Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold189
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: 2243555
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:557678 original size:12 final size:12
Alignment explanation
Indices: 557661--557699 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
557651 AAAAATTATG
557661 TATTTATATTTT
1 TATTTATATTTT
*
557673 TATTTATATTTA
1 TATTTATATTTT
*
557685 TATTTTTATTATT
1 TATTTATATT-TT
557698 TA
1 TA
557700 AAGTATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:557766 original size:35 final size:37
Alignment explanation
Indices: 557723--557818 Score: 99
Period size: 35 Copynumber: 2.6 Consensus size: 37
557713 TTATATAATA
557723 TTTA-TTTATTTTATATTTTTA-TATTCTTA-TCATG
1 TTTATTTTATTTTATATTTTTATTATTCTTAGTCATG
* * * *
557757 TTTATTTTATATTATATTTTAATTATTTTTATGTCGTG
1 TTTATTTTATTTTATATTTTTATTATTCTTA-GTCATG
*
557795 TTTATATTATATTTTATATATTTA
1 TTTAT-TT-TATTTTATATTTTTA
557819 AAATATTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
34 4 0.08
35 15 0.31
36 7 0.14
38 9 0.18
39 2 0.04
40 12 0.24
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (37 bp):
TTTATTTTATTTTATATTTTTATTATTCTTAGTCATG
Found at i:559401 original size:17 final size:16
Alignment explanation
Indices: 559373--559416 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
559363 AATTTAAATA
559373 AATAAAA-T-ATTTTT
1 AATAAAATTAATTTTT
559387 AATAAAATTTAATTTTT
1 AATAAAA-TTAATTTTT
*
559404 ATTAAAATTAATT
1 AATAAAATTAATT
559417 AAAAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.27
16 7 0.27
17 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATAAAATTAATTTTT
Found at i:560212 original size:16 final size:16
Alignment explanation
Indices: 560169--560217 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
560159 CATTTATTAA
*
560169 ATTTATCAATTAAATTT
1 ATTTATAAATTAAA-TT
*
560186 ATTTAAAAATTAAATT
1 ATTTATAAATTAAATT
* *
560202 ATTTATTAATTTAATT
1 ATTTATAAATTAAATT
560218 TAAATTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATAAATTAAATT
Found at i:560226 original size:16 final size:17
Alignment explanation
Indices: 560207--560245 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
560197 AAATTATTTA
560207 TTAATTTAA-TTTAAAT
1 TTAATTTAATTTTAAAT
560223 TTAA-TTAATTTTAAAT
1 TTAATTTAATTTTAAAT
*
560239 ATAATTT
1 TTAATTT
560246 TTTTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 4 0.20
16 14 0.70
17 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTTAATTTTAAAT
Found at i:560431 original size:19 final size:17
Alignment explanation
Indices: 560406--560455 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
560396 ATTCAATGTT
560406 AATAAATTAATATATTA
1 AATAAATTAATATATTA
560423 ATCATAAA-TAA-AT-TTA
1 A--ATAAATTAATATATTA
560439 AATAAATTAAATATATT
1 AATAAATT-AATATATT
560456 TTCTCAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
14 5 0.19
15 1 0.04
16 6 0.22
17 5 0.19
18 5 0.19
19 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAAATTAATATATTA
Found at i:563969 original size:21 final size:20
Alignment explanation
Indices: 563922--563969 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
563912 GTTCTGTAAA
563922 AAAAAATTTAAATTATTTTT
1 AAAAAATTTAAATTATTTTT
* *
563942 TATAAATTTAAAATTATTTTT
1 AAAAAATTT-AAATTATTTTT
563963 AAAAAAT
1 AAAAAAT
563970 AATATTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAAAATTTAAATTATTTTT
Found at i:563983 original size:16 final size:16
Alignment explanation
Indices: 563964--563994 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
563954 ATTATTTTTA
*
563964 AAAAATAATATTTAAT
1 AAAAATAAAATTTAAT
563980 AAAAATAAAATTTAA
1 AAAAATAAAATTTAA
563995 ATTTCAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATAAAATTTAAT
Found at i:569704 original size:23 final size:23
Alignment explanation
Indices: 569667--569795 Score: 79
Period size: 23 Copynumber: 5.6 Consensus size: 23
569657 TAATTATGTA
* *
569667 AATATTTTATTTATAAAATATTT
1 AATATTTAATATATAAAATATTT
* *
569690 AATATTTAATATATATAAT-TTA
1 AATATTTAATATATAAAATATTT
*
569712 AAT-TTTATATAATATAAATTA-TT
1 AATATTTA-AT-ATATAAAATATTT
* * *
569735 AATATATTAAAATTTAAAATA-TA
1 AATAT-TTAATATATAAAATATTT
*
569758 AATTATTTAAATATAATAAAATATAT
1 AA-TATTT-AATAT-ATAAAATATTT
*
569784 AA-ATATAATATA
1 AATATTTAATATA
569796 AATTTATAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
21 4 0.05
22 8 0.10
23 45 0.56
24 12 0.15
25 10 0.12
26 2 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATATTTAATATATAAAATATTT
Found at i:569710 original size:21 final size:21
Alignment explanation
Indices: 569678--569752 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
569668 ATATTTTATT
*
569678 TATAAAAT-ATTTAATATTTAA
1 TATAATATAATTTAA-ATTTAA
*
569699 TAT-ATATAATTTAAATTTTA
1 TATAATATAATTTAAATTTAA
*
569719 TATAATATAAATT--A-TTAA
1 TATAATATAATTTAAATTTAA
* *
569737 TATATTAAAATTTAAA
1 TATAATATAATTTAAA
569753 ATATAAATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
18 13 0.30
19 1 0.02
20 12 0.28
21 17 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATAATATAATTTAAATTTAA
Found at i:569719 original size:39 final size:39
Alignment explanation
Indices: 569676--569752 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
569666 AAATATTTTA
* *
569676 TTTATAAAATATTTAA-TATTTAATATA-TATAATTTAAAT
1 TTTATAAAATA-TAAATTA-TTAATATATTAAAATTTAAAT
*
569715 TTTATATAATATAAATTATTAATATATTAAAATTTAAA
1 TTTATAAAATATAAATTATTAATATATTAAAATTTAAA
569753 ATATAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 11 0.33
39 22 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (39 bp):
TTTATAAAATATAAATTATTAATATATTAAAATTTAAAT
Found at i:569739 original size:18 final size:18
Alignment explanation
Indices: 569702--569799 Score: 79
Period size: 16 Copynumber: 5.8 Consensus size: 18
569692 TATTTAATAT
*
569702 ATATAATTTAAATT-TT-
1 ATATAATATAAATTATTA
569718 ATATAATATAAATTATTA
1 ATATAATATAAATTATTA
569736 ATAT-AT-TAAA--ATT-
1 ATATAATATAAATTATTA
*
569749 -TAAAATATAAATTATTTAA
1 ATATAATATAAATTA-TT-A
*
569768 ATATAATA-AAATATATAA
1 ATATAATATAAAT-TATTA
569786 ATATAATATAAATT
1 ATATAATATAAATT
569800 TATAAACTAT
Statistics
Matches: 66, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
12 2 0.03
13 2 0.03
14 7 0.11
16 18 0.27
17 6 0.09
18 14 0.21
19 9 0.14
20 8 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATATAAATTATTA
Found at i:569745 original size:32 final size:33
Alignment explanation
Indices: 569709--569791 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 33
569699 TATATATAAT
*
569709 TTAAATTTTATATAATATAAATTA-TT-AATATA
1 TTAAAATTTATA-AATATAAATTATTTAAATATA
569741 TTAAAATTTA-AAATATAAATTATTTAAATATA
1 TTAAAATTTATAAATATAAATTATTTAAATATA
* *
569773 ATAAAATATATAAATATAA
1 TTAAAATTTATAAATATAA
569792 TATAAATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.24
31 3 0.07
32 23 0.51
33 8 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
TTAAAATTTATAAATATAAATTATTTAAATATA
Found at i:569758 original size:30 final size:33
Alignment explanation
Indices: 569717--569791 Score: 104
Period size: 30 Copynumber: 2.4 Consensus size: 33
569707 ATTTAAATTT
*
569717 TATAT-AATATAAATTA-TT-AATATATTAAAA
1 TATATAAATATAAATTATTTAAATATAATAAAA
*
569747 TTTA-AAATATAAATTATTTAAATATAATAAAA
1 TATATAAATATAAATTATTTAAATATAATAAAA
569779 TATATAAATATAA
1 TATATAAATATAA
569792 TATAAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 14 0.37
31 2 0.05
32 14 0.37
33 8 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TATATAAATATAAATTATTTAAATATAATAAAA
Found at i:569760 original size:46 final size:47
Alignment explanation
Indices: 569678--569816 Score: 113
Period size: 46 Copynumber: 2.8 Consensus size: 47
569668 ATATTTTATT
* * * * *
569678 TATAAAATATTTAATAT-TTAATATATATAATTTAAATTTT-ATATAA
1 TATAAATTA-TTAATATATTAAAATTTAAAATATAAATTTTAATATAA
569724 TATAAATTATTAATATATTAAAATTTAAAATATAAATTATTTAAATATAA
1 TATAAATTATTAATATATTAAAATTTAAAATATAAA-T-TTT-AATATAA
* *
569774 TA-AAATATATAAATATAATATAAATTTATAAACTATTAAATTT
1 TATAAAT-TATTAATATATTA-AAATTTA-AAA-TA-TAAATTT
569817 ACCGTAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
45 7 0.09
46 23 0.30
47 1 0.01
48 3 0.04
49 4 0.05
50 19 0.25
51 7 0.09
52 5 0.07
53 3 0.04
54 4 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (47 bp):
TATAAATTATTAATATATTAAAATTTAAAATATAAATTTTAATATAA
Found at i:569769 original size:39 final size:39
Alignment explanation
Indices: 569678--569769 Score: 91
Period size: 39 Copynumber: 2.4 Consensus size: 39
569668 ATATTTTATT
* * *
569678 TATAAAATATTT-AA-TATTTAATATATATAATTTAAAT
1 TATAAATTATTTAAATTATTTAATATATAAAATTTAAAA
* * * *
569715 TTTATATAATATAAATTA-TTAATATATTAAAATTTAAAA
1 TATAAATTATTTAAATTATTTAATATA-TAAAATTTAAAA
569754 TATAAATTATTTAAAT
1 TATAAATTATTTAAAT
569770 ATAATAAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
37 7 0.17
38 10 0.24
39 24 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (39 bp):
TATAAATTATTTAAATTATTTAATATATAAAATTTAAAA
Found at i:571311 original size:19 final size:18
Alignment explanation
Indices: 571289--571324 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
571279 ATTTTAATAT
*
571289 TTGTAATTATTTTTTTTAG
1 TTGTAATT-TTTTATTTAG
571308 TTGTAATTTTTTATTTA
1 TTGTAATTTTTTATTTA
571325 AAAAATCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (18 bp):
TTGTAATTTTTTATTTAG
Found at i:572642 original size:13 final size:13
Alignment explanation
Indices: 572624--572650 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
572614 CTATGTAGAA
572624 TCTTTAAAATTAC
1 TCTTTAAAATTAC
572637 TCTTTAAAATTAC
1 TCTTTAAAATTAC
572650 T
1 T
572651 TAGAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TCTTTAAAATTAC
Found at i:574563 original size:22 final size:23
Alignment explanation
Indices: 574530--574575 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
574520 GTTTTAGAAA
574530 TAGATATATGAAGGGTTTTTTAT
1 TAGATATATGAAGGGTTTTTTAT
574553 TAGA-ATATGAAGGGTTTTTTAT
1 TAGATATATGAAGGGTTTTTTAT
574575 T
1 T
574576 TTATAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (23 bp):
TAGATATATGAAGGGTTTTTTAT
Found at i:576258 original size:19 final size:20
Alignment explanation
Indices: 576225--576289 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 20
576215 TAAAATTTAT
* *
576225 TAAAAAGATATTTTTATATG
1 TAAAAATATAATTTTATATG
* *
576245 TAAAAATA-AATTTTAAATT
1 TAAAAATATAATTTTATATG
**
576264 TAAAAATATAATAATATATG
1 TAAAAATATAATTTTATATG
576284 -AAAAAT
1 TAAAAAT
576290 CAACGATCCA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 22 0.61
20 14 0.39
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATATAATTTTATATG
Found at i:577154 original size:17 final size:18
Alignment explanation
Indices: 577120--577162 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
577110 TTTATTATAA
577120 TTATATTTA-AAAATATT
1 TTATATTTATAAAATATT
*
577137 TTATATTTATATAA-ATT
1 TTATATTTATAAAATATT
577154 TTAT-TTTAT
1 TTATATTTAT
577163 TGATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 16 0.67
18 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTTATAAAATATT
Found at i:577187 original size:14 final size:14
Alignment explanation
Indices: 577143--577203 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
577133 TATTTTATAT
*
577143 TTATATAAATTTTA
1 TTATATTAATTTTA
*
577157 TTTTATTGATTATTTTA
1 TTATATT-A--ATTTTA
577174 TTATATTAATTTTA
1 TTATATTAATTTTA
**
577188 AAATATTAATTTTA
1 TTATATTAATTTTA
577202 TT
1 TT
577204 TTTTATTATG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
14 23 0.62
15 1 0.03
16 1 0.03
17 12 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATATTAATTTTA
Found at i:577870 original size:32 final size:33
Alignment explanation
Indices: 577798--577870 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
577788 TAAAATAAAA
*
577798 ATATATATTTGATATAAGTATTAATTTAATTTT
1 ATATATATTTAATATAAGTATTAATTTAATTTT
* *
577831 TTAATATATTTAATA-AATTA-TAATTTAATATTT
1 AT-ATATATTTAATATAAGTATTAATTTAAT-TTT
577864 ATATATA
1 ATATATA
577871 AATATTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
32 14 0.41
33 9 0.26
34 11 0.32
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (33 bp):
ATATATATTTAATATAAGTATTAATTTAATTTT
Found at i:578280 original size:31 final size:32
Alignment explanation
Indices: 578223--578422 Score: 143
Period size: 28 Copynumber: 6.3 Consensus size: 32
578213 CAAAAGTAAA
*
578223 ATTTATTATTTAAGATAAATATAATTTTAATT
1 ATTTATTATTTAAAATAAATATAATTTTAATT
578255 ATTTATT-TTTAAAAATAAATA-AATTTTAATT
1 ATTTATTATTT-AAAATAAATATAATTTTAATT
* **
578286 A---A-TATTCAATGTAAATATAATTTT-ATT
1 ATTTATTATTTAAAATAAATATAATTTTAATT
* *
578313 A--AAAT-TTTAAATATAAATATAA-TTTAATAT
1 ATTTATTATTTAAA-ATAAATATAATTTTAAT-T
* * *
578343 TTTTAGTTATTATTCAATATAAATATAATTTTATTTAT
1 ATTTA-TTA-T-TT-AAAATAAATATAATTTTA-AT-T
*
578381 ATTTATTATTTAATATAAATATAATTTTTAATT
1 ATTTATTATTTAAAATAAATATAA-TTTTAATT
578414 ATTTATTAT
1 ATTTATTAT
578423 ATATATATAC
Statistics
Matches: 136, Mismatches: 14, Indels: 35
0.74 0.08 0.19
Matches are distributed among these distances:
27 13 0.10
28 17 0.12
29 12 0.09
30 1 0.01
31 14 0.10
32 17 0.12
33 11 0.08
34 14 0.10
35 8 0.06
36 13 0.10
37 9 0.07
38 7 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
ATTTATTATTTAAAATAAATATAATTTTAATT
Found at i:578387 original size:34 final size:33
Alignment explanation
Indices: 578225--578422 Score: 150
Period size: 34 Copynumber: 6.2 Consensus size: 33
578215 AAAGTAAAAT
* * *
578225 TTATTATTTAAGATAAATATAATTTTAATTAT-
1 TTATTATTCAATATAAATATAATTTTATTTATA
* * *
578257 TTATTTTTAAAAATAAATA-AA---T-TTTA-A
1 TTATTATTCAATATAAATATAATTTTATTTATA
* *
578284 TTAATATTCAATGTAAATATAATTTTA-TTA-A
1 TTATTATTCAATATAAATATAATTTTATTTATA
* * *
578315 -AATT-TTAAATATAAATATAATTTAATATTTTTA
1 TTATTATTCAATATAAATATAATTT--TATTTATA
578348 GTTATTATTCAATATAAATATAATTTTATTTATA
1 -TTATTATTCAATATAAATATAATTTTATTTATA
* *
578382 TTTATTATTTAATATAAATATAATTTTTAATTAT-
1 -TTATTATTCAATATAAATATAA-TTTTATTTATA
578416 TTATTAT
1 TTATTAT
578423 ATATATATAC
Statistics
Matches: 132, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
27 17 0.13
28 3 0.02
29 17 0.13
30 2 0.02
31 9 0.07
32 18 0.14
33 8 0.06
34 28 0.21
35 12 0.09
36 18 0.14
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (33 bp):
TTATTATTCAATATAAATATAATTTTATTTATA
Found at i:578410 original size:18 final size:18
Alignment explanation
Indices: 578358--578412 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
578348 GTTATTATTC
578358 AATATAAATATAA-TTTT
1 AATATAAATATAATTTTT
* * *
578375 -ATTTATAT-TTATTATTT
1 AATATAAATATAATT-TTT
578392 AATATAAATATAATTTTT
1 AATATAAATATAATTTTT
578410 AAT
1 AAT
578413 TATTTATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 7
0.68 0.15 0.17
Matches are distributed among these distances:
15 2 0.07
16 7 0.25
17 3 0.11
18 12 0.43
19 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATAAATATAATTTTT
Found at i:578431 original size:34 final size:34
Alignment explanation
Indices: 578322--578445 Score: 114
Period size: 34 Copynumber: 3.6 Consensus size: 34
578312 TAAAATTTTA
*
578322 AATATAAATATAA--TTTAATATTTTTAGTTATTATT
1 AATATAAATATAATTTTTAATATATTTA-TTA-TA-T
* *
578357 CAATATAAATATAA-TTTTATTTATATTTATTATTT
1 -AATATAAATATAATTTTTA-ATATATTTATTATAT
578392 AATATAAATATAATTTTTAAT-TATTTATTATAT
1 AATATAAATATAATTTTTAATATATTTATTATAT
*
578425 ATATATACATA-AATATTTTAA
1 A-ATATAAATATAAT-TTTTAA
578446 CCAAATATCT
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
33 15 0.19
34 28 0.36
35 6 0.08
36 14 0.18
37 7 0.09
38 7 0.09
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (34 bp):
AATATAAATATAATTTTTAATATATTTATTATAT
Found at i:579823 original size:22 final size:20
Alignment explanation
Indices: 579775--579828 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
579765 TTCATCCAAT
*
579775 TAATTTAAAAATTAATATTAA
1 TAATTT-AAAATTAATACTAA
579796 TAAATTTAAAATTCAAATACTAA
1 T-AATTTAAAATT--AATACTAA
579819 TAA-TTAAAAT
1 TAATTTAAAAT
579829 CATTTTCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 14 0.48
22 7 0.24
23 8 0.28
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTTAAAATTAATACTAA
Found at i:583129 original size:21 final size:21
Alignment explanation
Indices: 583058--583131 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
583048 TAATTACTCG
*
583058 TTAAAATTATATAAAAAGTTA
1 TTAAAATCATATAAAAAGTTA
* * *
583079 TTAAAATAATATTAAAAGCTA
1 TTAAAATCATATAAAAAGTTA
*
583100 TTAATATCATATAAAAAGTTA
1 TTAAAATCATATAAAAAGTTA
*
583121 TCAAAATCATA
1 TTAAAATCATA
583132 GATTATATTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (21 bp):
TTAAAATCATATAAAAAGTTA
Found at i:583938 original size:2 final size:2
Alignment explanation
Indices: 583931--583957 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
583921 ATGTGTAATT
583931 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 T
583958 TTAGGGTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:584809 original size:78 final size:78
Alignment explanation
Indices: 584710--584976 Score: 261
Period size: 78 Copynumber: 3.4 Consensus size: 78
584700 AAAATTTTTA
* *
584710 ATCATTTCAAGTTAAATCAAATCTTATAAAATT-ATAAAATTTCATAATATACATTTTATCCAAA
1 ATCATTTCAAGTTAAATCAAATCTTAAAAAATTAATAAAATTTCAT-ATATACATCTTATCCAAA
*
584774 GCAAAAAAAATTAT
65 ACAAAAAAAATTAT
* * * * * * *
584788 ATTATTTCAAATTGAATCAAATCTTAAAAAATTAATAAATTTTTATGTGTACATCTTATCCAAAA
1 ATCATTTCAAGTTAAATCAAATCTTAAAAAATTAATAAAATTTCATATATACATCTTATCCAAAA
*
584853 CAAGAAAAATTAT
66 CAAAAAAAATTAT
* * * * ** *
584866 ATCATTTCGAGTTAAATCAAATCTTAAAATATCACA-AAACTTTCATGA-ACGCACCTTATCCAA
1 ATCATTTCAAGTTAAATCAAATCTTAAAAAATTA-ATAAAATTTCAT-ATATACATCTTATCCAA
*
584929 AACAAAAAAAAATTAC
64 AAC-AAAAAAAATTAT
* * * * *
584945 GTCATTTTAAATTAAATTAAATTTTAAAAAAT
1 ATCATTTCAAGTTAAATCAAATCTTAAAAAAT
584977 CACAAAAAAC
Statistics
Matches: 152, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
78 106 0.70
79 46 0.30
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (78 bp):
ATCATTTCAAGTTAAATCAAATCTTAAAAAATTAATAAAATTTCATATATACATCTTATCCAAAA
CAAAAAAAATTAT
Found at i:594575 original size:2 final size:2
Alignment explanation
Indices: 594568--594599 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
594558 TCTTCATTAA
594568 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
594600 TTTACTCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:596437 original size:19 final size:19
Alignment explanation
Indices: 596406--596445 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
596396 TCAAGTTACC
596406 TATTTAAATTT-AAAGATT
1 TATTTAAATTTAAAAGATT
596424 TATTTAATATTTAAAAGATT
1 TATTTAA-ATTTAAAAGATT
596444 TA
1 TA
596446 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TATTTAAATTTAAAAGATT
Found at i:598135 original size:12 final size:12
Alignment explanation
Indices: 598118--598147 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
598108 ACGTGTTGGA
*
598118 AATTTTATTTTT
1 AATTTTATATTT
598130 AATTTTATATTT
1 AATTTTATATTT
598142 AATTTT
1 AATTTT
598148 GGACATTGGG
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
AATTTTATATTT
Found at i:598357 original size:3 final size:3
Alignment explanation
Indices: 598351--598392 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
598341 AAGGATGATG
*
598351 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA CTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT
598393 CATCCAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:617550 original size:21 final size:21
Alignment explanation
Indices: 617511--617551 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
617501 CCTTAATTAA
*
617511 AATATAATATAAAATATTATT
1 AATATAATATAAAACATTATT
617532 AATATAATA-AATAACATTAT
1 AATATAATATAA-AACATTAT
617552 ATACAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATAATATAAAACATTATT
Found at i:617671 original size:19 final size:18
Alignment explanation
Indices: 617625--617673 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
617615 AAAAATATAA
*
617625 AATATAA-TTGTAA-TAT
1 AATATAATTTATAACTAT
*
617641 AATATTATTTATAACTAT
1 AATATAATTTATAACTAT
617659 AATATAAATTTATAA
1 AATAT-AATTTATAA
617674 ATTAAAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 6 0.22
17 5 0.19
18 8 0.30
19 8 0.30
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AATATAATTTATAACTAT
Found at i:618502 original size:16 final size:17
Alignment explanation
Indices: 618483--618518 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
618473 ATTTTTTCTC
*
618483 TTTCAAT-TTTTTATTT
1 TTTCAATATTTTCATTT
618499 TTTCAATATTTTCATTT
1 TTTCAATATTTTCATTT
618516 TTT
1 TTT
618519 AAGTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCAATATTTTCATTT
Found at i:618709 original size:18 final size:19
Alignment explanation
Indices: 618686--618726 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
618676 TATTATTTTT
*
618686 TAATATATTTAAT-AAAAA
1 TAATATATTAAATAAAAAA
618704 TAATATATTAAATAAAAAA
1 TAATATATTAAATAAAAAA
618723 TAAT
1 TAAT
618727 TAATTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATATATTAAATAAAAAA
Found at i:619335 original size:22 final size:20
Alignment explanation
Indices: 619305--619344 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
619295 ATAAATTTAA
619305 AAATAAATTTACATTTATAAGT
1 AAATAAA-TTA-ATTTATAAGT
*
619327 AAATTAATTAATTTATAA
1 AAATAAATTAATTTATAA
619345 ATGAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATAAATTAATTTATAAGT
Found at i:619709 original size:3 final size:3
Alignment explanation
Indices: 619701--619736 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
619691 CTCTCTAGCT
619701 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
619737 CGCAAGTCTC
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:620156 original size:2 final size:2
Alignment explanation
Indices: 620149--620174 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
620139 TGTGTACAAC
620149 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
620175 CATACTACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:623178 original size:17 final size:17
Alignment explanation
Indices: 623149--623182 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
623139 ATATATAGTT
*
623149 TTTATTAATTTAAAAAA
1 TTTATTAAGTTAAAAAA
623166 TTTATTAAGTTAAAAAA
1 TTTATTAAGTTAAAAAA
623183 AAATAGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTATTAAGTTAAAAAA
Found at i:627818 original size:11 final size:10
Alignment explanation
Indices: 627802--627893 Score: 52
Period size: 10 Copynumber: 9.3 Consensus size: 10
627792 ACATTAAAAA
627802 ATAATTTAAAT
1 ATAA-TTAAAT
627813 ATAATTAAAT
1 ATAATTAAAT
627823 AT--TTAAAT
1 ATAATTAAAT
627831 AT-ATTAAA-
1 ATAATTAAAT
* *
627839 ATTTATATAACAC
1 A-TAAT-TAA-AT
*
627852 AT-ATAAAAT
1 ATAATTAAAT
*
627861 AT-ATAAAAT
1 ATAATTAAAT
627870 ATAATTATAAT
1 ATAATTA-AAT
*
627881 ATAATAAAAT
1 ATAATTAAAT
627891 ATA
1 ATA
627894 TATGAATAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
8 9 0.13
9 18 0.26
10 21 0.30
11 18 0.26
12 2 0.03
13 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
ATAATTAAAT
Found at i:627828 original size:18 final size:17
Alignment explanation
Indices: 627800--627843 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
627790 ATACATTAAA
627800 AAATAATTTAAATATAATT
1 AAAT-ATTTAAATAT-ATT
627819 AAATATTTAAATATATT
1 AAATATTTAAATATATT
627836 AAA-ATTTA
1 AAATATTTA
627844 TATAACACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 6 0.24
18 10 0.40
19 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATATTTAAATATATT
Found at i:627864 original size:9 final size:9
Alignment explanation
Indices: 627809--627895 Score: 59
Period size: 9 Copynumber: 9.0 Consensus size: 9
627799 AAAATAATTT
*
627809 AAATATAATT
1 AAATAT-ATA
*
627819 AAATAT-TT
1 AAATATATA
627827 AAATATATTA
1 AAATATA-TA
627837 AAATTTATATA
1 AAA--TATATA
* *
627848 ACACATATA
1 AAATATATA
627857 AAATATATA
1 AAATATATA
627866 AAATATAATTA
1 AAATAT-A-TA
*
627877 TAATATAATA
1 AAATAT-ATA
627887 AAATATATA
1 AAATATATA
627896 TGAATAATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
8 8 0.12
9 21 0.33
10 18 0.28
11 13 0.20
12 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
AAATATATA
Found at i:627888 original size:30 final size:30
Alignment explanation
Indices: 627809--627895 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
627799 AAAATAATTT
*
627809 AAATATAATTA-AATAT--TTAAATATATTA
1 AAATATAATTATAATATAATAAAATATA-TA
* * *
627837 AAAT-TTA-TATAACACATATAAAATATATA
1 AAATATAATTATAATATA-ATAAAATATATA
627866 AAATATAATTATAATATAATAAAATATATA
1 AAATATAATTATAATATAATAAAATATATA
627896 TGAATAATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
26 2 0.04
27 5 0.11
28 4 0.09
29 6 0.13
30 22 0.48
31 7 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATATAATTATAATATAATAAAATATATA
Found at i:627902 original size:23 final size:21
Alignment explanation
Indices: 627854--627908 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
627844 TATAACACAT
627854 ATAA-AATAT-ATAAAATATA
1 ATAATAATATAATAAAATATA
*
627873 ATTATAATATAATAAAATATA
1 ATAATAATATAATAAAATATA
627894 TATGAATAAT-TAATA
1 -AT-AATAATATAATA
627909 CTTCGTCGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.10
20 5 0.17
21 10 0.33
22 7 0.23
23 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATAATATAATAAAATATA
Found at i:630803 original size:19 final size:20
Alignment explanation
Indices: 630770--630813 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
630760 GTTACAGAAC
630770 AGTGAGTTAAAATTTGATCG
1 AGTGAGTTAAAATTTGATCG
630790 AGTGAGTT-AAATTTGATCG
1 AGTGAGTTAAAATTTGATCG
630809 AGTGA
1 AGTGA
630814 ACACTGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (20 bp):
AGTGAGTTAAAATTTGATCG
Found at i:635085 original size:13 final size:13
Alignment explanation
Indices: 635067--635091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
635057 TCTTTGTTCT
635067 AATGTAATACCAC
1 AATGTAATACCAC
635080 AATGTAATACCA
1 AATGTAATACCA
635092 GAGCTAAGAC
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:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
AATGTAATACCAC
Found at i:644171 original size:2 final size:2
Alignment explanation
Indices: 644164--644200 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
644154 ATTTGATAAG
644164 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
644201 TGATGAAAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:649815 original size:2 final size:2
Alignment explanation
Indices: 649808--649851 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
649798 ATTAAAACAC
649808 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
649850 AG
1 AG
649852 TGGTCCTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:650240 original size:18 final size:18
Alignment explanation
Indices: 650217--650256 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
650207 AGATTATTAA
650217 ATTATTT-TTTTATAAAAT
1 ATTATTTATTTTA-AAAAT
650235 ATTATTTATTTTAAAAAT
1 ATTATTTATTTTAAAAAT
650253 ATTA
1 ATTA
650257 ATAAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTTATTTTAAAAAT
Found at i:651802 original size:2 final size:2
Alignment explanation
Indices: 651795--651819 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
651785 ACAAAAGTTG
651795 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
651820 GTAGTATACA
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:660546 original size:17 final size:17
Alignment explanation
Indices: 660512--660559 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
660502 AATTTTAATT
* *
660512 AAAATAATAT-ATTTTA
1 AAAAAAATATAATTATA
660528 AAAAAAATATAATTATA
1 AAAAAAATATAATTATA
*
660545 AAAAATATATAATTA
1 AAAAAAATATAATTA
660560 ATTTTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAAAATATAATTATA
Found at i:660571 original size:34 final size:33
Alignment explanation
Indices: 660533--660596 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 33
660523 TTTTAAAAAA
*
660533 AATATAATTATA-AAAAATATATAATTAATTTTTT
1 AATATAATTAAATAAAAATAT-TAA-TAATTTTTT
**
660567 AATATTTTTAAATAAAAATATTAATAATTT
1 AATATAATTAAATAAAAATATTAATAATTT
660597 AGGTCTACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
33 6 0.23
34 12 0.46
35 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
AATATAATTAAATAAAAATATTAATAATTTTTT
Found at i:661548 original size:17 final size:17
Alignment explanation
Indices: 661526--661562 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
661516 ATTGATAGTG
661526 TATAAAATTATATATAA
1 TATAAAATTATATATAA
* *
661543 TATAAATTTATATATTA
1 TATAAAATTATATATAA
661560 TAT
1 TAT
661563 GCATAAAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAAAATTATATATAA
Found at i:662675 original size:14 final size:15
Alignment explanation
Indices: 662656--662684 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
662646 TTAATTAATG
662656 TTTATAAT-ATATTA
1 TTTATAATAATATTA
662670 TTTATAATAATATTA
1 TTTATAATAATATTA
662685 ATATTAAATA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATAATAATATTA
Found at i:662860 original size:2 final size:2
Alignment explanation
Indices: 662853--662877 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
662843 TAAACCCAAG
662853 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
662878 AAGTGGGATT
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:667645 original size:13 final size:14
Alignment explanation
Indices: 667627--667655 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
667617 GATTATTAAA
667627 TATAAAAAA-TATT
1 TATAAAAAACTATT
667640 TATAAAAAACTATT
1 TATAAAAAACTATT
667654 TA
1 TA
667656 ATTATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
TATAAAAAACTATT
Found at i:667664 original size:25 final size:26
Alignment explanation
Indices: 667636--667692 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
667626 ATATAAAAAA
*
667636 TATTTATAAAAAACTATTTAAT-TAT
1 TATTTATAAAAAACTAATTAATATAT
* * *
667661 TATTTTTAACAAATTAATTAATATAT
1 TATTTATAAAAAACTAATTAATATAT
667687 TATTTA
1 TATTTA
667693 ATTAATTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTTATAAAAAACTAATTAATATAT
Found at i:670955 original size:65 final size:65
Alignment explanation
Indices: 670859--670982 Score: 239
Period size: 65 Copynumber: 1.9 Consensus size: 65
670849 GGCCATTTGC
670859 ACTTTTATTTTGGTGTTTATCTTTGGTCTTGTTTATTAATATTATAAAGGGCATGTATTGCACTT
1 ACTTTTATTTTGGTGTTTATCTTTGGTCTTGTTTATTAATATTATAAAGGGCATGTATTGCACTT
*
670924 ACTTTTATTTTGGTGTTTATCTTTGGTCTTGTTTATTAATATTATAAAGGGTATGTATT
1 ACTTTTATTTTGGTGTTTATCTTTGGTCTTGTTTATTAATATTATAAAGGGCATGTATT
670983 CGATATCTCT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.22, C:0.07, G:0.17, T:0.54
Consensus pattern (65 bp):
ACTTTTATTTTGGTGTTTATCTTTGGTCTTGTTTATTAATATTATAAAGGGCATGTATTGCACTT
Found at i:673726 original size:22 final size:22
Alignment explanation
Indices: 673700--673749 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
673690 GTATATATAT
** * *
673700 ATATATATTTGGTATAATTTTA
1 ATATATATTTAATAAAATCTTA
673722 ATATATATTTAATAAAATCTTA
1 ATATATATTTAATAAAATCTTA
673744 ATATAT
1 ATATAT
673750 GATATTTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
ATATATATTTAATAAAATCTTA
Found at i:674063 original size:2 final size:2
Alignment explanation
Indices: 674016--674050 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
674006 TACACATTAG
*
674016 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
674051 CACTCAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:675976 original size:24 final size:23
Alignment explanation
Indices: 675949--676043 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 23
675939 TATAATATAG
*
675949 TATTTATGT-TATGTTCATTTATTT
1 TATTTAT-TATAT-TTCAATTATTT
*
675973 TATTATATTATATTTTAATTATTT
1 TATT-TATTATATTTCAATTATTT
675997 TATTTAATTATATTT-AATTATATT
1 TATTT-ATTATATTTCAATTAT-TT
*
676021 TAATATTATTAAATTT-AATTATT
1 T-AT-TTATTATATTTCAATTATT
676044 AATCAATAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
23 7 0.11
24 31 0.50
25 22 0.35
26 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTTATTATATTTCAATTATTT
Found at i:675999 original size:16 final size:15
Alignment explanation
Indices: 675968--676010 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
675958 TATGTTCATT
675968 TATTTTATTATATTA
1 TATTTTATTATATTA
675983 TATTTTAATTAT-TT-
1 TATTTT-ATTATATTA
*
675997 TATTTAATTATATT
1 TATTTTATTATATT
676011 TAATTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 8 0.32
16 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTATTATATTA
Found at i:676031 original size:25 final size:22
Alignment explanation
Indices: 675967--676043 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 22
675957 TTATGTTCAT
675967 TTATTTTATTATATTATATTTTAA
1 TTATTTTATT-TATTATA-TTTAA
675991 TTATTTTATTTAATTATATTTAA
1 TTATTTTATTT-ATTATATTTAA
*
676014 TTATATTTAATATTATTAAATTTAA
1 TTAT-TTT-AT-TTATTATATTTAA
676039 TTATT
1 TTATT
676044 AATCAATAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
23 10 0.21
24 20 0.42
25 16 0.33
26 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTTTATTTATTATATTTAA
Found at i:676041 original size:10 final size:10
Alignment explanation
Indices: 675997--676024 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
675987 TTAATTATTT
675997 TATTTAATTA
1 TATTTAATTA
676007 TATTTAATTA
1 TATTTAATTA
676017 TATTTAAT
1 TATTTAAT
676025 ATTATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTAATTA
Found at i:680724 original size:89 final size:89
Alignment explanation
Indices: 680479--680929 Score: 517
Period size: 89 Copynumber: 5.0 Consensus size: 89
680469 TCTTTGGATG
* * * * *
680479 ATGATGGGCCGAGAGATTTGTTTTACACTTGCTTCTCAAATGCCTTCACTTGGACATGACTATAA
1 ATGATGGGCTGAGAGA--T-TTTTACACGTGCTTCTCAAATGCCTTCACATGGACACGACTGTAA
* *
680544 CGGAGAGGGCCAAAACCGTTAAATAGC
63 TGGAGAGGGCCAAAACCGCTAAATAGC
* * * * ** *
680571 ATAATGGGCCGAGA-TTTTTTACACGTGCTTCTCAAATGCCTTCACACGGATGCTACTGTAATGG
1 ATGATGGGCTGAGAGATTTTTACACGTGCTTCTCAAATGCCTTCACATGGACACGACTGTAATGG
*
680635 AGAGGGCCAAAACTGCTAAATAGC
66 AGAGGGCCAAAACCGCTAAATAGC
** * * * * * *
680659 ATGATGGGCTGAGAGATTTTTACACACGCTTCTCAGATGACGTCACATGGGCACTAATGTAATGG
1 ATGATGGGCTGAGAGATTTTTACACGTGCTTCTCAAATGCCTTCACATGGACACGACTGTAATGG
**
680724 AGAGGGCCAAAACTACTAAATAGC
66 AGAGGGCCAAAACCGCTAAATAGC
* * * *
680748 ATGATGGGCTGAGAGCTTTTTTACATGTGCTTCTCAAATGCCTTCACTTGGACACGACTGTAACG
1 ATGATGGGCTGAGAG-ATTTTTACACGTGCTTCTCAAATGCCTTCACATGGACACGACTGTAATG
*
680813 GAGAGGGCCAAAAGCGCTAAATAGC
65 GAGAGGGCCAAAACCGCTAAATAGC
* * * * *
680838 ACGATGGGCTTAGGGATTTTTTTACACTTGCTTCTCAAATGCCTTCACTTGGACACGACTGTAAT
1 ATGATGGGCTGAGAGA--TTTTTACACGTGCTTCTCAAATGCCTTCACATGGACACGACTGTAAT
*
680903 GAAGAGGGCCAAAACCGCTAAATAGC
64 GGAGAGGGCCAAAACCGCTAAATAGC
680929 A
1 A
680930 GCTGTGGCAT
Statistics
Matches: 304, Mismatches: 51, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
88 73 0.24
89 78 0.26
90 71 0.23
91 69 0.23
92 13 0.04
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (89 bp):
ATGATGGGCTGAGAGATTTTTACACGTGCTTCTCAAATGCCTTCACATGGACACGACTGTAATGG
AGAGGGCCAAAACCGCTAAATAGC
Found at i:680818 original size:179 final size:178
Alignment explanation
Indices: 680481--680929 Score: 515
Period size: 179 Copynumber: 2.5 Consensus size: 178
680471 TTTGGATGAT
* ** * * * * * * *
680481 GATGGGCCGAGAGATTTGTTTTACACTTGCTTCTCAAATGCCTTCACTTGGACATGACTATAACG
1 GATGGGCTGAGAGA-TT-TTTTACACACGCTTCTCAAATGACGTCACATGGACACGAATGTAATG
*
680546 GAGAGGGCCAAAACCGTTAAATAGCATAATGGGCCGAGATTTTTTACACGTGCTTCTCAAATGCC
64 GAGAGGGCCAAAACCGCTAAATAGCATAATGGGCCGAGATTTTTTACACGTGCTTCTCAAATGCC
** * * *
680611 TTCACACGGATGCTACTGTAATGGAGAGGGCCAAAA-CTGCTAAATAGCAT
129 TTCACACGGACACGACTGTAACGGAGAGGGCCAAAAGC-GCTAAATAGCAC
* * *
680661 GATGGGCTGAGAGA-TTTTTACACACGCTTCTCAGATGACGTCACATGGGCACTAATGTAATGGA
1 GATGGGCTGAGAGATTTTTTACACACGCTTCTCAAATGACGTCACATGGACACGAATGTAATGGA
** * * *
680725 GAGGGCCAAAACTACTAAATAGCATGATGGGCTGAGAGCTTTTTTACATGTGCTTCTCAAATGCC
66 GAGGGCCAAAACCGCTAAATAGCATAATGGGCCGAGA--TTTTTTACACGTGCTTCTCAAATGCC
**
680790 TTCACTTGGACACGACTGTAACGGAGAGGGCCAAAAGCGCTAAATAGCAC
129 TTCACACGGACACGACTGTAACGGAGAGGGCCAAAAGCGCTAAATAGCAC
* * ** * * * * *
680840 GATGGGCTTAGGGATTTTTTTACACTTGCTTCTCAAATGCCTTCACTTGGACACGACTGTAATGA
1 GATGGGCTGAGAGA-TTTTTTACACACGCTTCTCAAATGACGTCACATGGACACGAATGTAATGG
680905 AGAGGGCCAAAACCGCTAAATAGCA
65 AGAGGGCCAAAACCGCTAAATAGCA
680930 GCTGTGGCAT
Statistics
Matches: 224, Mismatches: 40, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
177 69 0.31
178 1 0.00
179 78 0.35
180 14 0.06
181 62 0.28
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (178 bp):
GATGGGCTGAGAGATTTTTTACACACGCTTCTCAAATGACGTCACATGGACACGAATGTAATGGA
GAGGGCCAAAACCGCTAAATAGCATAATGGGCCGAGATTTTTTACACGTGCTTCTCAAATGCCTT
CACACGGACACGACTGTAACGGAGAGGGCCAAAAGCGCTAAATAGCAC
Found at i:701807 original size:23 final size:23
Alignment explanation
Indices: 701780--701833 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 23
701770 AATGATCGAT
701780 TATTTTGTATAAAAATTTAAATAA
1 TATTTT-TATAAAAATTTAAATAA
*
701804 -A--TTTATACAAATTTAAATAA
1 TATTTTTATAAAAATTTAAATAA
701824 TATTTTTATA
1 TATTTTTATA
701834 TAATTAAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
23 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TATTTTTATAAAAATTTAAATAA
Found at i:702828 original size:27 final size:28
Alignment explanation
Indices: 702740--702839 Score: 78
Period size: 32 Copynumber: 3.4 Consensus size: 28
702730 AAAATACTGT
* * *
702740 AAATATTATATAATTATGTAAAAATATTA
1 AAAT-TTATATAAATATATAATAATATTA
* * *
702769 AAATTTATATAATATAAATTATTAACATGTTA
1 AAATTTATATAA-ATATA-TAAT-A-ATATTA
702801 AAATTTATATAAATATATAATAAT-TTA
1 AAATTTATATAAATATATAATAATATTA
702828 AATATTT-TATAA
1 AA-ATTTATATAA
702840 TTTAAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
27 10 0.17
28 14 0.24
29 7 0.12
30 5 0.09
31 5 0.09
32 17 0.29
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (28 bp):
AAATTTATATAAATATATAATAATATTA
Found at i:702831 original size:16 final size:16
Alignment explanation
Indices: 702810--702845 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
702800 AAAATTTATA
702810 TAAATATATAATAATT
1 TAAATATATAATAATT
* *
702826 TAAATATTTTATAATT
1 TAAATATATAATAATT
702842 TAAA
1 TAAA
702846 AAATATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATATATAATAATT
Found at i:702918 original size:106 final size:106
Alignment explanation
Indices: 702802--703014 Score: 383
Period size: 106 Copynumber: 2.0 Consensus size: 106
702792 AACATGTTAA
702802 AATTTATATAAATATATAATAATTTAAATA-TTTTATAATTTAAAAAATATATTAATTATAAAAA
1 AATTTATATAAATATATAATAATTTAAATATTTTTATAATTTAAAAAATATATTAATTAT-AAAA
* *
702866 AAATAAAAAATACTATCAAATTTACGTGGCTCTTTCAAGCAG
65 AAATAAAAAATACTATCAAATCTACCTGGCTCTTTCAAGCAG
702908 AATTTATATAAATATATAATAATTTAAATATTTTTATAATTTAAAAAATATATTAATTATAAAAA
1 AATTTATATAAATATATAATAATTTAAATATTTTTATAATTTAAAAAATATATTAATTATAAAAA
*
702973 AATAAAAAATACTGTCAAATCTACCTGGCTCTTTCAAGCAG
66 AATAAAAAATACTATCAAATCTACCTGGCTCTTTCAAGCAG
703014 A
1 A
703015 TTAGCATAGC
Statistics
Matches: 103, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
106 74 0.72
107 29 0.28
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (106 bp):
AATTTATATAAATATATAATAATTTAAATATTTTTATAATTTAAAAAATATATTAATTATAAAAA
AATAAAAAATACTATCAAATCTACCTGGCTCTTTCAAGCAG
Found at i:708473 original size:11 final size:11
Alignment explanation
Indices: 708459--708545 Score: 75
Period size: 11 Copynumber: 8.6 Consensus size: 11
708449 TTATACGATA
708459 AAATATAATAT
1 AAATATAATAT
708470 AAATAT-ATA-
1 AAATATAATAT
*
708479 AAAT-TTATAT
1 AAATATAATAT
708489 AAATA-AA-A-
1 AAATATAATAT
708497 AAATTATAATAT
1 AAA-TATAATAT
*
708509 AATTATAA-A-
1 AAATATAATAT
*
708518 AAAAAT-ATAT
1 AAATATAATAT
708528 AAATATAATAT
1 AAATATAATAT
708539 AAATATA
1 AAATATA
708546 TATTTTATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
8 5 0.08
9 15 0.25
10 16 0.26
11 23 0.38
12 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATATAATAT
Found at i:708490 original size:19 final size:19
Alignment explanation
Indices: 708456--708548 Score: 71
Period size: 19 Copynumber: 4.7 Consensus size: 19
708446 TAATTATACG
*
708456 ATAAAATATAATATAAATAT
1 ATAAAAT-TTATATAAATAT
708476 ATAAAATTTATATAAATA-
1 ATAAAATTTATATAAATAT
* *
708494 AAAAAATTATAATATAATTAT
1 ATAAAATT-T-ATATAAATAT
* **
708515 AAAAAAAATATATAAATAT
1 ATAAAATTTATATAAATAT
*
708534 AATATAAATATATAT
1 -ATA-AAATTTATAT
708549 TTTATTTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
18 7 0.12
19 20 0.33
20 18 0.30
21 15 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAATTTATATAAATAT
Found at i:708505 original size:39 final size:38
Alignment explanation
Indices: 708458--708532 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
708448 ATTATACGAT
* **
708458 AAAATATAATATAAATATATAAAATTTATATAAATAAA
1 AAAATATAATATAAATATAAAAAAAATATATAAATAAA
*
708496 AAAATTATAATATAATTATAAAAAAAATATATAAATA
1 AAAA-TATAATATAAATATAAAAAAAATATATAAATA
708533 TAATATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 4 0.12
39 28 0.88
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (38 bp):
AAAATATAATATAAATATAAAAAAAATATATAAATAAA
Found at i:708528 original size:24 final size:23
Alignment explanation
Indices: 708485--708541 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
708475 TATAAAATTT
708485 ATATAA-AT-AAAAAAATTAT-A
1 ATATAATATAAAAAAAATTATAA
708505 ATATAATTATAAAAAAAATATATAA
1 ATATAA-TATAAAAAAAAT-TATAA
708530 ATATAATATAAA
1 ATATAATATAAA
708542 TATATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.19
22 2 0.06
23 8 0.25
24 9 0.28
25 7 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
ATATAATATAAAAAAAATTATAA
Found at i:711868 original size:34 final size:32
Alignment explanation
Indices: 711830--711941 Score: 98
Period size: 32 Copynumber: 3.2 Consensus size: 32
711820 TTGCAATATT
**
711830 ATATAAAATAATAATATAAATATAAATTTATGTA
1 ATATAAAATAATAATAT-AATA-AAATTTATAAA
* *
711864 ATATAAATTAATAATATATTAAAATTTATAAA
1 ATATAAAATAATAATATAATAAAATTTATAAA
* *
711896 ATATAAAATATTTTAAATATAATTAAAATATAATAAA
1 ATATAAAATA--AT-AATATAA-TAAAAT-TTATAAA
711933 ATAATAAAA
1 AT-ATAAAA
711942 ATACATAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
32 18 0.28
33 3 0.05
34 17 0.27
35 6 0.09
36 6 0.09
37 8 0.12
38 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
ATATAAAATAATAATATAATAAAATTTATAAA
Found at i:711880 original size:13 final size:15
Alignment explanation
Indices: 711843--711902 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
711833 TAAAATAATA
711843 ATATAAATATAAATTT
1 ATAT-AATATAAATTT
* *
711859 ATGTAATATAAATTA
1 ATATAATATAAATTT
711874 ATA-ATATATTAAAATTT
1 ATATA-ATA-T-AAATTT
*
711891 ATAAAATATAAA
1 ATATAATATAAA
711903 ATATTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 1 0.03
15 18 0.50
16 5 0.14
17 11 0.31
18 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
ATATAATATAAATTT
Found at i:711893 original size:25 final size:23
Alignment explanation
Indices: 711865--711940 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 23
711855 ATTTATGTAA
711865 TATAAATTAATAATATATTAAAATT
1 TATAAATTAA-AATATATTAAAA-T
*
711890 TATAAAATATAAAATAT-TTTAAA-
1 TAT-AAAT-TAAAATATATTAAAAT
*
711913 TAT-AATTAAAATATAATAAAAT
1 TATAAATTAAAATATATTAAAAT
*
711935 AATAAA
1 TATAAA
711941 AATACATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 8 0.19
21 7 0.17
22 2 0.05
23 5 0.12
25 8 0.19
26 9 0.21
27 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TATAAATTAAAATATATTAAAAT
Found at i:711894 original size:17 final size:17
Alignment explanation
Indices: 711868--711924 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
711858 TATGTAATAT
*
711868 AAATTAATAATATATTA
1 AAATTTATAATATATTA
*
711885 AAATTTATAAAATA-TA
1 AAATTTATAATATATTA
*
711901 AAATATTTTAAATATAATTA
1 AAAT-TTAT-AATAT-ATTA
711921 AAAT
1 AAAT
711925 ATAATAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.19
17 15 0.47
18 4 0.12
19 1 0.03
20 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTTATAATATATTA
Found at i:711899 original size:32 final size:34
Alignment explanation
Indices: 711830--711905 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 34
711820 TTGCAATATT
**
711830 ATATAAAATAATAATATAAATATAAATTTATGTA
1 ATATAAAATAATAATATAAATATAAATTTATAAA
* *
711864 ATATAAATTAATAATAT-ATTA-AAATTTATAAA
1 ATATAAAATAATAATATAAATATAAATTTATAAA
711896 ATATAAAATA
1 ATATAAAATA
711906 TTTTAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 18 0.49
33 3 0.08
34 16 0.43
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (34 bp):
ATATAAAATAATAATATAAATATAAATTTATAAA
Found at i:712682 original size:14 final size:15
Alignment explanation
Indices: 712659--712695 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
712649 TTGGTGGCGG
712659 AAAG-GAAAAA-GGA
1 AAAGAGAAAAAGGGA
712672 AAAGAGAAAAAGGGA
1 AAAGAGAAAAAGGGA
712687 AAA-AGAAAA
1 AAAGAGAAAA
712696 GAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 12 0.55
15 6 0.27
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAGAGAAAAAGGGA
Found at i:716464 original size:31 final size:31
Alignment explanation
Indices: 716426--716487 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
716416 ATTTGTACAG
*
716426 AAATCACATGTAAATTGATAATACTTGCCGA
1 AAATCACATATAAATTGATAATACTTGCCGA
* *
716457 AAATCACATATAAATTGATAGTCCTTGCCGA
1 AAATCACATATAAATTGATAATACTTGCCGA
716488 CTCTACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (31 bp):
AAATCACATATAAATTGATAATACTTGCCGA
Found at i:720530 original size:12 final size:13
Alignment explanation
Indices: 720511--720543 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
720501 AAAATATAAT
720511 ATTTAATTATTAA
1 ATTTAATTATTAA
720524 A-TTAATTATTAA
1 ATTTAATTATTAA
720536 ATTTAATT
1 ATTTAATT
720544 TTTTAACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTAATTATTAA
Found at i:720985 original size:26 final size:26
Alignment explanation
Indices: 720956--721006 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
720946 GGGAAAAAAA
720956 AAAGAAAA-A-GAAAGAGATAAAGGAAG
1 AAAGAAAAGATGAAAG-GA-AAAGGAAG
720982 AAAGAAAAGATGAAAGGAAAAGGAA
1 AAAGAAAAGATGAAAGGAAAAGGAA
721007 AAGGGAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 15 0.65
27 3 0.13
28 5 0.22
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (26 bp):
AAAGAAAAGATGAAAGGAAAAGGAAG
Found at i:720987 original size:20 final size:20
Alignment explanation
Indices: 720962--721018 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
720952 AAAAAAAGAA
720962 AAAGAAAGAGAT-AAAGGAAG
1 AAAGAAA-AGATGAAAGGAAG
720982 AAAGAAAAGATGAAAGGAA-
1 AAAGAAAAGATGAAAGGAAG
* *
721001 AAGGAAAAG-GGAAAGGAA
1 AAAGAAAAGATGAAAGGAA
721019 AGATAATGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
19 12 0.35
20 14 0.41
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.04
Consensus pattern (20 bp):
AAAGAAAAGATGAAAGGAAG
Found at i:721478 original size:14 final size:14
Alignment explanation
Indices: 721461--721518 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 14
721451 ACCTCTCTTC
*
721461 CTCTATATCTATCT
1 CTCTATATCTTTCT
721475 CTC--TATCTTTCT
1 CTCTATATCTTTCT
*
721487 CTCTATCTC-TT-T
1 CTCTATATCTTTCT
*
721499 CTCTATATCTTTCC
1 CTCTATATCTTTCT
721513 CTCTAT
1 CTCTAT
721519 TCCTCTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 20 0.56
13 4 0.11
14 12 0.33
ACGTcount: A:0.14, C:0.33, G:0.00, T:0.53
Consensus pattern (14 bp):
CTCTATATCTTTCT
Found at i:721501 original size:26 final size:26
Alignment explanation
Indices: 721460--721518 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
721450 TACCTCTCTT
*
721460 CCTCTATATCTATCTCTCTATCTTTC
1 CCTCTATATCTATCTCTATATCTTTC
* * *
721486 TCTCTATCTCTTTCTCTATATCTTTC
1 CCTCTATATCTATCTCTATATCTTTC
721512 CCTCTAT
1 CCTCTAT
721519 TCCTCTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.53
Consensus pattern (26 bp):
CCTCTATATCTATCTCTATATCTTTC
Found at i:721796 original size:40 final size:40
Alignment explanation
Indices: 721752--721922 Score: 236
Period size: 40 Copynumber: 4.3 Consensus size: 40
721742 ATAAAGTTCT
* *
721752 AGAACCTTCCACATTATTCTAAAACATTCTAGAATCTTCC
1 AGAACCTTCCACAATATTCTAGAACATTCTAGAATCTTCC
*
721792 AGAACCTCCCACAATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCACAATATTCTAGAACATTCTAGAATCTTCC
* *
721832 AGAGCCTCCCACAATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCACAATATTCTAGAACATTCTAGAATCTTCC
* * * *
721872 AGAGCCTTCCACGATATTCTAGAACATTCCAGAA-CATTCT
1 AGAACCTTCCACAATATTCTAGAACATTCTAGAATC-TTCC
*
721912 AGAACATTCCA
1 AGAACCTTCCA
721923 AAGTGTTCTA
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 119 0.99
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.28
Consensus pattern (40 bp):
AGAACCTTCCACAATATTCTAGAACATTCTAGAATCTTCC
Found at i:721900 original size:10 final size:10
Alignment explanation
Indices: 721887--721920 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
721877 CTTCCACGAT
721887 ATTCTAGAAC
1 ATTCTAGAAC
*
721897 ATTCCAGAAC
1 ATTCTAGAAC
721907 ATTCTAGAAC
1 ATTCTAGAAC
721917 ATTC
1 ATTC
721921 CAAAGTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:721934 original size:20 final size:20
Alignment explanation
Indices: 721748--721922 Score: 79
Period size: 20 Copynumber: 8.8 Consensus size: 20
721738 CTCCATAAAG
* * **
721748 TTCTAGAACCTTCCACATTA
1 TTCTAGAACATTCCAGAACA
* *
721768 TTCTAAAACATTCTAGAATC-
1 TTCTAGAACATTCCAGAA-CA
* * * * *
721788 TTCCAGAACCTCCCACAATA
1 TTCTAGAACATTCCAGAACA
*
721808 TTCTAGAACATTCTAGAATC-
1 TTCTAGAACATTCCAGAA-CA
* * * * * *
721828 TTCCAGAGCCTCCCACAATA
1 TTCTAGAACATTCCAGAACA
*
721848 TTCTAGAACATTCTAGAATC-
1 TTCTAGAACATTCCAGAA-CA
* * * *
721868 TTCCAGAGCCTTCCACG-ATA
1 TTCTAGAACATTCCA-GAACA
721888 TTCTAGAACATTCCAGAACA
1 TTCTAGAACATTCCAGAACA
721908 TTCTAGAACATTCCA
1 TTCTAGAACATTCCA
721923 AAGTGTTCTA
Statistics
Matches: 105, Mismatches: 42, Indels: 16
0.64 0.26 0.10
Matches are distributed among these distances:
19 1 0.01
20 103 0.98
21 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.29
Consensus pattern (20 bp):
TTCTAGAACATTCCAGAACA
Found at i:725911 original size:14 final size:14
Alignment explanation
Indices: 725894--725951 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 14
725884 ACCTCTCTTC
*
725894 CTCTATATCTATCT
1 CTCTATATCTTTCT
725908 CTC--TATCTTTCT
1 CTCTATATCTTTCT
*
725920 CTCTATCTC-TT-T
1 CTCTATATCTTTCT
*
725932 CTCTATATCTTTCC
1 CTCTATATCTTTCT
725946 CTCTAT
1 CTCTAT
725952 TCCTCTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 20 0.56
13 4 0.11
14 12 0.33
ACGTcount: A:0.14, C:0.33, G:0.00, T:0.53
Consensus pattern (14 bp):
CTCTATATCTTTCT
Found at i:725934 original size:26 final size:26
Alignment explanation
Indices: 725893--725951 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
725883 TACCTCTCTT
*
725893 CCTCTATATCTATCTCTCTATCTTTC
1 CCTCTATATCTATCTCTATATCTTTC
* * *
725919 TCTCTATCTCTTTCTCTATATCTTTC
1 CCTCTATATCTATCTCTATATCTTTC
725945 CCTCTAT
1 CCTCTAT
725952 TCCTCTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.53
Consensus pattern (26 bp):
CCTCTATATCTATCTCTATATCTTTC
Found at i:726254 original size:40 final size:40
Alignment explanation
Indices: 726199--726338 Score: 226
Period size: 40 Copynumber: 3.5 Consensus size: 40
726189 CTTTCTACAT
726199 TATTCTAGAACATTCTAGAATCTTCCAGAGCCTCCCACAA
1 TATTCTAGAACATTCTAGAATCTTCCAGAGCCTCCCACAA
*
726239 TATTCTAGAACATTCTAGAATCTTTCAGAGCCTCCCACAA
1 TATTCTAGAACATTCTAGAATCTTCCAGAGCCTCCCACAA
* * *
726279 TATTCTAGAACATTTTAGAATCTTCCAGAGCCTTCCACGA
1 TATTCTAGAACATTCTAGAATCTTCCAGAGCCTCCCACAA
* *
726319 TATTCTAGAATATTCCAGAA
1 TATTCTAGAACATTCTAGAA
726339 CATTCTAGAA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 92 1.00
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.31
Consensus pattern (40 bp):
TATTCTAGAACATTCTAGAATCTTCCAGAGCCTCCCACAA
Found at i:727252 original size:18 final size:17
Alignment explanation
Indices: 727220--727253 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
727210 TTATGTCACT
*
727220 GAGCCATTTCCTCGTGG
1 GAGCCATTCCCTCGTGG
727237 GAGCCTATTCCCTCGTG
1 GAGCC-ATTCCCTCGTG
727254 ACCTCCCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.12, C:0.32, G:0.26, T:0.29
Consensus pattern (17 bp):
GAGCCATTCCCTCGTGG
Found at i:727599 original size:2 final size:2
Alignment explanation
Indices: 727592--727619 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
727582 GTGTCTTCCA
727592 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
727620 GCTTCTGCTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:727938 original size:24 final size:24
Alignment explanation
Indices: 727911--727964 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
727901 TTAAAAATTA
727911 ATTTT-TAGTTGAAATAATTTTATT
1 ATTTTATAGTTGAAA-AATTTTATT
* * *
727935 ATTTTATATTTTAAAATTTTTATT
1 ATTTTATAGTTGAAAAATTTTATT
727959 ATTTTA
1 ATTTTA
727965 AATATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTTATAGTTGAAAAATTTTATT
Found at i:727957 original size:16 final size:18
Alignment explanation
Indices: 727936--727971 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
727926 AATTTTATTA
727936 TTTTA-TATTTTAAA-AT
1 TTTTATTATTTTAAATAT
727952 TTTTATTATTTTAAATAT
1 TTTTATTATTTTAAATAT
727970 TT
1 TT
727972 ATTTTTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATTATTTTAAATAT
Found at i:727963 original size:17 final size:17
Alignment explanation
Indices: 727936--727979 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
727926 AATTTTATTA
727936 TTTTA-TATTTTAAAAT
1 TTTTATTATTTTAAAAT
727952 TTTTATTATTTT-AAAT
1 TTTTATTATTTTAAAAT
*
727968 ATTTATT-TTTTA
1 TTTTATTATTTTA
727980 CATTTTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 4 0.16
16 15 0.60
17 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATTATTTTAAAAT
Found at i:728568 original size:2 final size:2
Alignment explanation
Indices: 728561--728593 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
728551 AAAGTGTAGC
728561 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
728594 GGGTGCGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:729786 original size:18 final size:16
Alignment explanation
Indices: 729762--729810 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 16
729752 TTAAATAAAA
729762 TATAAATATAATATAT
1 TATAAATATAATATAT
729778 GTAATAAATATAATA-AT
1 -T-ATAAATATAATATAT
729795 TATAAA-ATAATATAT
1 TATAAATATAATATAT
729810 T
1 T
729811 TAACCACGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.20
15 8 0.27
16 1 0.03
17 3 0.10
18 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TATAAATATAATATAT
Found at i:735068 original size:16 final size:14
Alignment explanation
Indices: 735039--735095 Score: 55
Period size: 16 Copynumber: 4.0 Consensus size: 14
735029 ATAGGTTTAT
735039 ATTTATATTTTAAA
1 ATTTATATTTTAAA
735053 ATTTAATATATTTAAA
1 ATTT-ATAT-TTTAAA
* *
735069 ATTT-TATATT-AT
1 ATTTATATTTTAAA
735081 ATTTATATTTATAAA
1 ATTTATATTT-TAAA
735096 GAGAAAGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
12 5 0.15
13 6 0.18
14 8 0.24
15 5 0.15
16 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTATATTTTAAA
Found at i:741948 original size:2 final size:2
Alignment explanation
Indices: 741941--741965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
741931 TTCAATATTA
741941 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
741966 CATCATCATC
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:744346 original size:16 final size:16
Alignment explanation
Indices: 744325--744356 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
744315 TGCATTTGAT
744325 TAATTAAAATAAAATA
1 TAATTAAAATAAAATA
*
744341 TAATTATAATAAAATA
1 TAATTAAAATAAAATA
744357 ATTATTTTTA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAAAATAAAATA
Found at i:744415 original size:30 final size:30
Alignment explanation
Indices: 744381--744437 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
744371 AATAAAATAA
*
744381 AATAAAAT-AATTATAATAATAATTTAATTC
1 AATAAAATAAAATATAATAA-AATTTAATTC
*
744411 AATAAAATAAAATATTATAAAATTTAA
1 AATAAAATAAAATATAATAAAATTTAA
744438 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
AATAAAATAAAATATAATAAAATTTAATTC
Found at i:744674 original size:18 final size:19
Alignment explanation
Indices: 744646--744696 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
744636 CGCGTTTTAT
744646 ATTTTTATATTAAAAATTA
1 ATTTTTATATTAAAAATTA
**
744665 ATTTTT-TATTATTAATTA
1 ATTTTTATATTAAAAATTA
*
744683 ATTTTAAT-TTAAAA
1 ATTTTTATATTAAAA
744697 TATTTTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTATATTAAAAATTA
Found at i:748516 original size:8 final size:8
Alignment explanation
Indices: 748471--748595 Score: 78
Period size: 8 Copynumber: 15.2 Consensus size: 8
748461 ATTATTTTCA
*
748471 TATATTTT
1 TATATATT
748479 TATATATT
1 TATATATT
748487 ATAATTATATT
1 -T-A-TATATT
748498 TATCATA-T
1 TAT-ATATT
748506 TATATATT
1 TATATATT
748514 TATATATT
1 TATATATT
*
748522 T-TAATATA
1 TAT-ATATT
*
748530 TATAAAATT
1 TAT-ATATT
* *
748539 TTTATTATA
1 TATA-TATT
*
748548 TAGATATT
1 TATATATT
*
748556 AATATATT
1 TATATATT
748564 TATATATT
1 TATATATT
*
748572 TATATCTT
1 TATATATT
*
748580 TTTATA-T
1 TATATATT
748587 TATA-ATT
1 TATATATT
748594 TA
1 TA
748596 ATTATTATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
6 1 0.01
7 11 0.12
8 55 0.60
9 16 0.18
10 2 0.02
11 6 0.07
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (8 bp):
TATATATT
Found at i:748531 original size:20 final size:20
Alignment explanation
Indices: 748454--748532 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 20
748444 TTTTAGTTAG
*
748454 TATTTATATTATTTTCATATA
1 TATTTATA-TATTTTAATATA
* *
748475 TTTTTATATATTATAAT-TA
1 TATTTATATATTTTAATATA
748494 TATTTATCATA---T--TATA
1 TATTTAT-ATATTTTAATATA
748510 TATTTATATATTTTAATATA
1 TATTTATATATTTTAATATA
748530 TAT
1 TAT
748533 AAAATTTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
15 4 0.09
16 9 0.19
17 1 0.02
18 1 0.02
19 8 0.17
20 17 0.36
21 7 0.15
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTATATATTTTAATATA
Found at i:749016 original size:22 final size:22
Alignment explanation
Indices: 748991--749032 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
748981 AATTTAAAAA
748991 TAAAAT-AATCATATATTTTTAT
1 TAAAATAAATCATA-ATTTTTAT
*
749013 TAAATTAAATCATAATTTTT
1 TAAAATAAATCATAATTTTT
749033 TAGGTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAAATAAATCATAATTTTTAT
Found at i:749893 original size:3 final size:3
Alignment explanation
Indices: 749887--749925 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
749877 TAATAATAAT
749887 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
749926 TGGTGAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:752358 original size:4 final size:4
Alignment explanation
Indices: 752349--752385 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
752339 AAGGGTGATT
* *
752349 TACA TACA TACA TACA TACA TACA TAAA TGCA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
752386 GCATTCAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:757373 original size:14 final size:14
Alignment explanation
Indices: 757354--757380 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
757344 TTTATTCATC
757354 ATAGAATTAATATA
1 ATAGAATTAATATA
757368 ATAGAATTAATAT
1 ATAGAATTAATAT
757381 TCTAATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
ATAGAATTAATATA
Found at i:757401 original size:20 final size:21
Alignment explanation
Indices: 757361--757411 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
757351 ATCATAGAAT
*
757361 TAATATAATAGAATTAATATTC
1 TAATATAA-AGAATGAATATTC
757383 TAATATAAA-AATGAATATTC
1 TAATATAAAGAATGAATATTC
757403 TAATATAAA
1 TAATATAAA
757412 TTAGATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 19 0.68
21 1 0.04
22 8 0.29
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (21 bp):
TAATATAAAGAATGAATATTC
Found at i:757422 original size:14 final size:14
Alignment explanation
Indices: 757403--757460 Score: 77
Period size: 14 Copynumber: 4.4 Consensus size: 14
757393 ATGAATATTC
757403 TAATATAAATTAGA
1 TAATATAAATTAGA
*
757417 TAATATGAATT--A
1 TAATATAAATTAGA
757429 -AATATAAATTAGA
1 TAATATAAATTAGA
*
757442 TAATATAAATTAAA
1 TAATATAAATTAGA
757456 TAATA
1 TAATA
757461 AGATAATAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.24
12 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (14 bp):
TAATATAAATTAGA
Found at i:757469 original size:25 final size:25
Alignment explanation
Indices: 757404--757457 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
757394 TGAATATTCT
*
757404 AATATAAATTAGATAATATGAATTA
1 AATATAAATTAGATAATATAAATTA
757429 AATATAAATTAGATAATATAAATTA
1 AATATAAATTAGATAATATAAATTA
757454 AATA
1 AATA
757458 ATAAGATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (25 bp):
AATATAAATTAGATAATATAAATTA
Found at i:757583 original size:19 final size:16
Alignment explanation
Indices: 757542--757650 Score: 63
Period size: 15 Copynumber: 6.8 Consensus size: 16
757532 TCATTCATTT
757542 ATTAAATTAATAATTA
1 ATTAAATTAATAATTA
757558 A-TAAATTAATATATTTA
1 ATTAAATTAATA-A-TTA
757575 ACTTAAATTAA-AATTA
1 A-TTAAATTAATAATTA
* *
757591 AATAAA--AATAAATA
1 ATTAAATTAATAATTA
757605 A-TAATATTTAAATAATATA
1 ATTAA-A-TT-AATAAT-TA
757624 ATTATAA-TAATATATTA
1 ATTA-AATTAATA-ATTA
757641 A-TAAA-TAATA
1 ATTAAATTAATA
757651 TAAAATAATG
Statistics
Matches: 76, Mismatches: 3, Indels: 29
0.70 0.03 0.27
Matches are distributed among these distances:
13 5 0.07
14 6 0.08
15 21 0.28
16 8 0.11
17 12 0.16
18 9 0.12
19 11 0.14
20 3 0.04
21 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAATTAATAATTA
Found at i:757618 original size:11 final size:12
Alignment explanation
Indices: 757587--757659 Score: 53
Period size: 14 Copynumber: 5.8 Consensus size: 12
757577 TTAAATTAAA
757587 ATTAAATAA-A-
1 ATTAAATAATAT
*
757597 AATAAATAATAAT
1 ATTAAATAAT-AT
757610 ATTTAAATAATAT
1 A-TTAAATAATAT
757623 AATTATAATAATAT
1 -ATTA-AATAATAT
757637 ATT-AATAAATAAT
1 ATTAAAT-AAT-AT
*
757650 ATAAAATAAT
1 ATTAAATAAT
757660 GTAATAATTG
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
10 8 0.16
11 3 0.06
12 4 0.08
13 16 0.31
14 20 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATTAAATAATAT
Found at i:757618 original size:14 final size:13
Alignment explanation
Indices: 757599--757652 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 13
757589 TAAATAAAAA
757599 TAAATAATAATATT
1 TAAATAAT-ATATT
*
757613 TAAATAATATAAT
1 TAAATAATATATT
757626 TATAATAATATATT
1 TA-AATAATATATT
757640 AATAAATAATATA
1 --TAAATAATATA
757653 AAATAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 6 0.17
14 18 0.51
15 9 0.26
16 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAATAATATATT
Done.