Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold221
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: 2539808
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 5 of 19
Found at i:571740 original size:15 final size:15
Alignment explanation
Indices: 571722--571755 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
571712 GTTTAATTAA
*
571722 TAAAACTTTAAACCT
1 TAAAACTTCAAACCT
*
571737 TAAAACTTCAAATCT
1 TAAAACTTCAAACCT
571752 TAAA
1 TAAA
571756 TTTTAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAACTTCAAACCT
Found at i:573240 original size:24 final size:22
Alignment explanation
Indices: 573213--573267 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
573203 CATAAAGCTG
573213 ATTTTAAGATAAAATAATTTTATT
1 ATTTTAAGATAAAAT--TTTTATT
**
573237 ATTTTTATATTTAAAATTTTTATT
1 A-TTTTA-AGATAAAATTTTTATT
573261 ATTTTAA
1 ATTTTAA
573268 AAATCTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 5 0.19
24 9 0.33
25 5 0.19
26 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTTAAGATAAAATTTTTATT
Found at i:573255 original size:15 final size:17
Alignment explanation
Indices: 573237--573269 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
573227 TAATTTTATT
573237 ATTTTTA-TA-TTTAAA
1 ATTTTTATTATTTTAAA
573252 ATTTTTATTATTTTAAA
1 ATTTTTATTATTTTAAA
573269 A
1 A
573270 ATCTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTATTATTTTAAA
Found at i:573477 original size:12 final size:13
Alignment explanation
Indices: 573457--573489 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
573447 AGATCGTAAA
573457 TTAAATTTTTT-T
1 TTAAATTTTTTGT
*
573469 TTAATTTTTTTGT
1 TTAAATTTTTTGT
573482 TTAAATTT
1 TTAAATTT
573490 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (13 bp):
TTAAATTTTTTGT
Found at i:574334 original size:10 final size:10
Alignment explanation
Indices: 574312--574376 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
574302 AAAAATAAAT
574312 TATATATAAAA
1 TATATA-AAAA
574323 TATATAAAAA
1 TATATAAAAA
*
574333 TATTTAAAAA
1 TATATAAAAA
574343 T-TA-AAATAA
1 TATATAAA-AA
*
574352 TATATTAAAA
1 TATATAAAAA
* * *
574362 CATATTAATA
1 TATATAAAAA
574372 TATAT
1 TATAT
574377 TAATTAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
8 3 0.07
9 4 0.09
10 30 0.67
11 8 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
TATATAAAAA
Found at i:574353 original size:19 final size:19
Alignment explanation
Indices: 574298--574361 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
574288 ATTTTAGAGA
*
574298 ATTTAAAAA-T-AAATTAT
1 ATTTAAAAATTAAAATAAT
*
574315 ATAT-AAAATATATAAA-AAT
1 ATTTAAAAAT-TA-AAATAAT
574334 ATTTAAAAATTAAAATAAT
1 ATTTAAAAATTAAAATAAT
574353 ATATTAAAA
1 AT-TTAAAA
574362 CATATTAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
16 4 0.11
17 3 0.08
18 4 0.11
19 12 0.32
20 14 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTAAAAATTAAAATAAT
Found at i:574757 original size:30 final size:31
Alignment explanation
Indices: 574706--574798 Score: 102
Period size: 30 Copynumber: 3.0 Consensus size: 31
574696 TTATGATTCG
574706 AATTAATTTTAAATTATTATTTATATAATAAA
1 AATTAATTTTAAATTATTATTTA-ATAATAAA
* *
574738 AATTAATTTT-TATTA-TATTTAATTATAAA
1 AATTAATTTTAAATTATTATTTAATAATAAA
*
574767 ATATTAA-TTTAAATTAATTTTTTAAATAATAA
1 A-ATTAATTTTAAATT-ATTATTT-AATAATAA
574799 TTTAAATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
29 11 0.22
30 14 0.27
31 5 0.10
32 14 0.27
33 7 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AATTAATTTTAAATTATTATTTAATAATAAA
Found at i:574777 original size:28 final size:30
Alignment explanation
Indices: 574706--574776 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 30
574696 TTATGATTCG
574706 AATTAATTTTAAATTATTATTTATATAATAAA
1 AATTAATTTT--ATTATTATTTATATAATAAA
*
574738 AATTAATTTTTATTA-TATTTA-ATTATAAA
1 AATTAA-TTTTATTATTATTTATATAATAAA
574767 ATATTAATTT
1 A-ATTAATTT
574777 AAATTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 11 0.31
30 11 0.31
31 4 0.11
32 6 0.17
33 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
AATTAATTTTATTATTATTTATATAATAAA
Found at i:574790 original size:13 final size:13
Alignment explanation
Indices: 574757--574821 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 13
574747 TTATTATATT
* *
574757 TAATTATAAAATAT
1 TAATT-TAAATTAA
574771 TAATTTAAATTAA
1 TAATTTAAATTAA
**
574784 TTTTTTAAA-TAA
1 TAATTTAAATTAA
*
574796 TAATTTAAATTTA
1 TAATTTAAATTAA
*
574809 TAAATTAAATTAA
1 TAATTTAAATTAA
574822 ATTTGAGTTC
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
12 10 0.24
13 26 0.63
14 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTTAAATTAA
Found at i:574816 original size:25 final size:25
Alignment explanation
Indices: 574765--574818 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
574755 TTTAATTATA
* ***
574765 AAATATTAATTTAAATTAATTTTTT
1 AAATAATAATTTAAATTAATAAATT
*
574790 AAATAATAATTTAAATTTATAAATT
1 AAATAATAATTTAAATTAATAAATT
574815 AAAT
1 AAAT
574819 TAAATTTGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATAATAATTTAAATTAATAAATT
Found at i:575164 original size:25 final size:27
Alignment explanation
Indices: 575136--575191 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
575126 TAACTCTGAA
*
575136 AATAATTT-AAAT-TTAAATTTAAAAT
1 AATAATTTAAAATCATAAATTTAAAAT
575161 AATAATTTAAAATCGATAAATTTAAAAT
1 AATAATTTAAAATC-ATAAATTTAAAAT
575189 AAT
1 AAT
575192 TATTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.30
26 4 0.15
28 15 0.56
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
AATAATTTAAAATCATAAATTTAAAAT
Found at i:575184 original size:15 final size:14
Alignment explanation
Indices: 575149--575191 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
575139 AATTTAAATT
575149 TAAATTTAAAATAA
1 TAAATTTAAAATAA
*
575163 T-AATTTAAAATCGA
1 TAAATTTAAAAT-AA
575177 TAAATTTAAAATAA
1 TAAATTTAAAATAA
575191 T
1 T
575192 TATTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 10 0.40
14 5 0.20
15 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (14 bp):
TAAATTTAAAATAA
Found at i:577068 original size:16 final size:16
Alignment explanation
Indices: 577031--577066 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
577021 AAATTATTTA
*
577031 TTTTTAAAATTACTAC
1 TTTTTAAAATTACAAC
577047 TTTTTAAAATT-CAAC
1 TTTTTAAAATTACAAC
577062 TTTTT
1 TTTTT
577067 TATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTAAAATTACAAC
Found at i:584042 original size:25 final size:23
Alignment explanation
Indices: 584014--584086 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 23
584004 GATATTAATA
584014 TTAATTATATTTATATTATATATTT
1 TTAATTAT-TTTATATTAT-TATTT
584039 TTAAATTAATTTTTAATATTATTATTT
1 TT-AATT-A-TTTT-ATATTATTATTT
* *
584066 ATAATTATTTTTTATT-TTATT
1 TTAATTATTTTATATTATTATT
584087 AAATTTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
22 5 0.12
23 4 0.10
24 4 0.10
25 3 0.07
26 8 0.19
27 10 0.24
28 8 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTAATTATTTTATATTATTATTT
Found at i:584045 original size:26 final size:27
Alignment explanation
Indices: 584015--584087 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 27
584005 ATATTAATAT
*
584015 TAATTATATTTATATTATATATT-TTTA
1 TAATTATATTTTTATTAT-TATTATTTA
*
584042 -AATTA-ATTTTTAATATTATTATTTA
1 TAATTATATTTTTATTATTATTATTTA
584067 TAATTAT-TTTTTATT-TTATTA
1 TAATTATATTTTTATTATTATTA
584088 AATTTTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 4 0.10
25 19 0.47
26 17 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TAATTATATTTTTATTATTATTATTTA
Found at i:584052 original size:12 final size:11
Alignment explanation
Indices: 584034--584116 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 11
584024 TTATATTATA
584034 TATTTTTAAAT
1 TATTTTTAAAT
584045 TAATTTTTAATAT
1 T-ATTTTTAA-AT
584058 TATTATTTATAAT
1 TATT-TTTA-AAT
*
584071 TATTTTT-TAT
1 TATTTTTAAAT
*
584081 T-TTATTAAATTT
1 TATTTTTAAA--T
584093 TAAATTTTTAAATT
1 T--ATTTTTAAA-T
584107 TATTTTTAAA
1 TATTTTTAAA
584117 AAATATTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 1 0.02
12 25 0.43
13 13 0.22
14 4 0.07
15 7 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTTAAAT
Found at i:584065 original size:15 final size:15
Alignment explanation
Indices: 584008--584070 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
583998 TATTAAGATA
*
584008 TTAATATTAATTATAT
1 TTAATATT-ATTATTT
584024 TT-ATATTATATATTT
1 TTAATATTAT-TATTT
584039 TTAA-ATTA--ATTT
1 TTAATATTATTATTT
584051 TTAATATTATTATTT
1 TTAATATTATTATTT
*
584066 ATAAT
1 TTAAT
584071 TATTTTTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
12 8 0.20
13 4 0.10
14 2 0.05
15 23 0.57
16 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAATATTATTATTT
Found at i:584074 original size:13 final size:13
Alignment explanation
Indices: 584015--584080 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
584005 ATATTAATAT
584015 TAATTA-TATTTA
1 TAATTATTATTTA
*
584027 T-ATTATATATTTT
1 TAATTAT-TATTTA
584040 TAAATTAATT-TTTA
1 T-AATT-ATTATTTA
584054 -ATATTATTATTTA
1 TA-ATTATTATTTA
*
584067 TAATTATTTTTTA
1 TAATTATTATTTA
584080 T
1 T
584081 TTTATTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
11 4 0.09
12 5 0.12
13 24 0.56
14 4 0.09
15 4 0.09
16 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TAATTATTATTTA
Found at i:584139 original size:21 final size:21
Alignment explanation
Indices: 584115--584154 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
584105 TTTATTTTTA
**
584115 AAAAATATTTATTTCAATAAC
1 AAAAATATAAATTTCAATAAC
*
584136 AAAATTATAAATTTCAATA
1 AAAAATATAAATTTCAATA
584155 TTCTAAAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATATAAATTTCAATAAC
Found at i:584971 original size:2 final size:2
Alignment explanation
Indices: 584964--584988 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
584954 CTTAGAAGCG
584964 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 A
584989 GATTCACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:588009 original size:21 final size:21
Alignment explanation
Indices: 587972--588048 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
587962 TATTACTATT
* *
587972 TAAAATT-GAATTGAATTTAA
1 TAAAATTAAAATTAAATTTAA
587992 TAAAATTAAAATTAAATTTAA
1 TAAAATTAAAATTAAATTTAA
**
588013 TATTATTAAAATTTAATATTTAA
1 TAAAATTAAAA-TTAA-ATTTAA
*
588036 TAAATTTAAAATT
1 TAAAATTAAAATT
588049 TTAATTATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 7 0.15
21 20 0.43
22 6 0.13
23 14 0.30
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TAAAATTAAAATTAAATTTAA
Found at i:588040 original size:16 final size:16
Alignment explanation
Indices: 588004--588049 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
587994 AAATTAAAAT
*
588004 TAAATTTAATA-TTAT
1 TAAATTTAATATTTAA
588019 TAAAATTTAATATTTAA
1 T-AAATTTAATATTTAA
*
588036 TAAATTTAAAATTT
1 TAAATTTAATATTT
588050 TAATTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 1 0.04
16 22 0.81
17 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATTTAATATTTAA
Found at i:589223 original size:17 final size:19
Alignment explanation
Indices: 589201--589240 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
589191 ATACACTCAC
*
589201 AATTAAATT-T-ATTTATA
1 AATTAAATTATAATTTAAA
589218 AATTAAATTATAATTTAAA
1 AATTAAATTATAATTTAAA
589237 AATT
1 AATT
589241 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
19 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTAAATTATAATTTAAA
Found at i:590443 original size:3 final size:3
Alignment explanation
Indices: 590435--590463 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
590425 AATTTCATAT
590435 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
590464 TCAGGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:591075 original size:21 final size:20
Alignment explanation
Indices: 591047--591088 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
591037 ATCTAATTAA
*
591047 TTAAAAATTTAATATATAAT
1 TTAAAAATTTAATATAAAAT
591067 TTAATAAATTTAATATAAAAT
1 TTAA-AAATTTAATATAAAAT
591088 T
1 T
591089 AAATCAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAAAATTTAATATAAAAT
Found at i:591932 original size:21 final size:19
Alignment explanation
Indices: 591906--591944 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
591896 ATTTTAAATT
*
591906 TTAAATTTTATAAATAAAAAA
1 TTAAATATTA-AAA-AAAAAA
591927 TTAAATATTAAAAAAAAA
1 TTAAATATTAAAAAAAAA
591945 TTTCCTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAATATTAAAAAAAAAA
Found at i:592214 original size:2 final size:2
Alignment explanation
Indices: 592207--592240 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
592197 CTTTTTCTTC
*
592207 CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
592241 GCAATTTTTC
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:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:593715 original size:52 final size:52
Alignment explanation
Indices: 593651--593754 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
593641 TCTTTGTTGC
593651 TTGAAGTTTGATAGCCATTAGCTCTCATATGTTCTTCAATTTTTTATCATCA
1 TTGAAGTTTGATAGCCATTAGCTCTCATATGTTCTTCAATTTTTTATCATCA
*
593703 TTGAAGTTTGATAGCCATTAGCTCTCATATGTTCTTCGATTTTTTATCATCA
1 TTGAAGTTTGATAGCCATTAGCTCTCATATGTTCTTCAATTTTTTATCATCA
593755 ACTTACCTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.46
Consensus pattern (52 bp):
TTGAAGTTTGATAGCCATTAGCTCTCATATGTTCTTCAATTTTTTATCATCA
Found at i:595247 original size:239 final size:239
Alignment explanation
Indices: 594828--595306 Score: 958
Period size: 239 Copynumber: 2.0 Consensus size: 239
594818 TTTTAGTTGA
594828 AGGCTTCTTTTAGTTTATTACCAGAAACTAAATCTCTGTACAACAAGATTGAAACTATGTTACTT
1 AGGCTTCTTTTAGTTTATTACCAGAAACTAAATCTCTGTACAACAAGATTGAAACTATGTTACTT
594893 AGACTTGAGTGTGATTGTCGGATACGAGTATGTGTCTAGCACTGGATGTTCAATTTTTTAAAGTT
66 AGACTTGAGTGTGATTGTCGGATACGAGTATGTGTCTAGCACTGGATGTTCAATTTTTTAAAGTT
594958 TTTCCATTTATTTGGAGGGTCATATCTCTGTACCCACGTCCAGAAATGTGTTATGCACGGATACT
131 TTTCCATTTATTTGGAGGGTCATATCTCTGTACCCACGTCCAGAAATGTGTTATGCACGGATACT
595023 TCAAGAAAAATGAAGAATCTAAGCAACATAGGATTGAAGAGTGT
196 TCAAGAAAAATGAAGAATCTAAGCAACATAGGATTGAAGAGTGT
595067 AGGCTTCTTTTAGTTTATTACCAGAAACTAAATCTCTGTACAACAAGATTGAAACTATGTTACTT
1 AGGCTTCTTTTAGTTTATTACCAGAAACTAAATCTCTGTACAACAAGATTGAAACTATGTTACTT
595132 AGACTTGAGTGTGATTGTCGGATACGAGTATGTGTCTAGCACTGGATGTTCAATTTTTTAAAGTT
66 AGACTTGAGTGTGATTGTCGGATACGAGTATGTGTCTAGCACTGGATGTTCAATTTTTTAAAGTT
595197 TTTCCATTTATTTGGAGGGTCATATCTCTGTACCCACGTCCAGAAATGTGTTATGCACGGATACT
131 TTTCCATTTATTTGGAGGGTCATATCTCTGTACCCACGTCCAGAAATGTGTTATGCACGGATACT
595262 TCAAGAAAAATGAAGAATCTAAGCAACATAGGATTGAAGAGTGT
196 TCAAGAAAAATGAAGAATCTAAGCAACATAGGATTGAAGAGTGT
595306 A
1 A
595307 TTAAAATTCT
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
239 240 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (239 bp):
AGGCTTCTTTTAGTTTATTACCAGAAACTAAATCTCTGTACAACAAGATTGAAACTATGTTACTT
AGACTTGAGTGTGATTGTCGGATACGAGTATGTGTCTAGCACTGGATGTTCAATTTTTTAAAGTT
TTTCCATTTATTTGGAGGGTCATATCTCTGTACCCACGTCCAGAAATGTGTTATGCACGGATACT
TCAAGAAAAATGAAGAATCTAAGCAACATAGGATTGAAGAGTGT
Found at i:596288 original size:21 final size:21
Alignment explanation
Indices: 596264--596306 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
596254 CATATTGTAT
596264 AGCATTGGAACAATTTGATTA
1 AGCATTGGAACAATTTGATTA
596285 AGCATTGGAACAATTTGATTA
1 AGCATTGGAACAATTTGATTA
596306 A
1 A
596307 TGCCCCTGCA
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:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (21 bp):
AGCATTGGAACAATTTGATTA
Found at i:596945 original size:2 final size:2
Alignment explanation
Indices: 596938--596962 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
596928 GGATCTCATT
596938 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 T
596963 TGCAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:597546 original size:21 final size:22
Alignment explanation
Indices: 597520--597575 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
597510 TTCACTTTTA
597520 TTATATTATTAAAATAT-TATT
1 TTATATTATTAAAATATATATT
* *
597541 TTATATTAATAATTATATATATT
1 TTATATTATTAA-AATATATATT
*
597564 TT-TATAATTAAA
1 TTATATTATTAAA
597576 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 11 0.39
22 11 0.39
23 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATATTATTAAAATATATATT
Found at i:597561 original size:16 final size:17
Alignment explanation
Indices: 597518--597563 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
597508 TTTTCACTTT
597518 TATTATAT-TATTAAAA
1 TATTATATATATTAAAA
* *
597534 TATTATTTTATATTAATA
1 TATTA-TATATATTAAAA
597552 -ATTATATATATT
1 TATTATATATATT
597564 TTTATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 12 0.48
17 6 0.24
18 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATATATATTAAAA
Found at i:598389 original size:2 final size:2
Alignment explanation
Indices: 598382--598413 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
598372 TACCTGTAAA
598382 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
598414 GTCATGAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:599608 original size:18 final size:18
Alignment explanation
Indices: 599572--599618 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
599562 TACGATTATG
*
599572 ATATGATAAAATATTAAA
1 ATATGATAAAATATCAAA
599590 ATATGATATAAATA-CAAA
1 ATATGATA-AAATATCAAA
*
599608 A-ATGATCAAAT
1 ATATGATAAAAT
599619 TCGATATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 5 0.19
18 12 0.46
19 5 0.19
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (18 bp):
ATATGATAAAATATCAAA
Found at i:599609 original size:19 final size:18
Alignment explanation
Indices: 599572--599610 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
599562 TACGATTATG
**
599572 ATATGATAAAATATTAAA
1 ATATGATAAAATACAAAA
599590 ATATGATATAAATACAAAA
1 ATATGATA-AAATACAAAA
599609 AT
1 AT
599611 GATCAAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (18 bp):
ATATGATAAAATACAAAA
Found at i:601063 original size:15 final size:14
Alignment explanation
Indices: 601025--601065 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
601015 TAGTTTAATC
*
601025 AATTAAAATGATTA
1 AATTAAAATAATTA
601039 AATTAAAATAATTA
1 AATTAAAATAATTA
*
601053 ATTTAAAAATAAT
1 AATT-AAAATAAT
601066 GATATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
AATTAAAATAATTA
Found at i:601764 original size:20 final size:20
Alignment explanation
Indices: 601741--601779 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
601731 ATCATATCAC
601741 ATATAATACTTATAATTAAT
1 ATATAATACTTATAATTAAT
* * *
601761 ATATTATATTTATATTTAA
1 ATATAATACTTATAATTAA
601780 GAGTAAACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATAATACTTATAATTAAT
Found at i:601823 original size:16 final size:15
Alignment explanation
Indices: 601799--601832 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
601789 TATTTTAATA
601799 ATTTATATTATATTAT
1 ATTTATATTAT-TTAT
*
601815 ATTTTTATTATTTAT
1 ATTTATATTATTTAT
601830 ATT
1 ATT
601833 ATTTTTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTATATTATTTAT
Found at i:603354 original size:22 final size:20
Alignment explanation
Indices: 603326--603367 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
603316 TATTTATTTA
603326 AATTTTATATCAAATATCATAT
1 AATTTTA-ATCAAATAT-ATAT
*
603348 AATTTTAATTAAATATATAT
1 AATTTTAATCAAATATATAT
603368 TTTTATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTTAATCAAATATATAT
Found at i:603363 original size:21 final size:20
Alignment explanation
Indices: 603326--603393 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 20
603316 TATTTATTTA
*
603326 AATTTTATATCAAATATCATAT
1 AATTTTA-ATTAAATAT-ATAT
603348 AATTTTAATTAAATATATAT
1 AATTTTAATTAAATATATAT
603368 --TTTT-ATTAAATAT-TAT
1 AATTTTAATTAAATATATAT
*
603384 CATATTTAAT
1 AAT-TTTAAT
603394 ATTTACATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
16 3 0.07
17 9 0.22
18 5 0.12
19 3 0.07
20 6 0.15
21 8 0.20
22 7 0.17
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTTAATTAAATATATAT
Found at i:604566 original size:19 final size:19
Alignment explanation
Indices: 604540--604582 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
604530 ATAATATATA
*
604540 AAATTATTATAA-TTACAT
1 AAATTATTACAACTTACAT
604558 AAATATATTACAACTTACAT
1 AAAT-TATTACAACTTACAT
604578 AAATT
1 AAATT
604583 TTGCACGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTATTACAACTTACAT
Found at i:604633 original size:17 final size:17
Alignment explanation
Indices: 604598--604650 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
604588 CGACTGAAAA
* **
604598 AAATTAAAATAAAAAAT
1 AAATTATAATAATTAAT
*
604615 AAA-TATTATAATTACAT
1 AAATTATAATAATTA-AT
604632 AAATTATAATAATTAAT
1 AAATTATAATAATTAAT
604649 AA
1 AA
604651 TATAAGTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 7 0.24
17 12 0.41
18 10 0.34
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTATAATAATTAAT
Found at i:604654 original size:15 final size:17
Alignment explanation
Indices: 604613--604655 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
604603 AAAATAAAAA
*
604613 ATAAATATTATAATTAC
1 ATAAATATAATAATTAC
604630 ATAAATTATAATAATTA-
1 ATAAA-TATAATAATTAC
604647 AT-AATATAA
1 ATAAATATAA
604656 GTTAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 2 0.08
17 7 0.29
18 10 0.42
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAATATAATAATTAC
Found at i:605883 original size:5 final size:6
Alignment explanation
Indices: 605867--605891 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
605857 GTAAAATACC
605867 GTTTTT GTTTTT GTTTTT GTTTTT G
1 GTTTTT GTTTTT GTTTTT GTTTTT G
605892 GCTTGTCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (6 bp):
GTTTTT
Found at i:616932 original size:37 final size:36
Alignment explanation
Indices: 616863--616933 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
616853 TTTTAAAAAT
* *
616863 ATAAATTAAAATTTTATTTAAAATTTATTTATATCA
1 ATAAATTAAAAATTTATTTAAAATTTAATTATATCA
616899 ATAAATTAATAACATTTATTT-AAATTTAATTATAT
1 ATAAATTAA-AA-ATTTATTTAAAATTTAATTATAT
616934 TGTATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 9 0.29
37 15 0.48
38 7 0.23
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (36 bp):
ATAAATTAAAAATTTATTTAAAATTTAATTATATCA
Found at i:616984 original size:32 final size:33
Alignment explanation
Indices: 616915--616987 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
616905 TAATAACATT
* *
616915 TATTTAA-ATTTAATTATATTGTATATTTTTAA
1 TATTTAATATTTAATAATATTATATATTTTTAA
*
616947 TATTTAATATTTAATAATA-TAT-TATTTTTAT
1 TATTTAATATTTAATAATATTATATATTTTTAA
616978 TAATTTAATA
1 T-ATTTAATA
616988 AAATTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 9 0.25
32 17 0.47
33 10 0.28
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTTAATATTTAATAATATTATATATTTTTAA
Found at i:617177 original size:11 final size:9
Alignment explanation
Indices: 617143--617196 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 9
617133 AATTTTATTT
617143 TTTAT-ATA
1 TTTATAATA
617151 TTTTATAAT-
1 -TTTATAATA
617160 TTTATAATTA
1 TTTATAA-TA
617170 TATTATAATA
1 T-TTATAATA
617180 TTTATAA-A
1 TTTATAATA
*
617188 ATTATAATA
1 TTTATAATA
617197 CGTTGATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 14 0.36
9 13 0.33
10 6 0.15
11 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTATAATA
Found at i:617185 original size:20 final size:20
Alignment explanation
Indices: 617153--617264 Score: 74
Period size: 20 Copynumber: 5.6 Consensus size: 20
617143 TTTATATATT
617153 TTATAAT-TTTATAATTATA
1 TTATAATATTTATAATTATA
617172 TTATAATATTTATAA--A-A
1 TTATAATATTTATAATTATA
*
617189 TTATAATACGTTGATAATTTATA
1 TTATAATA--TTTATAA-TTATA
* * *
617212 TTATAAAATTTTAAAATATTTA
1 TTATAATA-TTTATAAT-TATA
*
617234 TT-TAATATTT-TAATTATT
1 TTATAATATTTATAATTATA
*
617252 TTAATTATATTTA
1 TT-ATAATATTTA
617265 AATAAAAATA
Statistics
Matches: 71, Mismatches: 11, Indels: 20
0.70 0.11 0.20
Matches are distributed among these distances:
17 9 0.13
18 5 0.07
19 16 0.23
20 17 0.24
21 5 0.07
22 11 0.15
23 8 0.11
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATAATATTTATAATTATA
Found at i:619482 original size:25 final size:24
Alignment explanation
Indices: 619454--619513 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 24
619444 TGTAATATAG
*
619454 TTATTTATGTTTAAATATT-TATTTT
1 TTATTTAT-TTT-AATATTATATATT
619479 TTATTTATTTTAATATTAATATATT
1 TTATTTATTTTAATATT-ATATATT
619504 TTATTTATTT
1 TTATTTATTT
619514 ATTTATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 6 0.19
24 3 0.09
25 23 0.72
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TTATTTATTTTAATATTATATATT
Found at i:619487 original size:29 final size:31
Alignment explanation
Indices: 619454--619522 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
619444 TGTAATATAG
*
619454 TTATTTATGTTTAA-ATA-TTTATTT-TTTAT
1 TTATTTAT-ATTAATATATTTTATTTATTTAT
619483 TTATTTTAATATTAATATATTTTATTTATTTAT
1 TTA-TTT-ATATTAATATATTTTATTTATTTAT
619516 TTATTTA
1 TTATTTA
619523 AAACTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
29 3 0.09
30 7 0.21
31 6 0.18
32 10 0.29
33 8 0.24
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (31 bp):
TTATTTATATTAATATATTTTATTTATTTAT
Found at i:621521 original size:3 final size:3
Alignment explanation
Indices: 621513--621552 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
621503 CAATTTACTG
*
621513 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
621553 TTAATTAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:622029 original size:13 final size:13
Alignment explanation
Indices: 622011--622040 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
622001 TTTTTTAATG
622011 TCGAATAATCAAT
1 TCGAATAATCAAT
*
622024 TCGAATAATCACT
1 TCGAATAATCAAT
622037 TCGA
1 TCGA
622041 CTAGCGACTT
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:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (13 bp):
TCGAATAATCAAT
Found at i:623343 original size:16 final size:16
Alignment explanation
Indices: 623316--623378 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
623306 ATTTTTTTTG
*
623316 TTATTTTAATTTTATA
1 TTATTTTAATTTTAAA
623332 TT-TTTTATATTTTAAA
1 TTATTTTA-ATTTTAAA
*
623348 TTATTTTAAATTTAAA
1 TTATTTTAATTTTAAA
* *
623364 TAATTTTAGTTTTAA
1 TTATTTTAATTTTAA
623379 GCTGATTGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 5 0.12
16 30 0.75
17 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTATTTTAATTTTAAA
Found at i:623610 original size:13 final size:13
Alignment explanation
Indices: 623588--623621 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
623578 ATATTTAATT
623588 AAAATATAAAAATA
1 AAAAT-TAAAAATA
*
623602 ATAATTAAAAATA
1 AAAATTAAAAATA
623615 AAAATTA
1 AAAATTA
623622 TACTTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAATTAAAAATA
Found at i:625428 original size:30 final size:30
Alignment explanation
Indices: 625312--625427 Score: 148
Period size: 30 Copynumber: 3.9 Consensus size: 30
625302 AACTCTTAAT
*
625312 CTTTAATTTG--CCTAATATAAGCCCTTCAC
1 CTTTAATTTGTACCCAA-ATAAGCCCTTCAC
**
625341 CTTTAATTTGCCCCCAAATAAGCCCTTCAC
1 CTTTAATTTGTACCCAAATAAGCCCTTCAC
*
625371 CTTTAATTTGTACCCAAATAAACCCTT-ATC
1 CTTTAATTTGTACCCAAATAAGCCCTTCA-C
*
625401 CTTTAATTTGTACCTAAATAAGCCCTT
1 CTTTAATTTGTACCCAAATAAGCCCTT
625428 AATGTAAATC
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
29 11 0.14
30 63 0.81
31 4 0.05
ACGTcount: A:0.29, C:0.28, G:0.06, T:0.36
Consensus pattern (30 bp):
CTTTAATTTGTACCCAAATAAGCCCTTCAC
Found at i:628755 original size:22 final size:23
Alignment explanation
Indices: 628730--628773 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
628720 ATAATAAAGT
*
628730 TAAATA-CATTTTAAAATATATA
1 TAAATATCATTTGAAAATATATA
*
628752 TAAATATCGTTTGAAAATATAT
1 TAAATATCATTTGAAAATATAT
628774 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (23 bp):
TAAATATCATTTGAAAATATATA
Found at i:633683 original size:19 final size:19
Alignment explanation
Indices: 633656--633696 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
633646 TTTTAAAAAA
633656 TATAATTAATA-TATTAATT
1 TATAATTAA-ACTATTAATT
*
633675 TATATTTAAACTATTAATT
1 TATAATTAAACTATTAATT
633694 TAT
1 TAT
633697 TTTTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAATTAAACTATTAATT
Found at i:633709 original size:3 final size:3
Alignment explanation
Indices: 633701--633732 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
633691 ATTTATTTTT
633701 TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T
633733 GGTGCTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:641359 original size:16 final size:17
Alignment explanation
Indices: 641328--641360 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
641318 ATCGGTTATG
*
641328 CTTATTTTCTTCTTTTT
1 CTTATTCTCTTCTTTTT
641345 CTTATTCTC-TCTTTTT
1 CTTATTCTCTTCTTTTT
641361 TTTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (17 bp):
CTTATTCTCTTCTTTTT
Found at i:645310 original size:14 final size:14
Alignment explanation
Indices: 645291--645331 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
645281 TAAATAAAAT
*
645291 AATTTTTATTTTAA
1 AATTTTTATTATAA
645305 AATTTTTATTATAA
1 AATTTTTATTATAA
645319 ATATTTTT-TTATA
1 A-ATTTTTATTATA
645332 GATTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTTTATTATAA
Found at i:646958 original size:23 final size:22
Alignment explanation
Indices: 646899--646960 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 22
646889 TAATTTAAAT
646899 ATTTTAAGTAAAATATTAAAAATAA
1 ATTTTAA-TAAAATA--AAAAATAA
646924 A--TTAATAAAATAAAAAATAA
1 ATTTTAATAAAATAAAAAATAA
646944 ATTTTATATAAAATAAA
1 ATTTTA-ATAAAATAAA
646961 TATAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 9 0.26
22 10 0.29
23 14 0.41
25 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
ATTTTAATAAAATAAAAAATAA
Found at i:646971 original size:22 final size:23
Alignment explanation
Indices: 646907--646971 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 23
646897 ATATTTTAAG
646907 TAAAATATTAAAAAT-AAA-TTA-A
1 TAAAATA--AAAAATAAAATTTATA
*
646929 TAAAATAAAAAATAAATTTTATA
1 TAAAATAAAAAATAAAATTTATA
*
646952 TAAAAT-AAATATAAAATTTA
1 TAAAATAAAAAATAAAATTTA
646972 AAAATATAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 6 0.16
21 2 0.05
22 22 0.59
23 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAAATAAAAAATAAAATTTATA
Found at i:647363 original size:34 final size:34
Alignment explanation
Indices: 647317--647534 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
647307 GTAAAAACCA
*
647317 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
647351 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
647385 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
647419 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
647452 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
647486 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
647519 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
647535 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:647431 original size:68 final size:67
Alignment explanation
Indices: 647315--647534 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
647305 TGGTAAAAAC
* * *
647315 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
647380 AT
66 AT
* * *
647382 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
647447 AAT
65 AAT
* * * * * *
647450 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
647515 AT
66 AT
647517 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
647535 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:651997 original size:34 final size:34
Alignment explanation
Indices: 651951--652166 Score: 262
Period size: 34 Copynumber: 6.4 Consensus size: 34
651941 GTAAAAACCA
*
651951 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
651985 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
652019 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
652053 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
652086 TCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* *
652120 CCATTTAATCAACAATGGTAAACTACTAAATCAT-
1 CCATTTAATCAACAATGGTAACCTACCAAATC-TC
652154 -CATTTAATCAACA
1 CCATTTAATCAACA
652167 TCACCCTCTA
Statistics
Matches: 157, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
33 41 0.26
34 114 0.73
35 2 0.01
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:652065 original size:68 final size:67
Alignment explanation
Indices: 651949--652166 Score: 301
Period size: 67 Copynumber: 3.2 Consensus size: 67
651939 TGGTAAAAAC
* * *
651949 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
652014 AT
66 AT
* * *
652016 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
652081 AAT
65 AAT
** * * * * *
652084 CTTCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
652149 AT
66 AT
*
652151 CATCATTTAATCAACA
1 CACCATTTAATCAACA
652167 TCACCCTCTA
Statistics
Matches: 133, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 72 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:652710 original size:19 final size:19
Alignment explanation
Indices: 652686--652725 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
652676 GTTGCTGATT
* *
652686 TTTTTAAATAATAGATAAA
1 TTTTTAAAAAATAAATAAA
652705 TTTTTAAAAAATAAATAAA
1 TTTTTAAAAAATAAATAAA
652724 TT
1 TT
652726 ATTTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTTTTAAAAAATAAATAAA
Found at i:653183 original size:24 final size:23
Alignment explanation
Indices: 653140--653203 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
653130 TGGTGACCAT
* **
653140 TTTTATTAAAGTTTGTATTTAATA
1 TTTTATTAAAGTATAAATTT-ATA
653164 TTTTATTAAAGTATAAATTTATA
1 TTTTATTAAAGTATAAATTTATA
* *
653187 TTATTAATAAATTATAA
1 TT-TTATTAAAGTATAA
653204 TGATAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 5 0.15
24 29 0.85
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
TTTTATTAAAGTATAAATTTATA
Found at i:654175 original size:23 final size:24
Alignment explanation
Indices: 654149--654193 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
654139 TATAAGATGA
654149 AATAAAATTTT-AAATATTAAATT
1 AATAAAATTTTAAAATATTAAATT
**
654172 AATAATTTTTTAAAATATTAAA
1 AATAAAATTTTAAAATATTAAA
654194 ATAAAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AATAAAATTTTAAAATATTAAATT
Found at i:654760 original size:17 final size:20
Alignment explanation
Indices: 654716--654761 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
654706 TATTATATTT
654716 ATTATTTATTTAATATTAAA
1 ATTATTTATTTAATATTAAA
*
654736 AGTAATTT-TTT-AT-TTAAA
1 A-TTATTTATTTAATATTAAA
654754 ATTATTTA
1 ATTATTTA
654762 AATTTAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 2 0.09
20 4 0.18
21 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTTATTTAATATTAAA
Found at i:654840 original size:3 final size:3
Alignment explanation
Indices: 654834--654859 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
654824 TTAATTTTCG
654834 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
654860 TTTCTTGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:655388 original size:23 final size:22
Alignment explanation
Indices: 655362--655430 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 22
655352 TACTAAAAAT
655362 TATTTTTTATATTAATATTTATA
1 TATTTTTTATATTAA-ATTTATA
655385 TA-TTTTTATAATTAAATTTAAATA
1 TATTTTTTAT-ATTAAATTT--ATA
*
655409 AATTTTATTATATTAAATTTAT
1 TATTTT-TTATATTAAATTTAT
655431 TAAATAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 11 0.28
23 9 0.22
24 4 0.10
25 12 0.30
26 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTTTATATTAAATTTATA
Found at i:655756 original size:18 final size:19
Alignment explanation
Indices: 655720--655759 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
655710 ATAATAATTT
**
655720 ATTAAAAAATTATGTAAAA
1 ATTAAAAAATTATAAAAAA
655739 ATTAAAAAA-TATAAAAAA
1 ATTAAAAAATTATAAAAAA
655757 ATT
1 ATT
655760 TATATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
ATTAAAAAATTATAAAAAA
Found at i:661013 original size:2 final size:2
Alignment explanation
Indices: 661001--661037 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
660991 ATAATGACAC
661001 AT AT CAT 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
661038 CAATTCTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:662139 original size:26 final size:25
Alignment explanation
Indices: 662110--662161 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
662100 AAAATTAATT
662110 ATTATAATTAATATAAATA-TTTTAAA
1 ATTA-AATTAA-ATAAATATTTTTAAA
* *
662136 ATTAATTTTAATAAATATTTTTAAA
1 ATTAAATTAAATAAATATTTTTAAA
662161 A
1 A
662162 AAAATGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.30
25 12 0.52
26 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTAAATTAAATAAATATTTTTAAA
Found at i:662142 original size:24 final size:25
Alignment explanation
Indices: 662114--662161 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
662104 TTAATTATTA
662114 TAATTA-ATATAAATA-TTTTAAAAT
1 TAATTATA-ATAAATATTTTTAAAAT
*
662138 TAATTTTAATAAATATTTTTAAAA
1 TAATTATAATAAATATTTTTAAAA
662162 AAAATGTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATTATAATAAATATTTTTAAAAT
Found at i:662802 original size:22 final size:23
Alignment explanation
Indices: 662745--662803 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 23
662735 AATATAATTA
*
662745 TAATTAAATTTAAATAAAAATATTT
1 TAATTAAA-TTAAAT-AAAAGATTT
*
662770 TTATT-AA-TAAAT-AAAGATTT
1 TAATTAAATTAAATAAAAGATTT
662790 TAATTAAATTAAAT
1 TAATTAAATTAAAT
662804 TTTTCTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 10 0.34
24 2 0.07
25 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATTAAATTAAATAAAAGATTT
Found at i:662905 original size:25 final size:26
Alignment explanation
Indices: 662872--662920 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
662862 TTATAGAAGT
662872 AATTTTTATAT-TT-ATATATTTATAA
1 AATTTTTATATATTAATA-ATTTATAA
662897 AATTTTTATATATTAATAATTTAT
1 AATTTTTATATATTAATAATTTAT
662921 TTATATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.50
26 8 0.36
27 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
AATTTTTATATATTAATAATTTATAA
Found at i:662917 original size:17 final size:15
Alignment explanation
Indices: 662896--662988 Score: 59
Period size: 17 Copynumber: 5.9 Consensus size: 15
662886 TATATTTATA
662896 AAATTTTTATATATT
1 AAATTTTTATATATT
662911 AATAATTTATT-TATA-T
1 -A-AATTT-TTATATATT
*
662927 AAA-TTTTACTATGTT
1 AAATTTTTA-TATATT
*
662942 AAAATTTTTATTTATTT
1 -AAATTTTTATATA-TT
662959 ATATATTTTTATTATATT
1 A-A-ATTTTTA-TATATT
662977 AAA-TTTTATATA
1 AAATTTTTATATA
662989 ATATTTTAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
12 2 0.03
13 2 0.03
14 9 0.15
15 7 0.11
16 9 0.15
17 18 0.29
18 12 0.19
19 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (15 bp):
AAATTTTTATATATT
Found at i:662934 original size:30 final size:30
Alignment explanation
Indices: 662888--662985 Score: 83
Period size: 30 Copynumber: 3.1 Consensus size: 30
662878 TATATTTATA
662888 TATTTATAAAATTTTTA-TATATTAATAATT
1 TATTTATAAAATTTTTACTATATTAA-AATT
*
662918 TATTTATATAAA-TTTTACTATGTTAAAATTTT
1 TATTTATA-AAATTTTTACTATATTAAAA--TT
* * *
662950 TATTTATTTATATATTTTTATTATATTAAATTT
1 TATTTA--TA-AAATTTTTACTATATTAAAATT
662983 TAT
1 TAT
662986 ATAATATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
30 15 0.27
31 10 0.18
32 8 0.14
33 5 0.09
34 5 0.09
35 13 0.23
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (30 bp):
TATTTATAAAATTTTTACTATATTAAAATT
Found at i:662976 original size:19 final size:19
Alignment explanation
Indices: 662877--663007 Score: 66
Period size: 19 Copynumber: 7.3 Consensus size: 19
662867 GAAGTAATTT
*
662877 TTATATTTATATATTTATA
1 TTATATTTATATATTTTTA
** * * *
662896 AAATTTTTATATATTAATAA
1 TTATATTTATATATT-TTTA
*
662916 TT-TATTTATATAAATTTTA
1 TTATATTTATAT-ATTTTTA
* * *
662935 CTAT-GTTA-AAATTTTTA
1 TTATATTTATATATTTTTA
662952 TT-TATTTATATATTTTTA
1 TTATATTTATATATTTTTA
662970 TTATA-TTA-A-ATTTTATA
1 TTATATTTATATATTTT-TA
*
662987 TAATATTT-TA-ATTTTT-
1 TTATATTTATATATTTTTA
663003 TTATA
1 TTATA
663008 ACATATTTAT
Statistics
Matches: 82, Mismatches: 21, Indels: 21
0.66 0.17 0.17
Matches are distributed among these distances:
16 10 0.12
17 18 0.22
18 22 0.27
19 28 0.34
20 4 0.05
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (19 bp):
TTATATTTATATATTTTTA
Found at i:662979 original size:35 final size:35
Alignment explanation
Indices: 662915--663007 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 35
662905 TATATTAATA
* * *
662915 ATTTATTTATATAAATTTTACTATGTTAAAATTTT-T
1 ATTTATTTATAT-ATTTTTATTATATT-AAATTTTAT
662951 ATTTATTTATATATTTTTATTATATTAAATTTTAT
1 ATTTATTTATATATTTTTATTATATTAAATTTTAT
*
662986 ATAATATTT-TA-ATTTTT-TTATA
1 AT-TTATTTATATATTTTTATTATA
663008 ACATATTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
33 5 0.10
34 13 0.25
35 16 0.31
36 17 0.33
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (35 bp):
ATTTATTTATATATTTTTATTATATTAAATTTTAT
Found at i:662985 original size:15 final size:15
Alignment explanation
Indices: 662900--662985 Score: 52
Period size: 15 Copynumber: 5.4 Consensus size: 15
662890 TTTATAAAAT
662900 TTTTA-TATATTAATA
1 TTTTATTATATTAA-A
*
662915 ATTTATT-TATATAAA
1 TTTTATTATAT-TAAA
* *
662930 TTTTACTATGTTAAAA
1 TTTTATTATATT-AAA
662946 TTTTTATT-TATTTATATA
1 -TTTTATTATA-TTA-A-A
662964 TTTTTATTATATTAAA
1 -TTTTATTATATTAAA
662980 TTTTAT
1 TTTTAT
662986 ATAATATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
15 20 0.36
16 12 0.21
17 10 0.18
18 12 0.21
19 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (15 bp):
TTTTATTATATTAAA
Found at i:662994 original size:36 final size:35
Alignment explanation
Indices: 662918--663031 Score: 96
Period size: 35 Copynumber: 3.3 Consensus size: 35
662908 ATTAATAATT
* * * *
662918 TATTTATATAAATTTTACTATGTTAAAATTTT-TATT
1 TATTTATAT-ATTTTTATTATATT-AAATTTTATATA
662954 TATTTATATATTTTTATTATATTAAATTTTATATAA
1 TATTTATATATTTTTATTATATTAAATTTTATAT-A
*
662990 TATTT-TA-ATTTTT-TTATA--ACATATTTATATA
1 TATTTATATATTTTTATTATATTAAAT-TTTATATA
*
663021 TATTCATATAT
1 TATTTATATAT
663032 AAAAAAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
31 8 0.12
32 9 0.13
33 7 0.10
34 13 0.19
35 16 0.24
36 14 0.21
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.60
Consensus pattern (35 bp):
TATTTATATATTTTTATTATATTAAATTTTATATA
Found at i:665584 original size:5 final size:5
Alignment explanation
Indices: 665566--665599 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
665556 ACACAGTTTT
665566 ATTTA ATTTGA ATTTA ATTTA ATTTA ATTTA ATT
1 ATTTA ATTT-A ATTTA ATTTA ATTTA ATTTA ATT
665600 ATAACATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:668776 original size:2 final size:2
Alignment explanation
Indices: 668769--668794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
668759 AGTTCAATTG
668769 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
668795 TAAATTTTAG
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:668861 original size:20 final size:18
Alignment explanation
Indices: 668813--668862 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
668803 AGATAAATTT
*
668813 TTTATTAATTTAAATTGA
1 TTTAATAATTTAAATTGA
668831 TTTAATTTAATTTAAATTGATA
1 TTTAA--TAATTTAAATTG--A
668853 TTTAATAATT
1 TTTAATAATT
668863 AATTTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
20 17 0.63
22 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTAATAATTTAAATTGA
Found at i:670312 original size:2 final size:2
Alignment explanation
Indices: 670301--670336 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
670291 CAATAGTTTA
670301 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
670337 CAAAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:670913 original size:2 final size:2
Alignment explanation
Indices: 670908--670932 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
670898 ACACACACAC
670908 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 A
670933 AATTGATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:672760 original size:1 final size:1
Alignment explanation
Indices: 672754--672779 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
672744 AGGGCATTAG
672754 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
672780 CCAAGCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:674585 original size:76 final size:76
Alignment explanation
Indices: 674459--674606 Score: 278
Period size: 76 Copynumber: 1.9 Consensus size: 76
674449 TTAGAAATCC
*
674459 CACTCTCTTAATATCAAATATATATATATATATATATACAAACAAAATAGATGAAAAATGTGAAT
1 CACTCTCTTAATATCAAAAATATATATATATATATATACAAACAAAATAGATGAAAAATGTGAAT
674524 CAACGGTATCT
66 CAACGGTATCT
*
674535 CACTCTCTTAATATCAAAAATATATATATATATATATATAAACAAAATAGATGAAAAATGTGAAT
1 CACTCTCTTAATATCAAAAATATATATATATATATATACAAACAAAATAGATGAAAAATGTGAAT
674600 CAACGGT
66 CAACGGT
674607 TGAATTGAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (76 bp):
CACTCTCTTAATATCAAAAATATATATATATATATATACAAACAAAATAGATGAAAAATGTGAAT
CAACGGTATCT
Found at i:681755 original size:13 final size:13
Alignment explanation
Indices: 681739--681764 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
681729 ATAAAATAAT
681739 AAAATATTATATA
1 AAAATATTATATA
681752 AAAATATTATATA
1 AAAATATTATATA
681765 TTTTAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATATTATATA
Found at i:681763 original size:18 final size:16
Alignment explanation
Indices: 681746--681822 Score: 59
Period size: 17 Copynumber: 4.7 Consensus size: 16
681736 AATAAAATAT
681746 TATATAAAAATATTATA
1 TATATAAAAAT-TTATA
* *
681763 TATTTTAAAATTTATA
1 TATATAAAAATTTATA
**
681779 TA-ATACGAA-TTATTAA
1 TATATAAAAATTTA-T-A
681795 TATATAAAAATTTATA
1 TATATAAAAATTTATA
*
681811 TAAATATAAAAT
1 TATATA-AAAAT
681823 ATCTTAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
14 3 0.07
15 4 0.09
16 16 0.35
17 20 0.43
18 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
TATATAAAAATTTATA
Found at i:681933 original size:63 final size:64
Alignment explanation
Indices: 681856--681979 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 64
681846 GTCAAAATAT
* *
681856 AAAATCATAATACGAATTTATAAGTGATAAAATCTAATTAAAATTTAAT-GAAAGAGAATTTAC
1 AAAATCATAATACGAATTTATAAATGATAAAATCTAATTAAAATGTAATAGAAAGAGAATTTAC
* * * * * *
681919 AAAATCATAATACGAATTTGTAAATTATTAGATCTAGTTAAAATGTAATAGAAAGTGAATT
1 AAAATCATAATACGAATTTATAAATGATAAAATCTAATTAAAATGTAATAGAAAGAGAATT
681980 ATAATAGACT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
63 42 0.81
64 10 0.19
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (64 bp):
AAAATCATAATACGAATTTATAAATGATAAAATCTAATTAAAATGTAATAGAAAGAGAATTTAC
Found at i:686844 original size:3 final size:3
Alignment explanation
Indices: 686836--686868 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
686826 AGTATTCGTA
686836 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
686869 CGTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:687003 original size:28 final size:27
Alignment explanation
Indices: 686972--687036 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
686962 TTTAATATAT
686972 TTTATATTTTATTTTTAAATAAATAATA
1 TTTAT-TTTTATTTTTAAATAAATAATA
* *
687000 TTTATTTAATT-TTTTTATATTAATAATA
1 TTTATTT--TTATTTTTAAATAAATAATA
*
687028 TATATTTTT
1 TTTATTTTT
687037 TAAATTCGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 26 0.81
29 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTATTTTTATTTTTAAATAAATAATA
Found at i:688781 original size:13 final size:13
Alignment explanation
Indices: 688763--688796 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
688753 GTCTTGTATT
688763 AATACATTTATGA
1 AATACATTTATGA
688776 AATACATTTATGA
1 AATACATTTATGA
*
688789 AATGCATT
1 AATACATT
688797 GACATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (13 bp):
AATACATTTATGA
Found at i:689119 original size:18 final size:18
Alignment explanation
Indices: 689091--689137 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
689081 TGATAACTAA
*
689091 AAGAGATATTTTTCTTATT
1 AAGAGATA-TTTACTTATT
689110 AAGA-ATATTTACTTATT
1 AAGAGATATTTACTTATT
*
689127 AA-ATATATTTA
1 AAGAGATATTTA
689138 ACTATCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 18 0.69
18 3 0.12
19 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (18 bp):
AAGAGATATTTACTTATT
Found at i:689447 original size:2 final size:2
Alignment explanation
Indices: 689440--689474 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
689430 TTGCTTTGTA
*
689440 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
689475 AACTATTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:690164 original size:21 final size:18
Alignment explanation
Indices: 690117--690175 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 18
690107 TTATATATTT
690117 ATAATTAAATTTAAATAA
1 ATAATTAAATTTAAATAA
690135 ATAA-T-AATTTAAATCAA
1 ATAATTAAATTTAAAT-AA
* *
690152 ATCAATTAAAATTAAAAAA
1 AT-AATTAAATTTAAATAA
690171 ATAAT
1 ATAAT
690176 ATTTAAACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 9 0.26
17 5 0.14
18 9 0.26
19 5 0.14
20 7 0.20
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATTAAATTTAAATAA
Found at i:691155 original size:26 final size:27
Alignment explanation
Indices: 691106--691159 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
691096 TCGAAAACCC
* *
691106 AGATTCTTGGTGTTTTAGGGTGGGAGA
1 AGATACTTGGTGTTTTAGGATGGGAGA
691133 AGATACTTGGTG-TTTAGGATGGGAGA
1 AGATACTTGGTGTTTTAGGATGGGAGA
691159 A
1 A
691160 ACGGGGGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.24, C:0.04, G:0.39, T:0.33
Consensus pattern (27 bp):
AGATACTTGGTGTTTTAGGATGGGAGA
Found at i:691320 original size:3 final size:3
Alignment explanation
Indices: 691312--691337 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
691302 ATCAACTTAA
691312 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
691338 AGCAAAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:692952 original size:20 final size:18
Alignment explanation
Indices: 692929--692982 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
692919 GAATATTCAT
692929 ATTATATTTATATATTTAAA
1 ATTAT-TTTATATATTT-AA
*
692949 ATTATTATAATAATATTTAA
1 ATTATT-TTAT-ATATTTAA
692969 ATTATTTTATATAT
1 ATTATTTTATATAT
692983 AAATTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 4 0.13
19 4 0.13
20 16 0.53
21 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTTTATATATTTAA
Found at i:692984 original size:23 final size:24
Alignment explanation
Indices: 692928--692998 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 24
692918 TGAATATTCA
*
692928 TATTATATTTATATATTTAAA--AT
1 TATTATATATA-ATATTTAAATTAT
692951 TATTATA-ATAATATTTAAATTAT
1 TATTATATATAATATTTAAATTAT
*
692974 T-TTATATATAA-ATTTTAATATAT
1 TATTATATATAATATTTAAAT-TAT
692997 TA
1 TA
692999 ATAATTTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 9 0.22
22 14 0.34
23 18 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTATATATAATATTTAAATTAT
Found at i:694979 original size:31 final size:29
Alignment explanation
Indices: 694944--695008 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
694934 CACTACAAAA
*
694944 TTTAAAAAATTAAAAATAATTAATAATTATT
1 TTTAAAAAATTAAAAATAA-AAAT-ATTATT
** *
694975 TTTAAAATTTTTAAAATAAAAATATTATT
1 TTTAAAAAATTAAAAATAAAAATATTATT
695004 TTTAA
1 TTTAA
695009 TAATTTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 11 0.37
30 3 0.10
31 16 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTAAAAAATTAAAAATAAAAATATTATT
Found at i:694981 original size:29 final size:27
Alignment explanation
Indices: 694949--695013 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 27
694939 CAAAATTTAA
*
694949 AAAATTAAAAATAATTAATAATTATTTTT
1 AAAATTAAAAATAA-AAAT-ATTATTTTT
*
694978 AAAATTTTTAAAATAAAAATATTATTTTT
1 AAAA--TTAAAAATAAAAATATTATTTTT
695007 AATAATT
1 AA-AATT
695014 TTCTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
28 2 0.06
29 15 0.48
30 5 0.16
31 9 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAAATTAAAAATAAAAATATTATTTTT
Found at i:697842 original size:31 final size:29
Alignment explanation
Indices: 697806--697870 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
697796 TTCGATTTTA
697806 AATTTAAATAATATATTT-TATAATATAAATT
1 AATTTAAATAAT-TATTTATATAAT-TAAA-T
*
697837 AATTTAAATAATTATTTATTTAATTAAAT
1 AATTTAAATAATTATTTATATAATTAAAT
697866 AATTT
1 AATTT
697871 TTATTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 6 0.19
30 9 0.28
31 17 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
AATTTAAATAATTATTTATATAATTAAAT
Found at i:697891 original size:23 final size:20
Alignment explanation
Indices: 697835--697880 Score: 76
Period size: 19 Copynumber: 2.3 Consensus size: 20
697825 ATAATATAAA
697835 TTAATTTAAATAATTATTTAT
1 TTAA-TTAAATAATTATTTAT
697856 TTAATTAAATAATT-TTTAT
1 TTAATTAAATAATTATTTAT
697875 TTAATT
1 TTAATT
697881 TTAATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 11 0.44
20 10 0.40
21 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATTAAATAATTATTTAT
Found at i:700552 original size:14 final size:15
Alignment explanation
Indices: 700520--700553 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
700510 ATATTAAAAA
700520 AAATATTTATATATT
1 AAATATTTATATATT
700535 -AATATTTATA-ATT
1 AAATATTTATATATT
700548 AAATAT
1 AAATAT
700554 AAATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATATTTATATATT
Found at i:701498 original size:2 final size:2
Alignment explanation
Indices: 701493--701537 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
701483 TATACATCTC
701493 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
701535 AT A
1 AT A
701538 AATCAAAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:706393 original size:145 final size:143
Alignment explanation
Indices: 706114--706382 Score: 353
Period size: 145 Copynumber: 1.9 Consensus size: 143
706104 TTTTTACAAC
* * * **
706114 TCATGGTTAAATATTATGAATATGAGAAACAATTCCTTATTAATTCAGTGTGCTTTGACCAAAGA
1 TCATGGTTAAATATCATAAATATGAAAAACAATTCCTTATTAATTCAGTGCACTTTGACCAAAGA
* * * *
706179 CTTTATATTAAAATTCAGATCACACTCAATCGATTTAAAATATAAAAAATTTTAATAACAATTAA
66 CTTAATACTAAAAATCAGATCACACTCAATCGAATTAAAATATAAAAAATTTTAATAACAATTAA
706244 AATATCATAAATA
131 AATATCATAAATA
*
706257 TCATGGTTAAATATCATAAATTTATGAAAAACAACTT-CTTATTAATTTAGTGCACTTTGACCAA
1 TCATGGTTAAATATCATAAA--TATGAAAAACAA-TTCCTTATTAATTCAGTGCACTTTGACCAA
* * * *
706321 AGACTTAATGCTAAAAATCATATCATACTTAATCGAATTAAAATA-AAAATAATATTTAATAA
63 AGACTTAATACTAAAAATCAGATCACACTCAATCGAATTAAAATATAAAA-AAT-TTTAATAA
706383 TTATTAAATA
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
143 18 0.17
144 4 0.04
145 75 0.70
146 10 0.09
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (143 bp):
TCATGGTTAAATATCATAAATATGAAAAACAATTCCTTATTAATTCAGTGCACTTTGACCAAAGA
CTTAATACTAAAAATCAGATCACACTCAATCGAATTAAAATATAAAAAATTTTAATAACAATTAA
AATATCATAAATA
Found at i:708056 original size:18 final size:16
Alignment explanation
Indices: 708039--708100 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
708029 AAACTATTTA
708039 ATTAAATATATATTTTT
1 ATTAAATAT-TATTTTT
708056 ATTAAATATTATTATATT
1 ATTAAATATTATT-T-TT
708074 -TT-AATACTTATTTATT
1 ATTAAATA-TTATTT-TT
708090 ATTAAA-ATTAT
1 ATTAAATATTAT
708101 ATATTTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 16 0.40
17 20 0.50
18 4 0.10
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTAAATATTATTTTT
Found at i:708061 original size:17 final size:17
Alignment explanation
Indices: 708039--708105 Score: 70
Period size: 16 Copynumber: 4.0 Consensus size: 17
708029 AAACTATTTA
708039 ATTAAATATATATTT-TT
1 ATTAAATAT-TATTTATT
708056 ATTAAATATTATTATATT
1 ATTAAATATTATT-TATT
708074 -TT-AATACTTATTTATT
1 ATTAAATA-TTATTTATT
*
708090 ATTAAA-ATTATATATT
1 ATTAAATATTATTTATT
708106 TAATTTTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
16 20 0.45
17 20 0.45
18 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTAAATATTATTTATT
Found at i:708074 original size:37 final size:35
Alignment explanation
Indices: 708018--708110 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 35
708008 TCTCTTAATA
*
708018 TATTAAAAATTAAACTATTTAATTAAATA-TATATTT-T
1 TATT-AAAATTATA-TATTTAATT-AATACT-TATTTAT
708055 TATTAAATATTAT-TATATT--TTAATACTTATTTAT
1 TATTAAA-ATTATATAT-TTAATTAATACTTATTTAT
708089 TATTAAAATTATATATTTAATT
1 TATTAAAATTATATATTTAATT
708111 TTTAAATTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
33 16 0.33
34 14 0.29
35 5 0.10
36 5 0.10
37 8 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (35 bp):
TATTAAAATTATATATTTAATTAATACTTATTTAT
Found at i:709295 original size:16 final size:16
Alignment explanation
Indices: 709269--709307 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
709259 ATTTTAATAC
709269 ATTAATA-ATTTATAT
1 ATTAATATATTTATAT
*
709284 TTTAATATATTTATAT
1 ATTAATATATTTATAT
709300 ATTAATAT
1 ATTAATAT
709308 CGTATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTAATATATTTATAT
Found at i:712856 original size:11 final size:12
Alignment explanation
Indices: 712842--712883 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
712832 AAATATTAAA
712842 ATTAAT-TTTAT
1 ATTAATATTTAT
712853 ATTAATATTTAT
1 ATTAATATTTAT
* *
712865 A-TAATATTAAA
1 ATTAATATTTAT
712876 ATTAATAT
1 ATTAATAT
712884 AAATTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 15 0.56
12 12 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTAATATTTAT
Found at i:712856 original size:17 final size:17
Alignment explanation
Indices: 712828--712891 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 17
712818 AAAATATATA
712828 TAATA-AATATTAAAAT
1 TAATATAATATTAAAAT
* * *
712844 TAATTTTATATTAATAT
1 TAATATAATATTAAAAT
*
712861 TTATATAATATTAAAAT
1 TAATATAATATTAAAAT
712878 TAATATAA-ATTAAA
1 TAATATAATATTAAA
712892 TAATAATTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 10 0.26
17 29 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATAATATTAAAAT
Found at i:712860 original size:6 final size:6
Alignment explanation
Indices: 712833--712883 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
712823 ATATATAATA
* * * *
712833 AATATT AAAATT AAT-TT TATATT AATATT TATA-T AATATT AAAATT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
712879 AATAT
1 AATAT
712884 AAATTAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
5 8 0.23
6 27 0.77
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AATATT
Found at i:712898 original size:17 final size:17
Alignment explanation
Indices: 712827--712898 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 17
712817 TAAAATATAT
712827 ATAATA-AATATTAAAA
1 ATAATATAATATTAAAA
* * * *
712843 TTAATTTTATATTAATA
1 ATAATATAATATTAAAA
* *
712860 TTTATATAATATTAAAA
1 ATAATATAATATTAAAA
*
712877 TTAATATAA-ATTAAATA
1 ATAATATAATATTAAA-A
712894 ATAAT
1 ATAAT
712899 TCAAATCAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 10 0.23
17 34 0.77
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATATAATATTAAAA
Done.