Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold399
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: 184626
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 1 of 2
Found at i:2014 original size:53 final size:53
Alignment explanation
Indices: 1950--2056 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
1940 ACTATGTAGT
1950 TGGATCATCAATCAATTAACAGTAGTATCCTGGAATCCTAGAAGGTGGACTGC
1 TGGATCATCAATCAATTAACAGTAGTATCCTGGAATCCTAGAAGGTGGACTGC
*
2003 TGGATCATCAATCAATTCACAGTAGTATCCTGGAATCCTAGAAGGTGGACTGC
1 TGGATCATCAATCAATTAACAGTAGTATCCTGGAATCCTAGAAGGTGGACTGC
2056 T
1 T
2057 TGGAAGTGCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (53 bp):
TGGATCATCAATCAATTAACAGTAGTATCCTGGAATCCTAGAAGGTGGACTGC
Found at i:4603 original size:33 final size:33
Alignment explanation
Indices: 4561--4629 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
4551 TTCTAGCATT
4561 GTTCTTAGTCAAGCAAGGAAGAAGACAGTTGCA
1 GTTCTTAGTCAAGCAAGGAAGAAGACAGTTGCA
4594 GTTCTTAGTCAAGCAAGGAAGAAGACAGTTGCA
1 GTTCTTAGTCAAGCAAGGAAGAAGACAGTTGCA
4627 GTT
1 GTT
4630 GGAACACGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (33 bp):
GTTCTTAGTCAAGCAAGGAAGAAGACAGTTGCA
Found at i:5398 original size:17 final size:16
Alignment explanation
Indices: 5360--5398 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
5350 AAAAAATATT
5360 ATTTTTTATTTTAATCA
1 ATTTTTTATTTTAA-CA
5377 ATTTTTTATCTTTAA-A
1 ATTTTTTAT-TTTAACA
5393 ATTTTT
1 ATTTTT
5399 AAAATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 9 0.43
18 5 0.24
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTTTATTTTAACA
Found at i:6090 original size:2 final size:2
Alignment explanation
Indices: 6083--6108 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6073 TTGCTTTAAC
6083 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
6109 TACAAATAAA
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:9778 original size:17 final size:17
Alignment explanation
Indices: 9756--9789 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9746 TATCTGATAT
9756 AAAAAAGAAAACAAAAA
1 AAAAAAGAAAACAAAAA
*
9773 AAAAAAGAAAAGAAAAA
1 AAAAAAGAAAACAAAAA
9790 TCCCATGAAT
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:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAACAAAAA
Found at i:10108 original size:16 final size:17
Alignment explanation
Indices: 10083--10114 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
10073 TAGTGTTTAA
10083 TTTATATTTAAATAAAT
1 TTTATATTTAAATAAAT
10100 TTTAT-TTTAAATAAA
1 TTTATATTTAAATAAA
10115 ATATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATATTTAAATAAAT
Found at i:10116 original size:17 final size:17
Alignment explanation
Indices: 10083--10165 Score: 64
Period size: 17 Copynumber: 4.8 Consensus size: 17
10073 TAGTGTTTAA
10083 TTTATATTTAAA-TAAAT
1 TTTAT-TTTAAATTAAAT
*
10100 TTTATTTTAAATAAAAT
1 TTTATTTTAAATTAAAT
* * *
10117 ATTAATTTATATTTAAA-
1 TTTATTTTA-AATTAAAT
10134 TTTATTTATAAATTAAAT
1 TTTATTT-TAAATTAAAT
10152 TATT-TATTTAAATT
1 T-TTAT-TTTAAATT
10166 TTTTACATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
16 6 0.12
17 27 0.52
18 15 0.29
19 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTATTTTAAATTAAAT
Found at i:10142 original size:16 final size:16
Alignment explanation
Indices: 10121--10170 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
10111 TAAAATATTA
10121 ATTTATATTTAAATTT
1 ATTTATATTTAAATTT
*
10137 ATTTATAAATTAAA-TT
1 ATTTAT-ATTTAAATTT
10153 A-TT-TATTTAAATTT
1 ATTTATATTTAAATTT
10167 -TTTA
1 ATTTA
10171 CATTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
13 6 0.21
14 5 0.18
15 2 0.07
16 9 0.32
17 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTATATTTAAATTT
Found at i:10240 original size:20 final size:20
Alignment explanation
Indices: 10215--10255 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
10205 ATATATTTTT
10215 ATATAAAT-TTAATTATAAAA
1 ATATAAATATTAA-TATAAAA
10235 ATATAAATATTAATATAAAA
1 ATATAAATATTAATATAAAA
10255 A
1 A
10256 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATAAATATTAATATAAAA
Found at i:14101 original size:2 final size:2
Alignment explanation
Indices: 14096--14139 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
14086 ATATACCTGC
*
14096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
14138 AT
1 AT
14140 GCATAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14753 original size:2 final size:2
Alignment explanation
Indices: 14746--14774 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14736 GGTCAACAAT
14746 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
14775 GAATACATTA
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:15447 original size:15 final size:16
Alignment explanation
Indices: 15418--15455 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
15408 TAAATAAAAA
* *
15418 ATAATTTTTATAATAT
1 ATAATATTTAAAATAT
15434 A-AATATTTAAAATAT
1 ATAATATTTAAAATAT
15449 ATAATAT
1 ATAATAT
15456 AAATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATATTTAAAATAT
Found at i:15467 original size:29 final size:28
Alignment explanation
Indices: 15434--15529 Score: 86
Period size: 31 Copynumber: 3.3 Consensus size: 28
15424 TTTATAATAT
15434 AAATATTTAAAATATATAATATAAATTA
1 AAATATTTAAAATATATAATATAAATTA
* * *
15462 TTAATATATCTAAATTATATAAAAATAAATTA
1 --AA-ATATTTAAAATATAT-AATATAAATTA
* *
15494 AAAAATTTAAAATATAT-ATATACATATA
1 AAATATTTAAAATATATAATATAAAT-TA
*
15522 AAGTATTT
1 AAATATTT
15530 GAATTGTCGA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
27 6 0.11
28 8 0.15
29 12 0.23
30 4 0.08
31 13 0.25
32 10 0.19
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (28 bp):
AAATATTTAAAATATATAATATAAATTA
Found at i:15512 original size:31 final size:30
Alignment explanation
Indices: 15438--15513 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
15428 TAATATAAAT
* * * *
15438 ATTTAAAATATATAATATAAATTATTAATAT
1 ATTTAAAATATAT-ATAAAAATAATTAAAAA
*
15469 ATCT-AAAT-TATATAAAAATAAATTAAAAA
1 ATTTAAAATATATATAAAAAT-AATTAAAAA
15498 ATTTAAAATATATATA
1 ATTTAAAATATATATA
15514 TACATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 7 0.19
29 12 0.33
30 8 0.22
31 9 0.25
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (30 bp):
ATTTAAAATATATATAAAAATAATTAAAAA
Found at i:17747 original size:2 final size:2
Alignment explanation
Indices: 17740--17771 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17730 CATCCGTCTC
17740 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
17772 GAAGAATTTA
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:18748 original size:22 final size:22
Alignment explanation
Indices: 18707--18748 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
18697 TATATAAAGT
*
18707 TATTTAAATTAATTATTATTGA
1 TATTTAAATTAATTAATATTGA
18729 TATTT-AATTAATTAAATATT
1 TATTTAAATTAATT-AATATT
18749 TATTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTAAATTAATTAATATTGA
Found at i:18992 original size:20 final size:20
Alignment explanation
Indices: 18955--18992 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18945 ATATGATTTA
*
18955 TATTTATTTAATTTGATTAT
1 TATTTATTTAATTCGATTAT
18975 TATTT-TTTATATTCGATT
1 TATTTATTTA-ATTCGATT
18993 CTCATATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTATTTAATTCGATTAT
Found at i:19202 original size:14 final size:13
Alignment explanation
Indices: 19156--19208 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 13
19146 AAATTGAATG
19156 ATTAATTTACTAAA
1 ATTAATTTA-TAAA
*
19170 ATATAATCATATAAAA
1 AT-TAAT-TTAT-AAA
19186 ATTAATTGTATAAA
1 ATTAATT-TATAAA
19200 ATTAATTTA
1 ATTAATTTA
19209 ATTTTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 2 0.06
14 12 0.36
15 12 0.36
16 7 0.21
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (13 bp):
ATTAATTTATAAA
Found at i:19815 original size:21 final size:21
Alignment explanation
Indices: 19765--19815 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
19755 TGAATCGGTT
19765 AATTTAAATTAAAATAATTTTA
1 AATTTAAA-TAAAATAATTTTA
*
19787 AATATTAAA-AAAATACTTTTA
1 AAT-TTAAATAAAATAATTTTA
19808 ATATTTAA
1 A-ATTTAA
19816 TGAATAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 16 0.62
22 5 0.19
23 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTAAATAAAATAATTTTA
Found at i:26519 original size:25 final size:24
Alignment explanation
Indices: 26458--26520 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
26448 TACAGATTAA
26458 AAATTTAATT-TAAATTATTATTT
1 AAATTTAATTATAAATTATTATTT
* *
26481 AAATATTAA-AATAATATTTTTATTT
1 AAAT-TTAATTATAA-ATTATTATTT
26506 AAATTTAATTATAAA
1 AAATTTAATTATAAA
26521 AATTTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 4 0.12
24 12 0.36
25 17 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATTTAATTATAAATTATTATTT
Found at i:29800 original size:21 final size:21
Alignment explanation
Indices: 29776--29819 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
29766 TGAAATTATA
*
29776 TATTGGTTAGATGAAAGAATG
1 TATTGGTTAGATGAAAAAATG
** *
29797 TATTTTTTAGTTGAAAAAATG
1 TATTGGTTAGATGAAAAAATG
29818 TA
1 TA
29820 ACTTTTAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (21 bp):
TATTGGTTAGATGAAAAAATG
Found at i:29825 original size:21 final size:21
Alignment explanation
Indices: 29782--29826 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29772 TATATATTGG
* **
29782 TTAGATGAAAGAATGTATTTT
1 TTAGATGAAAAAATGTAACTT
*
29803 TTAGTTGAAAAAATGTAACTT
1 TTAGATGAAAAAATGTAACTT
29824 TTA
1 TTA
29827 ATAACCAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (21 bp):
TTAGATGAAAAAATGTAACTT
Found at i:33217 original size:21 final size:21
Alignment explanation
Indices: 33174--33217 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33164 GATATATTGG
* **
33174 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAAAATGCAACTT
*
33195 TTGGATGAAAAAATGTAACTT
1 TTGGATGAAAAAATGCAACTT
33216 TT
1 TT
33218 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGGATGAAAAAATGCAACTT
Found at i:34549 original size:17 final size:17
Alignment explanation
Indices: 34527--34560 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34517 TCTAATTTTA
*
34527 TTTTATTTTTTATATGT
1 TTTTATATTTTATATGT
*
34544 TTTTATATTTTGTATGT
1 TTTTATATTTTATATGT
34561 ATTACCACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTATATTTTATATGT
Found at i:36060 original size:2 final size:2
Alignment explanation
Indices: 36048--36086 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
36038 AATATCTATC
*
36048 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36087 TCTTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:36495 original size:18 final size:19
Alignment explanation
Indices: 36442--36496 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
36432 ATATAAGTAT
*
36442 AAAAATATAATTT-TTTAA
1 AAAAATATAATTTATATAA
*
36460 AAAAATATTAAATATATATAA
1 AAAAATA-T-AATTTATATAA
36481 AAAAATAT-ATTTATAT
1 AAAAATATAATTTATAT
36497 TTGATATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 14 0.45
19 1 0.03
20 5 0.16
21 11 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATATAATTTATATAA
Found at i:36618 original size:2 final size:2
Alignment explanation
Indices: 36611--36637 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36601 TGAATTAATG
36611 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
36638 GATGAAAATA
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:37302 original size:39 final size:39
Alignment explanation
Indices: 37228--37303 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
37218 ATATTTATGT
* *
37228 AAATCTTTTATATTAATATTTATAATTAAATTTAAATAA
1 AAATCTTTTATATTAATATATATAATTAAAGTTAAATAA
*
37267 AAATTTTTTATTATTAATATA-ATAAATT-AAGTTAAAT
1 AAATCTTTTA-TATTAATATATAT-AATTAAAGTTAAAT
37304 CAAATCAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 19 0.59
40 13 0.41
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (39 bp):
AAATCTTTTATATTAATATATATAATTAAAGTTAAATAA
Found at i:37459 original size:23 final size:25
Alignment explanation
Indices: 37432--37483 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
37422 GGTATAAGTT
*
37432 ATATTGATTTTTAAT-T-TTTTTAA
1 ATATTGATATTTAATATATTTTTAA
* *
37455 ATATTTATATTTAATATATTTTTTA
1 ATATTGATATTTAATATATTTTTAA
37480 ATAT
1 ATAT
37484 GAATATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.54
24 1 0.04
25 10 0.42
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
ATATTGATATTTAATATATTTTTAA
Found at i:38660 original size:12 final size:12
Alignment explanation
Indices: 38627--38681 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
38617 AAAAAAAATT
*
38627 AAAA-TAATATA
1 AAAATTAATTTA
*
38638 AAAATT-TTTTA
1 AAAATTAATTTA
38649 AAAATTAATTTA
1 AAAATTAATTTA
*
38661 ATAAA-TAAATTA
1 A-AAATTAATTTA
38673 AAAATTAAT
1 AAAATTAAT
38682 AAATATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 16 0.46
12 16 0.46
13 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTAATTTA
Found at i:38727 original size:14 final size:15
Alignment explanation
Indices: 38710--38741 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
38700 TTAATTTTTT
38710 TATTTTTAAAA-ATA
1 TATTTTTAAAATATA
38724 TA-TTTTAAAATATA
1 TATTTTTAAAATATA
38738 TATT
1 TATT
38742 ATTTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.50
14 7 0.44
15 1 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTTTAAAATATA
Found at i:40865 original size:23 final size:24
Alignment explanation
Indices: 40819--40866 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40809 GAAAAACTTT
* **
40819 AAATTATTAAATATTATTTTTTAA
1 AAATAATTAAATATTATTAATTAA
40843 AAATAATTAAATA-TATTAATTAA
1 AAATAATTAAATATTATTAATTAA
40866 A
1 A
40867 TTAACTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATAATTAAATATTATTAATTAA
Found at i:41469 original size:14 final size:15
Alignment explanation
Indices: 41430--41472 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
41420 TTATATTTAA
41430 TTTATAATTTA-AATT
1 TTTAT-ATTTATAATT
41445 TTTAATATTTATAATT
1 TTT-ATATTTATAATT
41461 TTT-TATTTATAA
1 TTTATATTTATAA
41473 AATTATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 9 0.35
15 8 0.31
16 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATTTATAATT
Found at i:42835 original size:13 final size:13
Alignment explanation
Indices: 42817--42843 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42807 GCTTCTATAT
42817 ACTCAATTTGGGG
1 ACTCAATTTGGGG
42830 ACTCAATTTGGGG
1 ACTCAATTTGGGG
42843 A
1 A
42844 AAGGAAAATT
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:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (13 bp):
ACTCAATTTGGGG
Found at i:43049 original size:5 final size:5
Alignment explanation
Indices: 43039--43092 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
43029 GACGTACGTA
* *
43039 TTCTT TTC-T TTCTT TATATA TTCTT TTCTT TTCTT TT-TAT TTC-T TTCTT
1 TTCTT TTCTT TTCTT T-TCTT TTCTT TTCTT TTCTT TTCT-T TTCTT TTCTT
43088 TTCTT
1 TTCTT
43093 CTACTATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
4 9 0.22
5 28 0.70
6 3 0.08
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (5 bp):
TTCTT
Found at i:43085 original size:19 final size:21
Alignment explanation
Indices: 43037--43092 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
43027 AAGACGTACG
43037 TATTCTTTTC-TTTCTTTATA
1 TATTCTTTTCTTTTCTTTATA
*
43057 TATTCTTTTCTTTTCTTTTTA
1 TATTCTTTTCTTTTCTTTATA
43078 T-TTC-TTTCTTTTCTT
1 TATTCTTTTCTTTTCTT
43093 CTACTATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 11 0.32
20 13 0.38
21 10 0.29
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (21 bp):
TATTCTTTTCTTTTCTTTATA
Found at i:43554 original size:3 final size:3
Alignment explanation
Indices: 43546--43587 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
43536 TCAATCAATT
43546 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43588 CATAGAAGCA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:44543 original size:21 final size:21
Alignment explanation
Indices: 44496--44544 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
44486 TTAAACTTAG
*
44496 TTAA-ATTTTTTTATTTTTAA
1 TTAATATTTTTTTACTTTTAA
44516 -TATATATTTTTTTACTTTTAA
1 TTA-ATATTTTTTTACTTTTAA
44537 TTAATATT
1 TTAATATT
44545 CAAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 20 0.80
22 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTAATATTTTTTTACTTTTAA
Found at i:44570 original size:12 final size:12
Alignment explanation
Indices: 44553--44577 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44543 TTCAAAAAAT
44553 TTTAATTCAAAC
1 TTTAATTCAAAC
44565 TTTAATTCAAAC
1 TTTAATTCAAAC
44577 T
1 T
44578 CGAATATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAATTCAAAC
Found at i:45993 original size:3 final size:3
Alignment explanation
Indices: 45985--46024 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
45975 ATGCTAAATC
45985 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
46025 TTAGAAGTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:46188 original size:16 final size:15
Alignment explanation
Indices: 46151--46209 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
46141 CAATTTTGAT
*
46151 AAATTTAATTTGAAA
1 AAATTTAATTTAAAA
* *
46166 ATATTAAATTTAAAA
1 AAATTTAATTTAAAA
* *
46181 AAATTTAAATTGAAAT
1 AAATTT-AATTTAAAA
*
46197 CAATTTAATTTAA
1 AAATTTAATTTAA
46210 TTAAAATATT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 22 0.65
16 12 0.35
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (15 bp):
AAATTTAATTTAAAA
Found at i:46275 original size:14 final size:14
Alignment explanation
Indices: 46246--46313 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
46236 TATATATTTT
46246 AAAT-TTAAT-TATA
1 AAATATTAATATA-A
46259 AAATATTAATATAA
1 AAATATTAATATAA
46273 AAATATTTTGAATATTAA
1 AAATA--TT-AATA-TAA
* *
46291 AAATAATAATTTAA
1 AAATATTAATATAA
*
46305 AAATTTTAA
1 AAATATTAA
46314 ATCTATCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
13 4 0.09
14 21 0.47
15 5 0.11
16 3 0.07
17 4 0.09
18 8 0.18
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (14 bp):
AAATATTAATATAA
Found at i:47111 original size:22 final size:22
Alignment explanation
Indices: 47083--47133 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
47073 ATTTATTTAT
47083 AAAATATATAAATATTAATATA
1 AAAATATATAAATATTAATATA
* *
47105 AAAATATTTAAATATTATTATA
1 AAAATATATAAATATTAATATA
47127 AATAATA
1 AA-AATA
47134 AAATGGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATATATAAATATTAATATA
Found at i:47383 original size:25 final size:24
Alignment explanation
Indices: 47315--47369 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 24
47305 GATGACATCA
*
47315 ATTTAGATTAATATAATTTAAATTATT
1 ATTTA-ATTAATAT-A-TAAAATTATT
47342 ATTTAATTAATACTATAAAATTATT
1 ATTTAATTAATA-TATAAAATTATT
47367 ATT
1 ATT
47370 AATATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 12 0.46
26 8 0.31
27 6 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTAATTAATATATAAAATTATT
Found at i:48241 original size:30 final size:29
Alignment explanation
Indices: 48142--48247 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 29
48132 AATTTATCAT
*
48142 TTTAT-TTAAATAAATTTTTATATT-TTTA
1 TTTATATTAAATAAATTTTTA-ATTATTAA
* *
48170 -TTACATGTAAATAAATTATTAATTATTAA
1 TTTATAT-TAAATAAATTTTTAATTATTAA
*
48199 TTTATATTAAATAAATTTTTAACTT-TTGA
1 TTTATATTAAATAAATTTTTAA-TTATTAA
*
48228 TTTTTACTTAAATAAATTTT
1 TTTATA-TTAAATAAATTTT
48248 ATATTTTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
27 3 0.05
28 4 0.06
29 38 0.58
30 20 0.31
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTATATTAAATAAATTTTTAATTATTAA
Found at i:48248 original size:29 final size:28
Alignment explanation
Indices: 48142--48261 Score: 88
Period size: 29 Copynumber: 4.1 Consensus size: 28
48132 AATTTATCAT
*
48142 TTTAT-TTAAATAAATTTTTATATT-TTTA
1 TTTATATTAAATAAA-TTTTA-ATTATTAA
*
48170 -TTACATGTAAATAAATTATTAATTATTAA
1 TTTATAT-TAAATAAATT-TTAATTATTAA
*
48199 TTTATATTAAATAAATTTTTAACTT-TTGA
1 TTTATATTAAATAAA-TTTTAA-TTATTAA
*
48228 TTTTTACTTAAATAAATTTTATATT-TTATA
1 TTTATA-TTAAATAAATTTTA-ATTATTA-A
48258 TTTA
1 TTTA
48262 ATAATTTATT
Statistics
Matches: 75, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
27 3 0.04
28 6 0.08
29 43 0.57
30 23 0.31
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTATATTAAATAAATTTTAATTATTAA
Found at i:48814 original size:29 final size:30
Alignment explanation
Indices: 48777--48850 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
48767 GTAAAATTAA
* *
48777 TTTATTTAATATAATTATTATATTTTAAAT
1 TTTATTTAATATAAATAATATATTTTAAAT
48807 TTTA-TTAATATAAATAATATATTTTAAAT
1 TTTATTTAATATAAATAATATATTTTAAAT
48836 TTTAATTTAAT-TAAA
1 TTT-ATTTAATATAAA
48851 ATATTTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 26 0.65
30 9 0.22
31 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTATTTAATATAAATAATATATTTTAAAT
Found at i:48854 original size:26 final size:27
Alignment explanation
Indices: 48773--48904 Score: 87
Period size: 25 Copynumber: 4.9 Consensus size: 27
48763 TGTTGTAAAA
* **
48773 TTAATTTATTTAATATAATTATTATATT
1 TTAAATTA-TTAATATAATTAAAATATT
* *
48801 TTAAATTTTATTAATATAAATAATATATT
1 TTAAA--TTATTAATATAATTAAAATATT
*
48830 TTAAATT-TTAATTTAATTAAAATA-T
1 TTAAATTATTAATATAATTAAAATATT
* *
48855 TT-AATTATTTATTTAA-TATAAA-ATT
1 TTAAATTATTAATATAATTA-AAATATT
48880 TT-AATTATTAAATATATATATAAAA
1 TTAAATTATT-AATATA-AT-TAAAA
48905 AATATATATT
Statistics
Matches: 86, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
24 7 0.08
25 24 0.28
26 18 0.21
27 3 0.03
28 7 0.08
29 24 0.28
30 3 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAAATTATTAATATAATTAAAATATT
Found at i:48856 original size:13 final size:13
Alignment explanation
Indices: 48840--48886 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
48830 TTAAATTTTA
48840 ATTTAATTAAAAT
1 ATTTAATTAAAAT
**
48853 ATTTAATT-ATTT
1 ATTTAATTAAAAT
48865 ATTTAATATAAAAT
1 ATTTAAT-TAAAAT
48879 -TTTAATTA
1 ATTTAATTA
48887 TTAAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 11 0.39
13 15 0.54
14 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTAATTAAAAT
Found at i:48898 original size:25 final size:26
Alignment explanation
Indices: 48808--48938 Score: 105
Period size: 26 Copynumber: 5.1 Consensus size: 26
48798 ATTTTAAATT
*
48808 TTATTAATATAA-ATAATATATTTTAAA
1 TTATTAATATAATATAAAATA-TTT-AA
*
48835 TT-TTAATTTAAT-TAAAATATTTAA
1 TTATTAATATAATATAAAATATTTAA
* *
48859 TTATTTATTTAATATAAAAT-TTTAA
1 TTATTAATATAATATAAAATATTTAA
* *
48884 TTATTAAATATATATATAAAAAATAT-A
1 TTATT-AATATA-ATATAAAATATTTAA
*
48911 -TATTTAACATAATAT-AAATATTTAA
1 TTA-TTAATATAATATAAAATATTTAA
48936 TTA
1 TTA
48939 AATAAAATTT
Statistics
Matches: 85, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
24 10 0.12
25 27 0.32
26 33 0.39
27 13 0.15
28 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
TTATTAATATAATATAAAATATTTAA
Found at i:48933 original size:18 final size:18
Alignment explanation
Indices: 48910--48959 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
48900 TAAAAAATAT
48910 ATATTTAACATAATATAA
1 ATATTTAACATAATATAA
*
48928 ATATTTAA-TTAA-ATAA
1 ATATTTAACATAATATAA
48944 A-ATTTAACATACATAT
1 ATATTTAACATA-ATAT
48960 TAACTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 6 0.22
16 7 0.26
17 4 0.15
18 10 0.37
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATTTAACATAATATAA
Found at i:49073 original size:32 final size:32
Alignment explanation
Indices: 49040--49099 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
49030 ATTTATTTAT
*
49040 TTTATGATA-TTT-ATATATTATTCATATCATA
1 TTTAT-ATATTTTAATATATTAATCATATCATA
*
49071 TTTATTTATTTTAATATATTAATCATATC
1 TTTATATATTTTAATATATTAATCATATC
49100 TAAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 2 0.08
31 8 0.32
32 15 0.60
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (32 bp):
TTTATATATTTTAATATATTAATCATATCATA
Found at i:49089 original size:18 final size:19
Alignment explanation
Indices: 49030--49090 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
49020 ATTAATTATA
*
49030 ATTTATTTATTTT-ATGAT
1 ATTTATTTATTTTAATCAT
*
49048 ATTTATATATTATTCATATCAT
1 ATTTATTTATT-TT-A-ATCAT
49070 ATTTATTTATTTTAAT-AT
1 ATTTATTTATTTTAATCAT
49088 ATT
1 ATT
49091 AATCATATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 15 0.42
19 4 0.11
20 1 0.03
21 2 0.06
22 14 0.39
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTATTTATTTTAATCAT
Found at i:49114 original size:27 final size:29
Alignment explanation
Indices: 49049--49114 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 29
49039 TTTTATGATA
* *
49049 TTTATATATTATTCATATCATATTTATTTAT
1 TTTATATATTAATCATATCATA--TAATTAT
49080 TTTAATATATTAATCATATC-TA-AATTAT
1 TTT-ATATATTAATCATATCATATAATTAT
49108 TTTATAT
1 TTTATAT
49115 TTATAAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 4 0.12
28 8 0.25
31 5 0.16
32 15 0.47
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTATATATTAATCATATCATATAATTAT
Found at i:49157 original size:15 final size:14
Alignment explanation
Indices: 49132--49212 Score: 66
Period size: 15 Copynumber: 5.9 Consensus size: 14
49122 ACTTTTAAAC
*
49132 ATTAATATATTTTA
1 ATTATTATATTTTA
49146 ATATATTATATTTTA
1 AT-TATTATATTTTA
*
49161 ATTATT-T-TTAT-
1 ATTATTATATTTTA
49172 ATTATTATA-TTTA
1 ATTATTATATTTTA
49185 A-TATTATGGATTTTA
1 ATTATTAT--ATTTTA
49200 ATTAATTA-ATTTT
1 ATT-ATTATATTTT
49213 TCAAGTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
11 6 0.11
12 12 0.22
13 2 0.04
14 12 0.22
15 18 0.33
16 1 0.02
17 4 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTATTATATTTTA
Found at i:49161 original size:25 final size:25
Alignment explanation
Indices: 49133--49188 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
49123 CTTTTAAACA
49133 TTAATATATTTTAATA-TATTATATT
1 TTAATATATTTTAATATTATTATA-T
*
49158 TTAAT-TATTTTTATATTATTATAT
1 TTAATATATTTTAATATTATTATAT
49182 TTAATAT
1 TTAATAT
49189 TATGGATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTAATATATTTTAATATTATTATAT
Found at i:50583 original size:21 final size:21
Alignment explanation
Indices: 50559--50601 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
50549 TTTTTATTTT
50559 TTTAATTTT-TTAAAATAATTA
1 TTTAATTTTATT-AAATAATTA
50580 TTTAATTTTATTAAATAATTA
1 TTTAATTTTATTAAATAATTA
50601 T
1 T
50602 GAATAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAATTTTATTAAATAATTA
Found at i:51530 original size:30 final size:30
Alignment explanation
Indices: 51471--51530 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
51461 TTTTATGCTG
* *
51471 AATTTAATAATATTGAAGACGAATATTATT
1 AATTTAATAATATTAAAGACAAATATTATT
* * *
51501 AATTTAATAGTATTAAAGATAAATGTTATT
1 AATTTAATAATATTAAAGACAAATATTATT
51531 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.42
Consensus pattern (30 bp):
AATTTAATAATATTAAAGACAAATATTATT
Found at i:51627 original size:52 final size:54
Alignment explanation
Indices: 51526--51649 Score: 141
Period size: 52 Copynumber: 2.3 Consensus size: 54
51516 AAGATAAATG
*
51526 TTATTTTTAAAAATTTTTAAAAATATAATTTAAAAGGATTATTAATAATT-T-TT
1 TTATTTTT-AAAATTTTTAAAAATATAATTTAAAAGGATAATTAATAATTATCTT
* *
51579 TTATCTTTAAAATTTTT-AAAATA-AATTTTTATAAA-GATAATTATTAATTATCTT
1 TTATTTTTAAAATTTTTAAAAATATAA--TTTA-AAAGGATAATTAATAATTATCTT
51633 TTATTTCTTAAAATTTT
1 TTATTT-TTAAAATTTT
51650 ATAATGTTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
50 2 0.03
51 6 0.10
52 25 0.41
53 11 0.18
54 7 0.11
55 10 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (54 bp):
TTATTTTTAAAATTTTTAAAAATATAATTTAAAAGGATAATTAATAATTATCTT
Found at i:52233 original size:14 final size:14
Alignment explanation
Indices: 52194--52253 Score: 77
Period size: 14 Copynumber: 4.4 Consensus size: 14
52184 AATATTTTAT
52194 ATATATTAAATATA
1 ATATATTAAATATA
*
52208 A-ATATAAAATATA
1 ATATATTAAATATA
*
52221 ATATTTTAAATATA
1 ATATATTAAATATA
* *
52235 AAAAATTAAATATA
1 ATATATTAAATATA
52249 ATATA
1 ATATA
52254 CATTCGATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 12 0.32
14 25 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATATTAAATATA
Found at i:60582 original size:4 final size:4
Alignment explanation
Indices: 60551--60667 Score: 135
Period size: 4 Copynumber: 29.2 Consensus size: 4
60541 TTCTACCATT
* * *
60551 TCTC TGTC TCTC TCTG TCTC TCTG TCTC TCTC TCTC TCTC TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
* * * * * * * *
60599 TCTC TGTC TCTG TCTC TGTC TGTC TGTC TGTC TGTC TGTC TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
60647 TCTC TCTC TCTC TCTC TCTC T
1 TCTC TCTC TCTC TCTC TCTC T
60668 TTTTAAATTT
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 101 1.00
ACGTcount: A:0.00, C:0.40, G:0.09, T:0.50
Consensus pattern (4 bp):
TCTC
Found at i:70129 original size:23 final size:23
Alignment explanation
Indices: 70099--70143 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
70089 AAAATTATAT
* * *
70099 TTTTATATTTATATTTTAAAAAG
1 TTTTATATATAAATATTAAAAAG
70122 TTTTATATATAAATATTAAAAA
1 TTTTATATATAAATATTAAAAA
70144 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTATATATAAATATTAAAAAG
Found at i:73262 original size:2 final size:2
Alignment explanation
Indices: 73249--73289 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
73239 ACAAATGCTT
*
73249 AC AC AT AC AC AC AC 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 AC AC AC AC AC AC AC A
73290 GAGACAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:73512 original size:2 final size:2
Alignment explanation
Indices: 73505--73533 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
73495 GAAATGTATC
73505 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73534 TCTTGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74003 original size:17 final size:18
Alignment explanation
Indices: 73977--74011 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
73967 AACATTAAAT
73977 AAATAAAATAAA-TATAA
1 AAATAAAATAAATTATAA
*
73994 AAATATAATAAATTATAA
1 AAATAAAATAAATTATAA
74012 TTAATTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAAATAAATTATAA
Found at i:74012 original size:10 final size:9
Alignment explanation
Indices: 73974--74012 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
73964 TTAAACATTA
*
73974 AATAAATAA
1 AATAAATAT
73983 AATAAATAT
1 AATAAATAT
73992 AA-AAATAT
1 AATAAATAT
74000 AATAAATTAT
1 AATAAA-TAT
74010 AAT
1 AAT
74013 TAATTAAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 8 0.30
9 13 0.48
10 6 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAAATAT
Found at i:74266 original size:16 final size:17
Alignment explanation
Indices: 74227--74266 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
74217 CAAATACTTC
*
74227 AATATAAA-AAACTTAA
1 AATATAAATAAACTGAA
74243 AA-ATAAATAAA-TGAA
1 AATATAAATAAACTGAA
74258 AATATAAAT
1 AATATAAAT
74267 TATATGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (17 bp):
AATATAAATAAACTGAA
Found at i:74361 original size:2 final size:2
Alignment explanation
Indices: 74356--74392 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
74346 ATTTGTAGTT
74356 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
74393 CAGTGACTAA
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:75219 original size:21 final size:21
Alignment explanation
Indices: 75195--75236 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
75185 ATATTTTATA
75195 ATTATTTTTAA-ATAAAAATAT
1 ATTA-TTTTAATATAAAAATAT
*
75216 ATTATTTTAATTTAAAAATAT
1 ATTATTTTAATATAAAAATAT
75237 TGTTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTTTAATATAAAAATAT
Found at i:75793 original size:2 final size:2
Alignment explanation
Indices: 75778--75814 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
75768 ACAACTACAT
75778 TA TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
75815 TACATTCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:76100 original size:5 final size:5
Alignment explanation
Indices: 76092--76152 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
76082 TAATACGATT
* * *
76092 ATATA ATATAA AAATA AT-TA ATA-A TATAAA ATATA ATATA ATATA AAATA
1 ATATA ATAT-A ATATA ATATA ATATA -ATATA ATATA ATATA ATATA ATATA
*
76142 AAATA ATATA A
1 ATATA ATATA A
76153 AAATAAATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
4 5 0.11
5 37 0.79
6 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
ATATA
Found at i:76114 original size:7 final size:8
Alignment explanation
Indices: 76094--76161 Score: 52
Period size: 8 Copynumber: 8.4 Consensus size: 8
76084 ATACGATTAT
76094 ATAATATA
1 ATAATATA
*
76102 AAAATAATTA
1 ATAAT-A-TA
76112 ATAATATA
1 ATAATATA
76120 A-AATATAA
1 ATAATAT-A
76128 TATAATATA
1 -ATAATATA
*
76137 A-AATAAA
1 ATAATATA
76144 ATAATATA
1 ATAATATA
*
76152 AAAATA-A
1 ATAATATA
76159 ATA
1 ATA
76162 CAAATATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
7 14 0.29
8 19 0.40
9 4 0.08
10 11 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
ATAATATA
Found at i:76124 original size:10 final size:10
Alignment explanation
Indices: 76094--76173 Score: 62
Period size: 10 Copynumber: 8.0 Consensus size: 10
76084 ATACGATTAT
76094 ATAATATAAAA
1 ATAATAT-AAA
76105 ATAAT-T--A
1 ATAATATAAA
76112 ATAATATAAAA
1 ATAATAT-AAA
*
76123 TATAATATAAT
1 -ATAATATAAA
*
76134 ATAAAATAAA
1 ATAATATAAA
76144 ATAATATAAAA
1 ATAATAT-AAA
76155 ATAA-ATACAA
1 ATAATATA-AA
76165 AT-ATATAAA
1 ATAATATAAA
76174 CATTATAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
7 6 0.11
8 1 0.02
9 4 0.07
10 24 0.42
11 15 0.26
12 7 0.12
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (10 bp):
ATAATATAAA
Found at i:76161 original size:15 final size:16
Alignment explanation
Indices: 76094--76159 Score: 89
Period size: 15 Copynumber: 4.0 Consensus size: 16
76084 ATACGATTAT
76094 ATAATATAAAAATAATTA
1 ATAATATAAAAATAA--A
*
76112 ATAATATAAAATATAAT
1 ATAATATAAAA-ATAAA
76129 ATAATAT-AAAATAAA
1 ATAATATAAAAATAAA
76144 ATAATATAAAAATAAA
1 ATAATATAAAAATAAA
76160 TACAAATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
15 11 0.25
16 11 0.25
17 7 0.16
18 11 0.25
19 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATATAAAAATAAA
Found at i:76199 original size:17 final size:17
Alignment explanation
Indices: 76092--76158 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
76082 TAATACGATT
76092 ATATAATATAAAA-ATA
1 ATATAATATAAAATATA
76108 ATTAATAATATAAAATATA
1 A-T-ATAATATAAAATATA
76127 ATATAATATAAAATA-A
1 ATATAATATAAAATATA
76143 A-ATAATATAAAA-ATA
1 ATATAATATAAAATATA
76158 A
1 A
76159 ATACAAATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.02
15 13 0.28
16 3 0.06
17 14 0.30
18 12 0.26
19 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATATAATATAAAATATA
Found at i:77944 original size:2 final size:2
Alignment explanation
Indices: 77937--77968 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
77927 AAATGTACTA
*
77937 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77969 GCATGCACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:79199 original size:22 final size:21
Alignment explanation
Indices: 79174--79215 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
79164 CTTTAATAAC
79174 AAATTGAATTAAATTTAACTCA
1 AAATTGAATTAAA-TTAACTCA
* *
79196 AAATTTAATTCAATTAACTC
1 AAATTGAATTAAATTAACTC
79216 GCAATAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATTGAATTAAATTAACTCA
Found at i:79251 original size:16 final size:15
Alignment explanation
Indices: 79225--79258 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
79215 CGCAATAACT
*
79225 TTTAAAAATATAATA
1 TTTAAAAATATAAAA
79240 TTTAACAAATATAAAA
1 TTTAA-AAATATAAAA
79256 TTT
1 TTT
79259 TAATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTAAAAATATAAAA
Found at i:81205 original size:20 final size:20
Alignment explanation
Indices: 81180--81222 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
81170 TTGAGAATGA
81180 ATGAGAACGAATTTGGTCAT
1 ATGAGAACGAATTTGGTCAT
*
81200 ATGAGAATGAATTTGGTCAT
1 ATGAGAACGAATTTGGTCAT
81220 ATG
1 ATG
81223 TTAACTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.33
Consensus pattern (20 bp):
ATGAGAACGAATTTGGTCAT
Found at i:84432 original size:8 final size:8
Alignment explanation
Indices: 84419--84443 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
84409 TTGAAGTTAA
84419 AAAAATTT
1 AAAAATTT
84427 AAAAATTT
1 AAAAATTT
84435 AAAAATTT
1 AAAAATTT
84443 A
1 A
84444 TATATTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAAATTT
Found at i:84459 original size:13 final size:12
Alignment explanation
Indices: 84441--84500 Score: 65
Period size: 11 Copynumber: 5.2 Consensus size: 12
84431 ATTTAAAAAT
84441 TTATATATTTATA
1 TTATATA-TTATA
84454 TTATATA-TATA
1 TTATATATTATA
84465 TTATAT-TTATA
1 TTATATATTATA
*
84476 -TATTTTATTATA
1 TTA-TATATTATA
84488 TTATA-ATTATA
1 TTATATATTATA
84499 TT
1 TT
84501 TAAAATATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 2 0.05
11 24 0.59
12 6 0.15
13 9 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATATATTATA
Found at i:84511 original size:29 final size:30
Alignment explanation
Indices: 84439--84522 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
84429 AAATTTAAAA
*
84439 ATTTATATATTTATATTATA-TATATATTAT
1 ATTTAAATATTT-TATTATATTATATATTAT
*
84469 ATTTATATATTTTATTATATTATA-ATTAT
1 ATTTAAATATTTTATTATATTATATATTAT
*
84498 ATTTAAA-ATATTTAATAT-TTATATA
1 ATTTAAATAT-TTTATTATATTATATA
84523 AATTTTAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
28 7 0.14
29 26 0.53
30 16 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTAAATATTTTATTATATTATATATTAT
Found at i:87917 original size:22 final size:24
Alignment explanation
Indices: 87892--87955 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
87882 ATAAGTTTAA
*
87892 TATAAAACT-TAAATAAATAT-GT
1 TATAAAAATATAAATAAATATAGT
* *
87914 TATAAAAATATAATTAAATATATT
1 TATAAAAATATAAATAAATATAGT
87938 TATAAATAAT-TAAA-AAAT
1 TATAAA-AATATAAATAAAT
87956 TAATGAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 8 0.23
23 14 0.40
24 10 0.29
25 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TATAAAAATATAAATAAATATAGT
Found at i:87931 original size:23 final size:23
Alignment explanation
Indices: 87875--87955 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 23
87865 TGATTCATTT
* * *
87875 AAATTAAATAAGTTTA-ATATAA
1 AAATTAAATAAATATAGTTATAA
*
87897 AACTTAAATAAATAT-GTTATAA
1 AAATTAAATAAATATAGTTATAA
* *
87919 AAATATAATTAAATATATTTATAA
1 AAAT-TAAATAAATATAGTTATAA
87943 ATAATTAAA-AAAT
1 A-AATTAAATAAAT
87956 TAATGAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
22 20 0.43
23 14 0.30
24 10 0.21
25 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATTAAATAAATATAGTTATAA
Found at i:90415 original size:13 final size:14
Alignment explanation
Indices: 90397--90426 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
90387 ATAAATATCA
90397 ATCATATATTAT-T
1 ATCATATATTATAT
90410 ATCATATATTATAT
1 ATCATATATTATAT
90424 ATC
1 ATC
90427 TAAATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (14 bp):
ATCATATATTATAT
Found at i:91826 original size:2 final size:2
Alignment explanation
Indices: 91819--91848 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
91809 AGCAAATAGA
91819 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
91849 GACAACATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92013 original size:3 final size:3
Alignment explanation
Indices: 92005--92053 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
91995 AAGAATTTAC
92005 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
92053 T
1 T
92054 TTGTGAAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:92717 original size:21 final size:20
Alignment explanation
Indices: 92693--92736 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
92683 AGATTAATTG
*
92693 TTATAGTAATAAAATTAAATA
1 TTATAATAATAAAATTAAA-A
* *
92714 TTATAATGATATAATTAAAA
1 TTATAATAATAAAATTAAAA
92734 TTA
1 TTA
92737 AAGATACGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TTATAATAATAAAATTAAAA
Found at i:95859 original size:31 final size:31
Alignment explanation
Indices: 95822--95881 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
95812 AATAATTACA
95822 ATAATATTTATTATATTTATAATTATGATAG
1 ATAATATTTATTATATTTATAATTATGATAG
95853 ATAATATTTATTATATTTATAATTATGAT
1 ATAATATTTATTATATTTATAATTATGAT
95882 CAATATGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (31 bp):
ATAATATTTATTATATTTATAATTATGATAG
Found at i:99318 original size:27 final size:30
Alignment explanation
Indices: 99287--99347 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
99277 TATAAATTAA
*
99287 ATATATGT-AAATTTTTTAATTTT-T-TTT
1 ATATATGTAAAATATTTTAATTTTATATTT
* *
99314 ATATATTTAAAATATTTTATTTTTATATTT
1 ATATATGTAAAATATTTTAATTTTATATTT
99344 ATAT
1 ATAT
99348 TTAATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.25
28 13 0.46
29 1 0.04
30 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (30 bp):
ATATATGTAAAATATTTTAATTTTATATTT
Found at i:99790 original size:20 final size:20
Alignment explanation
Indices: 99767--99860 Score: 56
Period size: 18 Copynumber: 4.8 Consensus size: 20
99757 AAATAATTTT
99767 ATATAATAAAATAAATATAA
1 ATATAATAAAATAAATATAA
**
99787 ATAT--TAAAATTTAT-TATA
1 ATATAATAAAATAAATATA-A
* *
99805 ATATATTAAATATAATTAT-A
1 ATATAATAAA-ATAAATATAA
* *
99825 ATAT-ATAAAAT-TATATTA
1 ATATAATAAAATAAATATAA
99843 ATATAATATAATATAAAT
1 ATATAATA-AA-ATAAAT
99861 GTTTGAATTA
Statistics
Matches: 55, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
17 5 0.09
18 20 0.36
19 7 0.13
20 15 0.27
21 5 0.09
22 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAATAAAATAAATATAA
Found at i:99857 original size:5 final size:5
Alignment explanation
Indices: 99767--99858 Score: 61
Period size: 5 Copynumber: 19.2 Consensus size: 5
99757 AAATAATTTT
* * * * * *
99767 ATATA ATAAA ATA-A ATATA A-ATA TTAAA ATTTA TTATA ATATA TTA-A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
99814 ATATA ATTATA ATAT- ATA-A A-ATT ATATTA ATATA ATATA ATATA A
1 ATATA A-TATA ATATA ATATA ATATA ATA-TA ATATA ATATA ATATA A
99859 ATGTTTGAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
3 1 0.02
4 15 0.23
5 41 0.62
6 9 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:100265 original size:16 final size:16
Alignment explanation
Indices: 100213--100265 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
100203 ATTAAAATAG
*
100213 ATTATTTTTAAGTT-AA
1 ATTA-TTTTAATTTGAA
100229 ATTATTTTAGATTTG--
1 ATTATTTTA-ATTTGAA
100244 ATTATTTTAATTTGAA
1 ATTATTTTAATTTGAA
100260 ATTATT
1 ATTATT
100266 CAAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 5 0.16
15 14 0.44
16 13 0.41
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (16 bp):
ATTATTTTAATTTGAA
Found at i:104424 original size:27 final size:28
Alignment explanation
Indices: 104376--104433 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
104366 ATGACAATTA
*
104376 ATAAATTAATATTTAAAGTATAAAG-AT
1 ATAAATTAATATTTAAACTATAAAGCAT
* *
104403 ATAAATTAA-ATATTAATCTATATAGCAT
1 ATAAATTAATAT-TTAAACTATAAAGCAT
104431 ATA
1 ATA
104434 TAATGGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 2 0.08
27 19 0.73
28 5 0.19
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38
Consensus pattern (28 bp):
ATAAATTAATATTTAAACTATAAAGCAT
Found at i:106067 original size:17 final size:17
Alignment explanation
Indices: 106045--106079 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
106035 ATATGGTATC
*
106045 ATAATTTTTTTAAAAAA
1 ATAATTTTTTGAAAAAA
106062 ATAATTTTTTGAAAAAA
1 ATAATTTTTTGAAAAAA
106079 A
1 A
106080 AACTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATAATTTTTTGAAAAAA
Found at i:115731 original size:23 final size:21
Alignment explanation
Indices: 115685--115737 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
115675 ATAAAATTAT
115685 TTTTATATTAATATTTATATA
1 TTTTATATTAATATTTATATA
115706 TTTTATAATTAA-ATTTAAATATA
1 TTTTAT-ATTAATATTT--ATATA
115729 TTTT-TATTA
1 TTTTATATTA
115738 CTTAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 14 0.48
22 6 0.21
23 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATATTAATATTTATATA
Found at i:121736 original size:12 final size:12
Alignment explanation
Indices: 121695--121747 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
121685 ATTTGATACG
*
121695 ATAT-AAATATT
1 ATATAAAATATA
*
121706 ATATAAAAAAATA
1 ATAT-AAAATATA
121719 AT-TAAAATATA
1 ATATAAAATATA
*
121730 ATATAAAATATG
1 ATATAAAATATA
121742 ATATAA
1 ATATAA
121748 TAAAAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 13 0.37
12 15 0.43
13 7 0.20
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:121747 original size:17 final size:17
Alignment explanation
Indices: 121724--121764 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
121714 AAATAATTAA
* *
121724 AATATAATATAAAATAT
1 AATATAATAAAAAAAAT
*
121741 GATATAATAAAAAAAAT
1 AATATAATAAAAAAAAT
121758 AATATAA
1 AATATAA
121765 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AATATAATAAAAAAAAT
Found at i:121775 original size:36 final size:36
Alignment explanation
Indices: 121698--121776 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
121688 TGATACGATA
* *
121698 TAAATATTATATAAAAAAATAATTAAAATATAATAT
1 TAAATATGATATAAAAAAATAAATAAAATATAATAT
* *
121734 AAAATATGATATAATAAAAA-AAATAATATA-AATATT
1 TAAATATGATATAA-AAAAATAAATAAAATATAATA-T
121770 TAAATAT
1 TAAATAT
121777 ATTTAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 4 0.11
36 27 0.75
37 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (36 bp):
TAAATATGATATAAAAAAATAAATAAAATATAATAT
Found at i:121878 original size:19 final size:22
Alignment explanation
Indices: 121854--121893 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
121844 AATTATTATA
121854 AAAAAT-AA-AAAT-ATAACAT
1 AAAAATCAATAAATAATAACAT
121873 AAAAATCAATAAATAATAACA
1 AAAAATCAATAAATAATAACA
121894 ATTATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 4 0.22
22 6 0.33
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAAATCAATAAATAATAACAT
Found at i:121975 original size:21 final size:21
Alignment explanation
Indices: 121937--121999 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
121927 TTTAATTTGT
*
121937 ATTTGAACTTTAAAATTTTAG
1 ATTTGAAATTTAAAATTTTAG
** *
121958 ATTTGAAATTTATGATTTTCAA
1 ATTTGAAATTTAAAATTTT-AG
*
121980 ATTTAAAAATTTAAAATTTT
1 ATTT-GAAATTTAAAATTTT
122000 TTGTTTCGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 16 0.48
22 5 0.15
23 12 0.36
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.49
Consensus pattern (21 bp):
ATTTGAAATTTAAAATTTTAG
Found at i:124659 original size:20 final size:19
Alignment explanation
Indices: 124604--124660 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
124594 CTTAACCTAA
* * *
124604 TTATTTTTTATTATAATAT
1 TTATATTTTATTATATTAG
*
124623 TTATATTTTATAATATTAG
1 TTATATTTTATTATATTAG
*
124642 TTATAATTTTATTTTATTA
1 TTAT-ATTTTATTATATTA
124661 ATTTTTGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATATTTTATTATATTAG
Found at i:126046 original size:29 final size:29
Alignment explanation
Indices: 125987--126046 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
125977 CTTATTTTTA
*
125987 AAAAATATATTAAAATAATAAAATTAAAT
1 AAAAATATATTAAAATAATAAAATAAAAT
126016 AAAAATATATTTAAAA-AATAAAA-AAATAT
1 AAAAATATA-TTAAAATAATAAAATAAA-AT
126045 AA
1 AA
126047 TATAAATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 20 0.71
30 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAAATATATTAAAATAATAAAATAAAAT
Found at i:126109 original size:14 final size:15
Alignment explanation
Indices: 126079--126134 Score: 69
Period size: 15 Copynumber: 3.6 Consensus size: 15
126069 TAAATTATTT
126079 AATTATAAATATAAAAA
1 AATT-TAAAT-TAAAAA
126096 AA-TTAAATTAAAAA
1 AATTTAAATTAAAAA
*
126110 AATTTAAATTAAATTA
1 AATTTAAATTAAA-AA
126126 AATTTAAAT
1 AATTTAAAT
126135 AAATTTATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 8 0.22
15 15 0.42
16 11 0.31
17 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTTAAATTAAAAA
Found at i:128665 original size:14 final size:15
Alignment explanation
Indices: 128628--128666 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 15
128618 ATTACTAAAT
128628 TTAATATTAACTTTTA
1 TTAA-ATTAACTTTTA
128644 TATAAATTAA-TTTTA
1 T-TAAATTAACTTTTA
128659 TTAAATTA
1 TTAAATTA
128667 TGTTGCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.32
15 6 0.27
16 6 0.27
17 3 0.14
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAAATTAACTTTTA
Found at i:130861 original size:29 final size:30
Alignment explanation
Indices: 130829--130885 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
130819 GAATTTGAAA
*
130829 ATAATTCCAT-TTACCCCTCTAAAGTTTGG
1 ATAATACCATCTTACCCCTCTAAAGTTTGG
* * *
130858 ATAATACCCTCTTTCTCCTCTAAAGTTT
1 ATAATACCATCTTACCCCTCTAAAGTTT
130886 AATACAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 8 0.35
30 15 0.65
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.40
Consensus pattern (30 bp):
ATAATACCATCTTACCCCTCTAAAGTTTGG
Found at i:131271 original size:17 final size:17
Alignment explanation
Indices: 131249--131286 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
131239 CCATTATTTT
131249 AAAATT-TTAAAGATAAA
1 AAAATTATTAAA-ATAAA
131266 AAAATTGATTAAAATAAA
1 AAAATT-ATTAAAATAAA
131284 AAA
1 AAA
131287 TAATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAATTATTAAAATAAA
Found at i:132413 original size:4 final size:4
Alignment explanation
Indices: 132404--132430 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
132394 TATTTTTATT
132404 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
132431 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:133188 original size:2 final size:2
Alignment explanation
Indices: 133181--133224 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
133171 TCTTTCAATA
133181 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
133223 AT
1 AT
133225 GATTGGAACT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134753 original size:19 final size:19
Alignment explanation
Indices: 134715--134753 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
134705 TGGTTATCGA
**
134715 GGCACTGTTCACGTACACG
1 GGCACTGTTCACACACACG
*
134734 GGCACTGTTCACACATACG
1 GGCACTGTTCACACACACG
134753 G
1 G
134754 TTACTATGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (19 bp):
GGCACTGTTCACACACACG
Found at i:136590 original size:14 final size:14
Alignment explanation
Indices: 136571--136597 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
136561 AAAAAAGAAT
136571 TTTTTATTATTTTA
1 TTTTTATTATTTTA
136585 TTTTTATTATTTT
1 TTTTTATTATTTT
136598 TAATTTTGTA
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:137730 original size:20 final size:20
Alignment explanation
Indices: 137705--137768 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
137695 CCTATCATTT
137705 CATGTTTTCTACAAGCTTCA
1 CATGTTTTCTACAAGCTTCA
*
137725 CATGTTTTCTACATGCTTCA
1 CATGTTTTCTACAAGCTTCA
*
137745 CAAGTTTTCTACAAGCTTCA
1 CATGTTTTCTACAAGCTTCA
137765 CATG
1 CATG
137769 ATGGCAACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (20 bp):
CATGTTTTCTACAAGCTTCA
Found at i:138600 original size:42 final size:42
Alignment explanation
Indices: 138520--139208 Score: 925
Period size: 42 Copynumber: 16.4 Consensus size: 42
138510 TCCAAAGTCA
* * * * *
138520 AAGCCGACAGACAGACTAAGGATAAGAAAAGTCTCCAGGGTCA
1 AAGCCGACAGGCAGACTAAGG-GAAGGAAAGTCTCCAGGGACG
* * ** *
138563 AAGCCGACAGGCAGATTGAGGGTTGAAAAGTCTCCAGGGACG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
138605 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
*
138647 AAGCCGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGACG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
* *
138689 AAGCCGATAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGACG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
*
138731 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGATG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
* *
138773 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTCA
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
* * * * *
138815 AAGCCGACAGGTAGACTAAGGGCAGGAAAATCTCC-GAGGTCA
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAG-GGACG
* *
138857 AAGCCGACAAGCAGACTAAGGGTAGGAAAGTCTCCAGGGACG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
* *
138899 AAGCCGACAGACAGACTAAGGGAAGGAAAGTCTCTAGGGACG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
* * * *
138941 AAGCCGACAGGCAGACTAAGGGAAGAAAAGTCTCCGGGGTCA
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
* * * * *
138983 AAGCCGACAGGCAAACTAAGGAAAAGAAAGTCTCC-GAGGTCA
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAG-GGACG
* * * *
139025 AAGCCGACAAGCAGACTAAGGGTAGGAAAGTCTCC-GAGGTCA
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAG-GGACG
* * *
139067 AAGTCGACAGGCAGACTAAGGGTAGGAAAGTCTCCAAGGACG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
* *
139109 AAGCCGACAGGCAGACTAAGAGAAAGAAAGTCTCCAGGGACG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
139151 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
1 AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
*
139193 AAGCCAACAGGCAGAC
1 AAGCCGACAGGCAGAC
139209 GAAGCCGACA
Statistics
Matches: 578, Mismatches: 64, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
41 2 0.00
42 557 0.96
43 19 0.03
ACGTcount: A:0.37, C:0.21, G:0.33, T:0.10
Consensus pattern (42 bp):
AAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
Found at i:139209 original size:17 final size:17
Alignment explanation
Indices: 139189--139225 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
139179 AGTCTCCAGG
*
139189 GACGAAGCCAACAGGCA
1 GACGAAGCCAACAAGCA
*
139206 GACGAAGCCGACAAGCA
1 GACGAAGCCAACAAGCA
139223 GAC
1 GAC
139226 TAAGGGAAGG
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:0.41, C:0.30, G:0.30, T:0.00
Consensus pattern (17 bp):
GACGAAGCCAACAAGCA
Found at i:139232 original size:42 final size:41
Alignment explanation
Indices: 139186--139316 Score: 111
Period size: 42 Copynumber: 3.1 Consensus size: 41
139176 GAAAGTCTCC
139186 AGGGACG-AAGCCAACAGGCAGACGAAGCCGACAAGCAGACTA
1 AGGGACGAAAGCCAACAGG--GACGAAGCCGACAAGCAGACTA
* * **
139228 AGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAAGCAGACTA
1 AGGG-ACGAAAGCCAACAGGGACGAAGCCGACAAGCAGACTA
* * ** * * * *
139270 AGGGAAGGAAAGTCTCCGGGGTCAAAGCCAACAAGCAGACTA
1 AGGG-ACGAAAGCCAACAGGGACGAAGCCGACAAGCAGACTA
139312 AGGGA
1 AGGGA
139317 AGGAAAGTCT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.01
42 68 0.86
43 2 0.03
44 8 0.10
ACGTcount: A:0.39, C:0.22, G:0.33, T:0.06
Consensus pattern (41 bp):
AGGGACGAAAGCCAACAGGGACGAAGCCGACAAGCAGACTA
Found at i:139239 original size:59 final size:59
Alignment explanation
Indices: 139147--139267 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 59
139137 AGTCTCCAGG
* *
139147 GACGAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCAACAGGCA
1 GACGAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCAACAAGCA
*
139206 GACGAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAAGCA
1 GACGAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCAACAAGCA
139265 GAC
1 GAC
139268 TAAGGGAAGG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.38, C:0.24, G:0.33, T:0.05
Consensus pattern (59 bp):
GACGAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCAACAAGCA
Found at i:139280 original size:101 final size:101
Alignment explanation
Indices: 139105--139309 Score: 338
Period size: 101 Copynumber: 2.0 Consensus size: 101
139095 AGTCTCCAAG
* *
139105 GACGAAGCCGACAGGCAGACTAAGAGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAA
1 GACGAAGCCGACAAGCAGACTAAGAGAAAGAAAGTCTCCAGGGACGAAGCCGACAAGCAGACTAA
* *
139170 GGGAAGGAAAGTCTCCAGGGACGAAGCCAACAGGCA
66 GGGAAGGAAAGTCTCCAGGGACAAAGCCAACAAGCA
* *
139206 GACGAAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAAGCAGACTAA
1 GACGAAGCCGACAAGCAGACTAAGAGAAAGAAAGTCTCCAGGGACGAAGCCGACAAGCAGACTAA
* *
139271 GGGAAGGAAAGTCTCCGGGGTCAAAGCCAACAAGCA
66 GGGAAGGAAAGTCTCCAGGGACAAAGCCAACAAGCA
139307 GAC
1 GAC
139310 TAAGGGAAGG
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.39, C:0.23, G:0.32, T:0.06
Consensus pattern (101 bp):
GACGAAGCCGACAAGCAGACTAAGAGAAAGAAAGTCTCCAGGGACGAAGCCGACAAGCAGACTAA
GGGAAGGAAAGTCTCCAGGGACAAAGCCAACAAGCA
Found at i:139317 original size:42 final size:42
Alignment explanation
Indices: 139210--139443 Score: 378
Period size: 42 Copynumber: 5.6 Consensus size: 42
139200 CAGGCAGACG
* * *
139210 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGGACG
1 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCA
139252 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCA
1 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCA
* *
139294 AAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCCGGAGTCA
1 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCA
* *
139336 AAGCTGACAGGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCA
1 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCA
* * *
139378 AAGCCGATAGGCAGACTAAGGGTAGGAAAGTCTCCGGGGTCA
1 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCA
139420 AAGCCGACAAGCAGACTAAGGGAA
1 AAGCCGACAAGCAGACTAAGGGAA
139444 AACAAAAAAG
Statistics
Matches: 177, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 177 1.00
ACGTcount: A:0.37, C:0.21, G:0.33, T:0.10
Consensus pattern (42 bp):
AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCA
Found at i:139346 original size:143 final size:143
Alignment explanation
Indices: 139071--139351 Score: 411
Period size: 143 Copynumber: 2.0 Consensus size: 143
139061 AGGTCAAAGT
* * *
139071 CGACAGGCAGACTAAGGGTAGGAAAGTCTCCAAGGACGAAGCCGACAGGCAGACTAAGAGAAAGA
1 CGACAAGCAGACTAAGGGAAGGAAAGTCTCCAAGGACGAAGCCGACAAGCAGACTAAGAGAAAGA
* * * *
139136 AAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCAAC
66 AAGTCTCCAGGGACAAAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGGACAAAGCCAAC
139201 AGGCAGACGAAGC
131 AGGCAGACGAAGC
* * *
139214 CGACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAAGCAGACTAAGGGAAGGA
1 CGACAAGCAGACTAAGGGAAGGAAAGTCTCCAAGGACGAAGCCGACAAGCAGACTAAGAGAAAGA
* * * **
139279 AAGTCTCCGGGGTCAAAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCC-GGAGTCAAAGCTGA
66 AAGTCTCCAGGGACAAAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCCAGG-GACAAAGCCAA
139343 CAGGCAGAC
130 CAGGCAGAC
139352 TAAGGGAAGG
Statistics
Matches: 122, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
142 2 0.02
143 120 0.98
ACGTcount: A:0.38, C:0.22, G:0.32, T:0.08
Consensus pattern (143 bp):
CGACAAGCAGACTAAGGGAAGGAAAGTCTCCAAGGACGAAGCCGACAAGCAGACTAAGAGAAAGA
AAGTCTCCAGGGACAAAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCCAGGGACAAAGCCAAC
AGGCAGACGAAGC
Found at i:139347 original size:185 final size:185
Alignment explanation
Indices: 139025--139393 Score: 508
Period size: 185 Copynumber: 2.0 Consensus size: 185
139015 TCCGAGGTCA
* * * * *
139025 AAGCCGACAAGCAGACTAAGGGTAGGAAAGTCTCCGAGGTCAAAGTCGACAGGCAGACTAAGGGT
1 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGAGGACAAAGCCGACAAGCAGACTAAGGGA
* * * *
139090 AGGAAAGTCTCCAAGGACGAAGCCGACAGGCAGACTAAGAGAAAGAAAGTCTCCAGGGACGAAGC
66 AGGAAAGTCTCCAAGGACAAAGCCAACAAGCAGACTAAGAGAAAGAAAGTCTCCAGGGACAAAGC
*
139155 CGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCAACAGGCAGACG
131 CGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACAAAGCCAACAGGCAGACG
*
139210 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCC-AGGGACGAAGCCGACAAGCAGACTAAGGG
1 AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGA-GGACAAAGCCGACAAGCAGACTAAGGG
** * * * *
139274 AAGGAAAGTCTCCGGGGTCAAAGCCAACAAGCAGACTAAGGGAAGGAAAGTCTCC-GGAGTCAAA
65 AAGGAAAGTCTCCAAGGACAAAGCCAACAAGCAGACTAAGAGAAAGAAAGTCTCCAGG-GACAAA
* * * * *
139338 GCTGACAGGCAGACTAAGGGAAGGAAAGTCTCCGGGGTCAAAGCCGATAGGCAGAC
129 GCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACAAAGCCAACAGGCAGAC
139394 TAAGGGTAGG
Statistics
Matches: 160, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
184 3 0.02
185 157 0.98
ACGTcount: A:0.37, C:0.21, G:0.33, T:0.09
Consensus pattern (185 bp):
AAGCCGACAAGCAGACTAAGGGAAGGAAAGTCTCCGAGGACAAAGCCGACAAGCAGACTAAGGGA
AGGAAAGTCTCCAAGGACAAAGCCAACAAGCAGACTAAGAGAAAGAAAGTCTCCAGGGACAAAGC
CGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGACAAAGCCAACAGGCAGACG
Done.