Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015048.1 Kokia drynarioides strain JFW-HI SEQ_130092, whole genome shotgun sequence
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: 250950
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:37 original size:17 final size:17
Alignment explanation
Indices: 12--54 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2 TCAACCAAAT
*
12 TTAAATTTAGAATAAAC
1 TTAAATTTAAAATAAAC
* *
29 TTAATTTTAAAATAAAT
1 TTAAATTTAAAATAAAC
*
46 TTAAGTTTA
1 TTAAATTTA
55 TTGGGCCCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAAATAAAC
Found at i:1207 original size:13 final size:13
Alignment explanation
Indices: 1189--1215 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1179 TTTGAGTGAT
1189 ATGGTGACATAGG
1 ATGGTGACATAGG
1202 ATGGTGACATAGG
1 ATGGTGACATAGG
1215 A
1 A
1216 GTTAAGGTAG
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:0.33, C:0.07, G:0.37, T:0.22
Consensus pattern (13 bp):
ATGGTGACATAGG
Found at i:5535 original size:24 final size:24
Alignment explanation
Indices: 5504--5559 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
5494 TATGTATATG
5504 TATACATATACATACATATACACA
1 TATACATATACATACATATACACA
* * *
5528 TATGCATATACATACATTTATACA
1 TATACATATACATACATATACACA
5552 TATACATA
1 TATACATA
5560 CATATGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (24 bp):
TATACATATACATACATATACACA
Found at i:5540 original size:12 final size:10
Alignment explanation
Indices: 5505--5564 Score: 61
Period size: 10 Copynumber: 5.8 Consensus size: 10
5495 ATGTATATGT
5505 ATACATATAC
1 ATACATATAC
5515 ATACATATACAC
1 ATACATAT--AC
5527 ATATGCATATAC
1 ATA--CATATAC
*
5539 ATACAT-T-T
1 ATACATATAC
5547 ATACATATAC
1 ATACATATAC
5557 ATACATAT
1 ATACATAT
5565 GTATGTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
8 6 0.14
9 2 0.05
10 19 0.45
12 10 0.24
14 5 0.12
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (10 bp):
ATACATATAC
Found at i:5542 original size:18 final size:18
Alignment explanation
Indices: 5507--5561 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
5497 GTATATGTAT
* *
5507 ACATATACATACATATAC
1 ACATATACATATACATAC
*
5525 ACATATGCATATACATAC
1 ACATATACATATACATAC
**
5543 ATTTATACATATACATAC
1 ACATATACATATACATAC
5561 A
1 A
5562 TATGTATGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (18 bp):
ACATATACATATACATAC
Found at i:5573 original size:24 final size:23
Alignment explanation
Indices: 5500--5573 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 23
5490 TATGTATGTA
5500 TATGTATACATATACATACATAT
1 TATGTATACATATACATACATAT
* ** *
5523 ACACATATGCATATACATAC--A-
1 -TATGTATACATATACATACATAT
5544 T-T-TATACATATACATACATAT
1 TATGTATACATATACATACATAT
5565 GTATGTATA
1 -TATGTATA
5574 TGTATATAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
18 14 0.38
20 1 0.03
22 2 0.05
23 1 0.03
24 19 0.51
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.36
Consensus pattern (23 bp):
TATGTATACATATACATACATAT
Found at i:14549 original size:20 final size:19
Alignment explanation
Indices: 14520--14558 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
14510 TTATTTTAAA
14520 ATTTTAAAAAATTAAAAATT
1 ATTTT-AAAAATTAAAAATT
*
14540 ATTTTTAAAATTAAAAATT
1 ATTTTAAAAATTAAAAATT
14559 GTTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTTAAAAATTAAAAATT
Found at i:14556 original size:28 final size:30
Alignment explanation
Indices: 14508--14570 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
14498 GTAAACAATT
*
14508 AATTA-TTTTAAAATTTTAAAA-AATTAAA
1 AATTATTTTTAAAATTTAAAAATAATTAAA
**
14536 AATTATTTTTAAAA-TTAAAAATTGTTAAA
1 AATTATTTTTAAAATTTAAAAATAATTAAA
14565 AATTAT
1 AATTAT
14571 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
AATTATTTTTAAAATTTAAAAATAATTAAA
Found at i:16523 original size:15 final size:15
Alignment explanation
Indices: 16503--16556 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
16493 ATACTACAAA
16503 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
16518 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
16535 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
16552 ATATT
1 ATATT
16557 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:16757 original size:13 final size:14
Alignment explanation
Indices: 16735--16766 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
16725 ATATTGAAAA
16735 AATA-TAATATTTT
1 AATATTAATATTTT
16748 -ATATTAATATTTT
1 AATATTAATATTTT
16761 AATATT
1 AATATT
16767 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 9 0.53
14 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTAATATTTT
Found at i:24298 original size:26 final size:26
Alignment explanation
Indices: 24262--24311 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
24252 ACATATTTTC
*
24262 TCAAAATTTTACTTGGGGTAAAATCG
1 TCAAAATTTTACTTAGGGTAAAATCG
*
24288 TCAAAATTTTACTTAGGTTAAAAT
1 TCAAAATTTTACTTAGGGTAAAAT
24312 AGGGATGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (26 bp):
TCAAAATTTTACTTAGGGTAAAATCG
Found at i:25551 original size:106 final size:106
Alignment explanation
Indices: 25366--25582 Score: 434
Period size: 106 Copynumber: 2.0 Consensus size: 106
25356 GGCAACACAC
25366 TAATGACAATGTCATTGGACAAAACATAAATCTAAGTTTCTTTCATAATGGTATGTAATGTGGGG
1 TAATGACAATGTCATTGGACAAAACATAAATCTAAGTTTCTTTCATAATGGTATGTAATGTGGGG
25431 ATTAATCATGGTACTTTTAGTGGATTGAATATACGAGTAAA
66 ATTAATCATGGTACTTTTAGTGGATTGAATATACGAGTAAA
25472 TAATGACAATGTCATTGGACAAAACATAAATCTAAGTTTCTTTCATAATGGTATGTAATGTGGGG
1 TAATGACAATGTCATTGGACAAAACATAAATCTAAGTTTCTTTCATAATGGTATGTAATGTGGGG
25537 ATTAATCATGGTACTTTTAGTGGATTGAATATACGAGTAAA
66 ATTAATCATGGTACTTTTAGTGGATTGAATATACGAGTAAA
25578 TAATG
1 TAATG
25583 TTGCAATTAT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 111 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (106 bp):
TAATGACAATGTCATTGGACAAAACATAAATCTAAGTTTCTTTCATAATGGTATGTAATGTGGGG
ATTAATCATGGTACTTTTAGTGGATTGAATATACGAGTAAA
Found at i:37386 original size:21 final size:21
Alignment explanation
Indices: 37362--37405 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
37352 TAACCAACAA
37362 AAGG-AGAAAGAAGAAGAAGAG
1 AAGGAAGAAA-AAGAAGAAGAG
37383 AAGGAAGAAAAAGAAGAAGAG
1 AAGGAAGAAAAAGAAGAAGAG
37404 AA
1 AA
37406 TGAAATGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAGGAAGAAAAAGAAGAAGAG
Found at i:37410 original size:18 final size:16
Alignment explanation
Indices: 37360--37410 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
37350 GATAACCAAC
*
37360 AAAAGGAGAA-AGAAG
1 AAAAAGAGAAGAGAAG
*
37375 AAGAAGAGAAG-GAAG
1 AAAAAGAGAAGAGAAG
37390 AAAAAGAAGAAGAGAATG
1 AAAAAG-AGAAGAGAA-G
37408 AAA
1 AAA
37411 TGAAGGAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 17 0.59
16 5 0.17
17 3 0.10
18 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (16 bp):
AAAAAGAGAAGAGAAG
Found at i:38503 original size:22 final size:21
Alignment explanation
Indices: 38475--38515 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
38465 TCATTTGAAA
*
38475 AAGAAAAAAAATGAGAAAAAAG
1 AAGAAAAAAAA-AAGAAAAAAG
38497 AAGAAAAAAAAAAGAAAAA
1 AAGAAAAAAAAAAGAAAAA
38516 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (21 bp):
AAGAAAAAAAAAAGAAAAAAG
Found at i:40827 original size:34 final size:34
Alignment explanation
Indices: 40787--40857 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
40777 TTATTTATAC
40787 ATAGTAATTATGATTATGACATACAAAATAACAT
1 ATAGTAATTATGATTATGACATACAAAATAACAT
40821 ATAGTAATTATGATTATGACATACAAAATAACAT
1 ATAGTAATTATGATTATGACATACAAAATAACAT
40855 ATA
1 ATA
40858 ATAACTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (34 bp):
ATAGTAATTATGATTATGACATACAAAATAACAT
Found at i:43623 original size:25 final size:25
Alignment explanation
Indices: 43594--43645 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
43584 GAAGGAGAAG
43594 AGTAGGAAGATCATTTCAAACTCAA
1 AGTAGGAAGATCATTTCAAACTCAA
43619 AGTAGGAAGATCATTTCAAACTCAA
1 AGTAGGAAGATCATTTCAAACTCAA
43644 AG
1 AG
43646 ATGGTGGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.23
Consensus pattern (25 bp):
AGTAGGAAGATCATTTCAAACTCAA
Found at i:55126 original size:25 final size:25
Alignment explanation
Indices: 55098--55174 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
55088 TAAGGCTTAT
55098 TATTACTCTCTGGATGGCTATTAGC
1 TATTACTCTCTGGATGGCTATTAGC
* *
55123 TATTACGC-C-GGTAAGGCCTA-T---
1 TATTACTCTCTGG-ATGG-CTATTAGC
*
55144 TATTACTCTCTAGATGGCTATTAGC
1 TATTACTCTCTGGATGGCTATTAGC
55169 TATTAC
1 TATTAC
55175 GCTGGAAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 16
0.65 0.08 0.27
Matches are distributed among these distances:
21 10 0.26
22 5 0.13
23 3 0.08
24 5 0.13
25 16 0.41
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (25 bp):
TATTACTCTCTGGATGGCTATTAGC
Found at i:55153 original size:46 final size:46
Alignment explanation
Indices: 55086--55176 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
55076 TATTGCGACT
* *
55086 GGTAAGGCTTATTATTACTCTCTGGATGGCTATTAGCTATTACGCC
1 GGTAAGGCCTATTATTACTCTCTAGATGGCTATTAGCTATTACGCC
55132 GGTAAGGCCTATTATTACTCTCTAGATGGCTATTAGCTATTACGC
1 GGTAAGGCCTATTATTACTCTCTAGATGGCTATTAGCTATTACGC
55177 TGGAAGATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (46 bp):
GGTAAGGCCTATTATTACTCTCTAGATGGCTATTAGCTATTACGCC
Found at i:59908 original size:9 final size:8
Alignment explanation
Indices: 59889--59957 Score: 56
Period size: 7 Copynumber: 8.8 Consensus size: 8
59879 TCAGTCACCT
59889 GAAAAAGA
1 GAAAAAGA
*
59897 -AAAATGA
1 GAAAAAGA
59904 GAAAAAGGAA
1 GAAAAA-G-A
59914 GAAAAAGA
1 GAAAAAGA
*
59922 -AAAATGA
1 GAAAAAGA
59929 GAAAAAG-
1 GAAAAAGA
*
59936 GAAGAAAAA
1 GAA-AAAGA
59945 GAAAAAGA
1 GAAAAAGA
59953 -AAAAA
1 GAAAAA
59958 ATTATGACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
7 20 0.41
8 17 0.35
9 5 0.10
10 7 0.14
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (8 bp):
GAAAAAGA
Found at i:59922 original size:16 final size:15
Alignment explanation
Indices: 59889--59956 Score: 61
Period size: 16 Copynumber: 4.4 Consensus size: 15
59879 TCAGTCACCT
*
59889 GAAAAAGAA-AAATGA
1 GAAAAAGAAGAAA-AA
59904 GAAAAAGGAAGAAAAA
1 GAAAAA-GAAGAAAAA
59920 GAAAAATG-AGAAAAA
1 GAAAAA-GAAGAAAAA
59935 GGAAGAAA-AAGAAAAA
1 -GAA-AAAGAAGAAAAA
59951 GAAAAA
1 GAAAAA
59957 AATTATGACA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
14 3 0.07
15 16 0.35
16 21 0.46
17 6 0.13
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (15 bp):
GAAAAAGAAGAAAAA
Found at i:59923 original size:25 final size:25
Alignment explanation
Indices: 59889--59958 Score: 124
Period size: 25 Copynumber: 2.8 Consensus size: 25
59879 TCAGTCACCT
59889 GAAAAAGAAAAATGAGAAAAAGGAA
1 GAAAAAGAAAAATGAGAAAAAGGAA
59914 GAAAAAGAAAAATGAGAAAAAGGAA
1 GAAAAAGAAAAATGAGAAAAAGGAA
*
59939 GAAAAAGAAAAA-GAAAAAAA
1 GAAAAAGAAAAATGAGAAAAA
59959 TTATGACAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 7 0.16
25 37 0.84
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (25 bp):
GAAAAAGAAAAATGAGAAAAAGGAA
Found at i:59955 original size:5 final size:6
Alignment explanation
Indices: 59889--59956 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
59879 TCAGTCACCT
** **
59889 GAAAAA GAAAAA TGAGAAAA -AGGAA GAAAAA GAAAAA TGAGAAAA -AGGAA
1 GAAAAA GAAAAA -GA-AAAA GAAAAA GAAAAA GAAAAA -GA-AAAA GAAAAA
59939 GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA
59957 AATTATGACA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
5 4 0.08
6 32 0.67
7 4 0.08
8 8 0.17
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:62094 original size:13 final size:13
Alignment explanation
Indices: 62076--62109 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
62066 TTACTGGTAA
62076 GAAATTTCGGGAT
1 GAAATTTCGGGAT
*
62089 GAAATTTTGGGAT
1 GAAATTTCGGGAT
62102 GAAATTTC
1 GAAATTTC
62110 CTTAAAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (13 bp):
GAAATTTCGGGAT
Found at i:63368 original size:18 final size:18
Alignment explanation
Indices: 63321--63369 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
63311 TCTTCTATCC
*
63321 GAATGCAACCACAATCTG
1 GAATGCAATCACAATCTG
*
63339 GAATGCAATCACAATCTT
1 GAATGCAATCACAATCTG
*
63357 GAATGCAGTCACA
1 GAATGCAATCACA
63370 TTACCACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.20
Consensus pattern (18 bp):
GAATGCAATCACAATCTG
Found at i:69461 original size:19 final size:18
Alignment explanation
Indices: 69437--69473 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
69427 AAGATGACCA
*
69437 GAAGAAAGAGAAGGAAAAG
1 GAAGAAAAAGAA-GAAAAG
69456 GAAGAAAAAGAAGAAAAG
1 GAAGAAAAAGAAGAAAAG
69474 AATGACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
GAAGAAAAAGAAGAAAAG
Found at i:77642 original size:17 final size:17
Alignment explanation
Indices: 77612--77645 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
77602 TATTTGATTC
**
77612 TTTAAATTTTTAAAAAT
1 TTTAAATTAATAAAAAT
77629 TTTAAATTAATAAAAAT
1 TTTAAATTAATAAAAAT
77646 AAAATTATAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTAATAAAAAT
Found at i:77751 original size:25 final size:25
Alignment explanation
Indices: 77714--77772 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
77704 TAAAAATATA
* * *
77714 AATTATTTAATTTTGAATCATCTAT
1 AATTTTTTTATTTCGAATCATCTAT
*
77739 AATTTTTTTATTTCGAATCGTCTAT
1 AATTTTTTTATTTCGAATCATCTAT
77764 AATTTTTTT
1 AATTTTTTT
77773 CTAAGTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.58
Consensus pattern (25 bp):
AATTTTTTTATTTCGAATCATCTAT
Found at i:94143 original size:15 final size:15
Alignment explanation
Indices: 94107--94144 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
94097 AAATGACATG
94107 AAAATAAATAACAAC
1 AAAATAAATAACAAC
*
94122 AATATAAATAAACAA-
1 AAAATAAAT-AACAAC
94137 AAAATAAA
1 AAAATAAA
94145 AATAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAAATAACAAC
Found at i:95212 original size:49 final size:48
Alignment explanation
Indices: 95143--95935 Score: 273
Period size: 49 Copynumber: 16.2 Consensus size: 48
95133 TTCAATCTGT
* * *
95143 TCCCTCTTTGGTTTTAAGGTGTTAGGTCCGTCGTCTTGCCTTCAACCTA
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGT-TTGCCTTCAACCTA
* * * * * *
95192 TCCCTCTTCGATTTT-GAGGTGTAAGATTCATTG-TTGCAACTTCAACCTT
1 TCCCTCTTCGATTTTAG-GGTGTTAGGTCCGTCGTTTGC--CTTCAACCTA
*
95241 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTTGTGGCTTCAACCTA
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTT-TGCCTTCAACCTA
* * ** * *
95290 TCCTTTTTCGATTTTAGGGTGTTAGGTCCG-CCATTACAGTTTCAACCTA
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTTTGC--CTTCAACCTA
* * ** * * * * *
95339 TCCCTCTTC-AGTTTTAAGGTGTAAGGTTTGCCATTGAGGCTTCAACCTT
1 TCCCTCTTCGA-TTTTAGGGTGTTAGGTCCGTCGTT-TGCCTTCAACCTA
* * * * * ** * *
95388 TCCCTTTTTGGTTTTAGGGTGTTAGATCC-ACCATTGCAGCTTCAATCAA
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTTTGC--CTTCAACCTA
* * * * *
95437 TCCCTCTTCGATTTTAAGGTGTTTGGTCTGTCGTTGTGACTTCAACCAA
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTT-TGCCTTCAACCTA
* * * * *** * * * *
95486 TCCCTTTTCGATTTTAAGGTGTAAGATATATCGTTAGGACTTCAATCTT
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTT-TGCCTTCAACCTA
* * * * * * * *
95535 TCCCTATTCGGTTTTTGGGTGTTAGGTTCGCCGTTACGGCTTCAACCGA
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTT-TGCCTTCAACCTA
* * * * ** *
95584 TCCCTCTT-TAGTTTTAAGGTGTAAGGTCCGTCGTTACGATTTCAACCTT
1 TCCCTCTTCGA-TTTTAGGGTGTTAGGTCCGTCGTT-TGCCTTCAACCTA
** * * * * * * **
95633 TTTCTCTTTGATTTTAGGGTGTTAGATCCGCCATTACGAC-TCTAATATA
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTT-TGCCTTC-AACCTA
* * * * * * *
95682 TCTCTCTTCGAATTTAGAGTGTTAGGTCCATCGTTACGACTTCAATCTA
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTT-TGCCTTCAACCTA
* * * * * * * *
95731 TCCCTCTTCGATTTTAAGATGTAAGATTCATCG-TTGCGGCTTCAATCTT
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTTTGC--CTTCAACCTA
* *
95780 TCCCTCTTC-AGTTTTAAGGTGTTAGGTCCATCG-TTGCGGCTTCAACCTA
1 TCCCTCTTCGA-TTTTAGGGTGTTAGGTCCGTCGTTTGC--CTTCAACCTA
** * * * ** *
95829 TCTTTCGTC-AGTTTTAAGGTGTAAGGTTTG-C-TGTTGCGGCTTCAACCTT
1 TCCCTCTTCGA-TTTTAGGGTGTTAGGTCCGTCGT-TTGC--CTTCAACCTA
* * **
95878 TCCCTGTTCGATTTTAGGATGTTAGGTCCACCG-TTGCGGCTTCAACCTA
1 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTTTGC--CTTCAACCTA
*
95927 TCCTTCTTC
1 TCCCTCTTC
95936 AAACTCTATG
Statistics
Matches: 555, Mismatches: 161, Indels: 56
0.72 0.21 0.07
Matches are distributed among these distances:
47 7 0.01
48 10 0.02
49 523 0.94
50 11 0.02
51 4 0.01
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.40
Consensus pattern (48 bp):
TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTTTGCCTTCAACCTA
Found at i:95284 original size:98 final size:97
Alignment explanation
Indices: 95109--95935 Score: 428
Period size: 98 Copynumber: 8.4 Consensus size: 97
95099 TTTTTTCAAA
* * * * * *
95109 AGGTGTAAGATTCGCCGTTGCGACTTCAATCTGTTCCCTCTTTGGTTTTAAGGTGTTAGGTCCGT
1 AGGTGTAAGATCCACCGTTGCAACTTCAACCT-TTCCCTCTTCGATTTTAAGGTGTTAGGTCCGT
* *
95174 CGTCT-TGCCTTCAACCTATCCCTCTTCGATTTT
65 CGT-TGTGGCTTCAACCTATCCCTTTTCGATTTT
* ** *
95207 GAGGTGTAAGATTCATTGTTGCAACTTCAACCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGT
1 -AGGTGTAAGATCCACCGTTGCAACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGT
*
95272 CGTTGTGGCTTCAACCTATCCTTTTTCGATTTT
65 CGTTGTGGCTTCAACCTATCCCTTTTCGATTTT
* * * * * ** * * **
95305 AGGGTGTTAGGTCCGCCATTACAGTTTCAACCTATCCCTCTTC-AGTTTTAAGGTGTAAGGTTTG
1 A-GGTGTAAGATCCACCGTTGCAACTTCAACCTTTCCCTCTTCGA-TTTTAAGGTGTTAGGTCCG
* * * * * *
95369 CCATTGAGGCTTCAACCTTTCCCTTTTTGGTTTT
64 TCGTTGTGGCTTCAACCTATCCCTTTTCGATTTT
* * * * ** * *
95403 AGGGTGTTAGATCCACCATTGCAGCTTCAATCAATCCCTCTTCGATTTTAAGGTGTTTGGTCTGT
1 A-GGTGTAAGATCCACCGTTGCAACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGT
* *
95468 CGTTGTGACTTCAACCAATCCCTTTTCGATTTT
65 CGTTGTGGCTTCAACCTATCCCTTTTCGATTTT
** * * * * * ** *
95501 AAGGTGTAAGATATATCGTTAG-GACTTCAATCTTTCCCTATTCGGTTTTTGGGTGTTAGGTTCG
1 -AGGTGTAAGATCCACCGTT-GCAACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCG
* ** * *
95565 CCGTTACGGCTTCAACCGATCCCTCTTTAG-TTTT
64 TCGTTGTGGCTTCAACCTATCCCT-TTTCGATTTT
* ** * * * ** * * * *
95599 AAGGTGTAAGGTCCGTCGTTACGATTTCAACCTTTTTCTCTTTGATTTTAGGGTGTTAGATCCGC
1 -AGGTGTAAGATCCACCGTTGCAACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGT
* ** * ** * * *
95664 CATTACGAC-TCTAATATATCTCTCTTCGAATTT
65 CGTTGTGGCTTC-AACCTATCCCTTTTCGATTTT
* * * * * * * * * * * *
95697 AGAGTGTTAGGTCCATCGTTACGACTTCAATCTATCCCTCTTCGATTTTAAGATGTAAGATTCAT
1 AG-GTGTAAGATCCACCGTTGCAACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGT
* * * *
95762 CGTTGCGGCTTCAATCTTTCCCTCTTC-AGTTTT
65 CGTTGTGGCTTCAACCTATCCCTTTTCGA-TTTT
* * * ** * ** * * **
95795 AAGGTGTTAGGTCCATCGTTGCGGCTTCAACCTATCTTTCGTC-AGTTTTAAGGTGTAAGGTTTG
1 -AGGTGTAAGATCCACCGTTGCAACTTCAACCTTTCCCTCTTCGA-TTTTAAGGTGTTAGGTCCG
* * *
95859 -CTGTTGCGGCTTCAACCTTTCCCTGTTCGATTTT
64 TC-GTTGTGGCTTCAACCTATCCCTTTTCGATTTT
* * ** * *
95893 AGGATGTTAGGTCCACCGTTGCGGCTTCAACCTATCCTTCTTC
1 AGG-TGTAAGATCCACCGTTGCAACTTCAACCTTTCCCTCTTC
95936 AAACTCTATG
Statistics
Matches: 578, Mismatches: 132, Indels: 37
0.77 0.18 0.05
Matches are distributed among these distances:
97 16 0.03
98 523 0.90
99 39 0.07
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.40
Consensus pattern (97 bp):
AGGTGTAAGATCCACCGTTGCAACTTCAACCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCCGTC
GTTGTGGCTTCAACCTATCCCTTTTCGATTTT
Found at i:95481 original size:147 final size:144
Alignment explanation
Indices: 95143--95654 Score: 411
Period size: 147 Copynumber: 3.5 Consensus size: 144
95133 TTCAATCTGT
* * * *
95143 TCCCTCTTTGGTTTTAAGGTGTTAGGTCCGTCGTCTTGCCTTCAACCTATCCCTCTTCGATTTTG
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGT-TTGACTTCAACCTATCCCTCTTCGATTTTA
* * * * * * **
95208 AGGTGTAA-GATTCATTGTTGCAACTTCAACCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGT
65 AGGTGTAAGGTTTCATTG-AG--GCTTCAACCTTTCCCTATTCGGTTTTAGGGTGTTAGATCCAC
* ** *
95272 CGTTGTGGCTTCAACCTA
127 CATTGCAGCTTCAACCAA
* * * * * ** *
95290 TCCTTTTTCGATTTTAGGGTGTTAGGTCCGCCATTACAGTTTCAACCTATCCCTCTTC-AGTTTT
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTTGA-CTTCAACCTATCCCTCTTCGA-TTTT
* *
95354 AAGGTGTAAGGTTTGCCATTGAGGCTTCAACCTTTCCCTTTTTGGTTTTAGGGTGTTAGATCCAC
64 AAGGTGTAAGGTTT--CATTGAGGCTTCAACCTTTCCCTATTCGGTTTTAGGGTGTTAGATCCAC
*
95419 CATTGCAGCTTCAATCAA
127 CATTGCAGCTTCAACCAA
* * * *
95437 TCCCTCTTCGATTTTAAGGTGTTTGGTCTGTCGTTGTGACTTCAACCAATCCCTTTTCGATTTTA
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTT-TGACTTCAACCTATCCCTCTTCGATTTTA
* * * * * * *
95502 AGGTGTAAGATATATCGTT-AGGACTTCAATCTTTCCCTATTCGGTTTTTGGGTGTTAGGTTCGC
65 AGGTGTAAGGT-T-TCATTGAGG-CTTCAACCTTTCCCTATTCGGTTTTAGGGTGTTAGATCCAC
* * * *
95566 CGTTACGGCTTCAACCGA
127 CATTGCAGCTTCAACCAA
* * * * * ** *
95584 TCCCTCTT-TAGTTTTAAGGTGTAAGGTCCGTCGTTACGATTTCAACCTTTTTCTCTTTGATTTT
1 TCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGTCGTT-TGACTTCAACCTATCCCTCTTCGATTTT
*
95648 AGGGTGT
64 AAGGTGT
95655 TAGATCCGCC
Statistics
Matches: 288, Mismatches: 66, Indels: 22
0.77 0.18 0.06
Matches are distributed among these distances:
146 6 0.02
147 269 0.93
148 6 0.02
149 2 0.01
150 5 0.02
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (144 bp):
TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTTGACTTCAACCTATCCCTCTTCGATTTTAA
GGTGTAAGGTTTCATTGAGGCTTCAACCTTTCCCTATTCGGTTTTAGGGTGTTAGATCCACCATT
GCAGCTTCAACCAA
Found at i:97358 original size:6 final size:6
Alignment explanation
Indices: 97347--97375 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
97337 CCCTTTTCTC
97347 TCTTTT TCTTTT TCTTTT TCTTTT T-TTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
97376 GCTAGTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TCTTTT
Found at i:107056 original size:16 final size:16
Alignment explanation
Indices: 107032--107062 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
107022 TCGTTACAAA
*
107032 TTTATTCCTTTAACAG
1 TTTAGTCCTTTAACAG
107048 TTTAGTCCTTTAACA
1 TTTAGTCCTTTAACA
107063 TAAAAATTAC
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:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTAGTCCTTTAACAG
Found at i:123299 original size:21 final size:24
Alignment explanation
Indices: 123255--123302 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 24
123245 CAAGTGTCGA
123255 TAGTTGTGTTTACTGATGTATCGG
1 TAGTTGTGTTTACTGATGTATCGG
*
123279 TAGTT-TGTTTA-TTAT-TATCGG
1 TAGTTGTGTTTACTGATGTATCGG
123300 TAG
1 TAG
123303 AAGTTGCAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 6 0.26
24 5 0.22
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (24 bp):
TAGTTGTGTTTACTGATGTATCGG
Found at i:127160 original size:12 final size:13
Alignment explanation
Indices: 127135--127198 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
127125 AATAAATAAC
*
127135 AACAATATAAATA
1 AACAATAAAAATA
127148 AACAA-AAAAATA
1 AACAATAAAAATA
127160 AA-AATAAAAATTA
1 AACAATAAAAA-TA
* *
127173 AATACT-AAAATA
1 AACAATAAAAATA
127185 AACAATAAAAATA
1 AACAATAAAAATA
127198 A
1 A
127199 TTGAGATTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 2 0.05
12 19 0.44
13 20 0.47
14 2 0.05
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (13 bp):
AACAATAAAAATA
Found at i:127160 original size:16 final size:15
Alignment explanation
Indices: 127123--127161 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
127113 AAATAGCATG
*
127123 AAAATAAATAACAAC
1 AAAATAAATAACAAA
*
127138 AATATAAATAAACAAA
1 AAAATAAAT-AACAAA
127154 AAAATAAA
1 AAAATAAA
127162 AATAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAATAAATAACAAA
Found at i:127164 original size:37 final size:38
Alignment explanation
Indices: 127123--127198 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 38
127113 AAATAGCATG
127123 AAAATAAATAACAACAATA-T-AAATAAACAA-AAAAATA
1 AAAATAAA-AACAA-AATACTAAAATAAACAATAAAAATA
**
127160 AAAATAAAAATTAAATACTAAAATAAACAATAAAAATA
1 AAAATAAAAACAAAATACTAAAATAAACAATAAAAATA
127198 A
1 A
127199 TTGAGATTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 4 0.12
36 4 0.12
37 18 0.53
38 8 0.24
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (38 bp):
AAAATAAAAACAAAATACTAAAATAAACAATAAAAATA
Found at i:127168 original size:5 final size:6
Alignment explanation
Indices: 127123--127198 Score: 57
Period size: 6 Copynumber: 12.2 Consensus size: 6
127113 AAATAGCATG
* * *
127123 AAAATA AATAACA ACAATA TAAATA AACAA-A AAAATA AAAATA AAAAT-
1 AAAATA AA-AATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA
*
127171 TAAATA CTAAAATA AACAATA AAAATA A
1 AAAATA --AAAATA AA-AATA AAAATA A
127199 TTGAGATTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
5 6 0.11
6 32 0.58
7 12 0.22
8 5 0.09
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:127248 original size:15 final size:15
Alignment explanation
Indices: 127214--127255 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
127204 ATTGGGCATG
*
127214 AAAATAAAT-GACAA
1 AAAATAAATAAACAA
127228 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
*
127244 AAAATTAATAAA
1 AAAATAAATAAA
127256 TTAAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:129837 original size:3 final size:3
Alignment explanation
Indices: 129829--129907 Score: 77
Period size: 3 Copynumber: 26.3 Consensus size: 3
129819 CAATAAATCT
* * * ** * *
129829 AAC AAC AAC AAC AAC GAC AAT GAC AAC GGC AAC AAC AAT AAC AGC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* *
129877 AAC AAC AAC AAT AAT AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
129908 GAATTAAGTC
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.61, C:0.28, G:0.06, T:0.05
Consensus pattern (3 bp):
AAC
Found at i:129897 original size:21 final size:21
Alignment explanation
Indices: 129828--129907 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
129818 GCAATAAATC
* *
129828 TAACAACAACAACAACGACAA
1 TAACAACAACAACAACAATAA
* **
129849 TGACAACGGCAACAACAATAA
1 TAACAACAACAACAACAATAA
* *
129870 CAGCAACAACAACAACAATAA
1 TAACAACAACAACAACAATAA
129891 TAACAACAACAACAACA
1 TAACAACAACAACAACA
129908 GAATTAAGTC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.60, C:0.28, G:0.06, T:0.06
Consensus pattern (21 bp):
TAACAACAACAACAACAATAA
Found at i:138378 original size:16 final size:16
Alignment explanation
Indices: 138357--138390 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
138347 TGAAGGAAAT
138357 AATGGGTATAGTCCAC
1 AATGGGTATAGTCCAC
138373 AATGGGTATAGTCCAC
1 AATGGGTATAGTCCAC
138389 AA
1 AA
138391 GAAATGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (16 bp):
AATGGGTATAGTCCAC
Found at i:140879 original size:22 final size:23
Alignment explanation
Indices: 140817--140880 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
140807 TAATTGATTT
*
140817 TTAAAAATTATAAAAAAATGTTA
1 TTAAAAATTATATAAAAATGTTA
* * *
140840 TTAAAAACTATTTTAAAA-GTTA
1 TTAAAAATTATATAAAAATGTTA
140862 -TAGAAAATTATATAAAAAT
1 TTA-AAAATTATATAAAAAT
140881 ATTTAAATGA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 2 0.06
22 16 0.50
23 14 0.44
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (23 bp):
TTAAAAATTATATAAAAATGTTA
Found at i:140947 original size:7 final size:7
Alignment explanation
Indices: 140912--140936 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
140902 AAAGGAATAG
140912 TAATTTT
1 TAATTTT
140919 TAATTTT
1 TAATTTT
140926 TAATTTT
1 TAATTTT
140933 TAAT
1 TAAT
140937 AATATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TAATTTT
Found at i:141260 original size:19 final size:17
Alignment explanation
Indices: 141224--141340 Score: 60
Period size: 19 Copynumber: 6.5 Consensus size: 17
141214 ATTTTTTTTC
*
141224 TATAATTTTTACTATTTT
1 TATAATTTTTAATA-TTT
*
141242 TAGTAATTTTTAATGTTT
1 TA-TAATTTTTAATATTT
* *
141260 TATAATTTTAAATAGATTA
1 TATAATTTTTAAT--ATTT
* *
141279 GATAATTTTTTATCA-TT
1 TATAATTTTTAAT-ATTT
*
141296 TAGTAATTTTT-ATATAAT
1 TA-TAATTTTTAATAT-TT
141314 TA-AATTTTTTATATATTT
1 TATAA-TTTTTA-ATATTT
*
141332 TAAAATTTT
1 TATAATTTT
141341 CTGATTTTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
16 3 0.04
17 19 0.25
18 26 0.34
19 28 0.37
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
TATAATTTTTAATATTT
Found at i:141463 original size:30 final size:27
Alignment explanation
Indices: 141409--141482 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 27
141399 TGATATTTAC
*
141409 CATATTTACTA-AATTTTTATATTATTTTT
1 CATATTT-CTATAATATTT-TATTA-TTTT
141438 CTATAATTTCTATAATATTTTATTATTTT
1 C-AT-ATTTCTATAATATTTTATTATTTT
*
141467 CATATTTTTATAATAT
1 CATATTTCTATAATAT
141483 ATTAATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 12 0.30
28 2 0.05
29 6 0.15
30 10 0.25
31 10 0.25
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (27 bp):
CATATTTCTATAATATTTTATTATTTT
Found at i:143213 original size:19 final size:21
Alignment explanation
Indices: 143191--143237 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
143181 AAAAAAATTA
143191 AAAATATAT-AAAATTAT-TT
1 AAAATATATAAAAATTATATT
143210 AAAA-AGTATAAAAATTATATT
1 AAAATA-TATAAAAATTATATT
*
143231 TAAATAT
1 AAAATAT
143238 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 7 0.30
20 8 0.35
21 6 0.26
22 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATATATAAAAATTATATT
Found at i:143213 original size:20 final size:20
Alignment explanation
Indices: 143188--143227 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
143178 TTTAAAAAAA
143188 TTAAAAA-TATATAAAATTAT
1 TTAAAAAGTATA-AAAATTAT
143208 TTAAAAAGTATAAAAATTAT
1 TTAAAAAGTATAAAAATTAT
143228 ATTTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TTAAAAAGTATAAAAATTAT
Found at i:144417 original size:2 final size:2
Alignment explanation
Indices: 144410--144453 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
144400 TATTAATAAA
144410 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
144452 AT
1 AT
144454 GTACAATTGA
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:145444 original size:20 final size:20
Alignment explanation
Indices: 145398--145446 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
145388 TTTCTTTGGC
*
145398 ATTTCTACAAGTTCAATTTA
1 ATTTCTTCAAGTTCAATTTA
145418 ATTTCTTCAAGTTCAATTTA
1 ATTTCTTCAAGTTCAATTTA
145438 ATTTCTTCA
1 ATTTCTTCA
145447 TGCATCTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (20 bp):
ATTTCTTCAAGTTCAATTTA
Found at i:154138 original size:10 final size:10
Alignment explanation
Indices: 154123--154226 Score: 51
Period size: 10 Copynumber: 10.6 Consensus size: 10
154113 AAGAAAAATC
154123 ATAAAATATT
1 ATAAAATATT
154133 ATAAAA-ATTT
1 ATAAAATA-TT
154143 ATATAAA-ATT
1 ATA-AAATATT
* *
154153 CTAATGA-ATT
1 ATAA-AATATT
154163 ATAAAA-ATTT
1 ATAAAATA-TT
*
154173 ATAAGAATAAT
1 ATAA-AATATT
* *
154184 AAAAAATGTT
1 ATAAAATATT
*
154194 A-AACATATT
1 ATAAAATATT
154203 A-AAAATATT
1 ATAAAATATT
*
154212 A-AAAAAATT
1 ATAAAATATT
154221 ATAAAA
1 ATAAAA
154227 GAACTTGTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
9 27 0.36
10 37 0.49
11 10 0.13
12 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (10 bp):
ATAAAATATT
Found at i:154435 original size:11 final size:12
Alignment explanation
Indices: 154411--154445 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
154401 TATATAAATT
154411 TAATATTTTATG
1 TAATATTTTATG
154423 TAATATTTT-TG
1 TAATATTTTATG
*
154434 TATTATTTTATG
1 TAATATTTTATG
154446 ATTTTATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (12 bp):
TAATATTTTATG
Found at i:154478 original size:18 final size:18
Alignment explanation
Indices: 154385--154481 Score: 61
Period size: 20 Copynumber: 5.1 Consensus size: 18
154375 TAAGAAATTT
**
154385 TATATTTTTATAAGTTTA
1 TATATTTTTATATTTTTA
* * *
154403 TATAAATTTAATATTTTATG
1 TAT-ATTTTTATATTTT-TA
*
154423 TAATATTTTTGTATTATTT-
1 T-ATATTTTTATATT-TTTA
*
154442 TATGATTTTATGATTTTTTTA
1 TAT-ATTTT-T-ATATTTTTA
154463 TATATTTTTATATTTTTA
1 TATATTTTTATATTTTTA
154481 T
1 T
154482 TGGAAAACAA
Statistics
Matches: 60, Mismatches: 11, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
18 14 0.23
19 16 0.27
20 20 0.33
21 10 0.17
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TATATTTTTATATTTTTA
Found at i:159492 original size:24 final size:25
Alignment explanation
Indices: 159446--159495 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
159436 GTTGAAGTTG
159446 TTGAAGTGTGTTTGTGATGGGAGAA
1 TTGAAGTGTGTTTGTGATGGGAGAA
*
159471 TTGAATTGTG-TTGTGAAT-GGAGAA
1 TTGAAGTGTGTTTGTG-ATGGGAGAA
159495 T
1 T
159496 AATGATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (25 bp):
TTGAAGTGTGTTTGTGATGGGAGAA
Found at i:159634 original size:30 final size:30
Alignment explanation
Indices: 159598--159680 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
159588 TCTACCTCAA
*
159598 ATTGGCTTTGCGGAGGCACGATAATGATAT
1 ATTGGCTTTGCGGAGGTACGATAATGATAT
* * *
159628 ATTGGCTTTGTGGAGGTATGGTAATGATAT
1 ATTGGCTTTGCGGAGGTACGATAATGATAT
* * *
159658 AATGGATTTGCAGAGGTACGATA
1 ATTGGCTTTGCGGAGGTACGATA
159681 TGTCGGGATC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.08, G:0.31, T:0.33
Consensus pattern (30 bp):
ATTGGCTTTGCGGAGGTACGATAATGATAT
Found at i:160626 original size:23 final size:21
Alignment explanation
Indices: 160600--160652 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
160590 TTAATATTTT
160600 ATTTTAATAAAAAATTCAGTTCA
1 ATTTTAAT-AAAAATTCAGTT-A
* * *
160623 ATTTAAATACAAATTTAGTTA
1 ATTTTAATAAAAATTCAGTTA
160644 ATATTTAAT
1 AT-TTTAAT
160653 TTATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 3 0.12
22 15 0.60
23 7 0.28
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (21 bp):
ATTTTAATAAAAATTCAGTTA
Found at i:161822 original size:16 final size:15
Alignment explanation
Indices: 161797--161831 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
161787 TTTTAAGTTT
161797 ATATTATTTTATATG
1 ATATTATTTTATATG
161812 ATATTATTTT-TAT-
1 ATATTATTTTATATG
161825 ATATTAT
1 ATATTAT
161832 GTAATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 3 0.15
15 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
ATATTATTTTATATG
Found at i:168911 original size:10 final size:11
Alignment explanation
Indices: 168892--168920 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
168882 TAAAAAAATA
168892 TATATTTATTT
1 TATATTTATTT
168903 TAT-TTTATTT
1 TATATTTATTT
168913 TATATTTA
1 TATATTTA
168921 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATATTTATTT
Found at i:171088 original size:16 final size:16
Alignment explanation
Indices: 171067--171097 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
171057 TTCAAAACTC
171067 ATAAAAATAATATAAA
1 ATAAAAATAATATAAA
*
171083 ATAAAATTAATATAA
1 ATAAAAATAATATAA
171098 CTATTCGTAA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATAATATAAA
Found at i:171593 original size:82 final size:82
Alignment explanation
Indices: 171496--171658 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 82
171486 AAGAACCAAG
*
171496 TAAATTTCCATCCATTTTTATTTCTTTTTTTACACTTCTATCAAGCTAGAATTTATCTCTTAATC
1 TAAATTTCCATCCATTTTTATTTCTTTTTTTACACTTCTATCAAGCTAGAATTTATCTCCTAATC
*
171561 ATTTTCTATTAAAAAAA
66 ATTTTCTATCAAAAAAA
* *
171578 TAAATTTCCATCCATTTTTATTTCTTTTTTTACACTTCTATCAAGTTAGAATTTATCTCCTAATT
1 TAAATTTCCATCCATTTTTATTTCTTTTTTTACACTTCTATCAAGCTAGAATTTATCTCCTAATC
171643 ATTTTCTATCAAAAAA
66 ATTTTCTATCAAAAAA
171659 TATACCTACT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.49
Consensus pattern (82 bp):
TAAATTTCCATCCATTTTTATTTCTTTTTTTACACTTCTATCAAGCTAGAATTTATCTCCTAATC
ATTTTCTATCAAAAAAA
Found at i:173720 original size:18 final size:20
Alignment explanation
Indices: 173683--173721 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
173673 GCTGAAACTC
173683 ATATCATATGATAAATAGTT
1 ATATCATATGATAAATAGTT
*
173703 ATAT-ATATGA-ATATAGTT
1 ATATCATATGATAAATAGTT
173721 A
1 A
173722 GTTTAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (20 bp):
ATATCATATGATAAATAGTT
Found at i:174122 original size:21 final size:21
Alignment explanation
Indices: 174098--174150 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
174088 CCTTTGACAG
*
174098 TTCTACCGATACAAGTGAAGC
1 TTCTACCGATACAAGTCAAGC
* *
174119 TTCTACCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCAAGC
174140 TTCTACC-ATAC
1 TTCTACCGATAC
174151 TAAAAACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (21 bp):
TTCTACCGATACAAGTCAAGC
Found at i:175866 original size:19 final size:20
Alignment explanation
Indices: 175842--175890 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
175832 TCATTAAGCT
175842 TTAATTAACCCT-TTTA-ATC
1 TTAATTAACCCTATTTATA-C
*
175861 TTAATTAAACCTATTTATAC
1 TTAATTAACCCTATTTATAC
175881 TTAATATAAC
1 TTAAT-TAAC
175891 TCATGCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 11 0.44
20 10 0.40
21 4 0.16
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTAACCCTATTTATAC
Found at i:177434 original size:27 final size:27
Alignment explanation
Indices: 177390--177444 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
177380 TTCAATTCTT
*
177390 CTTCTTCTTCTTCAGTTCATTCAAACC
1 CTTCTTCTTCATCAGTTCATTCAAACC
* *
177417 CTTCTTCTTCATCTGTTCATTCGAACC
1 CTTCTTCTTCATCAGTTCATTCAAACC
177444 C
1 C
177445 CCAAAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.05, T:0.44
Consensus pattern (27 bp):
CTTCTTCTTCATCAGTTCATTCAAACC
Found at i:184400 original size:26 final size:25
Alignment explanation
Indices: 184371--184431 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
184361 AAATCATGTC
*
184371 ATTTTTTAATAATAAAAAATATATAA
1 ATTTTTTAATAAGAAAAAATA-ATAA
* **
184397 ATTTTTTTAT-AGAAAAAATAATTT
1 ATTTTTTAATAAGAAAAAATAATAA
184421 ATTTTTTAATA
1 ATTTTTTAATA
184432 TTATATATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 11 0.38
25 9 0.31
26 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTTTTTAATAAGAAAAAATAATAA
Found at i:188218 original size:14 final size:14
Alignment explanation
Indices: 188201--188254 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
188191 TTATTATTTT
188201 AATTTTAAAATAAA
1 AATTTTAAAATAAA
188215 AA-TTTAGAAATAAA
1 AATTTTA-AAATAAA
* *
188229 AAATTTCAAATATAA
1 AATTTTAAAATA-AA
*
188244 ATTTTTAAAAT
1 AATTTTAAAAT
188255 CCAAATTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 4 0.12
14 16 0.48
15 13 0.39
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (14 bp):
AATTTTAAAATAAA
Found at i:188232 original size:15 final size:13
Alignment explanation
Indices: 188204--188247 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
188194 TTATTTTAAT
188204 TTTAAAATAAAAA
1 TTTAAAATAAAAA
188217 TTTAGAAATAAAAAA
1 TTTA-AAAT-AAAAA
* *
188232 TTTCAAATATAAA
1 TTTAAAATAAAAA
188245 TTT
1 TTT
188248 TTAAAATCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.41
14 8 0.30
15 8 0.30
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (13 bp):
TTTAAAATAAAAA
Found at i:194268 original size:6 final size:6
Alignment explanation
Indices: 194257--194285 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
194247 TGATCAAAAT
194257 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
194286 TTAGAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:203740 original size:16 final size:17
Alignment explanation
Indices: 203708--203741 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
203698 ATGAGTTAGA
*
203708 ATAATGTTTATGTATTT
1 ATAATGGTTATGTATTT
203725 ATAATGGTTA-GTATTT
1 ATAATGGTTATGTATTT
203741 A
1 A
203742 GCGTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (17 bp):
ATAATGGTTATGTATTT
Found at i:215015 original size:17 final size:15
Alignment explanation
Indices: 214978--215009 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
214968 TGACCACAAT
214978 AACATTTCCATGCTA
1 AACATTTCCATGCTA
*
214993 AACATTTTCATGCTA
1 AACATTTCCATGCTA
215008 AA
1 AA
215010 AACATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (15 bp):
AACATTTCCATGCTA
Found at i:219406 original size:32 final size:30
Alignment explanation
Indices: 219360--219425 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
219350 ATTTAATTTT
* *
219360 AAAAAATAAAAAATAATAGAAAAAATGTGAA
1 AAAAAATAAAAAATAAAAGAAAAAA-CTGAA
* *
219391 AAAATAATAATAAATAAAAGAGAAAACTGAA
1 AAAA-AATAAAAAATAAAAGAAAAAACTGAA
219422 AAAA
1 AAAA
219426 GGAAGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (30 bp):
AAAAAATAAAAAATAAAAGAAAAAACTGAA
Found at i:220493 original size:36 final size:36
Alignment explanation
Indices: 220416--220515 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 36
220406 TCCAAACAAC
* * * *
220416 CAAAATAACAACCAAAACAGCAGCAAAAAATACCAG
1 CAAAATAACAACAAAAACAGCAACAAAAAACACCAA
* *
220452 CAAAATAACAACAAAAATAGCAAC-AAAAACAGCAA
1 CAAAATAACAACAAAAACAGCAACAAAAAACACCAA
* * * *
220487 CAAAAATAATAGCAAAAACAACACCAAAA
1 C-AAAATAACAACAAAAACAGCAACAAAA
220516 CAATAAAAAG
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 9 0.18
36 39 0.76
37 3 0.06
ACGTcount: A:0.66, C:0.22, G:0.06, T:0.06
Consensus pattern (36 bp):
CAAAATAACAACAAAAACAGCAACAAAAAACACCAA
Found at i:220497 original size:27 final size:27
Alignment explanation
Indices: 220458--220518 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
220448 CCAGCAAAAT
220458 AACAACAAAAATAGCAACAAA-AACAGC
1 AACAACAAAAATAGCAA-AAACAACAGC
*
220485 AACAA-AAATAATAGCAAAAACAACACC
1 AACAACAAA-AATAGCAAAAACAACAGC
220512 AA-AACAA
1 AACAACAA
220519 TAAAAAGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.69, C:0.21, G:0.05, T:0.05
Consensus pattern (27 bp):
AACAACAAAAATAGCAAAAACAACAGC
Found at i:220502 original size:24 final size:24
Alignment explanation
Indices: 220412--220515 Score: 86
Period size: 24 Copynumber: 4.3 Consensus size: 24
220402 AACATCCAAA
* * *
220412 CAACCAAAATAACAACCAAAACAG
1 CAACAAAAATAACAGCAAAAACAG
* *
220436 CAGCAAAAAATACCAGCAAAATA-A-
1 CAAC-AAAAATAACAGCAAAA-ACAG
* *
220460 CAACAAAAATAGCAACAAAAACAG
1 CAACAAAAATAACAGCAAAAACAG
* *
220484 CAACAAAAATAATAGCAAAAACAA
1 CAACAAAAATAACAGCAAAAACAG
*
220508 CACCAAAA
1 CAACAAAA
220516 CAATAAAAAG
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
22 1 0.02
23 15 0.24
24 33 0.52
25 13 0.21
26 1 0.02
ACGTcount: A:0.65, C:0.23, G:0.06, T:0.06
Consensus pattern (24 bp):
CAACAAAAATAACAGCAAAAACAG
Found at i:220514 original size:12 final size:12
Alignment explanation
Indices: 220453--220515 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
220443 AAATACCAGC
*
220453 AAAATAACAACA
1 AAAACAACAACA
* *
220465 AAAATAGCAACA
1 AAAACAACAACA
*
220477 AAAACAGCAACA
1 AAAACAACAACA
* * *
220489 AAAATAATAGCA
1 AAAACAACAACA
*
220501 AAAACAACACCA
1 AAAACAACAACA
220513 AAA
1 AAA
220516 CAATAAAAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.70, C:0.19, G:0.05, T:0.06
Consensus pattern (12 bp):
AAAACAACAACA
Found at i:220515 original size:23 final size:24
Alignment explanation
Indices: 220475--220520 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
220465 AAAATAGCAA
* *
220475 CAAAAACAGCAACAAAAATAATAG
1 CAAAAACAACAACAAAAACAATAG
*
220499 CAAAAACAAC-ACCAAAACAATA
1 CAAAAACAACAACAAAAACAATA
220521 AAAAGAAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.67, C:0.22, G:0.04, T:0.07
Consensus pattern (24 bp):
CAAAAACAACAACAAAAACAATAG
Found at i:220548 original size:92 final size:92
Alignment explanation
Indices: 220452--220651 Score: 203
Period size: 92 Copynumber: 2.2 Consensus size: 92
220442 AAAATACCAG
* *
220452 CAAAATAACAACAAAAA-T-AGCAACAAAAACAGCAACAAAAATAATAGCAAAAACAACACCAAA
1 CAAAATAACAACAAAAATTAAACAACAAAAAAAGCAACAAAAATAATA--AAAAACAACACCAAA
*
220515 ACAATAAAAAGA-AGC-ACCAAAACAGTAA
64 ACAATAAAAA-ACAACAACCAAAACAGTAA
* * * * * *
220543 CCAAAATAATAA-AAAAATTAAAACAGCAAAAAAAGTAACCAAAATAGTAAAAAACAACATCAAA
1 -CAAAATAACAACAAAAATT-AAACAACAAAAAAAGCAACAAAAATAATAAAAAACAACACCAAA
* *
220607 ACAGTAAAAAACAACAACCAAAATAGTAA
64 ACAATAAAAAACAACAACCAAAACAGTAA
* *
220636 AAAAATAACACCAAAA
1 CAAAATAACAACAAAA
220652 CAACAATATA
Statistics
Matches: 88, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
91 6 0.07
92 44 0.50
93 16 0.18
94 22 0.25
ACGTcount: A:0.68, C:0.17, G:0.06, T:0.09
Consensus pattern (92 bp):
CAAAATAACAACAAAAATTAAACAACAAAAAAAGCAACAAAAATAATAAAAAACAACACCAAAAC
AATAAAAAACAACAACCAAAACAGTAA
Found at i:220606 original size:21 final size:22
Alignment explanation
Indices: 220579--220639 Score: 97
Period size: 21 Copynumber: 2.8 Consensus size: 22
220569 CAAAAAAAGT
220579 AACCAAAATAGTAAAAAACAAC
1 AACCAAAATAGTAAAAAACAAC
* *
220601 -ATCAAAACAGTAAAAAACAAC
1 AACCAAAATAGTAAAAAACAAC
220622 AACCAAAATAGTAAAAAA
1 AACCAAAATAGTAAAAAA
220640 ATAACACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.10
Consensus pattern (22 bp):
AACCAAAATAGTAAAAAACAAC
Found at i:220616 original size:22 final size:21
Alignment explanation
Indices: 220580--220653 Score: 94
Period size: 21 Copynumber: 3.4 Consensus size: 21
220570 AAAAAAAGTA
*
220580 ACCAAAATAGTAAAAAACAAC
1 ACCAAAACAGTAAAAAACAAC
*
220601 ATCAAAACAGTAAAAAACAAC
1 ACCAAAACAGTAAAAAACAAC
* *
220622 AACCAAAATAGTAAAAAAATAAC
1 -ACCAAAACAGT-AAAAAACAAC
220645 ACCAAAACA
1 ACCAAAACA
220654 ACAATATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 19 0.42
22 17 0.38
23 9 0.20
ACGTcount: A:0.68, C:0.19, G:0.04, T:0.09
Consensus pattern (21 bp):
ACCAAAACAGTAAAAAACAAC
Found at i:220629 original size:43 final size:43
Alignment explanation
Indices: 220562--220653 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 43
220552 TAAAAAAATT
** *
220562 AAAACAGCAAAAAAAGTAACCAAAATAGT-AAAAAACAACATC
1 AAAACAGCAAAAAAAACAACCAAAATAGTAAAAAAACAACACC
* *
220604 AAAACAGTAAAAAACAACAACCAAAATAGTAAAAAAATAACACC
1 AAAACAGCAAAAAA-AACAACCAAAATAGTAAAAAAACAACACC
220648 AAAACA
1 AAAACA
220654 ACAATATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 13 0.30
43 13 0.30
44 17 0.40
ACGTcount: A:0.68, C:0.17, G:0.05, T:0.09
Consensus pattern (43 bp):
AAAACAGCAAAAAAAACAACCAAAATAGTAAAAAAACAACACC
Found at i:220804 original size:32 final size:32
Alignment explanation
Indices: 220763--220839 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
220753 AATGGGCCTC
*
220763 ATTTTTTGTCTAAGCCCATTTTTCGGGTC-TAT
1 ATTTTTTGTCCAAGCCCATTTTTCGGG-CATAT
220795 ATTTTTTGTCCAAGCCCATTTTTCGGGCATAT
1 ATTTTTTGTCCAAGCCCATTTTTCGGGCATAT
220827 ATTTTTTGTCCAA
1 ATTTTTTGTCCAA
220840 ACCCTTTCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 1 0.02
32 42 0.98
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.48
Consensus pattern (32 bp):
ATTTTTTGTCCAAGCCCATTTTTCGGGCATAT
Found at i:222577 original size:117 final size:119
Alignment explanation
Indices: 222430--222769 Score: 405
Period size: 117 Copynumber: 3.0 Consensus size: 119
222420 ATAAACTTGA
* * *
222430 ATAAATAAAAACCAACAAGCAGGTCTAAAGATGGAAGAAATTCAATAAAGAGATTAGATTT-TAA
1 ATAAATAAAAACCAACAAGCAGGTCCAAAGACGGAAGAAATTCAATAAAGAGATTAGATTTAAAA
222494 AAAAAA-TGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
66 AAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
222547 ATAAATAAAAACCAACAAGCAGGTCCAAAGACGGAAGAAATTCAATAAAGAGATTAGATTTAAAA
1 ATAAATAAAAACCAACAAGCAGGTCCAAAGACGGAAGAAATTCAATAAAGAGATTAGATTTAAAA
* ****
222612 AAAAAATTGATTAATAATGCTATCATGCAACAATA-CC-A-T-AAATAAAAACC
66 AAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
** ***
222662 A-ACAAGCAGGTCC-A-AAG-A--T--------GGAAGAAATTCAATAAAGAGATTAGATTTAAA
1 ATA-AATAAAAACCAACAAGCAGGTCCAAAGACGGAAGAAATTCAATAAAGAGATTAGATTT-AA
222713 AAAAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
64 AAAAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
222769 A
1 A
222770 CCATATTAGT
Statistics
Matches: 197, Mismatches: 18, Indels: 26
0.82 0.07 0.11
Matches are distributed among these distances:
102 29 0.15
103 39 0.20
104 2 0.01
105 1 0.01
106 1 0.01
107 7 0.04
110 1 0.01
112 1 0.01
113 3 0.02
114 2 0.01
115 12 0.06
116 1 0.01
117 60 0.30
118 10 0.05
119 28 0.14
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.24
Consensus pattern (119 bp):
ATAAATAAAAACCAACAAGCAGGTCCAAAGACGGAAGAAATTCAATAAAGAGATTAGATTTAAAA
AAAAAATTGATTAATAATGCTATCATGCAACAATATCCAATTGAATTTTGTACC
Found at i:222669 original size:102 final size:103
Alignment explanation
Indices: 222543--222749 Score: 398
Period size: 102 Copynumber: 2.0 Consensus size: 103
222533 TTGAATTTTG
222543 TACCATAAATAAAAACCAACAAGCAGGTCCAAAGACGGAAGAAATTCAATAAAGAGATTAGATTT
1 TACCATAAATAAAAACCAACAAGCAGGTCCAAAGACGGAAGAAATTCAATAAAGAGATTAGATTT
222608 -AAAAAAAAAATTGATTAATAATGCTATCATGCAACAA
66 AAAAAAAAAAATTGATTAATAATGCTATCATGCAACAA
*
222645 TACCATAAATAAAAACCAACAAGCAGGTCCAAAGATGGAAGAAATTCAATAAAGAGATTAGATTT
1 TACCATAAATAAAAACCAACAAGCAGGTCCAAAGACGGAAGAAATTCAATAAAGAGATTAGATTT
222710 AAAAAAAAAAATTGATTAATAATGCTATCATGCAACAA
66 AAAAAAAAAAATTGATTAATAATGCTATCATGCAACAA
222748 TA
1 TA
222750 TCCAATTGAA
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
102 64 0.62
103 39 0.38
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (103 bp):
TACCATAAATAAAAACCAACAAGCAGGTCCAAAGACGGAAGAAATTCAATAAAGAGATTAGATTT
AAAAAAAAAAATTGATTAATAATGCTATCATGCAACAA
Found at i:226406 original size:6 final size:6
Alignment explanation
Indices: 226385--226464 Score: 51
Period size: 6 Copynumber: 13.2 Consensus size: 6
226375 TTAAATGGGT
** * *
226385 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAG TTTATCTAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA---AA
226435 TTTAAA TTTAAA TTT-AA -TTAAA TTTGAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA T
226465 AGTTTTAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
4 4 0.07
5 6 0.10
6 37 0.64
7 6 0.10
9 5 0.09
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:226420 original size:17 final size:17
Alignment explanation
Indices: 226385--226464 Score: 72
Period size: 17 Copynumber: 4.4 Consensus size: 17
226375 TTAAATGGGT
*
226385 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TCTTAAA
226403 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
*
226420 TTTAAGTTTATCTATTTTAAA
1 TTTAAATTTATC----TTAAA
*
226441 TTTAAATTTA-ATTAAA
1 TTTAAATTTATCTTAAA
226457 TTTGAAAT
1 TTT-AAAT
226465 AGTTTTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
16 8 0.15
17 21 0.40
18 10 0.19
21 14 0.26
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:231374 original size:6 final size:6
Alignment explanation
Indices: 231353--231432 Score: 51
Period size: 6 Copynumber: 13.2 Consensus size: 6
231343 TTAAATGGGT
** * *
231353 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAG TTTATCTAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA---AA
231403 TTTAAA TTTAAA TTT-AA -TTAAA TTTGAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA T
231433 AGTTTTAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
4 4 0.07
5 6 0.10
6 37 0.64
7 6 0.10
9 5 0.09
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:231388 original size:17 final size:17
Alignment explanation
Indices: 231353--231432 Score: 72
Period size: 17 Copynumber: 4.4 Consensus size: 17
231343 TTAAATGGGT
*
231353 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TCTTAAA
231371 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
*
231388 TTTAAGTTTATCTATTTTAAA
1 TTTAAATTTATC----TTAAA
*
231409 TTTAAATTTA-ATTAAA
1 TTTAAATTTATCTTAAA
231425 TTTGAAAT
1 TTT-AAAT
231433 AGTTTTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
16 8 0.15
17 21 0.40
18 10 0.19
21 14 0.26
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:233248 original size:29 final size:27
Alignment explanation
Indices: 233173--233346 Score: 107
Period size: 29 Copynumber: 6.0 Consensus size: 27
233163 TCCCAAAGGT
* * *
233173 CCCTAAACTATCCAAAAATTACATTTTAAA
1 CCCTAAA-TTTCC-AAAATTCCATTTT-TA
* *
233203 CCTTAAACTTTCTAAAATTCCATTTTTGA
1 CCCTAAA-TTTCCAAAATTCCATTTTT-A
* * *
233232 CCCTGAATTCTCCAAAAATTACATTATTA
1 CCCTAAATT-TCC-AAAATTCCATTTTTA
*
233261 CCCTCACACTTTCCAAAATTCCATTTTTA
1 CCCT-A-AATTTCCAAAATTCCATTTTTA
**
233290 -CCTAAATTTTCCAAAAATTATATTTTTA
1 CCCTAAA-TTTCC-AAAATTCCATTTTTA
*
233318 CCCTCCAAACTTTCTAAAATTCCATTTTT
1 CCCT--AAA-TTTCCAAAATTCCATTTTT
233347 CACCTCAAAT
Statistics
Matches: 113, Mismatches: 21, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
26 1 0.01
27 6 0.05
28 18 0.16
29 41 0.36
30 37 0.33
31 10 0.09
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (27 bp):
CCCTAAATTTCCAAAATTCCATTTTTA
Found at i:233279 original size:59 final size:56
Alignment explanation
Indices: 233174--233409 Score: 233
Period size: 59 Copynumber: 4.1 Consensus size: 56
233164 CCCAAAGGTC
* * * *
233174 CCTAAACTATCCAAAAATTACATTTTAAACCTTAAACTTTCTAAAATTCCATTTTTGA
1 CCTAAATTCTCCAAAAATTACATTTT-ACCCTCAAACTTTCTAAAATTCCATTTTT-A
* * *
233232 CCCTGAATTCTCCAAAAATTACATTATTACCCTCACACTTTCCAAAATTCCATTTTTA
1 -CCTAAATTCTCCAAAAATTACATT-TTACCCTCAAACTTTCTAAAATTCCATTTTTA
* *
233290 CCTAAATTTTCCAAAAATTATATTTTTACCCTCCAAACTTTCTAAAATTCCATTTTTCA
1 CCTAAATTCTCCAAAAATTACA-TTTTACCCT-CAAACTTTCTAAAATTCCATTTTT-A
* ** * *
233349 CCTCAAATTTTTAAAAAATTACCATTTTACCC-CGAA-TTTCTTAAAATTTCATTTTTTA
1 CCT-AAATTCTCCAAAAATTA-CATTTTACCCTCAAACTTTC-TAAAATTCCA-TTTTTA
233407 CCT
1 CCT
233410 TGATTTTTCC
Statistics
Matches: 152, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
57 30 0.20
58 41 0.27
59 55 0.36
60 25 0.16
61 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.01, T:0.40
Consensus pattern (56 bp):
CCTAAATTCTCCAAAAATTACATTTTACCCTCAAACTTTCTAAAATTCCATTTTTA
Found at i:233367 original size:30 final size:28
Alignment explanation
Indices: 233275--233409 Score: 98
Period size: 30 Copynumber: 4.6 Consensus size: 28
233265 CACACTTTCC
*
233275 AAAATTCCATTTTTACCT-AAATTTTCCA
1 AAAATTCCATTTTTACCTCAAATTTT-TA
** *
233303 AAAATTATATTTTTACCCTCCAAACTTTCT-
1 AAAATTCCATTTTTA-CCT-CAAA-TTTTTA
233333 AAAATTCCATTTTTCACCTCAAATTTTTAA
1 AAAATTCCATTTTT-ACCTCAAATTTTT-A
* *
233363 AAAATTACCA-TTTTACCCCGAATTTCTT-
1 AAAATT-CCATTTTTACCTCAAATTT-TTA
*
233391 AAAATTTCATTTTTTACCT
1 AAAATTCCA-TTTTTACCT
233410 TGATTTTTCC
Statistics
Matches: 85, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.02
28 23 0.27
29 23 0.27
30 27 0.32
31 7 0.08
32 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.01, T:0.44
Consensus pattern (28 bp):
AAAATTCCATTTTTACCTCAAATTTTTA
Found at i:233394 original size:58 final size:58
Alignment explanation
Indices: 233211--233560 Score: 238
Period size: 58 Copynumber: 6.0 Consensus size: 58
233201 AACCTTAAAC
* * * * *
233211 TTTC-TAAAATTCCATTTTTGACCCTGAATTCTCCAAAAATTA-CATTATTACCCTCAC-AC
1 TTTCTTAAAATTCCATTTTTTA-CCTAAATTTTTCAAAAATTACCATT-TTACCC-C-CGAA
* * * *
233270 TTTC-CAAAATTCCA-TTTTTACCTAAATTTTCCAAAAATTA-TATTTTTACCCTCCAAA
1 TTTCTTAAAATTCCATTTTTTACCTAAATTTTTCAAAAATTACCA-TTTTACCC-CCGAA
* *
233327 CTTTC-TAAAATTCCATTTTTCACCTCAAATTTTTAAAAAATTACCATTTTA-CCCCGAA
1 -TTTCTTAAAATTCCATTTTTTACCT-AAATTTTTCAAAAATTACCATTTTACCCCCGAA
* ** *
233385 TTTCTTAAAATTTCATTTTTTACCTTGATTTTTCCAAAATTACCA-TTTACCCCCCGAA
1 TTTCTTAAAATTCCATTTTTTACCTAAATTTTTCAAAAATTACCATTTTA-CCCCCGAA
* * ** *
233443 CTTCCTAAAA-TCCTATTTTTTACCCTGATTTTTTTTC-AAAATTACCATTTTACCCCCGGA
1 TTTCTTAAAATTCC-ATTTTTTA-CCT-A-AATTTTTCAAAAATTACCATTTTACCCCCGAA
* * * ***
233503 TGTCTAAAAATTCCA-TTTTGACCCCGATTCTTTCTGAAAAATTACCATTTTACCCCCG
1 TTTCTTAAAATTCCATTTTTTACCTAAATT-TTTC--AAAAATTACCATTTTACCCCCG
233561 GATGTTTAAA
Statistics
Matches: 238, Mismatches: 34, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
56 7 0.03
57 54 0.23
58 67 0.28
59 31 0.13
60 65 0.27
61 14 0.06
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (58 bp):
TTTCTTAAAATTCCATTTTTTACCTAAATTTTTCAAAAATTACCATTTTACCCCCGAA
Found at i:233405 original size:117 final size:117
Alignment explanation
Indices: 233174--233521 Score: 293
Period size: 117 Copynumber: 3.0 Consensus size: 117
233164 CCCAAAGGTC
* * * * * * *
233174 CCTAAACTATCCAAAAATTACATTTTAAACCT-TAAACTTTCTAAAATTCCATTTTTGACC-CTG
1 CCTAAATTTTCCAAAAATTACATTTTTACCCTCCAAACTTTCTAAAATTCCATTTTTCACCTC-A
* ** *
233237 AATTCTCCAAAAATTA-CATTATTACCCTC-ACACTTTC-CAAAATTCCA-TTTTTA
65 AATTTTTAAAAAATTACCATT-TTACCC-CGA-A-TTTCTAAAAATTCCATTTTTTA
*
233290 CCTAAATTTTCCAAAAATTATATTTTTACCCTCCAAACTTTCTAAAATTCCATTTTTCACCTCAA
1 CCTAAATTTTCCAAAAATTACATTTTTACCCTCCAAACTTTCTAAAATTCCATTTTTCACCTCAA
* *
233355 ATTTTTAAAAAATTACCATTTTACCCCGAATTTCTTAAAATTTCATTTTTTA
66 ATTTTTAAAAAATTACCATTTTACCCCGAATTTCTAAAAATTCCATTTTTTA
* * * * * *
233407 CCTTGATTTTTCC-AAAATTACCA--TTTACCCCCCGAACTTCCTAAAA-TCCTATTTTTTACCC
1 CC-TAAATTTTCCAAAAATTA-CATTTTTACCCTCCAAACTTTCTAAAATTCC-ATTTTTCA-CC
* ** ** * *
233468 TGATTTTTTTTCAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTT
62 TCAAATTTTTAAAAAATTACCATTTTA-CCCCGAATTTCTAAAAATTCCATTTT
233522 GACCCCGATT
Statistics
Matches: 192, Mismatches: 29, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
115 7 0.04
116 64 0.33
117 85 0.44
118 36 0.19
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (117 bp):
CCTAAATTTTCCAAAAATTACATTTTTACCCTCCAAACTTTCTAAAATTCCATTTTTCACCTCAA
ATTTTTAAAAAATTACCATTTTACCCCGAATTTCTAAAAATTCCATTTTTTA
Found at i:233526 original size:29 final size:29
Alignment explanation
Indices: 233480--233574 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 29
233470 ATTTTTTTTC
233480 AAAATTACCATTTTACCCCCGGATGTCTA
1 AAAATTACCATTTTACCCCCGGATGTCTA
*
233509 AAAATT-CCATTTTGA-CCCC-GATTCTTTCTGA
1 AAAATTACCATTTT-ACCCCCGGA---TGTCT-A
*
233540 AAAATTACCATTTTACCCCCGGATGTTTA
1 AAAATTACCATTTTACCCCCGGATGTCTA
233569 AAAATT
1 AAAATT
233575 TTGTTTTTGA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
27 2 0.04
28 11 0.20
29 14 0.25
30 7 0.13
31 8 0.15
32 11 0.20
33 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGGATGTCTA
Found at i:233988 original size:96 final size:97
Alignment explanation
Indices: 233850--234037 Score: 256
Period size: 96 Copynumber: 1.9 Consensus size: 97
233840 GAAAACTTTA
* * * * *
233850 AAATCAAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
1 AAATCAAGGCAATATTCTTTTATCTCGAGTTCTGAAAATTTGTGCCTTAAATTACTAGGCGCAAC
*
233915 TTTTCTTCAAATTG-GAATAATCGAATACCCTT
66 TTTTCTTCAAATCGAG-ATAATCGAATACCCTT
* * *
233947 AAATCGAGGCAATGTT-TTTTATCTCTGA-TTCTGAAAATTTGTGCCTTAAATTACTAGGTGCAA
1 AAATCAAGGCAATATTCTTTTATCTC-GAGTTCTGAAAATTTGTGCCTTAAATTACTAGGCGCAA
234010 CTTTTCTTCAAATCGAGATAATCGAATA
65 CTTTTCTTCAAATCGAGATAATCGAATA
234038 TCTGTTTCCA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
96 63 0.79
97 17 0.21
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (97 bp):
AAATCAAGGCAATATTCTTTTATCTCGAGTTCTGAAAATTTGTGCCTTAAATTACTAGGCGCAAC
TTTTCTTCAAATCGAGATAATCGAATACCCTT
Found at i:240407 original size:18 final size:18
Alignment explanation
Indices: 240384--240426 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
240374 CAGATGTGAA
240384 GGAAAAGAAGAAAGAGAT
1 GGAAAAGAAGAAAGAGAT
**
240402 GGAAAA-AAGCGAGAGAT
1 GGAAAAGAAGAAAGAGAT
240419 GAGAAAAG
1 G-GAAAAG
240427 CACGACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.58, C:0.02, G:0.35, T:0.05
Consensus pattern (18 bp):
GGAAAAGAAGAAAGAGAT
Found at i:245298 original size:49 final size:48
Alignment explanation
Indices: 245239--245373 Score: 164
Period size: 49 Copynumber: 2.8 Consensus size: 48
245229 AAGCATAAAG
** *
245239 GGAAAGATTTAAACCGTAACAACGAATCCAGTATCACAGAGACGTGAA
1 GGAAAGATTTAAACCGTAACGGCGAATCCAGTACCACAGAGACGTGAA
* * * *
245287 GGAAA-ATATTTAACCTGGAACGGCAAATCCAATACCACAGAGACGTGAA
1 GGAAAGAT-TTAAACC-GTAACGGCGAATCCAGTACCACAGAGACGTGAA
*
245336 CGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCAC
1 -GGAAAGATTTAAACCGTAACGGCGAATCCAGTACCAC
245374 GAAGACACAA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
47 2 0.03
48 11 0.15
49 46 0.65
50 10 0.14
51 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (48 bp):
GGAAAGATTTAAACCGTAACGGCGAATCCAGTACCACAGAGACGTGAA
Found at i:245397 original size:49 final size:49
Alignment explanation
Indices: 245337--245594 Score: 222
Period size: 49 Copynumber: 5.3 Consensus size: 49
245327 AGACGTGAAC
* * *
245337 GGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGACACAAAG
1 GGAAAGGTTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAG
* * *
245386 GAAAAGGTTTAAG-TCGCAATGGCGAA-CCTAGTACCTC-AGAGACACAAAG
1 GGAAAGGTTTAAGCT-GCAACGGCGAATCC-AGTACCACGA-AGACACAAAG
* * * * * **
245435 GGAAAGGTTTAAGTTGTAATGACGAA-CCTAGTACCTC-AGAGACATGAAG
1 GGAAAGGTTTAAGCTGCAACGGCGAATCC-AGTACCACGA-AGACACAAAG
* * * *
245484 GGAAAGAG-TTAAGCTGCAACGGTGAATCCAATACCATGAAGATACAAAG
1 GGAAAG-GTTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAG
** * * *
245533 GGAAATATTTAAGCTGCAACGGCGAATCCAGTACCGCGAAAACACGAAG
1 GGAAAGGTTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAG
245582 GGAAAGGTTTAAG
1 GGAAAGGTTTAAG
245595 TCACAATGGC
Statistics
Matches: 168, Mismatches: 33, Indels: 16
0.77 0.15 0.07
Matches are distributed among these distances:
48 3 0.02
49 160 0.95
50 5 0.03
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.17
Consensus pattern (49 bp):
GGAAAGGTTTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAAG
Found at i:245426 original size:98 final size:97
Alignment explanation
Indices: 245164--245643 Score: 291
Period size: 98 Copynumber: 4.9 Consensus size: 97
245154 CCACAACGAT
* * * * * * * *
245164 GAATCCAGTACCATGAAGATATGGAA-GGAAAGGCTTAAGTCGCAACGGCGAACTGTGTACCTTA
1 GAATCCAGTACCACGAAGACA-CGAAGGGAAAGGTTTAAGTCGCAATGGCGAAC-CTATACCTCA
* * **
245228 GA-AGCATAAAGGGAAAGATTTAAACCGTAACAAC
64 GAGA-CATAAAGGGAAAGATTTAAGCTGTAACGGC
* ** * ** * * * * * *
245262 GAATCCAGTATCAC-AGAGACGTGAAGGAAAATATTTAA-CCTGGAACGGCAAATCCAATACCAC
1 GAATCCAGTACCACGA-AGACACGAAGGGAAAGGTTTAAGTC-GCAATGGCGAA-CCTATACCTC
* * * *
245325 AGAGACGTGAACGGAAAGATTTAAGCCGTAACGGC
63 AGAGACATAAAGGGAAAGATTTAAGCTGTAACGGC
* *
245360 GAATCCAGTACCACGAAGACACAAAGGAAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAG
1 GAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTA-TACCTCAG
* * * * *
245425 AGACACAAAGGGAAAGGTTTAAGTTGTAATGAC
65 AGACATAAAGGGAAAGATTTAAGCTGTAACGGC
* * * * *
245458 GAA-CCTAGTACCTC-AGAGACATGAAGGGAAAGAG-TTAAG-CTGCAACGGTGAATCCAATACC
1 GAATCC-AGTACCACGA-AGACACGAAGGGAAAG-GTTTAAGTC-GCAATGGCGAA-CCTATACC
* * * * *
245519 ATGA-AGATACAAAGGGAAATATTTAAGCTGCAACGGC
61 -TCAGAGACATAAAGGGAAAGATTTAAGCTGTAACGGC
* * * *
245556 GAATCCAGTACCGCGAAAACACGAAGGGAAAGGTTTAAGTCACAATGGCAAACCTTATACCTCAG
1 GAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCGCAATGGCGAACC-TATACCTCAG
245621 A-AGCATGAAA-GGAAA-ATTTAAGC
65 AGA-CAT-AAAGGGAAAGATTTAAGC
245644 AATAGCGGAT
Statistics
Matches: 290, Mismatches: 70, Indels: 45
0.72 0.17 0.11
Matches are distributed among these distances:
97 26 0.09
98 247 0.85
99 17 0.06
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (97 bp):
GAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTATACCTCAGA
GACATAAAGGGAAAGATTTAAGCTGTAACGGC
Found at i:245514 original size:196 final size:195
Alignment explanation
Indices: 245136--245641 Score: 506
Period size: 196 Copynumber: 2.6 Consensus size: 195
245126 CCACGAAACA
* ** * * * *
245136 TGAAGGGAAATATTTAAGCCACAACGATGAATCCAGTACCATGAAGATATGGAAGGAAAGGCTTA
1 TGAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACA-CGAAGGAAAGGTTTA
* * * *
245201 AGTCGCAACGGCGAA-CTGTGTACCTTAGAAGCATAAAGGGAAAGATTTAAACCGTAACAACGAA
65 AGTCGCAATGGCGAACCT-AGTACCTCAGAAGCACAAAGGGAAAGATTTAAACCGTAACAACGAA
* * * * * *
245265 TCCAGTATCACAGAGACGTGAAGGAAAATATTTAACCTGGAACGGCAAATCCAATACCA-CAGAG
129 TCCAGTACCACAGAGACATGAAGGAAAAGAGTTAACCTGCAACGGCAAATCCAATACCAGAAGAG
245329 AC
194 AC
* * * *
245331 GTGAACGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGACACAAAGGAAAAGGTTT
1 -TGAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGG-AAAGGTTT
* *** **
245396 AAGTCGCAATGGCGAACCTAGTACCTCAG-AGACACAAAGGGAAAGGTTTAAGTTGTAATGACGA
64 AAGTCGCAATGGCGAACCTAGTACCTCAGAAG-CACAAAGGGAAAGATTTAAACCGTAACAACGA
* * * **
245460 A-CCTAGTACCTCAGAGACATGAAGGGAAAGAGTTAAGCTGCAACGGTGAATCCAATACCATGAA
128 ATCC-AGTACCACAGAGACATGAAGGAAAAGAGTTAACCTGCAACGGCAAATCCAATACCA-GAA
*
245524 GATAC
191 GAGAC
* * * *
245529 -AAAGGGAAATATTTAAGCTGCAACGGCGAATCCAGTACCGCGAAAACACGAAGGGAAAGGTTTA
1 TGAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAA-GGAAAGGTTTA
* * *
245593 AGTCACAATGGCAAACCTTA-TACCTCAGAAGCATGAAA-GGAAA-ATTTAA
65 AGTCGCAATGGCGAACC-TAGTACCTCAGAAGCA-CAAAGGGAAAGATTTAA
245642 GCAATAGCGG
Statistics
Matches: 255, Mismatches: 45, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
195 13 0.05
196 226 0.89
197 11 0.04
198 5 0.02
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (195 bp):
TGAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGAAAGGTTTAA
GTCGCAATGGCGAACCTAGTACCTCAGAAGCACAAAGGGAAAGATTTAAACCGTAACAACGAATC
CAGTACCACAGAGACATGAAGGAAAAGAGTTAACCTGCAACGGCAAATCCAATACCAGAAGAGAC
Found at i:245610 original size:147 final size:147
Alignment explanation
Indices: 245318--245643 Score: 358
Period size: 147 Copynumber: 2.2 Consensus size: 147
245308 GGCAAATCCA
* * * * *
245318 ATACCACAGAGACGTGAACGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGACACA
1 ATACCTCAGAGACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGACACA
* * * *
245383 AAGGAAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACACAAAGGGAAAGGTTTAAG
66 AAGGAAAAGATTTAAGTCGCAACGGCGAACCTAGTACCGCAGAAACACAAAGGGAAAGGTTTAAG
*** *
245448 TTGTAATGACGAACC-T
131 TCACAATGACAAACCTT
* * * * * *
245464 AGTACCTCAGAGACATGAAGGGAAAGAGTTAAGCTGCAACGGTGAATCCAATACCATGAAGATAC
1 A-TACCTCAGAGACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGACAC
* * *
245529 AAAGGGAAATATTTAAG-CTGCAACGGCGAATCC-AGTACCGC-GAAAACACGAAGGGAAAGGTT
65 AAAGGAAAAGATTTAAGTC-GCAACGGCGAA-CCTAGTACCGCAG-AAACACAAAGGGAAAGGTT
*
245591 TAAGTCACAATGGCAAACCTT
127 TAAGTCACAATGACAAACCTT
245612 ATACCTCAGA-AGCATGAAAGGAAA-ATTTAAGC
1 ATACCTCAGAGA-CATGAAAGGAAAGATTTAAGC
245644 AATAGCGGAT
Statistics
Matches: 150, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
146 11 0.07
147 135 0.90
148 4 0.03
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (147 bp):
ATACCTCAGAGACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGACACA
AAGGAAAAGATTTAAGTCGCAACGGCGAACCTAGTACCGCAGAAACACAAAGGGAAAGGTTTAAG
TCACAATGACAAACCTT
Found at i:246888 original size:21 final size:20
Alignment explanation
Indices: 246859--246899 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
246849 TAAAGGCATT
*
246859 AATAATTATTGGTAATATTA
1 AATAATTATTGATAATATTA
*
246879 AATATATTATTTATAATATTA
1 AATA-ATTATTGATAATATTA
246900 TTAATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AATAATTATTGATAATATTA
Found at i:246906 original size:21 final size:21
Alignment explanation
Indices: 246856--246908 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
246846 AAATAAAGGC
*
246856 ATTAATAATTATTGGTAATATT
1 ATTAAT-ATTATTGATAATATT
* *
246878 A-AATATATTATTTATAATATT
1 ATTA-ATATTATTGATAATATT
246899 ATTAATATTA
1 ATTAATATTA
246909 ATAAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTAATATTATTGATAATATT
Found at i:248029 original size:29 final size:28
Alignment explanation
Indices: 247997--248132 Score: 89
Period size: 28 Copynumber: 4.8 Consensus size: 28
247987 GTTGATTTCG
247997 AATTCTCCAAAAATTACATTTTTACCCCA
1 AATT-TCCAAAAATTACATTTTTACCCCA
* * *
248026 AATTTTCAAAAATTA-TTTTTTACTCCTA
1 AATTTCCAAAAATTACATTTTTAC-CCCA
* *
248054 AACTTTCC-AAAATTCCATTTTTGACCCGA
1 AA-TTTCCAAAAATTACATTTTT-ACCCCA
* ** * *
248083 ATTTTAAAAAAATTACCA-TTTTACCTCG
1 AATTTCCAAAAATTA-CATTTTTACCCCA
* * *
248111 AACTTCCTAAAATTCCATTTTT
1 AATTTCCAAAAATTACATTTTT
248133 TACCATGATT
Statistics
Matches: 80, Mismatches: 20, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
27 9 0.11
28 40 0.50
29 27 0.34
30 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.40
Consensus pattern (28 bp):
AATTTCCAAAAATTACATTTTTACCCCA
Found at i:248215 original size:60 final size:61
Alignment explanation
Indices: 248091--248233 Score: 186
Period size: 62 Copynumber: 2.4 Consensus size: 61
248081 GAATTTTAAA
* * ** *
248091 AAAATTACCATTTTA--CCTCGAACTTCCTAAAATTCCATTTTTTACCATGATTTTTTTTCC
1 AAAATTACCATTTTACCCCTCGAACTTCCTAAAATCCCATTTTTAACCACAATATTTTTT-C
*
248151 AAAATTACCATTTTACCCCTCGAACTTCCTAAAATCCCATTTTTAACCCCAATATTTTTT-
1 AAAATTACCATTTTACCCCTCGAACTTCCTAAAATCCCATTTTTAACCACAATATTTTTTC
*
248211 AAAATTACTATTTTACCCC-CGAA
1 AAAATTACCATTTTACCCCTCGAA
248234 TGTCTAAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
59 4 0.05
60 33 0.45
62 37 0.50
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (61 bp):
AAAATTACCATTTTACCCCTCGAACTTCCTAAAATCCCATTTTTAACCACAATATTTTTTC
Found at i:248272 original size:29 final size:28
Alignment explanation
Indices: 248240--248310 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
248230 CGAATGTCTA
248240 AAAATT-CAATTTTTGACCTCTGAGTGTTC
1 AAAATTACAA-TTTTG-CCTCTGAGTGTTC
*
248269 AAAATTACCATTTTGCCTCTGAGTGTTC
1 AAAATTACAATTTTGCCTCTGAGTGTTC
*
248297 AAAATTACCATTTT
1 AAAATTACAATTTT
248311 ACCCTCGAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 27 0.68
29 11 0.28
30 2 0.05
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (28 bp):
AAAATTACAATTTTGCCTCTGAGTGTTC
Found at i:248294 original size:28 final size:29
Alignment explanation
Indices: 248250--248310 Score: 115
Period size: 28 Copynumber: 2.1 Consensus size: 29
248240 AAAATTCAAT
248250 TTTTGACCTCTGAGTGTTCAAAATTACCA
1 TTTTGACCTCTGAGTGTTCAAAATTACCA
248279 TTTTG-CCTCTGAGTGTTCAAAATTACCA
1 TTTTGACCTCTGAGTGTTCAAAATTACCA
248307 TTTT
1 TTTT
248311 ACCCTCGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTTGACCTCTGAGTGTTCAAAATTACCA
Found at i:248320 original size:28 final size:29
Alignment explanation
Indices: 248256--248320 Score: 107
Period size: 28 Copynumber: 2.3 Consensus size: 29
248246 CAATTTTTGA
*
248256 CCTCTGAGTGTTCAAAATTACCATTTT-G
1 CCTCTGAGTGTTCAAAATTACCATTTTAC
248284 CCTCTGAGTGTTCAAAATTACCATTTTAC
1 CCTCTGAGTGTTCAAAATTACCATTTTAC
248313 CCTC-GAGT
1 CCTCTGAGT
248321 ATACAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 31 0.89
29 4 0.11
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (29 bp):
CCTCTGAGTGTTCAAAATTACCATTTTAC
Found at i:248327 original size:28 final size:28
Alignment explanation
Indices: 248256--248328 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
248246 CAATTTTTGA
* * *
248256 CCTCTGAGTGTTCAAAATTACCATTTTG
1 CCTCTGAGTATACAAAATTACCATTTTC
* *
248284 CCTCTGAGTGTTCAAAATTACCATTTTAC
1 CCTCTGAGTATACAAAATTACCATTTT-C
248313 CCTC-GAGTATACAAAA
1 CCTCTGAGTATACAAAA
248329 AATCTCATCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 37 0.90
29 4 0.10
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (28 bp):
CCTCTGAGTATACAAAATTACCATTTTC
Done.