAATAAATCATCGTCAAGAGTCGTAAA
131 TAATTACATAATATTCGGGCACTAAAAGATTGGCCCCGAAATAAACCATCGTCAAGAGTCATAAA
* * *
329343 GCGACATACGAATACCCTTTATATA
196 GAGACATACGAACACCCTCTATATA
* * *
329368 GGATAATTCATTTTTTACATAAATTGCGTAATATTCTGGCACCAAGGGATTGGCCCTGAAACAAA
1 GGATAATTCATTTTTTACATAAATTACATAATATTCTGGCACCAAGGGATTGGCCCCGAAACAAA
* *
329433 TCATCGTCAAGAGTCGT-AAGCGACATACGAACGCCCTTTATATAGGATAATTCTATTTTTTGCA
66 TCATCGTCAAGAGTCGTAAAGCGACATACGAACGCCCTTTACATAGGATAATTC-ATTTTTTACA
** *
329497 TTAATTACATAA-ATTCGGGCACTAAAAGATTGGCCCCGAAATAGGCCATCGTCTAGAGTCATAA
130 TTAATTACATAATATTCGGGCACTAAAAGATTGGCCCCGAAATAAACCATCGTCAAGAGTCATAA
* * *
329561 A-ATAGCGTACGAACACCCTCTATGTAA
195 AGAGA-CATACGAACACCCTCTATAT-A
** * * *
329588 GG-TAATTCATTTTTTATGTAAATTACATAATATTTTGACACCAAGGGATTGGCTCCGAAA
1 GGATAATTCATTTTTTACATAAATTACATAATATTCTGGCACCAAGGGATTGGCCCCGAAA
329648 TAAGTCTCTC
Statistics
Matches: 240, Mismatches: 37, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
218 1 0.00
219 142 0.59
220 97 0.40
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (220 bp):
GGATAATTCATTTTTTACATAAATTACATAATATTCTGGCACCAAGGGATTGGCCCCGAAACAAA
TCATCGTCAAGAGTCGTAAAGCGACATACGAACGCCCTTTACATAGGATAATTCATTTTTTACAT
TAATTACATAATATTCGGGCACTAAAAGATTGGCCCCGAAATAAACCATCGTCAAGAGTCATAAA
GAGACATACGAACACCCTCTATATA
Found at i:329842 original size:10 final size:10
Alignment explanation
Indices: 329827--329856 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
329817 AGTCACCCTT
329827 ATAAAAAATA
1 ATAAAAAATA
329837 AT-AAAAATA
1 ATAAAAAATA
329846 ATAAAAAATA
1 ATAAAAAATA
329856 A
1 A
329857 AATAGTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:331559 original size:27 final size:27
Alignment explanation
Indices: 331529--331587 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
331519 TTATCATGTA
* *
331529 TTTAAAATAATTTATATTTATA-TAAAT
1 TTTAAAAT-ATTAATAATTATATTAAAT
* *
331556 TTTAATATATTAATAATTATATTATAT
1 TTTAAAATATTAATAATTATATTAAAT
331583 TTTAA
1 TTTAA
331588 TTTTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTAAAATATTAATAATTATATTAAAT
Found at i:332542 original size:21 final size:21
Alignment explanation
Indices: 332518--332559 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
332508 GTTTAAAAAG
*
332518 TATTAATA-ATTTTATCATTAA
1 TATTAATATA-TTTATAATTAA
*
332539 TATTTATATATTTATAATTAA
1 TATTAATATATTTATAATTAA
332560 ATTTAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTAATATATTTATAATTAA
Found at i:336019 original size:24 final size:23
Alignment explanation
Indices: 335975--336021 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
335965 TTATTTTATA
* * *
335975 TTAAGTTTAATATCATTAATTTT
1 TTAAGTTTAAAATAATAAATTTT
335998 TTAAGTTTTAAAATAATAAATTTT
1 TTAAG-TTTAAAATAATAAATTTT
336022 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
TTAAGTTTAAAATAATAAATTTT
Found at i:336039 original size:32 final size:31
Alignment explanation
Indices: 335990--336059 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
335980 TTTAATATCA
335990 TTAA-TTTTTTAAGTTTTA-AAATAATAA-ATT
1 TTAATTTTTTTAAGTTTTATAAATAA-AATA-T
*
336020 TTAATTTTTTTAAATTTTTATAAATAAAATAT
1 TTAATTTTTTT-AAGTTTTATAAATAAAATAT
336052 TTAATTTT
1 TTAATTTT
336060 ATATGATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 4 0.11
31 6 0.17
32 18 0.51
33 7 0.20
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TTAATTTTTTTAAGTTTTATAAATAAAATAT
Found at i:336292 original size:23 final size:22
Alignment explanation
Indices: 336254--336385 Score: 81
Period size: 23 Copynumber: 5.8 Consensus size: 22
336244 TTTCTCATTA
*
336254 AAAAAATA-AAAAATAATGATAT
1 AAAAAATATAAATATAAT-ATAT
* *
336276 AAAAAATATAAATATAAAATTTT
1 AAAAAATATAAATATAATA-TAT
* * *
336299 ATATAATATAAATTTTTAATATATT
1 AAAAAATATAAA--TATAATATA-T
*
336324 AAAATTTATATAAATATAATAT-T
1 AAAA--AATATAAATATAATATAT
** *
336347 -TTAAATATAATTATAATATAT
1 AAAAAATATAAATATAATATAT
336368 AAAAATATATAAATATAA
1 AAAAA-ATATAAATATAA
336386 AATTTAATTA
Statistics
Matches: 81, Mismatches: 19, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
20 14 0.17
21 1 0.01
22 12 0.15
23 31 0.38
24 1 0.01
25 15 0.19
27 7 0.09
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.39
Consensus pattern (22 bp):
AAAAAATATAAATATAATATAT
Found at i:336308 original size:17 final size:18
Alignment explanation
Indices: 336281--336349 Score: 83
Period size: 17 Copynumber: 4.1 Consensus size: 18
336271 GATATAAAAA
336281 ATATAAATATAAAATTTT
1 ATATAAATATAAAATTTT
*
336299 ATAT-AATATAAATTTTT
1 ATATAAATATAAAATTTT
*
336316 A-ATATAT-TAAAA-TTT
1 ATATAAATATAAAATTTT
*
336331 ATATAAATATAATATTTT
1 ATATAAATATAAAATTTT
336349 A
1 A
336350 AATATAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 4 0.10
16 11 0.26
17 19 0.45
18 8 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATAAATATAAAATTTT
Found at i:336311 original size:16 final size:17
Alignment explanation
Indices: 336281--336349 Score: 72
Period size: 16 Copynumber: 4.1 Consensus size: 17
336271 GATATAAAAA
336281 ATATAAATATAAAATTTT
1 ATATAAATAT-AAATTTT
336299 ATAT-AATATAAATTTT
1 ATATAAATATAAATTTT
* *
336315 -TA-ATATATTAAAATTT
1 ATATAAATA-TAAATTTT
336331 ATATAAATATAATATTTT
1 ATATAAATATAA-ATTTT
336349 A
1 A
336350 AATATAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 5 0.12
16 14 0.33
17 10 0.24
18 13 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATAAATATAAATTTT
Found at i:336330 original size:33 final size:34
Alignment explanation
Indices: 336290--336376 Score: 106
Period size: 35 Copynumber: 2.6 Consensus size: 34
336280 AATATAAATA
*
336290 TAAAATTT-TATATAATATAA-ATTTTTAATATAT
1 TAAAATTTATATA-AATATAATATTTTAAATATAT
336323 TAAAATTTATATAAATATAATATTTTAAATATAAT
1 TAAAATTTATATAAATATAATATTTTAAATAT-AT
* * *
336358 TATAATATATAAAAATATA
1 TAAAATTTATATAAATATA
336377 TAAATATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
33 15 0.32
34 14 0.30
35 18 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
TAAAATTTATATAAATATAATATTTTAAATATAT
Found at i:336332 original size:32 final size:35
Alignment explanation
Indices: 336290--336355 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 35
336280 AATATAAATA
*
336290 TAAAATTTTATAT-AATATAA-ATTTTTAATATAT
1 TAAAATTTTATATAAATATAATATTTTAAATATAT
336323 TAAAA-TTTATATAAATATAATATTTTAAATATA
1 TAAAATTTTATATAAATATAATATTTTAAATATA
336356 ATTATAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 7 0.23
33 12 0.40
34 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (35 bp):
TAAAATTTTATATAAATATAATATTTTAAATATAT
Found at i:336380 original size:29 final size:27
Alignment explanation
Indices: 336348--336415 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
336338 TATAATATTT
*
336348 TAAATATAATTATAATATATAAAAATATA
1 TAAATATAATT-TAAT-TATAAAAAAATA
336377 TAAATATAAAATTTAATTATAAAAAAATA
1 TAAATAT--AATTTAATTATAAAAAAATA
*
336406 TAAAGATAAT
1 TAAATATAAT
336416 AAAAAAGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 3 0.09
29 24 0.69
30 4 0.11
31 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (27 bp):
TAAATATAATTTAATTATAAAAAAATA
Found at i:336385 original size:16 final size:16
Alignment explanation
Indices: 336272--336414 Score: 67
Period size: 15 Copynumber: 9.4 Consensus size: 16
336262 AAAAATAATG
336272 ATATAAAAA-ATATAA
1 ATATAAAAATATATAA
* *
336287 ATATAAAATTTTATATA
1 ATATAAAAATATATA-A
* *
336304 ATAT--AAATTTTTAA
1 ATATAAAAATATATAA
*
336318 TATATTAAAATTTATATAA
1 -ATA-TAAAA-ATATATAA
* *
336337 ATAT-AATAT-TTTAA
1 ATATAAAAATATATAA
336351 ATAT---AAT-TATAA
1 ATATAAAAATATATAA
336363 TATATAAAAATATATAA
1 -ATATAAAAATATATAA
336380 ATAT-AAAAT-T-TAA
1 ATATAAAAATATATAA
* *
336393 TTATAAAAAAATATAA
1 ATATAAAAATATATAA
*
336409 AGATAA
1 ATATAA
336415 TAAAAAAGGA
Statistics
Matches: 97, Mismatches: 16, Indels: 29
0.68 0.11 0.20
Matches are distributed among these distances:
12 6 0.06
13 10 0.10
14 14 0.14
15 25 0.26
16 21 0.22
17 11 0.11
18 5 0.05
19 5 0.05
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (16 bp):
ATATAAAAATATATAA
Found at i:336911 original size:2 final size:2
Alignment explanation
Indices: 336904--336929 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
336894 TTTGACCTCC
336904 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
336930 GAAAAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:337464 original size:21 final size:21
Alignment explanation
Indices: 337403--337464 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
337393 TTTATTATTT
*
337403 TTTAAATAA-TAA-T-ATAAA
1 TTTAAATAATTAATTAATTAA
*
337421 TTTAAATTATT--TTAAGTTAAA
1 TTTAAATAATTAATTAA-TT-AA
337442 TTTAAATAATTAATTAATTAA
1 TTTAAATAATTAATTAATTAA
337463 TT
1 TT
337465 AAGATCTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
18 9 0.26
19 2 0.06
20 1 0.03
21 16 0.47
22 2 0.06
23 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTAAATAATTAATTAATTAA
Found at i:338383 original size:12 final size:13
Alignment explanation
Indices: 338368--338399 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
338358 AAAAATTAGA
338368 TTAATTTAAT-TT
1 TTAATTTAATATT
338380 TTAATTTAATATT
1 TTAATTTAATATT
338393 TT-ATTTA
1 TTAATTTA
338400 TCGATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTAATTTAATATT
Found at i:339144 original size:20 final size:20
Alignment explanation
Indices: 339115--339155 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
339105 ATTTAATAAA
*
339115 TTAATAATTTATATTATATT
1 TTAATAATTTATATAATATT
* *
339135 TTAATTATTTTTATAATATT
1 TTAATAATTTATATAATATT
339155 T
1 T
339156 ATATCATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAATAATTTATATAATATT
Found at i:339308 original size:13 final size:15
Alignment explanation
Indices: 339290--339322 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
339280 AAAAATTTAT
339290 ATTAATT-AATTAA-
1 ATTAATTCAATTAAG
339303 ATTAATTCAATTAAG
1 ATTAATTCAATTAAG
339318 ATTAA
1 ATTAA
339323 AATTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (15 bp):
ATTAATTCAATTAAG
Found at i:339615 original size:34 final size:33
Alignment explanation
Indices: 339574--339670 Score: 88
Period size: 39 Copynumber: 2.7 Consensus size: 33
339564 ATAATAAAAT
339574 TTAAATTTTTAATTTTATATTAAAAA-TTATATTA
1 TTAAATTTTTAATTTT-TATTAAAAATTTATA-TA
*
339608 TTAAATTTAATATATATTTTTTATTAAATATTTATCATA
1 TTAAATTT--T-TA-A-TTTTTATTAAAAATTTAT-ATA
*
339647 TTTAATTTTTAAATTTTTATTAAA
1 TTAAATTTTT-AATTTTTATTAAA
339671 CCTACTTCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
34 8 0.15
35 11 0.21
36 3 0.06
37 4 0.08
38 9 0.17
39 17 0.32
40 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (33 bp):
TTAAATTTTTAATTTTTATTAAAAATTTATATA
Found at i:339647 original size:23 final size:22
Alignment explanation
Indices: 339600--339663 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 22
339590 ATATTAAAAA
339600 TTATATTATTAAATTTAATATATAT
1 TTAT-TTATTAAATTT--TATATAT
339625 TT-TTTATTAAATATTTATCATAT
1 TTATTTATTAAAT-TTTAT-ATAT
339648 TTAATTT-TTAAATTTT
1 TT-ATTTATTAAATTTT
339664 TATTAAACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
22 3 0.09
23 18 0.51
24 9 0.26
25 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTTATTAAATTTTATATAT
Found at i:341509 original size:18 final size:18
Alignment explanation
Indices: 341472--341520 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
341462 ATCATATTTT
*
341472 TATTATTATATATATATA
1 TATTATAATATATATATA
341490 TATTATAATA-ATATAATA
1 TATTATAATATATAT-ATA
* *
341508 TAATCTAATATAT
1 TATTATAATATAT
341521 TCTTTAGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 20 0.77
19 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTATAATATATATATA
Found at i:342194 original size:10 final size:10
Alignment explanation
Indices: 342179--342211 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
342169 AAAAGGACAA
342179 ATATATGTAT
1 ATATATGTAT
342189 ATATA--TAT
1 ATATATGTAT
342197 ATATATGTAT
1 ATATATGTAT
342207 ATATA
1 ATATA
342212 ATGCTATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (10 bp):
ATATATGTAT
Found at i:345475 original size:16 final size:17
Alignment explanation
Indices: 345456--345488 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
345446 TTTTTTGTTA
345456 TTTAAAT-TTTATATTT
1 TTTAAATATTTATATTT
345472 TTTAAATATTTATATTT
1 TTTAAATATTTATATTT
345489 GATATTTATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATATTTATATTT
Found at i:345495 original size:13 final size:13
Alignment explanation
Indices: 345454--345512 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
345444 AATTTTTTGT
* *
345454 TATTTAAATTTTA
1 TATTTATATTTAA
*
345467 TATTT-T-TTAAA
1 TATTTATATTTAA
*
345478 TATTTATATTTGA
1 TATTTATATTTAA
*
345491 TATTTATTTTTAA
1 TATTTATATTTAA
*
345504 TATATATAT
1 TATTTATAT
345513 ATATATATGT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
11 8 0.23
12 1 0.03
13 26 0.74
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:347831 original size:24 final size:23
Alignment explanation
Indices: 347791--347836 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
347781 ATTAATTTTT
347791 TAAATTTAATTATAAAAAATATA
1 TAAATTTAATTATAAAAAATATA
347814 TAAATTTTAA-TAT-AAAAATATA
1 TAAA-TTTAATTATAAAAAATATA
347836 T
1 T
347837 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.45
23 7 0.32
24 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATTTAATTATAAAAAATATA
Found at i:347982 original size:21 final size:22
Alignment explanation
Indices: 347958--348013 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
347948 ATATTTTTAA
347958 TTTAATTAAATTAATTT-AAAT
1 TTTAATTAAATTAATTTAAAAT
**
347979 TTTAAAAAAATT-ATTTAAAAT
1 TTTAATTAAATTAATTTAAAAT
* *
348000 TTAAATTATATTAA
1 TTTAATTAAATTAA
348014 ATCGATGCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.15
21 22 0.81
22 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAATTAAATTAATTTAAAAT
Found at i:347994 original size:20 final size:21
Alignment explanation
Indices: 347956--348004 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
347946 AAATATTTTT
**
347956 AATTTAATTAAATTAATTTAA
1 AATTTAAAAAAATTAATTTAA
*
347977 ATTTTAAAAAAATT-ATTTAA
1 AATTTAAAAAAATTAATTTAA
347997 AATTTAAA
1 AATTTAAA
348005 TTATATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTAAAAAAATTAATTTAA
Found at i:348432 original size:12 final size:12
Alignment explanation
Indices: 348414--348454 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
348404 ATATAAAAAT
348414 AATATTTTTAAA
1 AATATTTTTAAA
*
348426 TATA-TTTTAAA
1 AATATTTTTAAA
*
348437 AATATTTTAAAA
1 AATATTTTTAAA
348449 AATATT
1 AATATT
348455 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATTTTTAAA
Found at i:348448 original size:11 final size:11
Alignment explanation
Indices: 348414--348454 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
348404 ATATAAAAAT
348414 AATATTTTTAAA
1 AATA-TTTTAAA
*
348426 TATATTTTAAA
1 AATATTTTAAA
348437 AATATTTTAAAA
1 AATATTTT-AAA
348449 AATATT
1 AATATT
348455 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 14 0.54
12 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AATATTTTAAA
Found at i:351913 original size:25 final size:25
Alignment explanation
Indices: 351879--351928 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
351869 GAAGGCTTTG
351879 CATTGCCAAATATCCTGCATCCGTC
1 CATTGCCAAATATCCTGCATCCGTC
*
351904 CATTGCCAAATATCCTGCATTCGTC
1 CATTGCCAAATATCCTGCATCCGTC
351929 AGATGTCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.34, G:0.12, T:0.30
Consensus pattern (25 bp):
CATTGCCAAATATCCTGCATCCGTC
Found at i:359842 original size:25 final size:24
Alignment explanation
Indices: 359783--359842 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
359773 AACATAATTT
* *
359783 TATTTATCTAAATTTTATTTAATA
1 TATTTATTTAAATTTTATTTAAGA
*
359807 TATTAATTTTAAATTTTATTTAAGA
1 TATTTA-TTTAAATTTTATTTAAGA
*
359832 TTGTTTATTTA
1 -TATTTATTTA
359843 TAAGTAAGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 5 0.17
25 20 0.69
26 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (24 bp):
TATTTATTTAAATTTTATTTAAGA
Found at i:359947 original size:35 final size:35
Alignment explanation
Indices: 359895--359979 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 35
359885 TTTTTAAAAA
* *
359895 AATATATTTTTAAAAATTTTAATAT-TCAATAATTT
1 AATAT-TTTTTAAAAATTTTAAAATATAAATAATTT
*
359930 AATATTTTTTATTAAATTTTAAAATATAAATAATTT
1 AATATTTTTTA-AAAATTTTAAAATATAAATAATTT
359966 AATAAATTTTTTAA
1 AAT--ATTTTTTAA
359980 TATTTATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
34 6 0.14
35 16 0.38
36 12 0.29
38 8 0.19
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (35 bp):
AATATTTTTTAAAAATTTTAAAATATAAATAATTT
Found at i:362852 original size:71 final size:74
Alignment explanation
Indices: 362762--362914 Score: 174
Period size: 75 Copynumber: 2.1 Consensus size: 74
362752 AACAAAATTT
**
362762 TAAAAAATAAAATTAAATT-AA-TTAAAAAAAT-TATGT-TGAAATT-AATATATTAATTATTAA
1 TAAAAAATAAAATTAAATTAAATTTAAAAAAATATAT-TAAAAAATTAAAT-TATTAATTATTAA
*
362822 TTTTAATAAAG
64 TTTTAATAAAA
* * *
362833 TAAAAAATAAAA-TATAATTAAATTTTAAAATAATATATTAAAAAATTAAATTTTTAATTTTTAA
1 TAAAAAATAAAATTA-AATTAAA-TTTAAAAAAATATATTAAAAAATTAAATTATTAATTATTAA
362897 TTTTAATAAAA
64 TTTTAATAAAA
362908 TAAAAAA
1 TAAAAAA
362915 ATTTACATTA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
70 2 0.03
71 16 0.23
72 2 0.03
74 10 0.14
75 36 0.52
76 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (74 bp):
TAAAAAATAAAATTAAATTAAATTTAAAAAAATATATTAAAAAATTAAATTATTAATTATTAATT
TTAATAAAA
Found at i:363070 original size:13 final size:13
Alignment explanation
Indices: 363044--363089 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
363034 AAATTTTAAT
*
363044 ATTTA-TAAAAAA
1 ATTTATTAAATAA
363056 ATTTATTAAATAA
1 ATTTATTAAATAA
363069 ATTT-TTAAAATATA
1 ATTTATT-AAATA-A
363083 ATTTATT
1 ATTTATT
363090 TTTAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 7 0.24
13 15 0.52
14 5 0.17
15 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTATTAAATAA
Found at i:363343 original size:14 final size:14
Alignment explanation
Indices: 363324--363354 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
363314 AAGTGGAATC
*
363324 AAATTTTTTTATTT
1 AAATTTTGTTATTT
363338 AAATTTTGTTATTT
1 AAATTTTGTTATTT
363352 AAA
1 AAA
363355 AATTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
AAATTTTGTTATTT
Found at i:363737 original size:22 final size:21
Alignment explanation
Indices: 363712--363767 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
363702 TTTAATAATT
* *
363712 TAATAATTAATTTTTATATTAA
1 TAATAATTAATATTAAT-TTAA
363734 TAATAATTAATATTAATTTAA
1 TAATAATTAATATTAATTTAA
363755 T-ATAATTACATAT
1 TAATAATTA-ATAT
363768 GCATAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 7 0.23
21 9 0.29
22 15 0.48
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATAATTAATATTAATTTAA
Found at i:372274 original size:24 final size:23
Alignment explanation
Indices: 372238--372283 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
372228 GATAGCATGT
*
372238 TATTTTATGATGTTGAAAATCAAA
1 TATTTTATCATGTT-AAAATCAAA
* *
372262 TATTTTGTCATGTTCAAATCAA
1 TATTTTATCATGTTAAAATCAA
372284 TGGAATTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (23 bp):
TATTTTATCATGTTAAAATCAAA
Found at i:374700 original size:2 final size:2
Alignment explanation
Indices: 374693--374721 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
374683 TGTGGACATG
374693 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
374722 ATACTTCTAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:375702 original size:8 final size:8
Alignment explanation
Indices: 375689--375713 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
375679 TATGTGTTGA
375689 ACATGAAT
1 ACATGAAT
375697 ACATGAAT
1 ACATGAAT
375705 ACATGAAT
1 ACATGAAT
375713 A
1 A
375714 AGAAGCTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (8 bp):
ACATGAAT
Found at i:375834 original size:2 final size:2
Alignment explanation
Indices: 375829--375869 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
375819 TGTGTGCGTG
375829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
375870 TATTCCTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:378459 original size:16 final size:15
Alignment explanation
Indices: 378399--378469 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
378389 ATGCATTGGA
378399 TTTTT-TTTAATTAT
1 TTTTTATTTAATTAT
*
378413 TTTTGTATTGT-ATTAA
1 TTTT-TATT-TAATTAT
* *
378429 TATGT-TTTAATTAT
1 TTTTTATTTAATTAT
378443 TTTTTATTTATATTAT
1 TTTTTATTTA-ATTAT
378459 TTTTTATTTAA
1 TTTTTATTTAA
378470 AAATTATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
13 1 0.02
14 13 0.29
15 7 0.16
16 23 0.51
17 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.70
Consensus pattern (15 bp):
TTTTTATTTAATTAT
Found at i:378492 original size:15 final size:15
Alignment explanation
Indices: 378471--378518 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
378461 TTTATTTAAA
378471 AATTATTAAAATTAT
1 AATTATTAAAATTAT
* *
378486 CATTATTGAAATTAT
1 AATTATTAAAATTAT
378501 AATTA-T--AATTAT
1 AATTATTAAAATTAT
378513 AATTAT
1 AATTAT
378519 GAATATGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 11 0.38
14 1 0.03
15 17 0.59
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
AATTATTAAAATTAT
Found at i:378687 original size:22 final size:20
Alignment explanation
Indices: 378656--378707 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
378646 AAATATTATG
378656 AGTTGATTTTTAAAA-TGAAA
1 AGTT-ATTTTTAAAATTGAAA
*
378676 AGGTGTATTTTTAAAATTGAAT
1 A-GT-TATTTTTAAAATTGAAA
378698 AGTTATTTTT
1 AGTTATTTTT
378708 TTAAAGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.29
21 14 0.50
22 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (20 bp):
AGTTATTTTTAAAATTGAAA
Found at i:378976 original size:99 final size:97
Alignment explanation
Indices: 378818--379010 Score: 248
Period size: 99 Copynumber: 2.0 Consensus size: 97
378808 AATAACATCT
*
378818 ACTCAATTAAAAAATAACAAAAAAATTATAAAATCAAAAATAAGTAATTTAATTTCTTTTAAATA
1 ACTCAATTAAAAAATAAAAAAAAAATTATAAAATCAAAAATAAGTAATTTAATTTCTTTTAAA-A
* *
378883 AA-TAAAA-GAAACTTTTAAACTTTTTCTTTCA
65 AATTAAAACAAAACTTTCAAACTTTTTCTTTCA
* ** *
378914 ACTCAATT-AAAAATAAAAATAAAAATATTATAAAATTAAGTTATATGTAATTTAATTTCTTTTA
1 ACTCAATTAAAAAAT-AAAA-AAAAA-ATTATAAAATCAA-AAATAAGTAATTTAATTTCTTTTA
*
378978 AAAAATTAAAACAAAACTTTCATACTTTTTCTT
62 AAAAATTAAAACAAAACTTTCAAACTTTTTCTT
379011 CTTTTAAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
95 6 0.07
96 11 0.13
97 5 0.06
98 15 0.18
99 28 0.34
100 18 0.22
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (97 bp):
ACTCAATTAAAAAATAAAAAAAAAATTATAAAATCAAAAATAAGTAATTTAATTTCTTTTAAAAA
ATTAAAACAAAACTTTCAAACTTTTTCTTTCA
Found at i:379214 original size:2 final size:2
Alignment explanation
Indices: 379202--379236 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
379192 GTAGGCTAGT
*
379202 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
379237 GTGGCAGCGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:384697 original size:19 final size:19
Alignment explanation
Indices: 384673--384714 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
384663 TTGAGCTCAG
384673 AATAATATTTTTAAATTAA
1 AATAATATTTTTAAATTAA
384692 AATAATATTTTTAAATTAA
1 AATAATATTTTTAAATTAA
384711 AATA
1 AATA
384715 GTATATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAATATTTTTAAATTAA
Found at i:384912 original size:19 final size:19
Alignment explanation
Indices: 384888--384926 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
384878 AATTTATATG
* *
384888 AAATAAGTCATTAACTTAA
1 AAATAAATCATTAACATAA
*
384907 AAATAAATCTTTAACATAA
1 AAATAAATCATTAACATAA
384926 A
1 A
384927 TTAATTTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATAAATCATTAACATAA
Found at i:385862 original size:2 final size:2
Alignment explanation
Indices: 385855--385882 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
385845 AGAAAAAGAA
385855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
385883 TTAGGAAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:386587 original size:30 final size:29
Alignment explanation
Indices: 386505--386588 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 29
386495 AATTCAACAA
*
386505 ATAAA-AATTTTATAAATATTAAAATTTAAAT
1 ATAAATAA-TTTATAAAT-TT-ATATTTAAAT
*
386536 ATAAATATTTTA-AAATTTTATATTTAATAT
1 ATAAATAATTTATAAA-TTTATATTTAA-AT
*
386566 ATTAATAATTTATAAATTTATAT
1 ATAAATAATTTATAAATTTATAT
386589 ATTATTAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
29 7 0.16
30 24 0.53
31 13 0.29
32 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAAATAATTTATAAATTTATATTTAAAT
Found at i:386597 original size:23 final size:23
Alignment explanation
Indices: 386520--386597 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
386510 AATTTTATAA
*
386520 ATATTAA-AA-TTTAAATATAAAT
1 ATATTAATAATTTTAAAT-TTAAT
* *
386542 ATTTTAA-AATTTTATATTTAAT
1 ATATTAATAATTTTAAATTTAAT
386564 ATATTAATAATTTATAAATTT-AT
1 ATATTAATAATTT-TAAATTTAAT
*
386587 ATATTATTAAT
1 ATATTAATAAT
386598 GAGTCATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
22 18 0.38
23 23 0.49
24 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTAATAATTTTAAATTTAAT
Found at i:388844 original size:26 final size:26
Alignment explanation
Indices: 388808--388878 Score: 142
Period size: 26 Copynumber: 2.7 Consensus size: 26
388798 GAGAAATAGT
388808 TAAATTTACCATTTTACTAAGTTTCA
1 TAAATTTACCATTTTACTAAGTTTCA
388834 TAAATTTACCATTTTACTAAGTTTCA
1 TAAATTTACCATTTTACTAAGTTTCA
388860 TAAATTTACCATTTTACTA
1 TAAATTTACCATTTTACTA
388879 TTTACTTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.46
Consensus pattern (26 bp):
TAAATTTACCATTTTACTAAGTTTCA
Found at i:392740 original size:2 final size:2
Alignment explanation
Indices: 392729--392777 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
392719 TTGTAAACTT
392729 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
392770 TA TA TA TA
1 TA TA TA TA
392778 AAATGAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:393833 original size:13 final size:12
Alignment explanation
Indices: 393810--393857 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 12
393800 AAACTCGAAA
393810 TAAATTTTAAACT
1 TAAA-TTTAAACT
*
393823 CTAAATTTAAAATT
1 -TAAATTT-AAACT
393837 TAAA-TTAAACT
1 TAAATTTAAACT
393848 TAAATTTAAA
1 TAAATTTAAA
393858 TCTTTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 8 0.27
12 7 0.23
13 7 0.23
14 8 0.27
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATTTAAACT
Found at i:394245 original size:23 final size:23
Alignment explanation
Indices: 394202--394245 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
394192 TTAATTTATT
* *
394202 TTTAAAATATAATATTTAATAAA
1 TTTAAAATAAAATATTCAATAAA
394225 TTTAAAATTAAAATA-TCAATA
1 TTTAAAA-TAAAATATTCAATA
394246 TTTATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAAATAAAATATTCAATAAA
Found at i:394699 original size:25 final size:26
Alignment explanation
Indices: 394648--394700 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
394638 TCACAGATAT
*
394648 AAAAATAAATATAATATTATATATTA
1 AAAAATAAATATAATATTAAATATTA
*
394674 AAAAATAAGATA-AAT-TTAAATTTTA
1 AAAAATAA-ATATAATATTAAATATTA
394699 AA
1 AA
394701 TATTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
26 11 0.46
27 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAAATAAATATAATATTAAATATTA
Found at i:394986 original size:3 final size:3
Alignment explanation
Indices: 394978--395011 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
394968 CCAAAACATG
394978 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
395012 TTGATTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:395149 original size:31 final size:31
Alignment explanation
Indices: 395079--395149 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
395069 TTTATACTAT
* * * *
395079 AAAAATATTTTTAATATTATTTTAAATAATT
1 AAAAAAATTTTTAATATTAATCTAAATAATA
* *
395110 ATATAAATTTTTAA-ATTAATCTAAATGAATA
1 AAAAAAATTTTTAATATTAATCTAAAT-AATA
395141 AAAAAAATT
1 AAAAAAATT
395150 ATAATTCACT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (31 bp):
AAAAAAATTTTTAATATTAATCTAAATAATA
Found at i:396620 original size:30 final size:30
Alignment explanation
Indices: 396568--396652 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
396558 ATTTATATTG
* **
396568 AAATTAAAACTTAAA-ACCTTATTTGCATAT
1 AAATTAAAAATTAAAGA-CTTATTTAAATAT
* * * *
396598 AAGTTTAAAATTAAATATTTATTTAAATAT
1 AAATTAAAAATTAAAGACTTATTTAAATAT
396628 AAATTAAAAATTAAAGACTTATTTA
1 AAATTAAAAATTAAAGACTTATTTA
396653 TTGATAATAA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
30 43 0.98
31 1 0.02
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (30 bp):
AAATTAAAAATTAAAGACTTATTTAAATAT
Found at i:398281 original size:18 final size:18
Alignment explanation
Indices: 398245--398285 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
398235 TAATTTATAA
*
398245 TATATAACAAATTGATTT
1 TATATAACAAATTCATTT
* *
398263 TATATAACAATTTCTTTT
1 TATATAACAAATTCATTT
398281 TATAT
1 TATAT
398286 TTTTTTATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (18 bp):
TATATAACAAATTCATTT
Found at i:398839 original size:102 final size:101
Alignment explanation
Indices: 398733--398926 Score: 223
Period size: 102 Copynumber: 1.9 Consensus size: 101
398723 TCTAATAATA
* * *
398733 TTAGTAAAATTTGATATAATTTT-GATAACATTATA-ATAACATT-TAAAATTTTTTATATATTT
1 TTAGTAAAATTTAATATAATTTTAG-TAACATTAGATATAACATTGTAAAATTTTATATA-ATTT
* *
398795 TTATATTTTTAATATAATTTTAATATATTTGATATAATTT
64 TTA-ACTTTT-ATATAATTTTAATAAATTTGATATAATTT
** * **
398835 TTAGTAACTTTTAATATAATTTTAGTAATATTAGATATAATTTTGGTAAAATTTTATATAATTTT
1 TTAGTAAAATTTAATATAATTTTAGTAACATTAGATATAACATT-GTAAAATTTTATATAATTTT
*
398900 TAACTTTTATATAATTTTGATAAATTT
65 TAACTTTTATATAATTTTAATAAATTT
398927 TTAGTAACTT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
102 45 0.58
103 12 0.16
104 7 0.09
105 13 0.17
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (101 bp):
TTAGTAAAATTTAATATAATTTTAGTAACATTAGATATAACATTGTAAAATTTTATATAATTTTT
AACTTTTATATAATTTTAATAAATTTGATATAATTT
Found at i:398852 original size:42 final size:41
Alignment explanation
Indices: 398741--398899 Score: 141
Period size: 42 Copynumber: 3.9 Consensus size: 41
398731 TATTAGTAAA
* * *
398741 ATTTGATATAATTTTGATAACATTATAATA-ACA-TTTAAAAT
1 ATTTGATATAATTTTTATAAC-TTTTAATATA-ATTTTAATAT
* * *
398782 TTTTTATAT-ATTTTTAT-ATTTTTAATATAATTTTAATAT
1 ATTTGATATAATTTTTATAACTTTTAATATAATTTTAATAT
*
398821 ATTTGATATAATTTTTAGTAACTTTTAATATAATTTTAGTAAT
1 ATTTGATATAATTTTTA-TAACTTTTAATATAATTTTAAT-AT
* *
398864 ATTAGATATAATTTTGGTA-AAATTTT-ATATAATTTT
1 ATTTGATATAATTTT--TATAACTTTTAATATAATTTT
398900 TAACTTTTAT
Statistics
Matches: 98, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
38 8 0.08
39 16 0.16
40 14 0.14
41 8 0.08
42 28 0.29
43 22 0.22
45 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (41 bp):
ATTTGATATAATTTTTATAACTTTTAATATAATTTTAATAT
Found at i:398857 original size:21 final size:20
Alignment explanation
Indices: 398782--398917 Score: 104
Period size: 21 Copynumber: 6.8 Consensus size: 20
398772 CATTTAAAAT
* * *
398782 TTTTTATATATTTTTA-TAT
1 TTTTAATATAATTTTAGTAA
*
398801 TTTTAATATAATTTTAAT-A
1 TTTTAATATAATTTTAGTAA
*
398820 TATTTGATATAATTTTTAGTAA
1 T-TTTAATATAA-TTTTAGTAA
398842 CTTTTAATATAATTTTAGTAA
1 -TTTTAATATAATTTTAGTAA
* *
398863 TATTAGATATAATTTTGGTAAAA
1 TTTTA-ATATAATTTTAGT--AA
398886 TTTT-ATATAATTTT--TAA
1 TTTTAATATAATTTTAGTAA
398903 CTTTT-ATATAATTTT
1 -TTTTAATATAATTTT
398918 GATAAATTTT
Statistics
Matches: 99, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
17 2 0.02
18 14 0.14
19 16 0.16
20 14 0.14
21 37 0.37
22 10 0.10
23 6 0.06
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTAATATAATTTTAGTAA
Found at i:398900 original size:11 final size:11
Alignment explanation
Indices: 398782--398929 Score: 63
Period size: 11 Copynumber: 14.5 Consensus size: 11
398772 CATTTAAAAT
398782 TTTTTATAT-A
1 TTTTTATATAA
398792 TTTTTATAT--
1 TTTTTATATAA
*
398801 TTTTAATATAA
1 TTTTTATATAA
*
398812 TTTTAATAT-A
1 TTTTTATATAA
*
398822 -TTTGATATAA
1 TTTTTATATAA
*
398832 TTTTTAGTA-AC
1 TTTTTA-TATAA
*
398843 TTTTAATATAA
1 TTTTTATATAA
*
398854 -TTTTA-GTAA
1 TTTTTATATAA
**
398863 TATTAGATATAA
1 T-TTTTATATAA
**
398875 TTTTGGTA-AA
1 TTTTTATATAA
*
398885 ATTTTATATAA
1 TTTTTATATAA
398896 --TTT-T-TAA
1 TTTTTATATAA
*
398903 CTTTTATATAA
1 TTTTTATATAA
*
398914 TTTTGATA-AA
1 TTTTTATATAA
398924 TTTTTA
1 TTTTTA
398930 GTAACTTTTA
Statistics
Matches: 105, Mismatches: 19, Indels: 28
0.69 0.12 0.18
Matches are distributed among these distances:
7 3 0.03
8 1 0.01
9 24 0.23
10 32 0.30
11 39 0.37
12 6 0.06
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.57
Consensus pattern (11 bp):
TTTTTATATAA
Found at i:399064 original size:21 final size:20
Alignment explanation
Indices: 399033--399089 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
399023 TAAATTAGAA
399033 TAATATAATTTTGTAAT-AGTT
1 TAATA-AATTTT-TAATAAGTT
*
399054 TAATAATATTTTTAATAATTT
1 TAATAA-ATTTTTAATAAGTT
399075 TAATAAA-TTTTAATA
1 TAATAAATTTTTAATA
399090 TTATTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.24
20 6 0.18
21 19 0.58
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TAATAAATTTTTAATAAGTT
Found at i:399075 original size:9 final size:9
Alignment explanation
Indices: 399057--399099 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
399047 AATAGTTTAA
*
399057 TAATATTTT
1 TAATAATTT
399066 TAATAATTT
1 TAATAATTT
399075 TAATAAATTT
1 TAAT-AATTT
*
399085 TAATATTATT
1 TAATAAT-TT
399095 TAATA
1 TAATA
399100 TGATTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 14 0.47
10 16 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAATAATTT
Found at i:399083 original size:10 final size:10
Alignment explanation
Indices: 399052--399089 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
399042 TTTGTAATAG
399052 TTTAATAATATT
1 TTTAATAA-A-T
399064 TTTAAT-AAT
1 TTTAATAAAT
399073 TTTAATAAAT
1 TTTAATAAAT
399083 TTTAATA
1 TTTAATA
399090 TTATTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.28
10 11 0.44
11 1 0.04
12 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTAATAAAT
Found at i:399805 original size:23 final size:22
Alignment explanation
Indices: 399758--399805 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
399748 AGGTAATATT
* *
399758 ATATTATAATTTATATATAACA
1 ATATTAAAATTTATATATAAAA
399780 ATATTAAAACTTTGATA-ATAAAA
1 ATATTAAAA-TTT-ATATATAAAA
399803 ATA
1 ATA
399806 CGAGAATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 11 0.50
24 3 0.14
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATTAAAATTTATATATAAAA
Found at i:399873 original size:32 final size:33
Alignment explanation
Indices: 399831--399896 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
399821 TTAAAATAAA
*
399831 AATAAAATATTA-ATATTAACTAAAAAATATTT
1 AATAAAATATTATATATTAAATAAAAAATATTT
* * *
399863 AATAATATATTATATATTAAATAAATAATGTTT
1 AATAAAATATTATATATTAAATAAAAAATATTT
399896 A
1 A
399897 CTTATTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (33 bp):
AATAAAATATTATATATTAAATAAAAAATATTT
Found at i:400510 original size:22 final size:22
Alignment explanation
Indices: 400450--400513 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 22
400440 TAAAATTATA
*
400450 TTATTTTTTAATT-TACTTATTT
1 TTATTTTTTAATTAT-TTTATTT
400472 TTATAGCTTTTTAATTATTTTATTT
1 TTAT---TTTTTAATTATTTTATTT
400497 TTATTTTTTAATTATTT
1 TTATTTTTTAATTATTT
400514 CAATTTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
22 17 0.46
25 19 0.51
26 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (22 bp):
TTATTTTTTAATTATTTTATTT
Found at i:400520 original size:22 final size:22
Alignment explanation
Indices: 400479--400521 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
400469 TTTTTATAGC
* *
400479 TTTTTAATTATTTTATTTTTAT
1 TTTTTAATTATTTCAATTTTAT
400501 TTTTTAATTATTTCAATTTTA
1 TTTTTAATTATTTCAATTTTA
400522 AACTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTAATTATTTCAATTTTAT
Found at i:400532 original size:19 final size:19
Alignment explanation
Indices: 400508--400544 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
400498 TATTTTTTAA
400508 TTATTTCAATTTTAAACTT
1 TTATTTCAATTTTAAACTT
*
400527 TTATTTGAATTTTAAACT
1 TTATTTCAATTTTAAACT
400545 CTTAGATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (19 bp):
TTATTTCAATTTTAAACTT
Found at i:400556 original size:20 final size:19
Alignment explanation
Indices: 400515--400558 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
400505 TAATTATTTC
* *
400515 AATTTTAAACTTTTATTTG
1 AATTTTAAACTCTTAATTG
400534 AATTTTAAACTCTTAGATTG
1 AATTTTAAACTCTTA-ATTG
400554 AATTT
1 AATTT
400559 CAATTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (19 bp):
AATTTTAAACTCTTAATTG
Found at i:407882 original size:21 final size:20
Alignment explanation
Indices: 407821--407880 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
407811 ATCTATTCAA
407821 AAATT-AAATAA-ATAATTTT
1 AAATTAAAATAATAT-ATTTT
*
407840 AAATTTTATAATAATA-ATTTT
1 AAA--TTAAAATAATATATTTT
407861 AAATTAAAATAATATATTTT
1 AAATTAAAATAATATATTTT
407881 TATTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 13 0.38
20 5 0.15
21 10 0.29
22 5 0.15
23 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTAAAATAATATATTTT
Found at i:407887 original size:20 final size:19
Alignment explanation
Indices: 407826--407888 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
407816 TTCAAAAATT
407826 AAATAAATAATTTTAAATTTTA
1 AAAT-AATAATTTT-AA-TTTA
* *
407848 TAATAATAATTTTAAATTA
1 AAATAATAATTTTAATTTA
*
407867 AAATAATATATTTTTATTTA
1 AAATAATA-ATTTTAATTTA
407887 AA
1 AA
407889 TTTAATTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 10 0.29
20 13 0.37
21 9 0.26
22 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATAATAATTTTAATTTA
Found at i:407889 original size:19 final size:19
Alignment explanation
Indices: 407824--407889 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
407814 TATTCAAAAA
407824 TTAAATAAATAATTTTAAATT
1 TTAAAT-AATAATTTTAAA-T
407845 TTATAATAATAATTTTAAAT
1 TTA-AATAATAATTTTAAAT
* *
407865 TAAAATAATATATTTT-TAT
1 TTAAATAATA-ATTTTAAAT
407884 TTAAAT
1 TTAAAT
407890 TTAATTATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 14 0.35
20 8 0.20
21 15 0.38
22 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATAATAATTTTAAAT
Found at i:408788 original size:14 final size:14
Alignment explanation
Indices: 408769--408796 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
408759 ATATCTAATT
408769 AAATCGATAATTTA
1 AAATCGATAATTTA
408783 AAATCGATAATTTA
1 AAATCGATAATTTA
408797 TTTAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AAATCGATAATTTA
Found at i:418443 original size:2 final size:2
Alignment explanation
Indices: 418436--418481 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
418426 ATAATTCTAC
418436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
418478 AT AT
1 AT AT
418482 CAATTCAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:419674 original size:16 final size:16
Alignment explanation
Indices: 419633--419675 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
419623 AATATTGAAT
*
419633 ATTAAATAAATATTTA
1 ATTAAATATATATTTA
* *
419649 ATAAAAATATATATTTG
1 AT-TAAATATATATTTA
419666 ATTAAATATA
1 ATTAAATATA
419676 AATAGTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTAAATATATATTTA
Found at i:420868 original size:2 final size:2
Alignment explanation
Indices: 420853--420887 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
420843 CTTTATATTC
*
420853 TA TA TA T- TA CA 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
420888 AAACAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:421501 original size:10 final size:10
Alignment explanation
Indices: 421486--421515 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
421476 TTATATTAAT
421486 AAATTAGTAA
1 AAATTAGTAA
421496 AAATTAGTAA
1 AAATTAGTAA
421506 AAATTAGTAA
1 AAATTAGTAA
421516 CTTATATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (10 bp):
AAATTAGTAA
Found at i:421791 original size:19 final size:19
Alignment explanation
Indices: 421759--421797 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
421749 TAAGAATAGA
*
421759 TATTATATAATTTGGTTGG
1 TATTATATAATTTGATTGG
**
421778 TATTATATTGTTTGATTGG
1 TATTATATAATTTGATTGG
421797 T
1 T
421798 TAAAATTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (19 bp):
TATTATATAATTTGATTGG
Found at i:422117 original size:16 final size:16
Alignment explanation
Indices: 422081--422118 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
422071 ACATTAAAAG
422081 TAATATTTTAAATATA
1 TAATATTTTAAATATA
*
422097 AAATATTTATAAATA-A
1 TAATATTT-TAAATATA
422113 TAATAT
1 TAATAT
422119 AATATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATTTTAAATATA
Done.