Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 28 of 33
Found at i:4715640 original size:25 final size:24
Alignment explanation
Indices: 4715598--4715645 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
4715588 CAGTAAAAAA
* *
4715598 TTTTAAAATATTATAAAATAATAT
1 TTTTAAAAAATTAAAAAATAATAT
4715622 TTTTAAAAAATTTAAAAAATAATA
1 TTTTAAAAAA-TTAAAAAATAATA
4715646 AATAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTTAAAAAATTAAAAAATAATAT
Found at i:4715661 original size:34 final size:34
Alignment explanation
Indices: 4715591--4715654 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
4715581 TTTAAATCAG
* * *
4715591 TAAAAAATTTTAAAATATTATAAAATAATATTTT
1 TAAAAAATTTTAAAAAATAATAAAATAAAATTTT
4715625 TAAAAAA-TTTAAAAAATAAT-AAATAAAATT
1 TAAAAAATTTTAAAAAATAATAAAATAAAATT
4715655 AATTTAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 9 0.33
33 11 0.41
34 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAATTTTAAAAAATAATAAAATAAAATTTT
Found at i:4718292 original size:2 final size:2
Alignment explanation
Indices: 4718285--4718311 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4718275 GAAAAACAAA
4718285 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
4718312 ACAAAACCGA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4719167 original size:2 final size:2
Alignment explanation
Indices: 4719155--4719187 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4719145 CATAAATTAG
*
4719155 TC TC TC GC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4719188 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
TC
Found at i:4719192 original size:2 final size:2
Alignment explanation
Indices: 4719187--4719215 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4719177 TCTCTCTCTC
4719187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4719216 GATAATGAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4727489 original size:28 final size:28
Alignment explanation
Indices: 4727458--4727537 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
4727448 TTTTTAATTA
*
4727458 AATTATATACTTATTTTTAAAAATTAAT
1 AATTATATAATTATTTTTAAAAATTAAT
* *
4727486 AATTAGTA-AATTTTTATTTAAAATTTAAT
1 AATTA-TATAATTATT-TTTAAAAATTAAT
*
4727515 -ATT-TATAATATATTTTTTAAAAT
1 AATTATATAAT-TATTTTTAAAAAT
4727538 GTGATTTCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
26 2 0.05
27 10 0.24
28 16 0.38
29 14 0.33
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (28 bp):
AATTATATAATTATTTTTAAAAATTAAT
Found at i:4727513 original size:29 final size:28
Alignment explanation
Indices: 4727471--4727537 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
4727461 TATATACTTA
* *
4727471 TTTTTAAAAATTAATAATTAGTAA-ATTT
1 TTTTTAAAATTTAATAATTA-TAATATAT
*
4727499 TTATTTAAAATTTAATATTTATAATATAT
1 TT-TTTAAAATTTAATAATTATAATATAT
4727528 TTTTTAAAAT
1 TTTTTAAAAT
4727538 GTGATTTCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
TTTTTAAAATTTAATAATTATAATATAT
Found at i:4731933 original size:14 final size:14
Alignment explanation
Indices: 4731914--4731943 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4731904 AAACGAGTTG
4731914 TTTCTCTTTTTTGT
1 TTTCTCTTTTTTGT
4731928 TTTCTCTTTTTTGT
1 TTTCTCTTTTTTGT
4731942 TT
1 TT
4731944 GTGCCCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (14 bp):
TTTCTCTTTTTTGT
Found at i:4732457 original size:15 final size:15
Alignment explanation
Indices: 4732437--4732466 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4732427 ATGTTCCCAT
4732437 GGAACTTAGTGAGAG
1 GGAACTTAGTGAGAG
4732452 GGAACTTAGTGAGAG
1 GGAACTTAGTGAGAG
4732467 CTGGTGCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.40, T:0.20
Consensus pattern (15 bp):
GGAACTTAGTGAGAG
Found at i:4733311 original size:7 final size:7
Alignment explanation
Indices: 4733275--4733325 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
4733265 TCGTATAATT
4733275 ATTTTAA
1 ATTTTAA
* *
4733282 AATATAA
1 ATTTTAA
4733289 ATTTAATAA
1 ATTT--TAA
4733298 A-TTTAA
1 ATTTTAA
4733304 ATTTTAA
1 ATTTTAA
4733311 ATTTTAA
1 ATTTTAA
*
4733318 CTTTTAA
1 ATTTTAA
4733325 A
1 A
4733326 ACTATAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
6 4 0.11
7 25 0.71
8 2 0.06
9 4 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (7 bp):
ATTTTAA
Found at i:4734212 original size:3 final size:3
Alignment explanation
Indices: 4734204--4734237 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4734194 TTGCCCTCCA
4734204 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4734238 GTAAATAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4739029 original size:2 final size:2
Alignment explanation
Indices: 4739022--4739052 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4739012 TGAACTGCAA
4739022 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4739053 AGGGGGGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4739519 original size:24 final size:24
Alignment explanation
Indices: 4739487--4739578 Score: 73
Period size: 24 Copynumber: 3.9 Consensus size: 24
4739477 AACATAACAT
* *
4739487 AAATATATATATATAATTATATTA
1 AAATTTATATATATAAATATATTA
4739511 AAATTTATATAATATAAAT-TATTA
1 AAATTTATAT-ATATAAATATATTA
* * *
4739535 ATATTAAATTTATATAAATATA-TA
1 AAATT-TATATATATAAATATATTA
* * *
4739559 ATATTT-TAAATATAATTATA
1 AAATTTATATATATAAATATA
4739579 ATATTTAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
22 11 0.20
24 33 0.59
25 12 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATTTATATATATAAATATATTA
Found at i:4739543 original size:29 final size:29
Alignment explanation
Indices: 4739489--4739568 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 29
4739479 CATAACATAA
*
4739489 ATAT-ATATATATAATTATATTAAAATTT
1 ATATAATATAAATAATTATATTAAAATTT
*
4739517 ATATAATATAAATTATTAATATT-AAATTT
1 ATATAATATAAATAATT-ATATTAAAATTT
* *
4739546 ATATAA-ATATATAA-TATTTTAAA
1 ATATAATATAAATAATTATATTAAA
4739569 TATAATTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 4 0.09
27 3 0.07
28 10 0.23
29 22 0.50
30 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATAATATAAATAATTATATTAAAATTT
Found at i:4739547 original size:15 final size:16
Alignment explanation
Indices: 4739505--4739551 Score: 64
Period size: 14 Copynumber: 3.1 Consensus size: 16
4739495 ATATATAATT
4739505 ATATTAAAATTTATATA
1 ATATT-AAATTTATATA
4739522 ATA-TAAA-TTAT-TA
1 ATATTAAATTTATATA
4739535 ATATTAAATTTATATA
1 ATATTAAATTTATATA
4739551 A
1 A
4739552 ATATATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.19
14 8 0.30
15 7 0.26
16 4 0.15
17 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTAAATTTATATA
Found at i:4739924 original size:3 final size:3
Alignment explanation
Indices: 4739916--4739951 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4739906 TTGTTAGCCA
4739916 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4739952 TATGTAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4740081 original size:3 final size:3
Alignment explanation
Indices: 4740073--4740118 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
4740063 CACCTGTCTT
4740073 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4740119 GATACATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4744078 original size:16 final size:16
Alignment explanation
Indices: 4744047--4744096 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
4744037 TTAATATATC
4744047 AAAAT-TTATATAAATA
1 AAAATATTAT-TAAATA
4744063 TAAAATATT-TTAAATA
1 -AAAATATTATTAAATA
*
4744079 AAATTATTATTAAA-A
1 AAAATATTATTAAATA
4744094 AAA
1 AAA
4744097 TATAAATATG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 11 0.37
16 11 0.37
17 6 0.20
18 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATATTATTAAATA
Found at i:4744081 original size:14 final size:15
Alignment explanation
Indices: 4744062--4744099 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
4744052 TTATATAAAT
4744062 ATAAAATATT-TTAA
1 ATAAAATATTATTAA
4744076 ATAAAATTATTATTAA
1 ATAAAA-TATTATTAA
4744092 A-AAAATAT
1 ATAAAATAT
4744100 AAATATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 8 0.36
16 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAAAATATTATTAA
Found at i:4745024 original size:16 final size:16
Alignment explanation
Indices: 4745003--4745034 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4744993 TTAATCAACG
*
4745003 AAAAATATATTTTTTA
1 AAAAATATATATTTTA
4745019 AAAAATATATATTTTA
1 AAAAATATATATTTTA
4745035 TTTTATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATATATATTTTA
Found at i:4745655 original size:20 final size:19
Alignment explanation
Indices: 4745610--4745660 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
4745600 AAAATAATAT
*
4745610 TCATATTAATTAATATTGA
1 TCATATAAATTAATATTGA
*
4745629 TCAATATCAATTAATATTCG-
1 TC-ATATAAATTAATATT-GA
4745649 TACATATAAATT
1 T-CATATAAATT
4745661 CATAATACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (19 bp):
TCATATAAATTAATATTGA
Found at i:4745857 original size:24 final size:24
Alignment explanation
Indices: 4745830--4745887 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
4745820 AATATATATT
*
4745830 TATTTAATATTTAAAAATTTTAAA
1 TATTTAATATTTAAAAATCTTAAA
* *
4745854 TATTAAATATTT-ATAATCTTAAA
1 TATTTAATATTTAAAAATCTTAAA
4745877 -ATTT-ATATTTA
1 TATTTAATATTTA
4745888 CATATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 6 0.21
22 3 0.10
23 9 0.31
24 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTAATATTTAAAAATCTTAAA
Found at i:4745859 original size:23 final size:22
Alignment explanation
Indices: 4745833--4745887 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
4745823 ATATATTTAT
*
4745833 TTAATATTTAAAAATTTTAAATA
1 TTAATATTTAAAAATCTTAAA-A
*
4745856 TTAAATATTT-ATAATCTTAAAA
1 TT-AATATTTAAAAATCTTAAAA
*
4745878 TTTATATTTA
1 TTAATATTTA
4745888 CATATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 6 0.22
22 3 0.11
23 11 0.41
24 7 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATATTTAAAAATCTTAAAA
Found at i:4745875 original size:16 final size:16
Alignment explanation
Indices: 4745834--4745883 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
4745824 TATATTTATT
*
4745834 TAATATTTAAAAATTT-
1 TAATA-TTAAATATTTA
4745850 TAAATATTAAATATTTA
1 T-AATATTAAATATTTA
*
4745867 TAATCTTAAA-ATTTA
1 TAATATTAAATATTTA
4745882 TA
1 TA
4745884 TTTACATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 7 0.23
16 18 0.60
17 5 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATATTAAATATTTA
Found at i:4748961 original size:2 final size:2
Alignment explanation
Indices: 4748956--4749006 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
4748946 TTCTTTTTTA
* *
4748956 AT AT AT AT AC AT AT AT AT AT AT AT AC 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
*
4748998 AT GT AT AT A
1 AT AT AT AT A
4749007 AGTCCTAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4748977 original size:16 final size:16
Alignment explanation
Indices: 4748956--4749006 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
4748946 TTCTTTTTTA
4748956 ATATATATACATATAT
1 ATATATATACATATAT
4748972 ATATATATACATATAT
1 ATATATATACATATAT
* *
4748988 ATATATATATATGTAT
1 ATATATATACATATAT
4749004 ATA
1 ATA
4749007 AGTCCTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (16 bp):
ATATATATACATATAT
Found at i:4749753 original size:15 final size:15
Alignment explanation
Indices: 4749735--4749764 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4749725 TCAAATATAA
4749735 AAATATTTTTAATAT
1 AAATATTTTTAATAT
4749750 AAATATTTTTAATAT
1 AAATATTTTTAATAT
4749765 TTAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATATTTTTAATAT
Found at i:4751439 original size:18 final size:19
Alignment explanation
Indices: 4751405--4751447 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
4751395 CTTAAGTATA
*
4751405 TAGATTTATGAAGTTGGTT
1 TAGATTTATGAAATTGGTT
*
4751424 TGGATTT-TGAAATTGGTT
1 TAGATTTATGAAATTGGTT
4751442 TAGATT
1 TAGATT
4751448 CTGACTTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (19 bp):
TAGATTTATGAAATTGGTT
Found at i:4753160 original size:16 final size:15
Alignment explanation
Indices: 4753127--4753174 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 15
4753117 CCAGCTTAAT
4753127 ATAATTTATTAATAAAA
1 ATAA-TTATTAA-AAAA
4753144 ATAATATATTTTAAAAAA
1 ATAAT-TA--TTAAAAAA
4753162 ATAATTATTAAAA
1 ATAATTATTAAAA
4753175 TATATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 6 0.21
16 1 0.04
17 8 0.29
18 9 0.32
19 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTATTAAAAAA
Found at i:4753163 original size:18 final size:18
Alignment explanation
Indices: 4753135--4753170 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4753125 ATATAATTTA
4753135 TTAATAAAAATAATATATT
1 TTAATAAAAATAAT-TATT
4753154 TTAA-AAAAATAATTATT
1 TTAATAAAAATAATTATT
4753171 AAAATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAATAAAAATAATTATT
Found at i:4753164 original size:15 final size:16
Alignment explanation
Indices: 4753134--4753174 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
4753124 AATATAATTT
*
4753134 ATTAATAAAAATAATA
1 ATTATTAAAAATAATA
4753150 TATT-TTAAAAA-AATA
1 -ATTATTAAAAATAATA
4753165 ATTATTAAAA
1 ATTATTAAAA
4753175 TATATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 6 0.27
17 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTATTAAAAATAATA
Found at i:4753198 original size:32 final size:34
Alignment explanation
Indices: 4753123--4753209 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 34
4753113 AAATCCAGCT
4753123 TAATATAATTTATTAATAAAAATAATATATTTTAA
1 TAATATAA-TTATTAATAAAAATAATATATTTTAA
* * *
4753158 AAAAATAATTATTAA-AATATATAA-ATA-TTTAA
1 TAATATAATTATTAATAA-AAATAATATATTTTAA
* *
4753190 TAATATAATAAATAATAAAA
1 TAATATAATTATTAATAAAA
4753210 TAAATTTTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
32 17 0.40
33 7 0.17
34 12 0.29
35 6 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
TAATATAATTATTAATAAAAATAATATATTTTAA
Found at i:4753202 original size:19 final size:17
Alignment explanation
Indices: 4753141--4753203 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 17
4753131 TTTATTAATA
*
4753141 AAAATA-ATATAT-TTT
1 AAAATATATAAATATTT
* *
4753156 AAAA-AAATAATTA-TT
1 AAAATATATAAATATTT
4753171 AAAATATATAAATATTT
1 AAAATATATAAATATTT
4753188 AATAATATAATAAATA
1 AA-AATAT-ATAAATA
4753204 ATAAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 1 0.03
15 14 0.37
16 7 0.18
17 4 0.11
18 5 0.13
19 7 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATATATAAATATTT
Found at i:4756491 original size:16 final size:16
Alignment explanation
Indices: 4756462--4756519 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
4756452 TTATTCAAAC
*
4756462 TCAAAATAAATTAAAT
1 TCAAAATAATTTAAAT
*
4756478 TTAAAAGT-ATTTAAAT
1 TCAAAA-TAATTTAAAT
*
4756494 TCAAAATAATTTAAAC
1 TCAAAATAATTTAAAT
4756510 TCAAAATAAT
1 TCAAAATAAT
4756520 CAAATTAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 1 0.03
16 34 0.94
17 1 0.03
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (16 bp):
TCAAAATAATTTAAAT
Found at i:4756508 original size:32 final size:32
Alignment explanation
Indices: 4756423--4756508 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
4756413 GAGCTAATCA
* * * *
4756423 ATTCAAACAC-AAATAAATCAAATTTATAATT
1 ATTCAAACTCAAAATAAATTAAATTTAAAAGT
4756454 ATTCAAACTCAAAATAAATTAAATTTAAAAGT
1 ATTCAAACTCAAAATAAATTAAATTTAAAAGT
* * *
4756486 ATTTAAATTCAAAATAATTTAAA
1 ATTCAAACTCAAAATAAATTAAA
4756509 CTCAAAATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 9 0.19
32 38 0.81
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (32 bp):
ATTCAAACTCAAAATAAATTAAATTTAAAAGT
Found at i:4759049 original size:20 final size:19
Alignment explanation
Indices: 4759024--4759074 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
4759014 TAATAATAAT
4759024 AATAATAATAAAATTGTTAA
1 AATAATAATAAAATT-TTAA
**
4759044 AATAATTTTGAAAATTTTAA
1 AATAATAAT-AAAATTTTAA
4759064 AATGAATAATA
1 AAT-AATAATA
4759075 TTTTATAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (19 bp):
AATAATAATAAAATTTTAA
Found at i:4763091 original size:2 final size:2
Alignment explanation
Indices: 4763084--4763110 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4763074 GTGTTTCTCT
4763084 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
4763111 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4767311 original size:2 final size:2
Alignment explanation
Indices: 4767304--4767334 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4767294 GCAGGAAAAC
4767304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4767335 GAAAACGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4770036 original size:2 final size:2
Alignment explanation
Indices: 4770029--4770058 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4770019 TACTGAGTTT
4770029 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4770059 AGATATGTGG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4771900 original size:2 final size:2
Alignment explanation
Indices: 4771893--4771917 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4771883 GTGACAGAAC
4771893 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
4771918 GAGAGAGAGA
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:4784011 original size:2 final size:2
Alignment explanation
Indices: 4784006--4784031 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4783996 ATATATATAT
4784006 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
4784032 TTTTGAAGCA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4784163 original size:2 final size:2
Alignment explanation
Indices: 4784156--4784217 Score: 88
Period size: 2 Copynumber: 31.0 Consensus size: 2
4784146 TGCCACTTAT
* * *
4784156 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4784198 TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA
4784218 ATTTAATCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4788561 original size:34 final size:33
Alignment explanation
Indices: 4788517--4788733 Score: 258
Period size: 34 Copynumber: 6.4 Consensus size: 33
4788507 AAAAACCACT
*
4788517 ATTTAATCAACAATGGCAACCTACCAAATCTACC
1 ATTTAATCAACAATGGTAACCTACCAAATC-ACC
*
4788551 ATTTAGTCAACAATGGTAAGCC-ACCAAATCACC
1 ATTTAATCAACAATGGTAA-CCTACCAAATCACC
* * **
4788584 AATTTAATCAATAATGGTAAGCTACCAAATTTCTC
1 -ATTTAATCAACAATGGTAACCTACCAAATCAC-C
* *
4788619 ATTTAATCAACAATGGTAAGCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATC-ACC
* *
4788653 ATTTAGTCAACAATGGCAAACC-ACCAAATCACCC
1 ATTTAATCAACAATGG-TAACCTACCAAATCA-CC
*
4788687 ATTTAATCAACAATGGTAAACTACCAAATCACC
1 ATTTAATCAACAATGGTAACCTACCAAATCACC
4788720 ATTTAATCAACAAT
1 ATTTAATCAACAAT
4788734 TCTCCCACTT
Statistics
Matches: 158, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.15
34 128 0.81
35 7 0.04
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.25
Consensus pattern (33 bp):
ATTTAATCAACAATGGTAACCTACCAAATCACC
Found at i:4788693 original size:102 final size:101
Alignment explanation
Indices: 4788517--4788733 Score: 335
Period size: 102 Copynumber: 2.1 Consensus size: 101
4788507 AAAAACCACT
* *
4788517 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATCA
* * **
4788582 CCAATTTAATCAATAATGGTAAGCTACCAAATTTCTC
66 CCAATTTAATCAACAATGGTAAACTACCAAATCAC-C
* * *
4788619 ATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATCA
*
4788684 CCCATTTAATCAACAATGGTAAACTACCAAATCACC
66 CCAATTTAATCAACAATGGTAAACTACCAAATCACC
4788720 ATTTAATCAACAAT
1 ATTTAATCAACAAT
4788734 TCTCCCACTT
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.25
Consensus pattern (101 bp):
ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATCA
CCAATTTAATCAACAATGGTAAACTACCAAATCACC
Found at i:4793181 original size:34 final size:34
Alignment explanation
Indices: 4793138--4793359 Score: 231
Period size: 34 Copynumber: 6.5 Consensus size: 34
4793128 TGGTAAAAAA
* *
4793138 CTACCATTTAATCAACAATGGCAACCTATCAAAT
1 CTACCATTTAATCAACAATGGTAACCTACCAAAT
*
4793172 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 CTACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
4793206 C-ACCAATTTAATCAATAATGGTAAGCTTACCAAAT
1 CTACC-ATTTAATCAACAATGGTAA-CCTACCAAAT
* *
4793241 -TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CTAC-CATTTAATCAACAATGGTAACCTACCAAAT
* **
4793275 CTCCCATTTAATCAACAATGACAAACC-ACCAAAT
1 CTACCATTTAATCAACAATG-GTAACCTACCAAAT
* * *
4793309 C-ACCCATTTAATCAAAAATGGTAAACTATCAAAT
1 CTA-CCATTTAATCAACAATGGTAACCTACCAAAT
4793343 C-ACCATTTAATCAACAA
1 CTACCATTTAATCAACAA
4793360 ACTTAAGAAC
Statistics
Matches: 158, Mismatches: 21, Indels: 19
0.80 0.11 0.10
Matches are distributed among these distances:
33 20 0.13
34 104 0.66
35 33 0.21
36 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (34 bp):
CTACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:4793256 original size:69 final size:67
Alignment explanation
Indices: 4793140--4793359 Score: 237
Period size: 69 Copynumber: 3.2 Consensus size: 67
4793130 GTAAAAAACT
* * * *
4793140 ACCATTTAATCAACAATGGC-AACCTATCAAATCTA-CCATTTAGTCAACAATGGTAAGCCACCA
1 ACCATTTAATCAACAATGACAAACC-ACCAAATC-ACCCATTTAATCAACAATGGTAAGCTACCA
4793203 AATC
64 AATC
* ** * * ** *
4793207 ACCAATTTAATCAATAATGGTAAGCTTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCA
1 ACC-ATTTAATCAACAATGACAAAC-CACCAAATCACCCATTTAATCAACAATGGTAAGCTACCA
4793272 AATC
64 AATC
* * * *
4793276 TCCCATTTAATCAACAATGACAAACCACCAAATCACCCATTTAATCAAAAATGGTAAACTATCAA
1 -ACCATTTAATCAACAATGACAAACCACCAAATCACCCATTTAATCAACAATGGTAAGCTACCAA
4793341 ATC
65 ATC
4793344 ACCATTTAATCAACAA
1 ACCATTTAATCAACAA
4793360 ACTTAAGAAC
Statistics
Matches: 125, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
67 18 0.14
68 51 0.41
69 54 0.43
70 2 0.02
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.26
Consensus pattern (67 bp):
ACCATTTAATCAACAATGACAAACCACCAAATCACCCATTTAATCAACAATGGTAAGCTACCAAA
TC
Found at i:4793321 original size:103 final size:101
Alignment explanation
Indices: 4793140--4793359 Score: 296
Period size: 103 Copynumber: 2.2 Consensus size: 101
4793130 GTAAAAAACT
* * ** *
4793140 ACCATTTAATCAACAATGGCAACCTATCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAA
1 ACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGACAAACCACCAAA
* * *
4793205 TCACCAATTTAATCAATAATGGTAAGCTTACCAAATT
66 TCACCAATTTAATCAAAAATGGTAAAC-TACCAAATC
* * * *
4793242 TCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGACAAACCACCAA
1 AC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGACAAACCACCAA
* *
4793307 ATCACCCATTTAATCAAAAATGGTAAACTATCAAATC
65 ATCACCAATTTAATCAAAAATGGTAAACTACCAAATC
4793344 ACCATTTAATCAACAA
1 ACCATTTAATCAACAA
4793360 ACTTAAGAAC
Statistics
Matches: 102, Mismatches: 15, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
101 14 0.14
102 9 0.09
103 79 0.77
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.26
Consensus pattern (101 bp):
ACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGACAAACCACCAAA
TCACCAATTTAATCAAAAATGGTAAACTACCAAATC
Found at i:4794530 original size:16 final size:14
Alignment explanation
Indices: 4794501--4794539 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
4794491 CACTAAAAAA
4794501 AATATTTT-AATTT
1 AATATTTTAAATTT
4794514 ATATATTATTAAATTT
1 A-ATATT-TTAAATTT
4794530 AATATTTTAA
1 AATATTTTAA
4794540 TGTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 9 0.39
15 7 0.30
16 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:4794549 original size:29 final size:30
Alignment explanation
Indices: 4794501--4794559 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
4794491 CACTAAAAAA
4794501 AATATTTTAATTTATATATTATT-AAATTT
1 AATATTTTAATTTATATATTATTGAAATTT
* *
4794530 AATATTTTAATGTT-TTTATTTTTGAAATTT
1 AATATTTTAAT-TTATATATTATTGAAATTT
4794560 TAGTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (30 bp):
AATATTTTAATTTATATATTATTGAAATTT
Found at i:4795317 original size:25 final size:24
Alignment explanation
Indices: 4795289--4795335 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4795279 TATATACACA
4795289 TTTTATAAATTTAAATAAAAATTAT
1 TTTTATAAA-TTAAATAAAAATTAT
* *
4795314 TTTTATTAATTAAATAATAATT
1 TTTTATAAATTAAATAAAAATT
4795336 TAAATTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTATAAATTAAATAAAAATTAT
Found at i:4795711 original size:6 final size:6
Alignment explanation
Indices: 4795700--4795728 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4795690 TTGTCGTTAA
4795700 ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
4795729 AAATAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:4795791 original size:21 final size:22
Alignment explanation
Indices: 4795767--4795811 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
4795757 TATATATTTA
4795767 TTTTTAAA-TTGTAATTTAAAT
1 TTTTTAAATTTGTAATTTAAAT
* *
4795788 TTTTTAAATTTTTTATTTAAAT
1 TTTTTAAATTTGTAATTTAAAT
4795810 TT
1 TT
4795812 GATATGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTTAAATTTGTAATTTAAAT
Found at i:4796251 original size:19 final size:19
Alignment explanation
Indices: 4796227--4796283 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
4796217 AGACTTGGAG
4796227 GCGGGAGCCAAGGGCTCGC
1 GCGGGAGCCAAGGGCTCGC
4796246 GCGGGAGCCAAGGGCTCGC
1 GCGGGAGCCAAGGGCTCGC
*
4796265 CCGGGAGCCAAGGGCTCGC
1 GCGGGAGCCAAGGGCTCGC
4796284 AACAGCTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.16, C:0.33, G:0.46, T:0.05
Consensus pattern (19 bp):
GCGGGAGCCAAGGGCTCGC
Found at i:4800226 original size:2 final size:2
Alignment explanation
Indices: 4800219--4800260 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4800209 TGTTTGTACA
4800219 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4800261 GTTTTTTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4802738 original size:15 final size:15
Alignment explanation
Indices: 4802720--4802769 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
4802710 TTATTATAAT
4802720 TTAAAAATATAAATA
1 TTAAAAATATAAATA
4802735 TT-AAAATATTAAAT-
1 TTAAAAATA-TAAATA
* *
4802749 TTAATAATATAAAAA
1 TTAAAAATATAAATA
4802764 TTAAAA
1 TTAAAA
4802770 TAAATATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAAATATAAATA
Found at i:4802757 original size:29 final size:30
Alignment explanation
Indices: 4802711--4802771 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
4802701 TTATTTTATT
*
4802711 TATTATAATTTAAAAATATAAATATTAAAA
1 TATTATAATTTAAAAATATAAAAATTAAAA
*
4802741 TATTA-AATTTAATAATATAAAAATTAAAA
1 TATTATAATTTAAAAATATAAAAATTAAAA
4802770 TA
1 TA
4802772 AATATTTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
TATTATAATTTAAAAATATAAAAATTAAAA
Found at i:4802775 original size:21 final size:21
Alignment explanation
Indices: 4802728--4802775 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4802718 ATTTAAAAAT
4802728 ATAAAT-ATTAAAATATTAAA
1 ATAAATAATTAAAATATTAAA
* *
4802748 TTTAATAATATAAAA-ATTAAA
1 ATAAATAAT-TAAAATATTAAA
4802769 ATAAATA
1 ATAAATA
4802776 TTTCGCCACA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAATAATTAAAATATTAAA
Found at i:4812680 original size:14 final size:14
Alignment explanation
Indices: 4812661--4812689 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4812651 GGAATAGATT
4812661 GTCGTCAGAGGTAG
1 GTCGTCAGAGGTAG
4812675 GTCGTCAGAGGTAG
1 GTCGTCAGAGGTAG
4812689 G
1 G
4812690 CAAAAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.45, T:0.21
Consensus pattern (14 bp):
GTCGTCAGAGGTAG
Found at i:4817459 original size:85 final size:87
Alignment explanation
Indices: 4817298--4817463 Score: 309
Period size: 85 Copynumber: 1.9 Consensus size: 87
4817288 TCAAAGGAGG
4817298 AAAGTAAGGTTGGATGAAAATTGGCAGACACTTAAAAAAAAAAAAAGAAAATACCTGCAAAATAT
1 AAAGTAAGGTTGGATGAAAATTGGCAGACACTT-AAAAAAAAAAAAGAAAATACCTGCAAAATAT
4817363 GATAACAGATAGAAAATACCTGC
65 GATAACAGATAGAAAATACCTGC
4817386 AAAGTAAGGTTGGATGAAAATTGGCAGACAC-T-AAAAAAAAAAAGAAAATACCTGCAAAATATG
1 AAAGTAAGGTTGGATGAAAATTGGCAGACACTTAAAAAAAAAAAAGAAAATACCTGCAAAATATG
4817449 ATAACAGATAGAAAA
66 ATAACAGATAGAAAA
4817464 GAAAGGCAGT
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
85 46 0.59
87 1 0.01
88 31 0.40
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (87 bp):
AAAGTAAGGTTGGATGAAAATTGGCAGACACTTAAAAAAAAAAAAGAAAATACCTGCAAAATATG
ATAACAGATAGAAAATACCTGC
Found at i:4820003 original size:301 final size:301
Alignment explanation
Indices: 4819461--4820367 Score: 1805
Period size: 301 Copynumber: 3.0 Consensus size: 301
4819451 TTCAGTGATG
4819461 AGACCCTTAACCAGCAACAAACAATTGAAAGAAAATACTTACCCACCACACTGAGGACAAAATAA
1 AGACCCTTAACCAGCAACAAACAATTGAAAGAAAATACTTACCCACCACACTGAGGACAAAATAA
4819526 ATTTTTCCAAATGGTCAATTGAAACGCACATAAATTACAGCATTTAATGTTCACTTATTAATCTT
66 ATTTTTCCAAATGGTCAATTGAAACGCACATAAATTACAGCATTTAATGTTCACTTATTAATCTT
4819591 TGGCTGGCTCTTTGACTCTAACAAATAGTAAGACTGTTACATAATGGAAAACATCAAATTATACT
131 TGGCTGGCTCTTTGACTCTAACAAATAGTAAGACTGTTACATAATGGAAAACATCAAATTATACT
4819656 TTAAAATTTTAAAATCCAAAATTATTGATTTTATGTTAATTTCTTTTAGTTTTGTTTTTTACCCG
196 TTAAAATTTTAAAATCCAAAATTATTGATTTTATGTTAATTTCTTTTAGTTTTGTTTTTTACCCG
4819721 TCTCTATTATTTTAGAATAAATGGACTCTGAAGTTGGCTTA
261 TCTCTATTATTTTAGAATAAATGGACTCTGAAGTTGGCTTA
4819762 AGACCCTTAACCAGCAACAAACAATTGAAAGAAAATACTTACCCACCACACTGAGGACAAAATAA
1 AGACCCTTAACCAGCAACAAACAATTGAAAGAAAATACTTACCCACCACACTGAGGACAAAATAA
4819827 ATTTTTCCAAATGGTCAATTGAAACGCACATAAATTACAGCATTTAATGTTCACTTATTAATCTT
66 ATTTTTCCAAATGGTCAATTGAAACGCACATAAATTACAGCATTTAATGTTCACTTATTAATCTT
*
4819892 TGGCTGGCTCTTTAACTCTAACAAATAGTAAGACTGTTACATAATGGAAAACATCAAATTATACT
131 TGGCTGGCTCTTTGACTCTAACAAATAGTAAGACTGTTACATAATGGAAAACATCAAATTATACT
4819957 TTAAAATTTTAAAATCCAAAATTATTGATTTTATGTTAATTTCTTTTAGTTTTGTTTTTTACCCG
196 TTAAAATTTTAAAATCCAAAATTATTGATTTTATGTTAATTTCTTTTAGTTTTGTTTTTTACCCG
4820022 TCTCTATTATTTTAGAATAAATGGACTCTGAAGTTGGCTTA
261 TCTCTATTATTTTAGAATAAATGGACTCTGAAGTTGGCTTA
4820063 AGACCCTTAACCAGCAACAAACAATTGAAAGAAAATACTTACCCACCACACTGAGGACAAAATAA
1 AGACCCTTAACCAGCAACAAACAATTGAAAGAAAATACTTACCCACCACACTGAGGACAAAATAA
4820128 ATTTTTCCAAATGGTCAATTGAAACGCACATAAATTACAGCATTTAATGTTCACTTATTAATCTT
66 ATTTTTCCAAATGGTCAATTGAAACGCACATAAATTACAGCATTTAATGTTCACTTATTAATCTT
4820193 TGGCTGGCTCTTTGACTCTAACAAATAGTAAGACTGTTACATAATGGAAAACATCAAATTATACT
131 TGGCTGGCTCTTTGACTCTAACAAATAGTAAGACTGTTACATAATGGAAAACATCAAATTATACT
4820258 TTAAAATTTTAAAATCCAAAATTATTGATTTTATGTTAATTTCTTTTAGTTTTGTTTTTTACCCG
196 TTAAAATTTTAAAATCCAAAATTATTGATTTTATGTTAATTTCTTTTAGTTTTGTTTTTTACCCG
4820323 TCTCTATTATTTTAGAATAAATGGACTCTGAAGTTGGCTTA
261 TCTCTATTATTTTAGAATAAATGGACTCTGAAGTTGGCTTA
4820364 AGAC
1 AGAC
4820368 AGCCCAAATT
Statistics
Matches: 604, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
301 604 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (301 bp):
AGACCCTTAACCAGCAACAAACAATTGAAAGAAAATACTTACCCACCACACTGAGGACAAAATAA
ATTTTTCCAAATGGTCAATTGAAACGCACATAAATTACAGCATTTAATGTTCACTTATTAATCTT
TGGCTGGCTCTTTGACTCTAACAAATAGTAAGACTGTTACATAATGGAAAACATCAAATTATACT
TTAAAATTTTAAAATCCAAAATTATTGATTTTATGTTAATTTCTTTTAGTTTTGTTTTTTACCCG
TCTCTATTATTTTAGAATAAATGGACTCTGAAGTTGGCTTA
Found at i:4822287 original size:4 final size:4
Alignment explanation
Indices: 4822280--4822324 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
4822270 AAAATACAAA
* * * *
4822280 AAAG AAAG AAAG AAAG AAAG AAAG AATG AATG AATG AATG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
4822325 GGAGAAAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (4 bp):
AAAG
Found at i:4822644 original size:137 final size:137
Alignment explanation
Indices: 4822398--4822671 Score: 548
Period size: 137 Copynumber: 2.0 Consensus size: 137
4822388 CATAATCAAA
4822398 AAGCATTGGTAGTGCTAAAAGCTGAAACAAGCACCTCTATGGCAAATCACCTGAAATGTCATCTT
1 AAGCATTGGTAGTGCTAAAAGCTGAAACAAGCACCTCTATGGCAAATCACCTGAAATGTCATCTT
4822463 AATGTCTTAAGAGACTTCTATAAAAAATCCATACTGTCAGCCTGACATTTATTGGCACAATAATC
66 AATGTCTTAAGAGACTTCTATAAAAAATCCATACTGTCAGCCTGACATTTATTGGCACAATAATC
4822528 AGTTAGT
131 AGTTAGT
4822535 AAGCATTGGTAGTGCTAAAAGCTGAAACAAGCACCTCTATGGCAAATCACCTGAAATGTCATCTT
1 AAGCATTGGTAGTGCTAAAAGCTGAAACAAGCACCTCTATGGCAAATCACCTGAAATGTCATCTT
4822600 AATGTCTTAAGAGACTTCTATAAAAAATCCATACTGTCAGCCTGACATTTATTGGCACAATAATC
66 AATGTCTTAAGAGACTTCTATAAAAAATCCATACTGTCAGCCTGACATTTATTGGCACAATAATC
4822665 AGTTAGT
131 AGTTAGT
4822672 CCAACAAACT
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (137 bp):
AAGCATTGGTAGTGCTAAAAGCTGAAACAAGCACCTCTATGGCAAATCACCTGAAATGTCATCTT
AATGTCTTAAGAGACTTCTATAAAAAATCCATACTGTCAGCCTGACATTTATTGGCACAATAATC
AGTTAGT
Found at i:4825176 original size:120 final size:120
Alignment explanation
Indices: 4824971--4825214 Score: 461
Period size: 120 Copynumber: 2.0 Consensus size: 120
4824961 CTTAATGATA
**
4824971 CTTGACAGCATAAAGAACTCATCAAATAACTGAAGAGAAACCATATTTCAGCACGGATAGTATCA
1 CTTGACAGCATAAAGAACTCATCAAATAACTGAAGAGAAACCATATTTCAGCACAAATAGTATCA
4825036 AATGTCATAAAAGGTAGACCAAAATGCCTATTAGTTATTATTTCTTCTAATGTTC
66 AATGTCATAAAAGGTAGACCAAAATGCCTATTAGTTATTATTTCTTCTAATGTTC
*
4825091 CTTGACAGGATAAAGAACTCATCAAATAACTGAAGAGAAACCATATTTCAGCACAAATAGTATCA
1 CTTGACAGCATAAAGAACTCATCAAATAACTGAAGAGAAACCATATTTCAGCACAAATAGTATCA
4825156 AATGTCATAAAAGGTAGACCAAAATGCCTATTAGTTATTATTTCTTCTAATGTTC
66 AATGTCATAAAAGGTAGACCAAAATGCCTATTAGTTATTATTTCTTCTAATGTTC
4825211 CTTG
1 CTTG
4825215 TCCTTATGTT
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (120 bp):
CTTGACAGCATAAAGAACTCATCAAATAACTGAAGAGAAACCATATTTCAGCACAAATAGTATCA
AATGTCATAAAAGGTAGACCAAAATGCCTATTAGTTATTATTTCTTCTAATGTTC
Found at i:4830910 original size:45 final size:44
Alignment explanation
Indices: 4830861--4831000 Score: 124
Period size: 45 Copynumber: 3.1 Consensus size: 44
4830851 TTTTAAATTG
*
4830861 AGTTTTATTATTTTTTTAATTAATTTTTAATTGGATTTAATTTTA
1 AGTTTTATTAATTTTTTAATTAA-TTTTAATTGGATTTAATTTTA
* * *
4830906 AG-TTTATATAAATTTTTAGTTAAATTTTAATTAGATTTGAA-TTTA
1 AGTTTTAT-TAATTTTTTAATT-AATTTTAATTGGATTT-AATTTTA
* * * * *
4830951 AGTTTATATAAATTTTTT-ATTTATGTTAAATGAATTTAATTTTTA
1 AGTTT-TATTAATTTTTTAATTAATTTTAATTGGATTTAA-TTTTA
4830996 AGTTT
1 AGTTT
4831001 AAATTTATAT
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
43 2 0.03
44 16 0.21
45 42 0.55
46 13 0.17
47 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.59
Consensus pattern (44 bp):
AGTTTTATTAATTTTTTAATTAATTTTAATTGGATTTAATTTTA
Found at i:4830920 original size:22 final size:22
Alignment explanation
Indices: 4830895--4831001 Score: 58
Period size: 22 Copynumber: 4.8 Consensus size: 22
4830885 TTTTAATTGG
4830895 ATTTAATTTTAAGTTTATATAA
1 ATTTAATTTTAAGTTTATATAA
* * * * *
4830917 ATTTTTAGTTAAATTTTA-ATTAG
1 A-TTTAATTTTAAGTTTATA-TAA
4830940 ATTTGAA-TTTAAGTTTATATAA
1 ATTT-AATTTTAAGTTTATATAA
** * * *
4830962 ATTTTTTATTTATG-TTAAATGA
1 ATTTAAT-TTTAAGTTTATATAA
4830984 ATTTAATTTTTAAGTTTA
1 ATTTAA-TTTTAAGTTTA
4831002 AATTTATATT
Statistics
Matches: 60, Mismatches: 17, Indels: 15
0.65 0.18 0.16
Matches are distributed among these distances:
22 34 0.57
23 26 0.43
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
ATTTAATTTTAAGTTTATATAA
Found at i:4830972 original size:23 final size:22
Alignment explanation
Indices: 4830902--4830973 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
4830892 TGGATTTAAT
4830902 TTTAAGTTTATATAAATTTTTA
1 TTTAAGTTTATATAAATTTTTA
* * * **
4830924 GTTAAATTT-TAATTAGATTTGAA
1 TTTAAGTTTAT-A-TAAATTTTTA
4830947 TTTAAGTTTATATAAATTTTTTA
1 TTTAAGTTTATATAAA-TTTTTA
4830970 TTTA
1 TTTA
4830974 TGTTAAATGA
Statistics
Matches: 36, Mismatches: 10, Indels: 7
0.68 0.19 0.13
Matches are distributed among these distances:
21 1 0.03
22 11 0.31
23 23 0.64
24 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (22 bp):
TTTAAGTTTATATAAATTTTTA
Found at i:4831001 original size:45 final size:45
Alignment explanation
Indices: 4830886--4831027 Score: 125
Period size: 45 Copynumber: 3.2 Consensus size: 45
4830876 TTAATTAATT
*
4830886 TTTAATTG-GATTTAATTTTAAGTTTATATAAATTTTTAGTTAAA
1 TTTAAATGAGATTTAATTTTAAGTTTATATAAATTTTTAGTTAAA
* * *
4830930 TTTTAATTAGATTTGAA-TTTAAGTTTATATAAATTTTTTA-TT-TA
1 TTTAAATGAGATTT-AATTTTAAGTTTATATAAA-TTTTTAGTTAAA
* **
4830974 TGTTAAATGA-ATTTAATTTTTAAGTTTAAATTTATATTTTA-TTAAA
1 T-TTAAATGAGATTTAA-TTTTAAGTTTATATAAAT-TTTTAGTTAAA
4831020 TATTAAAT
1 T-TTAAAT
4831028 TTCATTATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
43 2 0.03
44 12 0.15
45 49 0.62
46 16 0.20
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (45 bp):
TTTAAATGAGATTTAATTTTAAGTTTATATAAATTTTTAGTTAAA
Found at i:4831427 original size:16 final size:15
Alignment explanation
Indices: 4831406--4831440 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
4831396 AAACTTAATC
*
4831406 AATTAAATTTGTATTA
1 AATTAAATTTATA-TA
4831422 AATTAAATTTATATA
1 AATTAAATTTATATA
4831437 AATT
1 AATT
4831441 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
AATTAAATTTATATA
Found at i:4831544 original size:26 final size:24
Alignment explanation
Indices: 4831514--4831596 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 24
4831504 TTTAATTTTT
4831514 AATTTTAAATATTAATATTAAAATA
1 AATTTT-AATATTAATATTAAAATA
*
4831539 ATATTTTAATATTATTTATTATAAAATA
1 A-ATTTTAATATTA-ATA-T-TAAAATA
*
4831567 AATTTTAA-ATT-A-ATTCAAATAA
1 AATTTTAATATTAATATTAAAAT-A
4831589 AATTTTAA
1 AATTTTAA
4831597 ATAAAATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
21 5 0.10
22 10 0.20
23 1 0.02
25 8 0.16
26 10 0.20
27 8 0.16
28 8 0.16
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTTTAATATTAATATTAAAATA
Found at i:4833182 original size:22 final size:23
Alignment explanation
Indices: 4833137--4833188 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
4833127 TTAAATTATA
4833137 ATAAATAAAATTAATTAACAATTT
1 ATAAA-AAAATTAATTAACAATTT
*
4833161 -TAAAAAAATTATTTAA-ATATTT
1 ATAAAAAAATTAATTAACA-ATTT
4833183 ATAAAA
1 ATAAAA
4833189 TATTAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 15 0.60
23 9 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAAAAAAATTAATTAACAATTT
Found at i:4833279 original size:16 final size:17
Alignment explanation
Indices: 4833258--4833291 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4833248 ACTTATATCT
4833258 TAAATTT-ATTTTTAAA
1 TAAATTTAATTTTTAAA
4833274 TAAATTTAAATTTTTAAA
1 TAAATTT-AATTTTTAAA
4833292 ATATATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTTAATTTTTAAA
Found at i:4833345 original size:20 final size:20
Alignment explanation
Indices: 4833322--4833364 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4833312 TTATGAATAT
4833322 TTAAATAATT-TTTAATATTA
1 TTAAATAATTATTTAAT-TTA
* *
4833342 TTAATTAATTATTTTATTTA
1 TTAAATAATTATTTAATTTA
4833362 TTA
1 TTA
4833365 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAAATAATTATTTAATTTA
Found at i:4834894 original size:20 final size:20
Alignment explanation
Indices: 4834865--4834903 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4834855 GGAAAAAAAA
*
4834865 AATCTAAATAAAAAGATATG
1 AATCTAAATAAAAAAATATG
*
4834885 AATCTTAATAAAAAAATAT
1 AATCTAAATAAAAAAATAT
4834904 TATAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
AATCTAAATAAAAAAATATG
Found at i:4836789 original size:17 final size:17
Alignment explanation
Indices: 4836763--4836797 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4836753 CAAACTGAAG
*
4836763 TTTTCCTTTTTTTTTCT
1 TTTTCCTTTTTATTTCT
*
4836780 TTTTCTTTTTTATTTCT
1 TTTTCCTTTTTATTTCT
4836797 T
1 T
4836798 CTAATGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCCTTTTTATTTCT
Found at i:4841249 original size:22 final size:21
Alignment explanation
Indices: 4841198--4841250 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
4841188 TCATAAAATT
*
4841198 AGGAAAAAGTAATTTAATTAG
1 AGGAAAAAGTAATTTAATTAC
4841219 AGGGAAAAAGTAATTTAATTAC
1 A-GGAAAAAGTAATTTAATTAC
4841241 AGGACAAAAG
1 AGGA-AAAAG
4841251 AAGAAATCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGAAAAAGTAATTTAATTAC
Found at i:4844536 original size:25 final size:23
Alignment explanation
Indices: 4844482--4844536 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
4844472 AGCAGACACT
*
4844482 AAAAAAAAAAAAAAAATGAAGTC
1 AAAAAAAAAAAAAAAATGAAGGC
* *
4844505 AAGAAAAAGAAAAGAAAATGAAGAGG
1 AA-AAAAA-AAAAAAAAATGAAG-GC
4844531 AAAAAA
1 AAAAAA
4844537 TGGAGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 2 0.08
24 5 0.19
25 17 0.65
26 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.05
Consensus pattern (23 bp):
AAAAAAAAAAAAAAAATGAAGGC
Found at i:4854021 original size:2 final size:2
Alignment explanation
Indices: 4854014--4854050 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4854004 ACCTACAAAA
4854014 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4854051 TTATCACCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4860230 original size:2 final size:2
Alignment explanation
Indices: 4860223--4860269 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4860213 TGCAGATGAA
4860223 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
4860265 AT AT A
1 AT AT A
4860270 CCTGAGACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4866725 original size:64 final size:64
Alignment explanation
Indices: 4866624--4866751 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
4866614 CTCAAAACTA
* *
4866624 AAAAATCCACGAACAGTTGAGTTTGACAATTATACATCGTAGACAACATGTCCCTTTTATCCTT
1 AAAAATCCACGAACAGTTGAGTTTGACAATTATACATCGTAGACAACATCTCCCTTTTAACCTT
*
4866688 AAAAATCCACGAACAGTTGAGTTTGACAATTATACATCGTAGACAACATCTCCTTTTTAACCTT
1 AAAAATCCACGAACAGTTGAGTTTGACAATTATACATCGTAGACAACATCTCCCTTTTAACCTT
4866752 TGCACTGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (64 bp):
AAAAATCCACGAACAGTTGAGTTTGACAATTATACATCGTAGACAACATCTCCCTTTTAACCTT
Found at i:4869808 original size:33 final size:33
Alignment explanation
Indices: 4869766--4869833 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
4869756 AAAAATAAAA
4869766 TACACACAAGGAAAAACACAAAAGCCAAAAAGC
1 TACACACAAGGAAAAACACAAAAGCCAAAAAGC
4869799 TACACACAAGGAAAAACACAAAAGCCAAAAAGC
1 TACACACAAGGAAAAACACAAAAGCCAAAAAGC
4869832 TA
1 TA
4869834 ACTAATATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.60, C:0.24, G:0.12, T:0.04
Consensus pattern (33 bp):
TACACACAAGGAAAAACACAAAAGCCAAAAAGC
Found at i:4871264 original size:58 final size:57
Alignment explanation
Indices: 4871174--4871288 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 57
4871164 TTCCCCGGTT
4871174 ACAGGATCTGTTTATGCCCACCAATACAGAAACAAGCAATTTTCAATTCCAAGACATA
1 ACAGGATCTGTTTATGCCCACCAATACAGAAACAAGCAA-TTTCAATTCCAAGACATA
** * * *
4871232 ACAGGATCTGTTTATGCCTGCTAATACAGAAACAAGTAATTTCTATTCCAAGACATA
1 ACAGGATCTGTTTATGCCCACCAATACAGAAACAAGCAATTTCAATTCCAAGACATA
4871289 GCATGGCATT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
57 17 0.33
58 35 0.67
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (57 bp):
ACAGGATCTGTTTATGCCCACCAATACAGAAACAAGCAATTTCAATTCCAAGACATA
Found at i:4872891 original size:36 final size:35
Alignment explanation
Indices: 4872808--4872891 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 35
4872798 TTTAAAAAAA
4872808 TTAATAAATAAATATATATAAAATATGAATATATTT
1 TTAATAAATAAATATATATAAAATA-GAATATATTT
* *
4872844 TT--TAAAAAAATATAGTATTAAAA-A-ATTATCATTT
1 TTAATAAATAAATATA-TA-TAAAATAGAATAT-ATTT
4872878 TTAATAAATAAATA
1 TTAATAAATAAATA
4872892 GGTAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
33 4 0.10
34 17 0.43
35 3 0.08
36 16 0.40
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (35 bp):
TTAATAAATAAATATATATAAAATAGAATATATTT
Found at i:4872985 original size:18 final size:18
Alignment explanation
Indices: 4872964--4873017 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
4872954 ATTTAAATAA
4872964 TTTTTAAGAAATAAATTT
1 TTTTTAAGAAATAAATTT
* *
4872982 TTTTTAAGAAGTAAATAT
1 TTTTTAAGAAATAAATTT
* * *
4873000 TTTGTAAAAAATATATTT
1 TTTTTAAGAAATAAATTT
4873018 CATCGACGAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (18 bp):
TTTTTAAGAAATAAATTT
Found at i:4877461 original size:114 final size:114
Alignment explanation
Indices: 4877261--4877491 Score: 462
Period size: 114 Copynumber: 2.0 Consensus size: 114
4877251 AAATGTAGTC
4877261 ATTGCAGGCAGATCATCAAACGTATGAAATGGGTGCTTAAAAATGATAGAGCTCATATTGGAAAC
1 ATTGCAGGCAGATCATCAAACGTATGAAATGGGTGCTTAAAAATGATAGAGCTCATATTGGAAAC
4877326 TTAATAAAAAGAGCAAAAGTCCAATTTGAATACAATACAAAGGATGGCA
66 TTAATAAAAAGAGCAAAAGTCCAATTTGAATACAATACAAAGGATGGCA
4877375 ATTGCAGGCAGATCATCAAACGTATGAAATGGGTGCTTAAAAATGATAGAGCTCATATTGGAAAC
1 ATTGCAGGCAGATCATCAAACGTATGAAATGGGTGCTTAAAAATGATAGAGCTCATATTGGAAAC
4877440 TTAATAAAAAGAGCAAAAGTCCAATTTGAATACAATACAAAGGATGGCA
66 TTAATAAAAAGAGCAAAAGTCCAATTTGAATACAATACAAAGGATGGCA
4877489 ATT
1 ATT
4877492 CGTCAATTCT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 117 1.00
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (114 bp):
ATTGCAGGCAGATCATCAAACGTATGAAATGGGTGCTTAAAAATGATAGAGCTCATATTGGAAAC
TTAATAAAAAGAGCAAAAGTCCAATTTGAATACAATACAAAGGATGGCA
Found at i:4883910 original size:15 final size:14
Alignment explanation
Indices: 4883892--4883932 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 14
4883882 GATTTAATTT
4883892 TAATTATTATTTAAA
1 TAATT-TTATTTAAA
4883907 TAATTTTA---AAA
1 TAATTTTATTTAAA
4883918 TAATTTTATTTAAA
1 TAATTTTATTTAAA
4883932 T
1 T
4883933 TTTTATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 11 0.48
14 7 0.30
15 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAATTTTATTTAAA
Found at i:4885345 original size:19 final size:18
Alignment explanation
Indices: 4885314--4885354 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4885304 TCACTCTATT
4885314 ATTATATTTATAAAATAAA
1 ATTATATTTAT-AAATAAA
4885333 ATTA-ATTTAATAAAT-AA
1 ATTATATTT-ATAAATAAA
4885350 ATTAT
1 ATTAT
4885355 GCACATCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATATTTATAAATAAA
Found at i:4886249 original size:188 final size:184
Alignment explanation
Indices: 4885932--4886300 Score: 576
Period size: 188 Copynumber: 2.0 Consensus size: 184
4885922 TTACCACAAT
* *
4885932 GATTGTTACCGACATACCATCCAAAAATCTTGCCTCGACTAATCTTGCTTACTGCATGCTTTCTG
1 GATTGTTACCGACACACCATCCAAAAATCTTGCCTCGACTAATCTTGCTTACTGCATACTTTCTG
4885997 ATCTTCACAAGTTCGCCGTCACACCGGAGACGCCTCTCTTCTTTCTATCTCGTATCCTTTTTTGA
66 ATCTTCACAAGTTCGCCGTCACACCGGAGACGCCTCTCTTCTTTCTATCTCGTATCCTTTTTTGA
* * *
4886062 TTGTTTCTTTCTTTTTTTTTTTCCGCTTTATTTTCAGTGTTAATCGCAGTTTATATAA
131 ATGTTTC--T-TTTTTTTTTGT-CGCTTTATTTTCAGTGTTAATCACAGTTTATATAA
* * * *
4886120 GATTGTTACCGGCACACCATCCAAAGATGTTGCCTCGACTAATCTTGCTTACTGCATATTTTCTG
1 GATTGTTACCGACACACCATCCAAAAATCTTGCCTCGACTAATCTTGCTTACTGCATACTTTCTG
* * *
4886185 ATCTTCACAATTTCGCCGTCACACCGGCGACGCCTCTGTTCTTTCTATCTCGTATCCTTTTTTGA
66 ATCTTCACAAGTTCGCCGTCACACCGGAGACGCCTCTCTTCTTTCTATCTCGTATCCTTTTTTGA
* *
4886250 ATGTTTCTTTTTTTTTTGTCGTTTTATTTTCAGTTTTAATCACAGTTTATA
131 ATGTTTCTTTTTTTTTTGTCGCTTTATTTTCAGTGTTAATCACAGTTTATA
4886301 CGATATTTTT
Statistics
Matches: 167, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
184 29 0.17
185 10 0.06
186 1 0.01
188 127 0.76
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.43
Consensus pattern (184 bp):
GATTGTTACCGACACACCATCCAAAAATCTTGCCTCGACTAATCTTGCTTACTGCATACTTTCTG
ATCTTCACAAGTTCGCCGTCACACCGGAGACGCCTCTCTTCTTTCTATCTCGTATCCTTTTTTGA
ATGTTTCTTTTTTTTTTGTCGCTTTATTTTCAGTGTTAATCACAGTTTATATAA
Found at i:4888978 original size:20 final size:20
Alignment explanation
Indices: 4888953--4888992 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4888943 TTTGTTTCCA
4888953 TTCAAAGTAGAAGCAAAGCT
1 TTCAAAGTAGAAGCAAAGCT
4888973 TTCAAAGTAGAAGCAAAGCT
1 TTCAAAGTAGAAGCAAAGCT
4888993 GTCATAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (20 bp):
TTCAAAGTAGAAGCAAAGCT
Found at i:4889484 original size:8 final size:8
Alignment explanation
Indices: 4889471--4889498 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4889461 AACCATATTG
4889471 TTGAATTA
1 TTGAATTA
4889479 TTGAATTA
1 TTGAATTA
4889487 TTGAATTA
1 TTGAATTA
4889495 TTGA
1 TTGA
4889499 TTCCCATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (8 bp):
TTGAATTA
Found at i:4896745 original size:105 final size:106
Alignment explanation
Indices: 4896563--4896768 Score: 315
Period size: 105 Copynumber: 2.0 Consensus size: 106
4896553 TCTACTTAAC
* *
4896563 TTTTTCTTCCTCTTAATGTTTTCTTCTCTTTCTAGTGTTTGGTTACGTATTATTTATCCGTAGTG
1 TTTTTCTTCCTCTTAATATTTTCTTCTCATTCTAGTGTTTGGTTACGTATTATTTATCCGTAGTG
* *
4896628 TCGAATGATATTTGCATATCATATGCTGTAACTCCTTACTT
66 TCGAATGATATTTGCAGATCATATGCCGTAACTCCTTACTT
* * * **
4896669 TTTTTCTTCCTCTTCATATTTT-TTCTCATTGTAGTGTTTGGTTATGTATTATTTATTTGTAGTG
1 TTTTTCTTCCTCTTAATATTTTCTTCTCATTCTAGTGTTTGGTTACGTATTATTTATCCGTAGTG
*
4896733 TTGAATGATATTTGCAGATCATATGCCGTAACTCCT
66 TCGAATGATATTTGCAGATCATATGCCGTAACTCCT
4896769 GTGTATGAAG
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
105 70 0.78
106 20 0.22
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.51
Consensus pattern (106 bp):
TTTTTCTTCCTCTTAATATTTTCTTCTCATTCTAGTGTTTGGTTACGTATTATTTATCCGTAGTG
TCGAATGATATTTGCAGATCATATGCCGTAACTCCTTACTT
Found at i:4897227 original size:44 final size:44
Alignment explanation
Indices: 4897178--4897268 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
4897168 ATAACATGAT
*
4897178 AATTATTTTTTTCATTGGTTTCATAAATTTTTAGGTATCTTTCC
1 AATTATTTTTTTCATTGGTTTCATAAATTTCTAGGTATCTTTCC
*
4897222 AATTATTTTTTTCATTGGTTTCATAAATTTCTAGGTATCTTTTC
1 AATTATTTTTTTCATTGGTTTCATAAATTTCTAGGTATCTTTCC
4897266 AAT
1 AAT
4897269 GGTAGCATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (44 bp):
AATTATTTTTTTCATTGGTTTCATAAATTTCTAGGTATCTTTCC
Found at i:4900045 original size:33 final size:30
Alignment explanation
Indices: 4899976--4900070 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 30
4899966 TATATTAATT
*
4899976 TAATTTTAAATTATTATTTATATAATAAAA
1 TAATTTTAAATTATTATTAATATAATAAAA
4900006 TAATTTTAAATTATAAATATTAATATAA-AAATA
1 TAATTTTAAATTAT---TATTAATATAATAAA-A
*
4900039 TTATTTTAATATTATT-TTAA-ATAATAAAA
1 TAATTTTAA-ATTATTATTAATATAATAAAA
4900068 TAA
1 TAA
4900071 AATATTTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
29 7 0.12
30 21 0.38
31 1 0.02
32 3 0.05
33 19 0.34
34 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATTTTAAATTATTATTAATATAATAAAA
Found at i:4901138 original size:14 final size:14
Alignment explanation
Indices: 4901116--4901146 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4901106 CTTATTATTA
4901116 ATTTCTTTTAAAAT
1 ATTTCTTTTAAAAT
*
4901130 ATTTTTTTTAAAAT
1 ATTTCTTTTAAAAT
4901144 ATT
1 ATT
4901147 AGTTTCTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTCTTTTAAAAT
Found at i:4902837 original size:21 final size:19
Alignment explanation
Indices: 4902804--4902845 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
4902794 TTTTTAAATT
*
4902804 TATATAAATAAAATATAAA
1 TATATAAATAAAAAATAAA
4902823 TATATAAATTAAAAAAATAAA
1 TATATAAA-T-AAAAAATAAA
4902844 TA
1 TA
4902846 AATATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TATATAAATAAAAAATAAA
Found at i:4903619 original size:21 final size:21
Alignment explanation
Indices: 4903581--4903624 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
4903571 AATATTTTTT
4903581 AATATTATTTTAAATAA-TAA
1 AATATTATTTTAAATAATTAA
4903601 AATA-TATATTTAAATTAATTAA
1 AATATTAT-TTTAAA-TAATTAA
4903623 AA
1 AA
4903625 AATCGTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.14
20 10 0.48
21 3 0.14
22 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATTATTTTAAATAATTAA
Found at i:4905169 original size:36 final size:36
Alignment explanation
Indices: 4905129--4905202 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
4905119 TCATACAAAG
4905129 AAAAAAATGGTGTGATTAAACTCCAAAAAGAGATCC
1 AAAAAAATGGTGTGATTAAACTCCAAAAAGAGATCC
4905165 AAAAAAATGGTGTGATTAAACTCCAAAAAGAGATCC
1 AAAAAAATGGTGTGATTAAACTCCAAAAAGAGATCC
4905201 AA
1 AA
4905203 CTGTACTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (36 bp):
AAAAAAATGGTGTGATTAAACTCCAAAAAGAGATCC
Found at i:4905925 original size:16 final size:17
Alignment explanation
Indices: 4905906--4905944 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
4905896 ATTTTAAGAG
4905906 ATATTTATATTTT-ATT
1 ATATTTATATTTTAATT
4905922 ATA-TTATATTTTAATT
1 ATATTTATATTTTAATT
4905938 AT-TTTAT
1 ATATTTAT
4905945 TCATATTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTTATATTTTAATT
Found at i:4905930 original size:15 final size:16
Alignment explanation
Indices: 4905910--4905944 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4905900 TAAGAGATAT
4905910 TTATATTTT-ATTATA
1 TTATATTTTAATTATA
*
4905925 TTATATTTTAATTATT
1 TTATATTTTAATTATA
4905941 TTAT
1 TTAT
4905945 TCATATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATTTTAATTATA
Found at i:4905945 original size:19 final size:20
Alignment explanation
Indices: 4905917--4905961 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4905907 TATTTATATT
* *
4905917 TTATTATATT-ATATTTTAA
1 TTATTTTATTCATATTCTAA
*
4905936 TTATTTTATTCATATTCTAT
1 TTATTTTATTCATATTCTAA
4905956 TTATTT
1 TTATTT
4905962 AATCATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTCATATTCTAA
Found at i:4905962 original size:19 final size:19
Alignment explanation
Indices: 4905916--4905969 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
4905906 ATATTTATAT
*
4905916 TTTATTATATT-ATATTTTA
1 TTTATT-TATTCATATTCTA
*
4905935 ATTATTTTATTCATATTCTA
1 TTTA-TTTATTCATATTCTA
*
4905955 TTTATTTAATCATAT
1 TTTATTTATTCATAT
4905970 ATAAAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATTTATTCATATTCTA
Found at i:4906509 original size:21 final size:22
Alignment explanation
Indices: 4906485--4906531 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
4906475 GATTAAGAGT
* *
4906485 ATTTTGAATTTAAATT-ATTAA
1 ATTTTAAAATTAAATTAATTAA
*
4906506 ATTTTAAAATTAAATTAATTTA
1 ATTTTAAAATTAAATTAATTAA
4906528 ATTT
1 ATTT
4906532 CAATCAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTAAAATTAAATTAATTAA
Found at i:4907193 original size:2 final size:2
Alignment explanation
Indices: 4907186--4907223 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4907176 TAACTTGCAC
*
4907186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4907224 TCTACCTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4914085 original size:2 final size:2
Alignment explanation
Indices: 4914078--4914110 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4914068 TAATAAATAA
4914078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4914111 AAGAGAACCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4920571 original size:16 final size:16
Alignment explanation
Indices: 4920552--4920594 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
4920542 TTATAATATA
**
4920552 TAAATTTAAATTATTT
1 TAAATTTAAATTAACT
*
4920568 TAAATTTAATTTAACT
1 TAAATTTAAATTAACT
4920584 TAAATTTAAAT
1 TAAATTTAAAT
4920595 AAAATTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATTTAAATTAACT
Found at i:4920589 original size:11 final size:11
Alignment explanation
Indices: 4920552--4920607 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
4920542 TTATAATATA
4920552 TAAATTTAAAT
1 TAAATTTAAAT
*
4920563 T-ATTTTAAAT
1 TAAATTTAAAT
* *
4920573 TTAATTTAACT
1 TAAATTTAAAT
4920584 TAAATTTAAAT
1 TAAATTTAAAT
*
4920595 AAAATTTAAAT
1 TAAATTTAAAT
4920606 TA
1 TA
4920608 TAATAACACT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
10 9 0.24
11 28 0.76
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:4921054 original size:10 final size:10
Alignment explanation
Indices: 4921009--4921108 Score: 69
Period size: 10 Copynumber: 9.9 Consensus size: 10
4920999 TTAGTTGTGA
*
4921009 ATAAATCTAT
1 ATAAATATAT
*
4921019 TTAAATATAT
1 ATAAATATAT
*
4921029 CA-AAAGTATGT
1 -ATAAA-TATAT
4921040 ATAAATATAT
1 ATAAATATAT
4921050 ATAAATATATT
1 ATAAATATA-T
** *
4921061 ATGTACATAT
1 ATAAATATAT
4921071 ATAAATATAT
1 ATAAATATAT
* *
4921081 TTAAATGTAT
1 ATAAATATAT
**
4921091 A-ATTTATAT
1 ATAAATATAT
4921100 ATAAATATA
1 ATAAATATA
4921109 AATTATAAAT
Statistics
Matches: 66, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
9 6 0.09
10 46 0.70
11 14 0.21
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (10 bp):
ATAAATATAT
Found at i:4921074 original size:31 final size:29
Alignment explanation
Indices: 4921039--4921108 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
4921029 CAAAAGTATG
*
4921039 TATAAATATATATAAATATATTATGTACATA
1 TATAAATATATATAAATATATAAT-T-CATA
* * *
4921070 TATAAATATATTTAAATGTATAATTTATA
1 TATAAATATATATAAATATATAATTCATA
4921099 TATAAATATA
1 TATAAATATA
4921109 AATTATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 13 0.37
30 1 0.03
31 21 0.60
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (29 bp):
TATAAATATATATAAATATATAATTCATA
Found at i:4922950 original size:3 final size:3
Alignment explanation
Indices: 4922942--4922983 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
4922932 ACCCATTAGA
4922942 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4922984 CTTTGGCTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4923444 original size:41 final size:41
Alignment explanation
Indices: 4923399--4923555 Score: 102
Period size: 44 Copynumber: 4.0 Consensus size: 41
4923389 TTTAATTAAC
4923399 TTTAAAAAATTTACATTAATAAATTAAAATATTAATTATTT
1 TTTAAAAAATTTACATTAATAAATTAAAATATTAATTATTT
* * * * *
4923440 TTTAAAATAAAAATTAAATTAAAAAAGGTT-TATTATT-ATTATTT
1 TTT--AA-AAAATTTACATTAATAAA--TTAAAATATTAATTATTT
* * **
4923484 TTT-AATAA---A-ATTAA-AAA-TAATAT-TTAATTA-AG
1 TTTAAAAAATTTACATTAATAAATTAAAATATTAATTATTT
*
4923516 TTTAAAAATTTTACATTAATAAATTAAAATATTAATTATT
1 TTTAAAAAATTTACATTAATAAATTAAAATATTAATTATT
4923556 ATGGTTTTTA
Statistics
Matches: 85, Mismatches: 15, Indels: 32
0.64 0.11 0.24
Matches are distributed among these distances:
32 6 0.07
33 8 0.09
35 3 0.04
36 6 0.07
37 6 0.07
38 3 0.04
39 5 0.06
40 10 0.12
41 4 0.05
43 2 0.02
44 25 0.29
45 5 0.06
46 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (41 bp):
TTTAAAAAATTTACATTAATAAATTAAAATATTAATTATTT
Found at i:4927364 original size:22 final size:20
Alignment explanation
Indices: 4927337--4927390 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
4927327 TATAGATAAT
4927337 AAAATAAAAAATAAATTTCATA
1 AAAATAAAAAATAAATTT--TA
*
4927359 AAAATAAATTAAATTAATTTTA
1 AAAATAAA--AAATAAATTTTA
4927381 AAAATAAAAA
1 AAAATAAAAA
4927391 TAAGTTAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 2 0.07
22 18 0.62
24 9 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATAAAAAATAAATTTTA
Found at i:4927439 original size:23 final size:21
Alignment explanation
Indices: 4927336--4927442 Score: 58
Period size: 23 Copynumber: 4.9 Consensus size: 21
4927326 TTATAGATAA
* *
4927336 TAAAATAAAAAA-TAAATTTCA
1 TAAAA-AAAAAATTAAATTACT
* *
4927357 T-AAAAATAAATTAAATTAATTT
1 TAAAAAAAAAATTAAATT-A-CT
* *
4927379 TAAAAATAAAAA-TAAGTTAGATT
1 TAAAAA-AAAAATTAAATT--ACT
*
4927402 TAAAAAAAAATTTAAATTACT
1 TAAAAAAAAAATTAAATTACT
4927423 TAAAAAAATTAAATTAAATT
1 TAAAAAAA--AAATTAAATT
4927443 TATATAATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
19 5 0.08
20 9 0.14
21 11 0.17
22 5 0.08
23 31 0.47
24 5 0.08
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAAAAAAAATTAAATTACT
Found at i:4927821 original size:105 final size:110
Alignment explanation
Indices: 4927710--4927909 Score: 247
Period size: 104 Copynumber: 1.9 Consensus size: 110
4927700 ATTAAATATT
* * *
4927710 ATTTTTAATTTTATAAAA-AA-TAATAATTGATATATTATTTAT-TAAATTTTTTA-AA-T-TTA
1 ATTTTTTATTTTAAAAAATAATTAATAATTGA-AT-TTATTAATATAAATTTTTTATAATTATTA
4927769 AATA-ATTTTATTA-AAAAATAATAA-TAATAAACCCTTTTTAATTTA
64 AATATATTTT-TTATAAAAATAATAATTAATAAACCCTTTTTAATTTA
* *
4927814 ATTTTTTATTTTAAAAAATAATTAATATTTTAATTTATTAATATAAATTTTTTATAATTAATTAA
1 ATTTTTTATTTTAAAAAATAATTAATAATTGAATTTATTAATATAAATTTTTTATAATT-ATTAA
4927879 ATATATTTTTTATTAAAAATAATAATTAATA
65 ATATATTTTTTA-TAAAAATAATAATTAATA
4927910 TATTATTATT
Statistics
Matches: 80, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
104 23 0.29
105 15 0.19
106 10 0.12
107 1 0.01
109 10 0.12
110 5 0.06
111 11 0.14
112 5 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (110 bp):
ATTTTTTATTTTAAAAAATAATTAATAATTGAATTTATTAATATAAATTTTTTATAATTATTAAA
TATATTTTTTATAAAAATAATAATTAATAAACCCTTTTTAATTTA
Found at i:4927890 original size:23 final size:24
Alignment explanation
Indices: 4927844--4927891 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
4927834 ATTAATATTT
*
4927844 TAATTTATTAATATAAATTTTTTA
1 TAATTAATTAATATAAATTTTTTA
*
4927868 TAATTAATTAA-ATATATTTTTTA
1 TAATTAATTAATATAAATTTTTTA
4927891 T
1 T
4927892 TAAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATTAATTAATATAAATTTTTTA
Found at i:4927893 original size:20 final size:19
Alignment explanation
Indices: 4927847--4927894 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
4927837 AATATTTTAA
4927847 TTTATTAATATAAATTTTT
1 TTTATTAATATAAATTTTT
*
4927866 TATAATTAAT-TAAATATATTT
1 T-TTATTAATATAAAT-T-TTT
4927887 TTTATTAA
1 TTTATTAA
4927895 AAATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 6 0.25
20 14 0.58
21 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTATTAATATAAATTTTT
Found at i:4927941 original size:66 final size:69
Alignment explanation
Indices: 4927814--4927944 Score: 182
Period size: 69 Copynumber: 1.9 Consensus size: 69
4927804 TTTTAATTTA
* *
4927814 ATTTTTTATTTTAAAAAATAATTAATATTTTAATTTATTAATATAAATTTTTTATAATTAATTAA
1 ATTTTTTATTTAAAAAAATAATTAATATATTAATTTATTAATATAAATTTTTTATAATTAATTAA
4927879 ATAT
66 ATAT
*
4927883 ATTTTTTA-TTAAAAATAATAATTAATATATT-A-TTATTTAT-TAAATTTTTTA-AATTTAATT
1 ATTTTTTATTTAAAAA-AATAATTAATATATTAATTTATTAATATAAATTTTTTATAA-TTAATT
4927943 AA
64 AA
4927945 TTTATAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
65 2 0.04
66 19 0.33
67 7 0.12
68 7 0.12
69 22 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (69 bp):
ATTTTTTATTTAAAAAAATAATTAATATATTAATTTATTAATATAAATTTTTTATAATTAATTAA
ATAT
Found at i:4928999 original size:14 final size:14
Alignment explanation
Indices: 4928982--4929041 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
4928972 TTTATATAAT
4928982 TATATTTTATTTTA
1 TATATTTTATTTTA
*
4928996 TATATTTTATTATA
1 TATATTTTATTTTA
* *
4929010 TTATAATTATATTTAA
1 -TAT-ATTTTATTTTA
*
4929026 AATATTTTATATTTA
1 TATATTTTAT-TTTA
4929041 T
1 T
4929042 TTAAAATTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
14 19 0.54
15 8 0.23
16 8 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATTTTATTTTA
Found at i:4929030 original size:20 final size:20
Alignment explanation
Indices: 4929007--4929058 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4928997 ATATTTTATT
4929007 ATATTATA-ATTATATTTAAA
1 ATATTATATATT-TATTTAAA
*
4929027 ATATTTTATATTTATTTAAA
1 ATATTATATATTTATTTAAA
4929047 AT-TTGATATATT
1 ATATT-ATATATT
4929059 AGTAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATATTATATATTTATTTAAA
Found at i:4929031 original size:30 final size:30
Alignment explanation
Indices: 4928967--4929035 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
4928957 AGTTGGATTT
* * *
4928967 AATAATTTA-TATAATTATATTTTATTTTA
1 AATATTTTATTATAATTATATTATATTTAA
*
4928996 TATATTTTATTAT-ATTATAATTATATTTAA
1 AATATTTTATTATAATTAT-ATTATATTTAA
4929026 AATATTTTAT
1 AATATTTTAT
4929036 ATTTATTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
AATATTTTATTATAATTATATTATATTTAA
Found at i:4929069 original size:49 final size:48
Alignment explanation
Indices: 4929001--4929113 Score: 124
Period size: 49 Copynumber: 2.3 Consensus size: 48
4928991 TTTTATATAT
4929001 TTTATTATATTATAA-TTATATT-TAAAATATTTTATATTTAT-TTAAAA
1 TTTA-TATATTATAATTTATATTATAAAA-ATTTTATATTTATATTAAAA
* * *
4929048 TTTGATATATTAGTAATTTATATTATATAAATTTTATTTTTATATTAATA
1 TTT-ATATATTA-TAATTTATATTATAAAAATTTTATATTTATATTAAAA
*
4929098 TTTATATTTTAATAAT
1 TTTATATATT-ATAAT
4929114 ATTTTCATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
47 10 0.18
48 4 0.07
49 29 0.52
50 13 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (48 bp):
TTTATATATTATAATTTATATTATAAAAATTTTATATTTATATTAAAA
Found at i:4929092 original size:17 final size:18
Alignment explanation
Indices: 4929070--4929123 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
4929060 GTAATTTATA
4929070 TTATATAAATTTTAT-TT
1 TTATATAAATTTTATATT
*
4929087 TTATATTAATATTTATATT
1 TTATATAAAT-TTTATATT
4929106 TTA-ATAATATTTTCATAT
1 TTATATAA-ATTTT-ATAT
4929124 CATATTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 9 0.29
18 11 0.35
19 11 0.35
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATAAATTTTATATT
Done.