Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 12 of 19
Found at i:2560385 original size:17 final size:17
Alignment explanation
Indices: 2560363--2560414 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2560353 AAATTTATAT
2560363 AATATAAATTATTAATA
1 AATATAAATTATTAATA
*
2560380 AATATATAA-TATT-TTA
1 AATATA-AATTATTAATA
2560396 AATAT-AATTATTATATA
1 AATATAAATTATTA-ATA
2560413 AA
1 AA
2560415 ATACACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.07
15 4 0.14
16 7 0.24
17 14 0.48
18 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATAAATTATTAATA
Found at i:2560631 original size:18 final size:18
Alignment explanation
Indices: 2560608--2560653 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2560598 ATATGATTTT
*
2560608 TTTAATTAAATTATATC-A
1 TTTAATTAAA-GATATCAA
*
2560626 TTTAATTCAAGATATCAA
1 TTTAATTAAAGATATCAA
2560644 TTTAATTAAA
1 TTTAATTAAA
2560654 AGTTTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTAATTAAAGATATCAA
Found at i:2560667 original size:3 final size:3
Alignment explanation
Indices: 2560659--2560713 Score: 60
Period size: 3 Copynumber: 17.7 Consensus size: 3
2560649 TTAAAAGTTT
2560659 ATA ATA AT- ATA A-A TATAA ATA GATA AATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -AT-A ATA -ATA -ATA ATA ATA ATA ATA ATA ATA
2560706 ATA ATA AT
1 ATA ATA AT
2560714 TGATTCCAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
2 3 0.07
3 34 0.74
4 8 0.17
5 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2564405 original size:13 final size:13
Alignment explanation
Indices: 2564361--2564414 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
2564351 TATAATTAAA
* *
2564361 ATATTATATTTAT
1 ATATTAAATATAT
2564374 AT-TTAAATATAT
1 ATATTAAATATAT
*
2564386 A-A-AAAATATAT
1 ATATTAAATATAT
*
2564397 ATATTAAATATAA
1 ATATTAAATATAT
2564410 ATATT
1 ATATT
2564415 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
11 9 0.27
12 10 0.30
13 14 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTAAATATAT
Found at i:2564411 original size:30 final size:31
Alignment explanation
Indices: 2564349--2564413 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
2564339 TTAAAAATTT
* *
2564349 TATATAATTAAAATATTATATTTATATTTAAA
1 TATATAA-TAAAATATTATATTTAAATATAAA
2564381 TATATAA-AAAATA-TATATATTAAATATAAA
1 TATATAATAAAATATTATAT-TTAAATATAAA
2564411 TAT
1 TAT
2564414 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 18 0.60
32 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TATATAATAAAATATTATATTTAAATATAAA
Found at i:2568051 original size:13 final size:13
Alignment explanation
Indices: 2568035--2568096 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
2568025 AAATAATATA
2568035 ATTTTTTAATTAT
1 ATTTTTTAATTAT
*
2568048 A-TTTATATATTAT
1 ATTTTTTA-ATTAT
2568061 A-TTTTTAACTTA-
1 ATTTTTTAA-TTAT
2568073 ATTTTTTAA-TAT
1 ATTTTTTAATTAT
*
2568085 ATTTATTAATTA
1 ATTTTTTAATTA
2568097 AATTAATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
11 2 0.05
12 15 0.37
13 24 0.59
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTTTTAATTAT
Found at i:2568471 original size:3 final size:3
Alignment explanation
Indices: 2568463--2568526 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
2568453 TTGTTTTTCT
* *
2568463 TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2568511 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
2568527 ATTTAGCTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2569509 original size:14 final size:14
Alignment explanation
Indices: 2569455--2569509 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
2569445 TTTTAAAAAT
2569455 ATTTTTAT-ATT-A
1 ATTTTTATAATTAA
*
2569467 ATATTTATAATTAA
1 ATTTTTATAATTAA
* * *
2569481 TTTTTTAAAAATAA
1 ATTTTTATAATTAA
*
2569495 ATTTTTATTATTAA
1 ATTTTTATAATTAA
2569509 A
1 A
2569510 ATAATAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
12 7 0.22
13 3 0.09
14 22 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTTTATAATTAA
Found at i:2569517 original size:40 final size:38
Alignment explanation
Indices: 2569420--2569518 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 38
2569410 CATGGACTGA
2569420 TTTATTATTTAAAATAAT-ATTAAAATTTTAAAAATATT
1 TTTATTA-TTAAAATAATAATTAAAATTTTAAAAATATT
* * **
2569458 TTTA-TATTAATATTTATAATTAATTTTTTAAAAATAAATT
1 TTTATTATTAA-AATAATAATTAAAATTTTAAAAAT--ATT
2569498 TTTATTATTAAAATAATAATT
1 TTTATTATTAAAATAATAATT
2569519 TTAATCAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
36 4 0.08
37 6 0.12
38 19 0.38
40 15 0.30
41 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (38 bp):
TTTATTATTAAAATAATAATTAAAATTTTAAAAATATT
Found at i:2570140 original size:2 final size:2
Alignment explanation
Indices: 2570133--2570157 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2570123 GCAAATACAA
2570133 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
2570158 AAAGCAAATG
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:2571690 original size:38 final size:38
Alignment explanation
Indices: 2571623--2571721 Score: 94
Period size: 38 Copynumber: 2.6 Consensus size: 38
2571613 TAGTTATTTA
* * *
2571623 ATATAATAT-AAATATTTGTATATTATATATTATCTAAT
1 ATATAATATAAAATATATAT-TATTATATATAATCTAAT
* * *
2571661 ATATAATATAAAATATATATTATTTTATATAATTTTAT
1 ATATAATATAAAATATATATTATTATATATAATCTAAT
* *
2571699 AT-TATTATAAAAGTATATTTTAT
1 ATATAATATAAAA-TATATATTAT
2571722 AAAATAACGT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 9 0.18
38 34 0.67
39 8 0.16
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (38 bp):
ATATAATATAAAATATATATTATTATATATAATCTAAT
Found at i:2571721 original size:15 final size:16
Alignment explanation
Indices: 2571696--2571725 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2571686 TATATAATTT
2571696 TATATTATTATAAAAG
1 TATATTATTATAAAAG
2571712 TATATT-TTATAAAA
1 TATATTATTATAAAA
2571726 TAACGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TATATTATTATAAAAG
Found at i:2571744 original size:17 final size:19
Alignment explanation
Indices: 2571711--2571745 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2571701 TATTATAAAA
2571711 GTATATTTTATAAAATAAC
1 GTATATTTTATAAAATAAC
2571730 GTATA-TTTA-AAAATAA
1 GTATATTTTATAAAATAA
2571746 AATTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (19 bp):
GTATATTTTATAAAATAAC
Found at i:2575092 original size:16 final size:15
Alignment explanation
Indices: 2575072--2575125 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
2575062 AAAAATACTG
2575072 AAAATTTAAAATATAA
1 AAAATTTAAAATAT-A
2575088 CAAATATTTAAAATAATA
1 -AAA-ATTTAAAAT-ATA
*
2575106 AATATTTAAAGATATA
1 AAAATTTAAA-ATATA
2575122 AAAA
1 AAAA
2575126 ATAAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 13 0.41
17 7 0.22
18 10 0.31
19 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAATTTAAAATATA
Found at i:2581167 original size:12 final size:12
Alignment explanation
Indices: 2581150--2581180 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2581140 GAAAATAAAA
2581150 GCTGTTAACTGT
1 GCTGTTAACTGT
2581162 GCTGTTAACTGT
1 GCTGTTAACTGT
2581174 GC-GTTAA
1 GCTGTTAA
2581181 TTTTGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (12 bp):
GCTGTTAACTGT
Found at i:2581195 original size:13 final size:12
Alignment explanation
Indices: 2581177--2581228 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
2581167 TAACTGTGCG
2581177 TTAATTTTGAAAT
1 TTAA-TTTGAAAT
2581190 TTAATTTGAAAT
1 TTAATTTGAAAT
* *
2581202 AGTAAATGTTAAAAT
1 --TTAAT-TTGAAAT
2581217 TTAATTTGAAAT
1 TTAATTTGAAAT
2581229 AGTGAAGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 14 0.44
13 8 0.25
14 4 0.12
15 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (12 bp):
TTAATTTGAAAT
Found at i:2585915 original size:12 final size:12
Alignment explanation
Indices: 2585898--2585923 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2585888 GAAAACAAAG
2585898 GCTGCCAACTGT
1 GCTGCCAACTGT
2585910 GCTGCCAACTGT
1 GCTGCCAACTGT
2585922 GC
1 GC
2585924 CGTCAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.27, T:0.23
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:2585948 original size:12 final size:12
Alignment explanation
Indices: 2585926--2585976 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
2585916 AACTGTGCCG
2585926 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
2585939 TCAATTTGAAAT
1 TCAATTTGAAAT
*
2585951 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
2585966 TCAATTTGAAA
1 TCAATTTGAAA
2585977 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:2585988 original size:27 final size:27
Alignment explanation
Indices: 2585932--2585988 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
2585922 GCCGTCAATT
* *
2585932 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
2585959 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
2585986 TTG
1 TTG
2585989 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:2587061 original size:22 final size:22
Alignment explanation
Indices: 2587036--2587077 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2587026 TTTATTAAAA
2587036 ATAAA-TTAGATATTAAATATTT
1 ATAAATTTA-ATATTAAATATTT
2587058 ATAAATTTAATATTAAATAT
1 ATAAATTTAATATTAAATAT
2587078 ATTAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAAATTTAATATTAAATATTT
Found at i:2587097 original size:22 final size:22
Alignment explanation
Indices: 2587061--2587115 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2587051 AATATTTATA
* *
2587061 AATTTAATATTAAATATATTAATT
1 AATTTAATA-AAAATA-AATAATT
*
2587085 AA-TTAATAAAAATAAATATTT
1 AATTTAATAAAAATAAATAATT
2587106 AATTTAATAA
1 AATTTAATAA
2587116 TATAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.26
22 12 0.44
23 6 0.22
24 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTAATAAAAATAAATAATT
Found at i:2587126 original size:26 final size:25
Alignment explanation
Indices: 2587065--2587141 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 25
2587055 TTTATAAATT
2587065 TAATATTAAATATATTAATTAATTAATA
1 TAAT-TTAAATAT-TTAATTAA-TAATA
**
2587093 -AAAATAAATATTTAATTTAATAATA
1 TAATTTAAATATTTAA-TTAATAATA
*
2587118 TAATTTAAAATATATAATTAATAA
1 TAATTT-AAATATTTAATTAATAA
2587142 ATTAAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 9 0.22
26 21 0.51
27 11 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATTTAAATATTTAATTAATAATA
Found at i:2588500 original size:3 final size:3
Alignment explanation
Indices: 2588492--2588522 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2588482 TGATTTCGGG
2588492 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2588523 AAAAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2588716 original size:3 final size:3
Alignment explanation
Indices: 2588710--2588739 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2588700 TTCATAATAA
2588710 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2588740 CCTATATGGT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2588882 original size:25 final size:25
Alignment explanation
Indices: 2588853--2588935 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
2588843 AATTATATTT
2588853 TATAATTTTATATATAATATAATTA
1 TATAATTTTATATATAATATAATTA
* * *
2588878 TATAATTAAATATAAATAATATAAATA
1 TATAATT--TTATATATAATATAATTA
* *
2588905 -AT-ATTTTAAATATATAAAAAAATTA
1 TATAATTTT--ATATATAATATAATTA
2588930 TATAAT
1 TATAAT
2588936 AAAAATAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
23 1 0.02
25 22 0.50
26 4 0.09
27 17 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TATAATTTTATATATAATATAATTA
Found at i:2588891 original size:18 final size:18
Alignment explanation
Indices: 2588868--2588957 Score: 57
Period size: 18 Copynumber: 5.2 Consensus size: 18
2588858 TTTTATATAT
2588868 AATATAATTATATAATTA
1 AATATAATTATATAATTA
* *
2588886 AATATAAATAATATAAAT-
1 AATAT-AATTATATAATTA
* *
2588904 AATAT-TTTAAAT-ATATA
1 AATATAATTATATAAT-TA
*
2588921 AA-AAAATTATATAA-TA
1 AATATAATTATATAATTA
*
2588937 AAAATAATT-TATATATTA
1 AATATAATTATATA-ATTA
2588955 AAT
1 AAT
2588958 TTGATCTAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
15 1 0.02
16 14 0.26
17 13 0.25
18 15 0.28
19 10 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATAATTATATAATTA
Found at i:2588899 original size:27 final size:27
Alignment explanation
Indices: 2588861--2588943 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
2588851 TTTATAATTT
*
2588861 TATATATAATATAATTATATAATTAAA
1 TATAAATAATATAATTATATAATTAAA
* *
2588888 TATAAATAATATAAATA-ATATTTTAAA
1 TATAAATAATATAATTATATA-ATTAAA
2588915 TATATAA-AA-A-AATTATATAA-TAAA
1 TATA-AATAATATAATTATATAATTAAA
*
2588939 AATAA
1 TATAA
2588944 TTTATATATT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
23 1 0.02
24 7 0.15
25 4 0.09
26 7 0.15
27 26 0.55
28 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TATAAATAATATAATTATATAATTAAA
Found at i:2588900 original size:9 final size:9
Alignment explanation
Indices: 2588861--2588908 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
2588851 TTTATAATTT
*
2588861 TATATATAA
1 TATAAATAA
*
2588870 TAT-AATTA
1 TATAAATAA
*
2588878 TATAATTAAA
1 TATAAAT-AA
2588888 TATAAATAA
1 TATAAATAA
2588897 TATAAATAA
1 TATAAATAA
2588906 TAT
1 TAT
2588909 TTTAAATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 6 0.19
9 19 0.59
10 7 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TATAAATAA
Found at i:2589155 original size:15 final size:16
Alignment explanation
Indices: 2589117--2589157 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2589107 TTGATACGAT
2589117 AGAAAG-AAAATTGAA
1 AGAAAGAAAAATTGAA
* *
2589132 AGTATGAAAAATTG-A
1 AGAAAGAAAAATTGAA
2589147 AGAAAGAAAAA
1 AGAAAGAAAAA
2589158 GGATAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.15
Consensus pattern (16 bp):
AGAAAGAAAAATTGAA
Found at i:2592079 original size:16 final size:15
Alignment explanation
Indices: 2592058--2592105 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
2592048 TCTTCGTATA
*
2592058 ATATAAATTACATAAT
1 ATATAAATTA-AAAAT
2592074 ATATAAATATAAAAAT
1 ATATAAAT-TAAAAAT
*
2592090 ATATATATTATAAAAT
1 ATATAAATTA-AAAAT
2592106 TAAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATAAATTAAAAAT
Found at i:2601044 original size:17 final size:17
Alignment explanation
Indices: 2601005--2601044 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2600995 CGTTTATAAA
*
2601005 ATTAAAATTTTTACATT
1 ATTAATATTTTTACATT
2601022 ATTAATATTTTTACATT
1 ATTAATATTTTTACATT
*
2601039 GTTAAT
1 ATTAAT
2601045 GTATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTAATATTTTTACATT
Found at i:2602222 original size:24 final size:24
Alignment explanation
Indices: 2602195--2602241 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2602185 TTATTACCTT
2602195 CAATTCTTTTTCAGCTTCAGGAGG
1 CAATTCTTTTTCAGCTTCAGGAGG
2602219 CAATTCTTTTTCAGCTTCAGGAG
1 CAATTCTTTTTCAGCTTCAGGAG
2602242 AAGCAGCGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (24 bp):
CAATTCTTTTTCAGCTTCAGGAGG
Found at i:2604599 original size:12 final size:13
Alignment explanation
Indices: 2604582--2604610 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2604572 CAAAAGTATT
2604582 AATTTTT-TTTAA
1 AATTTTTATTTAA
2604594 AATTTTTATTTAA
1 AATTTTTATTTAA
2604607 AATT
1 AATT
2604611 AATAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATTTTTATTTAA
Found at i:2604675 original size:22 final size:22
Alignment explanation
Indices: 2604647--2604688 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2604637 TTTAACATAA
* *
2604647 TAAAATATTTTTATTTTAATAT
1 TAAAATATTTATAATTTAATAT
2604669 TAAAATATTTATAATTTAAT
1 TAAAATATTTATAATTTAAT
2604689 TTACATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAAAATATTTATAATTTAATAT
Found at i:2605457 original size:2 final size:2
Alignment explanation
Indices: 2605452--2605481 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2605442 ACTAAAAAAT
2605452 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
2605482 AAATTTGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2610893 original size:24 final size:24
Alignment explanation
Indices: 2610865--2610921 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
2610855 GGTTGAACCA
2610865 GATGCATTATGGGTTGGACATG-TC
1 GATGCATTATGGGTTGGACA-GATC
2610889 GATGCATTATGGGTTGGACAGATC
1 GATGCATTATGGGTTGGACAGATC
*
2610913 AATGCATTA
1 GATGCATTA
2610922 GAAGAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (24 bp):
GATGCATTATGGGTTGGACAGATC
Found at i:2613297 original size:32 final size:32
Alignment explanation
Indices: 2613260--2613320 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
2613250 AATTGAAGAA
*
2613260 TGAAAAATTATAAATATTCGAGATTGAACATT
1 TGAAAAATTATAAATATTCAAGATTGAACATT
2613292 TGAAAAATTATAAATATTCAAGATTGAAC
1 TGAAAAATTATAAATATTCAAGATTGAAC
2613321 GTTAATCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (32 bp):
TGAAAAATTATAAATATTCAAGATTGAACATT
Found at i:2613422 original size:16 final size:16
Alignment explanation
Indices: 2613403--2613434 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2613393 TTTCATTAAT
2613403 TTGTGATGAATTACCG
1 TTGTGATGAATTACCG
2613419 TTGTGATGAATTACCG
1 TTGTGATGAATTACCG
2613435 CGATGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (16 bp):
TTGTGATGAATTACCG
Found at i:2616558 original size:29 final size:25
Alignment explanation
Indices: 2616506--2616569 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
2616496 AAAGATTTGG
*
2616506 TTAATTATTTTCTTAAAAACATTTT
1 TTAATTATTTTATTAAAAACATTTT
2616531 TTAATTATTTATATTAAATAACATATTT
1 TTAATTATTT-TATTAAA-AACAT-TTT
2616559 TATAATATATT
1 T-TAAT-TATT
2616570 GAATCTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 10 0.30
26 6 0.18
27 5 0.15
28 4 0.12
29 4 0.12
30 4 0.12
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATTATTTTATTAAAAACATTTT
Found at i:2617088 original size:17 final size:17
Alignment explanation
Indices: 2617066--2617118 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
2617056 GTTGTTAAGA
2617066 TATAAATGAAAAATGAT
1 TATAAATGAAAAATGAT
** *
2617083 TATAAATAGAAAAAAAAA
1 TATAAAT-GAAAAATGAT
*
2617101 TAAAAAT-AAAAATGAT
1 TATAAATGAAAAATGAT
2617117 TA
1 TA
2617119 GTGGTATGTT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25
Consensus pattern (17 bp):
TATAAATGAAAAATGAT
Found at i:2618206 original size:19 final size:21
Alignment explanation
Indices: 2618181--2618227 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
2618171 TTAATAAAAT
*
2618181 TTAAATTATTATTTA-ATTAA
1 TTAAATTATTATTTATATAAA
2618201 -TAAA-T-TTATTTATATAAA
1 TTAAATTATTATTTATATAAA
2618219 TTAAATTAT
1 TTAAATTAT
2618228 AAAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
17 7 0.32
18 5 0.23
19 8 0.36
20 1 0.05
21 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAATTATTATTTATATAAA
Found at i:2618219 original size:14 final size:13
Alignment explanation
Indices: 2618164--2618230 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 13
2618154 TCATATTTTT
2618164 ATTTAATTTAATAAA
1 ATTTAA-TTAAT-AA
*
2618179 ATTTAAATT-AT-T
1 ATTT-AATTAATAA
2618191 ATTTAATTAATAA
1 ATTTAATTAATAA
*
2618204 ATTTATTTATATAA
1 ATTTAATTA-ATAA
*
2618218 ATTAAATT-ATAA
1 ATTTAATTAATAA
2618230 A
1 A
2618231 AATATTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
11 4 0.09
12 11 0.26
13 8 0.19
14 12 0.28
15 6 0.14
16 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTAATTAATAA
Found at i:2618554 original size:25 final size:25
Alignment explanation
Indices: 2618525--2618578 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
2618515 TGATCTATTT
*
2618525 TATTCACATT-GATAATGTACTTATA
1 TATTCAAATTCGAT-ATGTACTTATA
*
2618550 TATTCAAATTCGATATGTATTTATA
1 TATTCAAATTCGATATGTACTTATA
2618575 TATT
1 TATT
2618579 TAATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (25 bp):
TATTCAAATTCGATATGTACTTATA
Found at i:2618628 original size:17 final size:17
Alignment explanation
Indices: 2618601--2618650 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
2618591 ATTTTTTTTA
2618601 AAATAATTTAATAAATTT
1 AAAT-ATTTAATAAATTT
*
2618619 AAATATTTAACAAATTT
1 AAATATTTAATAAATTT
*
2618636 AAATATCTAATAAAT
1 AAATATTTAATAAAT
2618651 ATCACTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 25 0.86
18 4 0.14
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATTTAATAAATTT
Found at i:2618699 original size:19 final size:17
Alignment explanation
Indices: 2618675--2618709 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
2618665 AGAATACAAA
2618675 TTTAAATAATAATTTAAAT
1 TTTAAAT-AT-ATTTAAAT
2618694 TTTAAATATATTTAAA
1 TTTAAATATATTTAAA
2618710 AATTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAATATATTTAAAT
Found at i:2618844 original size:14 final size:14
Alignment explanation
Indices: 2618825--2618859 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2618815 TATATTAAAA
2618825 AAATTATTTTTAAT
1 AAATTATTTTTAAT
*
2618839 AAATTATTTTTACT
1 AAATTATTTTTAAT
2618853 AAATTAT
1 AAATTAT
2618860 AAATTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (14 bp):
AAATTATTTTTAAT
Found at i:2618864 original size:7 final size:7
Alignment explanation
Indices: 2618852--2618878 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2618842 TTATTTTTAC
2618852 TAAATTA
1 TAAATTA
2618859 TAAATTA
1 TAAATTA
2618866 TAAATTA
1 TAAATTA
2618873 TAAATT
1 TAAATT
2618879 TTTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAAATTA
Found at i:2624176 original size:32 final size:33
Alignment explanation
Indices: 2624125--2624189 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
2624115 TTATATTTAA
* *
2624125 AATATTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATATTTATATAAATTTTAAAATATT
2624158 AATAATTTATA-TTATATAAATTTTAAAATATT
1 AATAATTTATATTTATATAAATTTTAAAATATT
2624190 TATATATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATAATTTATATTTATATAAATTTTAAAATATT
Found at i:2624182 original size:16 final size:17
Alignment explanation
Indices: 2624115--2624245 Score: 76
Period size: 18 Copynumber: 7.5 Consensus size: 17
2624105 TATATTATAA
*
2624115 TTATATT-TAAAATATT
1 TTATATTATATAATATT
2624131 TTATATTTATATAA-ATT
1 TTATA-TTATATAATATT
*
2624148 TTA-A-TATATTAATAAT
1 TTATATTATA-TAATATT
2624164 TTATATTATATAA-ATT
1 TTATATTATATAATATT
*
2624180 TTAAAATATTTATATATTATT
1 TT---ATA-TTATATAATATT
* * *
2624201 ATCATATTTATATTATTTT
1 -TTATA-TTATATAATATT
*
2624220 TATATATTATATTATATT
1 T-TATATTATATAATATT
2624238 TTA-ATTAT
1 TTATATTAT
2624246 TTTCTTCGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
14 4 0.04
15 3 0.03
16 20 0.22
17 14 0.15
18 21 0.23
19 19 0.21
20 7 0.08
21 3 0.03
22 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTATATAATATT
Found at i:2624199 original size:27 final size:27
Alignment explanation
Indices: 2624120--2624241 Score: 93
Period size: 32 Copynumber: 4.2 Consensus size: 27
2624110 TATAATTATA
2624120 TTTAAAATATTT-TATATTTATATAAAT
1 TTTAAAATATTTATATA-TTATATAAAT
*
2624147 TTTAATATATTAATAATTTATATTATATAAAT
1 TTTAAAATATT--T-A--TATATTATATAAAT
*
2624179 TTTAAAATATTTATATATTATTATCATAT
1 TTTAAAATATTTATATATTA-TAT-AAAT
** * *
2624208 TTATATTATTTTTATATATTATATTATAT
1 TT-TAAAATATTTATATATTATA-TAAAT
2624237 TTTAA
1 TTTAA
2624242 TTATTTTCTT
Statistics
Matches: 78, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
27 17 0.22
28 5 0.06
29 15 0.19
30 17 0.22
32 20 0.26
33 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAAAATATTTATATATTATATAAAT
Found at i:2624207 original size:19 final size:18
Alignment explanation
Indices: 2624090--2624237 Score: 66
Period size: 19 Copynumber: 8.2 Consensus size: 18
2624080 ATAATTAAGG
2624090 TATTATT-TAT-TTTAATA
1 TATTATTATATATTT-ATA
* *
2624107 TATTATAATTATATTTAAAA
1 TATTATTA-TATATTT-ATA
2624127 TATT-TTATAT-TTATATA
1 TATTATTATATATT-TATA
*
2624144 AATT-TTA-ATATATTA-A
1 TATTATTATATAT-TTATA
2624160 TA--ATT-TATATTATATA
1 TATTATTATATATT-TATA
* *
2624176 AATT-TTAAAATATTTATA
1 TATTATT-ATATATTTATA
2624194 TATTATTATCATATTTATA
1 TATTATTAT-ATATTTATA
*
2624213 TTATTTTTATATATTATATTA
1 -TATTATTATATATT-TA-TA
2624234 TATT
1 TATT
2624238 TTAATTATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
14 1 0.01
15 8 0.08
16 6 0.06
17 21 0.21
18 13 0.13
19 26 0.26
20 24 0.24
21 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATTATATATTTATA
Found at i:2635239 original size:3 final size:3
Alignment explanation
Indices: 2635231--2635262 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2635221 TAACAATATC
2635231 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2635263 TTAAATTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2635391 original size:24 final size:28
Alignment explanation
Indices: 2635363--2635420 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
2635353 ATAAAATATG
2635363 TATTAAT-T-TAATA-AAA-ATTTTATT
1 TATTAATATATAATATAAATATTTTATT
2635387 TATTAATATATAATATAAATATTTTATT
1 TATTAATATATAATATAAATATTTTATT
*
2635415 TTTTAA
1 TATTAA
2635421 AAATTAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 7 0.24
25 1 0.03
26 5 0.17
27 3 0.10
28 13 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TATTAATATATAATATAAATATTTTATT
Found at i:2635428 original size:28 final size:25
Alignment explanation
Indices: 2635370--2635428 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 25
2635360 ATGTATTAAT
*
2635370 TTAATAAAAATTTTATTTATTAATA
1 TTAATAAAAATTTTATTTATTAAAA
*
2635395 TATAATATAAATATTTTATTTTTTAAAAA
1 T-TAATA-AAA-ATTTTATTTATT-AAAA
2635424 TTAAT
1 TTAAT
2635429 TTTTTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.04
26 5 0.18
27 3 0.11
28 15 0.54
29 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTAATAAAAATTTTATTTATTAAAA
Found at i:2643211 original size:20 final size:19
Alignment explanation
Indices: 2643167--2643216 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
2643157 ATTTAATCAA
*
2643167 TTTA-ATTAAAATTAAATT
1 TTTATATTAAATTTAAATT
* *
2643185 ATAATATTAAATTTATAATT
1 TTTATATTAAATTTA-AATT
2643205 TTTATATTAAAT
1 TTTATATTAAAT
2643217 AAATATTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
20 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATATTAAATTTAAATT
Found at i:2644726 original size:13 final size:13
Alignment explanation
Indices: 2644708--2644737 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2644698 AATTATTAAA
2644708 AAAATTATATTTT
1 AAAATTATATTTT
2644721 AAAATTATATTTT
1 AAAATTATATTTT
2644734 AAAA
1 AAAA
2644738 ATATTATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAAATTATATTTT
Found at i:2644783 original size:21 final size:21
Alignment explanation
Indices: 2644757--2644798 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2644747 GATTAATATA
2644757 TAAAAAT-ATAAGTAAATTATT
1 TAAAAATAAT-AGTAAATTATT
*
2644778 TAAAAATAATAGTTAATTATT
1 TAAAAATAATAGTAAATTATT
2644799 AAAGTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAGTAAATTATT
Found at i:2644799 original size:24 final size:24
Alignment explanation
Indices: 2644723--2644799 Score: 58
Period size: 24 Copynumber: 3.3 Consensus size: 24
2644713 TATATTTTAA
*
2644723 AATTA-TATTTTAAAAATATTA-TT
1 AATTATTA-TTTAAAAATAATAGTT
* *
2644746 AGATTAATATATAAAAAT-ATAAG-T
1 A-ATTATTATTTAAAAATAAT-AGTT
2644770 AA--ATTATTTAAAAATAATAGTT
1 AATTATTATTTAAAAATAATAGTT
2644792 AATTATTA
1 AATTATTA
2644800 AAGTAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
21 13 0.31
22 5 0.12
23 3 0.07
24 19 0.45
25 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AATTATTATTTAAAAATAATAGTT
Found at i:2644939 original size:19 final size:18
Alignment explanation
Indices: 2644904--2644943 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2644894 GTTTTTTAAA
2644904 AAAATTTGAGTAGTTTTT
1 AAAATTTGAGTAGTTTTT
* *
2644922 AAAATTTTAGTATTTTTT
1 AAAATTTGAGTAGTTTTT
2644940 AAAA
1 AAAA
2644944 AATAAATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (18 bp):
AAAATTTGAGTAGTTTTT
Found at i:2645116 original size:2 final size:2
Alignment explanation
Indices: 2645109--2645229 Score: 57
Period size: 2 Copynumber: 65.0 Consensus size: 2
2645099 ATATCATACC
* *
2645109 AT AT AT AT AT AT AT AT AT AT A- AT TT GAC AT AT -T A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
* * * * *
2645148 TT A- AT -T AT AT AA AT -T TT A- AT AT AT AC AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
2645186 CGT AT TT AT AT -T AT -T TT AT AT AT AT AT AT AT AT AT AT -T AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2645226 AT AT
1 AT AT
2645230 TGGTCTAGTC
Statistics
Matches: 88, Mismatches: 18, Indels: 26
0.67 0.14 0.20
Matches are distributed among these distances:
1 11 0.12
2 76 0.86
3 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2648723 original size:8 final size:8
Alignment explanation
Indices: 2648710--2648766 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
2648700 AAATATAACA
2648710 TAAATATT
1 TAAATATT
2648718 TAAATATT
1 TAAATATT
2648726 TAAAT-TT
1 TAAATATT
*
2648733 TATATAATT
1 TAAAT-ATT
2648742 TAAAT-TAT
1 TAAATAT-T
2648750 T-AATATTT
1 TAAATA-TT
2648758 TAAA-ATT
1 TAAATATT
2648765 TA
1 TA
2648767 TATAAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
7 14 0.34
8 18 0.44
9 9 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TAAATATT
Found at i:2648742 original size:16 final size:16
Alignment explanation
Indices: 2648710--2648771 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
2648700 AAATATAACA
*
2648710 TAAATATTTAAAT-ATT
1 TAAAT-TTTATATAATT
2648726 TAAATTTTATATAATT
1 TAAATTTTATATAATT
*
2648742 TAAATTATTA-ATATTT
1 TAAATT-TTATATAATT
*
2648758 TAAAATTTATATAA
1 TAAATTTTATATAA
2648772 ATATAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.23
16 27 0.69
17 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATTTTATATAATT
Found at i:2655238 original size:12 final size:12
Alignment explanation
Indices: 2655217--2655246 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2655207 ACAGCCAATT
*
2655217 CATAGCCATAGC
1 CATAGGCATAGC
2655229 CATAGGCATAGC
1 CATAGGCATAGC
2655241 CATAGG
1 CATAGG
2655247 TGTTGCTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (12 bp):
CATAGGCATAGC
Found at i:2655792 original size:17 final size:17
Alignment explanation
Indices: 2655766--2655801 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2655756 TTCATGATAA
2655766 ATATTATATAAAAATAT
1 ATATTATATAAAAATAT
* *
2655783 ATATTTTATATAAATAT
1 ATATTATATAAAAATAT
2655800 AT
1 AT
2655802 TTAATTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTATATAAAAATAT
Found at i:2655793 original size:19 final size:20
Alignment explanation
Indices: 2655769--2655819 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2655759 ATGATAAATA
2655769 TTATATAAAAATATAT-ATT
1 TTATATAAAAATATATAATT
* *
2655788 TTATATAAATATATTTAATT
1 TTATATAAAAATATATAATT
2655808 TTGAT-TAAAAAT
1 TT-ATATAAAAAT
2655820 TCATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.52
20 11 0.41
21 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTATATAAAAATATATAATT
Found at i:2656142 original size:16 final size:17
Alignment explanation
Indices: 2656091--2656163 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 17
2656081 AAGATGAATT
* *
2656091 TAATTTAAATAATTTATA
1 TAATTTTAATATTTTA-A
*
2656109 TAATTATAATAATATTTAA
1 TAATTTTAAT-AT-TTTAA
2656128 TAATTTTAA-ATTTTAA
1 TAATTTTAATATTTTAA
*
2656144 TATTTTTAATATTTATAA
1 TAATTTTAATATTT-TAA
2656162 TA
1 TA
2656164 TTAACTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
16 13 0.28
17 6 0.13
18 13 0.28
19 10 0.22
20 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTTTAATATTTTAA
Found at i:2656150 original size:9 final size:9
Alignment explanation
Indices: 2656123--2656165 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
2656113 TATAATAATA
*
2656123 TTTAATAAT
1 TTTAATATT
2656132 TTTAA-A-T
1 TTTAATATT
2656139 TTTAATATT
1 TTTAATATT
2656148 TTTAATATT
1 TTTAATATT
*
2656157 TATAATATT
1 TTTAATATT
2656166 AACTTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 6 0.19
8 2 0.06
9 23 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTAATATT
Found at i:2657009 original size:24 final size:24
Alignment explanation
Indices: 2656958--2657009 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2656948 ATTCGTTATG
* * *
2656958 ATTATTATATATAATAATATTTTT
1 ATTAATATATATAATAAAATTTTA
2656982 ATTAATATATA-AATAAAATTATTA
1 ATTAATATATATAATAAAATT-TTA
2657006 ATTA
1 ATTA
2657010 TTGCATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTAATATATATAATAAAATTTTA
Found at i:2657147 original size:21 final size:21
Alignment explanation
Indices: 2657099--2657147 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
2657089 TGGGAGTGGG
2657099 TATTTT-TT-TTTAAAAAAAT
1 TATTTTATTATTTAAAAAAAT
* *
2657118 TA-TTAATTATTTTAAAAAAT
1 TATTTTATTATTTAAAAAAAT
2657138 TATTTTATTA
1 TATTTTATTA
2657148 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.08
19 4 0.17
20 12 0.50
21 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATTATTTAAAAAAAT
Found at i:2657218 original size:21 final size:21
Alignment explanation
Indices: 2657164--2657225 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2657154 TTAAAAATAA
2657164 TAATATTTTA-AATTTATATT
1 TAATATTTTATAATTTATATT
* *
2657184 TATTATTAATATAATTTA-ATT
1 TAATATT-TTATAATTTATATT
2657205 TAATATTTTGATAATTT-TATT
1 TAATATTTT-ATAATTTATATT
2657226 ATATCATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 7 0.21
21 21 0.62
22 6 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATATTTTATAATTTATATT
Found at i:2658114 original size:2 final size:2
Alignment explanation
Indices: 2658107--2658133 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2658097 TCCTTCATGG
2658107 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 A
2658134 AAAGGCTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2658979 original size:2 final size:2
Alignment explanation
Indices: 2658941--2658970 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
2658931 AACTTGTTAA
2658941 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
2658971 AGGTATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2659243 original size:22 final size:22
Alignment explanation
Indices: 2659215--2659261 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2659205 GTGGGATTGG
* *
2659215 TATAAAA-ATTTAAATTATTATT
1 TATAAAATATTAAAAATATT-TT
2659237 TATAAAATATTAAAAATATTTT
1 TATAAAATATTAAAAATATTTT
2659259 TAT
1 TAT
2659262 TAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATAAAATATTAAAAATATTTT
Found at i:2662759 original size:2 final size:2
Alignment explanation
Indices: 2662752--2662800 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
2662742 TCAATCTTCA
* * *
2662752 AT AT AT AT AT AT AT AT AT AG AT AT AT AT TT CAT AT AA 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
*
2662795 TT AT AT
1 AT AT AT
2662801 TTTTTTTACA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 37 0.97
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2663790 original size:27 final size:27
Alignment explanation
Indices: 2663740--2663792 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2663730 GACCTGTCTG
**
2663740 AAATTTCAGTTTAAGTGGTCCTAAGTA
1 AAATTTCAGTTTAAGTGGAACTAAGTA
2663767 AAATTTCAGTTTACA-TGGAACTAAGT
1 AAATTTCAGTTTA-AGTGGAACTAAGT
2663793 TAGACAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (27 bp):
AAATTTCAGTTTAAGTGGAACTAAGTA
Found at i:2664053 original size:3 final size:3
Alignment explanation
Indices: 2664045--2664091 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
2664035 AAACCTTAAT
2664045 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
2664091 T
1 T
2664092 TAGCAGAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2667474 original size:16 final size:16
Alignment explanation
Indices: 2667455--2667496 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2667445 AATTTAGATT
*
2667455 ATTTTGGGTTCGGATC
1 ATTTTGAGTTCGGATC
*
2667471 ATTTTGAGTTCGGATT
1 ATTTTGAGTTCGGATC
*
2667487 ATTTCGAGTT
1 ATTTTGAGTT
2667497 TGAGTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.48
Consensus pattern (16 bp):
ATTTTGAGTTCGGATC
Found at i:2668107 original size:16 final size:17
Alignment explanation
Indices: 2668080--2668111 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2668070 CAATAATAAT
2668080 TTAAAAATTTAAATTAA
1 TTAAAAATTTAAATTAA
2668097 TTAAAAA-TTAAATTA
1 TTAAAAATTTAAATTA
2668112 TTATAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATTTAAATTAA
Found at i:2670152 original size:21 final size:21
Alignment explanation
Indices: 2670104--2670166 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2670094 ATAATATGTT
* *
2670104 AAATTAATTTA-TATTTAAGAA
1 AAATTTATTTATTATTTAA-TA
2670125 TAAATTTATTT-TTAATTTAATA
1 -AAATTTATTTATT-ATTTAATA
2670147 AAATTTATTTATTATTTAAT
1 AAATTTATTTATTATTTAAT
2670167 TATAATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 17 0.47
22 13 0.36
23 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AAATTTATTTATTATTTAATA
Found at i:2670218 original size:47 final size:50
Alignment explanation
Indices: 2670149--2670249 Score: 145
Period size: 47 Copynumber: 2.1 Consensus size: 50
2670139 ATTTAATAAA
*
2670149 ATTTATTTATTATTTAATTATAATATAATTAATAATATTATTAT-TTA-T
1 ATTTAATTATTATTTAATTATAATATAATTAATAATATTATTATATTATT
* * *
2670197 ATTTAATT-TTATTTATTTATAATGTAATTAATAATATTTTTATATTATT
1 ATTTAATTATTATTTAATTATAATATAATTAATAATATTATTATATTATT
2670246 ATTT
1 ATTT
2670250 TATATCTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
47 32 0.68
48 10 0.21
49 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (50 bp):
ATTTAATTATTATTTAATTATAATATAATTAATAATATTATTATATTATT
Found at i:2670308 original size:14 final size:15
Alignment explanation
Indices: 2670280--2670308 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2670270 TTATTTATTC
2670280 AAATTTGTTTATTAT
1 AAATTTGTTTATTAT
2670295 AAATTT-TTTATTAT
1 AAATTTGTTTATTAT
2670309 TTGAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
AAATTTGTTTATTAT
Found at i:2670370 original size:19 final size:19
Alignment explanation
Indices: 2670348--2670396 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
2670338 AACATATTCA
2670348 TAAATAAATTTATTTAATT
1 TAAATAAATTTATTTAATT
*
2670367 TAAATAAATATATTTAATT
1 TAAATAAATTTATTTAATT
2670386 TAAAATAAATT
1 T-AAATAAATT
2670397 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATAAATTTATTTAATT
Found at i:2670542 original size:2 final size:2
Alignment explanation
Indices: 2670502--2670529 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2670492 AAGACTATTA
2670502 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
2670530 TAAAGCTATA
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:2675306 original size:16 final size:17
Alignment explanation
Indices: 2675273--2675308 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2675263 CAAGAGCATG
2675273 TTTTATTATAATATTTA
1 TTTTATTATAATATTTA
2675290 TTTTATTATAA-ATTTA
1 TTTTATTATAATATTTA
2675306 TTT
1 TTT
2675309 AATATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTATAATATTTA
Found at i:2675550 original size:11 final size:11
Alignment explanation
Indices: 2675511--2675552 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2675501 TAAATTAATA
*
2675511 TTATAATTATT
1 TTATATTTATT
2675522 TTAT-TTTATT
1 TTATATTTATT
* *
2675532 TGAAATTTATT
1 TTATATTTATT
2675543 TTATATTTAT
1 TTATATTTAT
2675553 AAATAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TTATATTTATT
Found at i:2678791 original size:138 final size:139
Alignment explanation
Indices: 2678543--2678823 Score: 519
Period size: 138 Copynumber: 2.0 Consensus size: 139
2678533 AGCCCAGAAA
*
2678543 TAGTTGTCAGAGCTACTCACATCCTTGGAATGAATTTGATCGTTGTATAATGAGGACAATCAATT
1 TAGTTGTCAGAGCTACTCACATCCTTGGAATGAATTTGATAGTTGTATAATGAGGACAATCAATT
*
2678608 CTTTTATTTGCCAGATGGCTTAAGTTTCTACCTACTATTACTCTTGGAA-TTATTGCAAAAAGAA
66 CTTTTATTTGCCAGATGGCTTAAGTTTCTACCTACTATTACTCTTGGAATTTATTACAAAAAGAA
2678672 GATTAGCGT
131 GATTAGCGT
* *
2678681 TAGTTGTCGGAGCTACTTACATCCTTGGAATGAATTTGATAGTTGTATAATGAGGACAATCAATT
1 TAGTTGTCAGAGCTACTCACATCCTTGGAATGAATTTGATAGTTGTATAATGAGGACAATCAATT
2678746 CTTTTATTTGCCAGATGGCTTAAGTTTCTACCTACTATTACTCTTGGAATTTATTACAAAAAGAA
66 CTTTTATTTGCCAGATGGCTTAAGTTTCTACCTACTATTACTCTTGGAATTTATTACAAAAAGAA
2678811 GATTAGCGT
131 GATTAGCGT
2678820 TAGT
1 TAGT
2678824 AGCATAGCCG
Statistics
Matches: 138, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
138 111 0.80
139 27 0.20
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (139 bp):
TAGTTGTCAGAGCTACTCACATCCTTGGAATGAATTTGATAGTTGTATAATGAGGACAATCAATT
CTTTTATTTGCCAGATGGCTTAAGTTTCTACCTACTATTACTCTTGGAATTTATTACAAAAAGAA
GATTAGCGT
Found at i:2685832 original size:8 final size:7
Alignment explanation
Indices: 2685821--2685850 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2685811 ACAAAAGGGG
2685821 AAAAAAT
1 AAAAAAT
2685828 AAAAAAT
1 AAAAAAT
2685835 AAAAAAT
1 AAAAAAT
2685842 AAATAAAT
1 AAA-AAAT
2685850 A
1 A
2685851 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAAAT
Found at i:2685853 original size:2 final size:2
Alignment explanation
Indices: 2685848--2685876 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2685838 AAATAAATAA
2685848 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
2685877 ACGAAAAAGG
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:2696719 original size:28 final size:28
Alignment explanation
Indices: 2696661--2696719 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
2696651 TTAATTTAAA
*
2696661 AAAAATTATTTAATAAATAAAATATCTT
1 AAAAATTATTTAATAAATAAAATATCAT
*
2696689 AAAATTTATTTAATTATAA-AAAATAT-AT
1 AAAAATTATTTAA-TA-AATAAAATATCAT
2696717 AAA
1 AAA
2696720 TATAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 16 0.59
29 9 0.33
30 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAAATTATTTAATAAATAAAATATCAT
Found at i:2700054 original size:55 final size:55
Alignment explanation
Indices: 2699975--2700114 Score: 165
Period size: 55 Copynumber: 2.5 Consensus size: 55
2699965 CAAATTCAAC
* *
2699975 CAACTCTTAACAAATGCTAGATACACAATAAAGTGGTCTTGCTAC-AAAGGAAATT
1 CAACTCTTAACAAATGCTAGATACACAA-AAAGTGCTCTTGCTACAAAAGGAAATG
* * * * * *
2700030 CAACTCTTAACAAATGCTAGATACAACAAAGATTGCTGTTTCTACAAAAGGTACTG
1 CAACTCTTAACAAATGCTAGATAC-ACAAAAAGTGCTCTTGCTACAAAAGGAAATG
**
2700086 CAGTTCTTAACAAATGCTAGATACACAAA
1 CAACTCTTAACAAATGCTAGATACACAAA
2700115 GATTAGAATG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
55 40 0.55
56 33 0.45
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (55 bp):
CAACTCTTAACAAATGCTAGATACACAAAAAGTGCTCTTGCTACAAAAGGAAATG
Found at i:2701112 original size:21 final size:21
Alignment explanation
Indices: 2701083--2701136 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2701073 AGCTTCATAG
*
2701083 TTTCTTGTAGTTC-CAGATTCT
1 TTTCATGTAGTTCTC-GATTCT
*
2701104 TTTCATGTAATTCTCGATTCT
1 TTTCATGTAGTTCTCGATTCT
*
2701125 GTTCATGTAGTT
1 TTTCATGTAGTT
2701137 GATGTATGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.52
Consensus pattern (21 bp):
TTTCATGTAGTTCTCGATTCT
Found at i:2709169 original size:13 final size:13
Alignment explanation
Indices: 2709151--2709175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2709141 AAAACATGAA
2709151 TGAAGAAAGAAAC
1 TGAAGAAAGAAAC
2709164 TGAAGAAAGAAA
1 TGAAGAAAGAAA
2709176 TGATTCTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.24, T:0.08
Consensus pattern (13 bp):
TGAAGAAAGAAAC
Found at i:2709706 original size:15 final size:15
Alignment explanation
Indices: 2709678--2709719 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
2709668 ATTTATAAAT
2709678 AATTTAATTAAATAA
1 AATTTAATTAAATAA
2709693 AATTATAATT-AATAA
1 AATT-TAATTAAATAA
*
2709708 AATTTATTTAAA
1 AATTTAATTAAA
2709720 AATAATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.17
15 15 0.62
16 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTAATTAAATAA
Found at i:2710240 original size:11 final size:10
Alignment explanation
Indices: 2710224--2710261 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
2710214 AATACATAAA
2710224 TTTTTTCTCTT
1 TTTTTTCT-TT
2710235 TTTTTTCTTT
1 TTTTTTCTTT
2710245 CTTTTTTCTTT
1 -TTTTTTCTTT
2710256 TTTTTT
1 TTTTTT
2710262 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:2710420 original size:16 final size:17
Alignment explanation
Indices: 2710399--2710431 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2710389 ATAGTTAACG
*
2710399 ATATTTTTAATT-TTTT
1 ATATTTGTAATTATTTT
2710415 ATATTTGTAATTATTTT
1 ATATTTGTAATTATTTT
2710432 TAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATATTTGTAATTATTTT
Found at i:2710687 original size:12 final size:12
Alignment explanation
Indices: 2710654--2710687 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2710644 AAAATATGAC
2710654 ATAAAAAATAAT
1 ATAAAAAATAAT
*
2710666 -TAAAACATAAT
1 ATAAAAAATAAT
2710677 ATAAAAAATAA
1 ATAAAAAATAA
2710688 ATATGACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:2711019 original size:16 final size:15
Alignment explanation
Indices: 2710887--2711035 Score: 54
Period size: 14 Copynumber: 9.2 Consensus size: 15
2710877 CACGATATTT
*
2710887 ATAAAAAATATTTAA
1 ATAAAAAATATATAA
*
2710902 TATAAAAATAATATATAT
1 -AT-AAAA-AATATATAA
*
2710920 ATGACATAAATATATATAT
1 AT-A-A-AAA-ATATATAA
* * *
2710939 GTATAAAA-ATATAC
1 ATAAAAAATATATAA
2710953 ATAAAAAAT-TATTAA
1 ATAAAAAATATA-TAA
*
2710968 TATATATAAAATTTATAA
1 -ATA-A-AAAATATATAA
*
2710986 A-AAATATAATATTTTAA
1 ATAAA-A-AATA-TATAA
2711003 ATAAAAAATAATATAA
1 ATAAAAAAT-ATATAA
*
2711019 AT-ACAAATATATAA
1 ATAAAAAATATATAA
2711033 ATA
1 ATA
2711036 TTTTTTTTCT
Statistics
Matches: 103, Mismatches: 13, Indels: 35
0.68 0.09 0.23
Matches are distributed among these distances:
14 22 0.21
15 10 0.10
16 21 0.20
17 16 0.16
18 21 0.20
19 13 0.13
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (15 bp):
ATAAAAAATATATAA
Found at i:2711048 original size:4 final size:4
Alignment explanation
Indices: 2711041--2711099 Score: 54
Period size: 4 Copynumber: 15.8 Consensus size: 4
2711031 AAATATTTTT
* * * *
2711041 TTTC TTTC CTT- TTTC TTTG TTTC --TC TTTC TTTT TTTC ATT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
2711085 TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTT
2711100 TTGGGCTGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
2 2 0.05
3 4 0.09
4 37 0.86
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:2711063 original size:15 final size:15
Alignment explanation
Indices: 2711036--2711092 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
2711026 TATATAAATA
2711036 TTTTT-TTTCTTTCC
1 TTTTTCTTTCTTTCC
*
2711050 TTTTTCTTTGTTT-C
1 TTTTTCTTTCTTTCC
* * *
2711064 TCTTTCTTTTTTTCA
1 TTTTTCTTTCTTTCC
2711079 TTTTTCTTTCTTTC
1 TTTTTCTTTCTTTC
2711093 TTTCTTTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
14 17 0.49
15 18 0.51
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTCTTTCTTTCC
Found at i:2711083 original size:29 final size:27
Alignment explanation
Indices: 2711040--2711101 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
2711030 TAAATATTTT
* *
2711040 TTTTCTTTCCTTTTTCTTTGTTTCTCTTTC
1 TTTT-TTTCATTTTTCTTT-CTT-TCTTTC
2711070 TTTTTTTCATTTTTCTTTCTTTCTTTC
1 TTTTTTTCATTTTTCTTTCTTTCTTTC
2711097 TTTTT
1 TTTTT
2711102 GGGCTGAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 11 0.37
28 2 0.07
29 13 0.43
30 4 0.13
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (27 bp):
TTTTTTTCATTTTTCTTTCTTTCTTTC
Found at i:2711101 original size:19 final size:18
Alignment explanation
Indices: 2711038--2711101 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
2711028 TATAAATATT
*
2711038 TTTTTTCTTTCCTTTTTC
1 TTTTTTCTTTCTTTTTTC
2711056 TTTGTTTCTCTTTCTTTTTTTC
1 -TT-TTT-TCTTTC-TTTTTTC
*
2711078 ATTTTTCTTTCTTTCTTTC
1 TTTTTTCTTTCTTT-TTTC
2711097 TTTTT
1 TTTTT
2711102 GGGCTGAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.08
19 16 0.42
20 6 0.16
21 7 0.18
22 6 0.16
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTTCTTTCTTTTTTC
Found at i:2712704 original size:19 final size:21
Alignment explanation
Indices: 2712682--2712724 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
2712672 TATGAAATTA
*
2712682 TTTATTTAA-ATTAA-TAAAT
1 TTTATTTAATATAAATTAAAT
2712701 TTTATTTAATATAAATTAAAT
1 TTTATTTAATATAAATTAAAT
2712722 TTT
1 TTT
2712725 GGTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 4 0.19
21 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTATTTAATATAAATTAAAT
Found at i:2712858 original size:3 final size:3
Alignment explanation
Indices: 2712850--2712874 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2712840 AATAAATAAT
2712850 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2712875 AATCTATCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2713759 original size:3 final size:3
Alignment explanation
Indices: 2713746--2713774 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2713736 AAATTTGGTG
2713746 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2713775 CAAATGGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2722500 original size:12 final size:12
Alignment explanation
Indices: 2722485--2722509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2722475 AGAAAAAGAA
2722485 AGAAATAGAAAT
1 AGAAATAGAAAT
2722497 AGAAATAGAAAT
1 AGAAATAGAAAT
2722509 A
1 A
2722510 AAGAAAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AGAAATAGAAAT
Found at i:2722500 original size:22 final size:21
Alignment explanation
Indices: 2722475--2722525 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
2722465 TAAAAAAAGG
* *
2722475 AGAAAAAGAAAGAAATAGAAAT
1 AGAAAAAGAAAGAAAGA-AAAA
* *
2722497 AGAAATAGAAATAAAGAAAAA
1 AGAAAAAGAAAGAAAGAAAAA
2722518 AGAAAAAG
1 AGAAAAAG
2722526 TTGCTTTAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.08
Consensus pattern (21 bp):
AGAAAAAGAAAGAAAGAAAAA
Found at i:2729511 original size:1 final size:1
Alignment explanation
Indices: 2729507--2729531 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2729497 TTTAAAAATT
2729507 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2729532 CTCACTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2730856 original size:21 final size:21
Alignment explanation
Indices: 2730832--2730874 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2730822 TTAGATTTTC
2730832 TCTCTT-TCTCCTCTCTAAAAT
1 TCTCTTAT-TCCTCTCTAAAAT
*
2730853 TCTCTTATTTCTCTCTAAAAT
1 TCTCTTATTCCTCTCTAAAAT
2730874 T
1 T
2730875 TTATAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (21 bp):
TCTCTTATTCCTCTCTAAAAT
Found at i:2730885 original size:21 final size:21
Alignment explanation
Indices: 2730842--2730887 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2730832 TCTCTTTCTC
* * *
2730842 CTCTCTAAAATTCTCTTATTT
1 CTCTCTAAAATTCTATAAATT
*
2730863 CTCTCTAAAATTTTATAAATT
1 CTCTCTAAAATTCTATAAATT
2730884 CTCT
1 CTCT
2730888 TATTTCTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (21 bp):
CTCTCTAAAATTCTATAAATT
Found at i:2731134 original size:15 final size:15
Alignment explanation
Indices: 2731114--2731153 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2731104 TATTATGTGA
2731114 AATTAGGTTTA-GAGT
1 AATTA-GTTTAGGAGT
*
2731129 AATTAGTTTAGGGGT
1 AATTAGTTTAGGAGT
2731144 AATTAGTTTA
1 AATTAGTTTA
2731154 AAGCCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (15 bp):
AATTAGTTTAGGAGT
Found at i:2736645 original size:75 final size:75
Alignment explanation
Indices: 2736538--2736786 Score: 336
Period size: 75 Copynumber: 3.3 Consensus size: 75
2736528 ATGTGAAATA
* *
2736538 TGCAGATTATCTCGGATTAATTGTTAATAGTAGTAATGTGAAATATGCAGAAATATTTTTTGATT
1 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAATATTTTTTGATT
2736603 GTAGTTATCG
66 GTAGTTATCG
* * * * * * *
2736613 TGCAGATTATCTCGGGTTAGTTGTTGATAGTAGTACTCTAAAATATGTAGAAACATTTGTTGATT
1 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAATATTTTTTGATT
2736678 GTAGTTATCG
66 GTAGTTATCG
* * *
2736688 TGCATATTATCTCGGATTAGTTGTTGGTAGTAGTAATGTGAAATATGCAGTAACATTTGTTTATT
1 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAG-AA-ATAT-TTT-TT
*
2736753 GATTGTAGTTATCA
62 GATTGTAGTTATCG
*
2736767 TGCAGATTATCTCAGATTAG
1 TGCAGATTATCTCGGATTAG
2736787 AGTTTCATCT
Statistics
Matches: 148, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
75 109 0.74
76 2 0.01
77 2 0.01
78 2 0.01
79 33 0.22
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.41
Consensus pattern (75 bp):
TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAATATTTTTTGATT
GTAGTTATCG
Found at i:2736712 original size:39 final size:39
Alignment explanation
Indices: 2736597--2736713 Score: 98
Period size: 39 Copynumber: 3.1 Consensus size: 39
2736587 GAAATATTTT
* *
2736597 TTGATTGTAGTTATCGTGCAGATTATCTCGGGTTAGTTG
1 TTGATTGTAGTTATCGTGCAAATTATCTCGGATTAGTTG
* * * * * ** *
2736636 TTGATAGTAG-TA-C-T-CTAAAATATGTAGAAACATTTG
1 TTGATTGTAGTTATCGTGC-AAATTATCTCGGATTAGTTG
*
2736672 TTGATTGTAGTTATCGTGCATATTATCTCGGATTAGTTG
1 TTGATTGTAGTTATCGTGCAAATTATCTCGGATTAGTTG
2736711 TTG
1 TTG
2736714 GTAGTAGTAA
Statistics
Matches: 54, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
35 1 0.02
36 21 0.39
37 3 0.06
38 3 0.06
39 25 0.46
40 1 0.02
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (39 bp):
TTGATTGTAGTTATCGTGCAAATTATCTCGGATTAGTTG
Found at i:2738636 original size:23 final size:23
Alignment explanation
Indices: 2738613--2738699 Score: 63
Period size: 24 Copynumber: 3.7 Consensus size: 23
2738603 ATAAATGAAT
2738613 TTAAATAAATTTAAATTATT-AA
1 TTAAATAAATTTAAATTATTAAA
* * *
2738635 TT-TACAAATATAAATATATTTAAA
1 TTAAATAAATTTAAAT-TA-TTAAA
* *
2738659 TAAAATTAAGATTTATATT-TTAAA
1 TTAAA-TAA-ATTTAAATTATTAAA
2738683 TTAAATAAAATTTAAAT
1 TTAAAT-AAATTTAAAT
2738700 AAATATAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
21 10 0.21
22 4 0.08
23 10 0.21
24 14 0.29
25 1 0.02
26 3 0.06
27 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (23 bp):
TTAAATAAATTTAAATTATTAAA
Found at i:2738645 original size:41 final size:38
Alignment explanation
Indices: 2738600--2738717 Score: 105
Period size: 41 Copynumber: 2.9 Consensus size: 38
2738590 TTTAAAAAAT
2738600 AATATAAATGAATTTAAATAAATTTAAATTATTAATTTACA
1 AATATAAAT-AATTTAAATAAATTTAAA-TATTAATTT-CA
* *
2738641 AATATAAATATATTTAAATAAAATTAAGAT-TTATATTTTA
1 AATATAAATA-ATTTAAATAAATTTAA-ATATTA-ATTTCA
*
2738681 AAT-TAAATAAAATTTAAATAAATATAAAAATATTAAT
1 AATATAAAT--AATTTAAATAAAT-T-TAAATATTAAT
2738718 ATTATATTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
39 5 0.08
40 19 0.29
41 35 0.54
42 6 0.09
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (38 bp):
AATATAAATAATTTAAATAAATTTAAATATTAATTTCA
Found at i:2738683 original size:24 final size:24
Alignment explanation
Indices: 2738648--2738696 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2738638 ACAAATATAA
*
2738648 ATATATTTAAATAAAATTAAGATTT
1 ATATATTTAAATAAAA-TAAAATTT
*
2738673 ATAT-TTTAAATTAAATAAAATTT
1 ATATATTTAAATAAAATAAAATTT
2738696 A
1 A
2738697 AATAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 10 0.45
25 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATATATTTAAATAAAATAAAATTT
Found at i:2745965 original size:7 final size:7
Alignment explanation
Indices: 2745953--2745978 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2745943 TTCAGGTTCA
2745953 GGTTTAG
1 GGTTTAG
2745960 GGTTTAG
1 GGTTTAG
2745967 GGTTTAG
1 GGTTTAG
2745974 GGTTT
1 GGTTT
2745979 GGACCAGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:2749434 original size:2 final size:2
Alignment explanation
Indices: 2749429--2749489 Score: 70
Period size: 2 Copynumber: 30.5 Consensus size: 2
2749419 GAATTTTTTC
* *
2749429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT CAA 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
* *
2749472 AT TT AT AT -T TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2749490 CTTTTAATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2750542 original size:9 final size:9
Alignment explanation
Indices: 2750511--2750552 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
2750501 AAAATAATAA
2750511 ATTAA-ATT
1 ATTAATATT
*
2750519 ATTAATTTT
1 ATTAATATT
*
2750528 AATAATATT
1 ATTAATATT
2750537 ATTAATATT
1 ATTAATATT
2750546 ATTAATA
1 ATTAATA
2750553 AAACCCTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 5 0.17
9 24 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTAATATT
Found at i:2751390 original size:16 final size:16
Alignment explanation
Indices: 2751358--2751397 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2751348 TATTATCACT
**
2751358 TAAAAAATAATTTTAA
1 TAAAAAATAATAATAA
2751374 TAAAAAATAATAATAA
1 TAAAAAATAATAATAA
2751390 TAACAAAA
1 TAA-AAAA
2751398 ATCTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAAATAATAATAA
Found at i:2751449 original size:19 final size:20
Alignment explanation
Indices: 2751412--2751452 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2751402 ATTTTTTATC
* *
2751412 AAATTTTTATTAATTTATTA
1 AAATTTTTAATAATATATTA
2751432 AAATTTTTAAT-ATATATTA
1 AAATTTTTAATAATATATTA
2751451 AA
1 AA
2751453 TATTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTTTTAATAATATATTA
Done.