Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014927.1 Kokia drynarioides strain JFW-HI SEQ_129970, 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: 457488
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 273 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3748 original size:9 final size:9
Alignment explanation
Indices: 3737--3794 Score: 55
Period size: 9 Copynumber: 6.1 Consensus size: 9
3727 TAAATAATTT
*
3737 AAAATTTAT
1 AAAATTTAA
3746 AAAATATTAA
1 AAAAT-TTAA
3756 AAAATTAAATAA
1 AAAATT---TAA
*
3768 AAAATTT-T
1 AAAATTTAA
3776 AAAATTTAA
1 AAAATTTAA
3785 AAAATTTAA
1 AAAATTTAA
3794 A
1 A
3795 TTTAAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
8 7 0.17
9 17 0.41
10 8 0.20
12 9 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAATTTAA
Found at i:3788 original size:30 final size:31
Alignment explanation
Indices: 3737--3795 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 31
3727 TAAATAATTT
3737 AAAATTTATAAAATATTAAAAAATTAAATAA
1 AAAATTTATAAAATATTAAAAAATTAAATAA
3768 AAAATTT-TAAAAT-TTAAAAAATTTAAAT
1 AAAATTTATAAAATATTAAAAAA-TTAAAT
3796 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.30
30 12 0.44
31 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAATTTATAAAATATTAAAAAATTAAATAA
Found at i:3795 original size:15 final size:15
Alignment explanation
Indices: 3747--3803 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
3737 AAAATTTATA
3747 AAATATTAAAAAA-TT
1 AAAT-TTAAAAAATTT
3762 AAA--TAAAAAATTTT
1 AAATTTAAAAAA-TTT
3776 AAAATTTAAAAAATTT
1 -AAATTTAAAAAATTT
3792 AAATTTAAAAAA
1 AAATTTAAAAAA
3804 AAAAAATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 7 0.19
14 2 0.05
15 18 0.49
16 3 0.08
17 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTTAAAAAATTT
Found at i:3804 original size:16 final size:16
Alignment explanation
Indices: 3754--3804 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
3744 ATAAAATATT
3754 AAAAAA-TTAAA--TA
1 AAAAAATTTAAATTTA
*
3767 AAAAATTTTAAAATTT-
1 AAAAAATTT-AAATTTA
3783 AAAAAATTTAAATTTA
1 AAAAAATTTAAATTTA
3799 AAAAAA
1 AAAAAA
3805 AAAAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 5 0.16
14 2 0.06
15 9 0.29
16 14 0.45
17 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAAATTTAAATTTA
Found at i:4101 original size:32 final size:32
Alignment explanation
Indices: 4039--4099 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
4029 TAAAAGATAT
* *
4039 TATTTTCATACTTATTTTTATTTTACTTTTTC
1 TATTTTCAAAATTATTTTTATTTTACTTTTTC
4071 TATTTTCAAAATT-TTTTTATTTT-CTTTTT
1 TATTTTCAAAATTATTTTTATTTTACTTTTT
4100 TTATGAGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 6 0.22
31 10 0.37
32 11 0.41
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (32 bp):
TATTTTCAAAATTATTTTTATTTTACTTTTTC
Found at i:6737 original size:4 final size:4
Alignment explanation
Indices: 6717--6778 Score: 60
Period size: 4 Copynumber: 16.2 Consensus size: 4
6707 AACAAATTAC
* * *
6717 CTTT CTTT CCTT C-TT CTTT CTTT C-TT C-TT C-TT CTTC CTTC CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
6761 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
6779 CTGTTTATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
3 12 0.23
4 36 0.69
5 4 0.08
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:6777 original size:17 final size:18
Alignment explanation
Indices: 6717--6778 Score: 83
Period size: 17 Copynumber: 3.5 Consensus size: 18
6707 AACAAATTAC
6717 CTTTCTTTCCTTCTTCTTT
1 CTTTCTTT-CTTCTTCTTT
*
6736 CTTTC-TTCTTCTTCTTC
1 CTTTCTTTCTTCTTCTTT
*
6753 CTTCCTTTCTT-TTCTTT
1 CTTTCTTTCTTCTTCTTT
6770 CTTTCTTTC
1 CTTTCTTTC
6779 CTGTTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 26 0.68
18 7 0.18
19 5 0.13
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTCTTTCTTCTTCTTT
Found at i:9447 original size:18 final size:19
Alignment explanation
Indices: 9424--9459 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9414 GAGACCGGCC
*
9424 AATTGTTTGTGG-TGCCAA
1 AATTGTTTATGGTTGCCAA
9442 AATTGTTTATGGTTGCCA
1 AATTGTTTATGGTTGCCA
9460 TTTCAGCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (19 bp):
AATTGTTTATGGTTGCCAA
Found at i:10573 original size:15 final size:16
Alignment explanation
Indices: 10553--10583 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
10543 CAATCCATTT
10553 AAAATAGG-TAAAAAA
1 AAAATAGGATAAAAAA
10568 AAAATAGGATAAAAAA
1 AAAATAGGATAAAAAA
10584 TTAATGATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAATAGGATAAAAAA
Found at i:20038 original size:2 final size:2
Alignment explanation
Indices: 20031--20055 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20021 ACTAATCAGG
20031 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
20056 TACAATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:21283 original size:16 final size:16
Alignment explanation
Indices: 21262--21295 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
21252 ATGAAAATGG
21262 TTATGATTAGGAGTGA
1 TTATGATTAGGAGTGA
21278 TTATGATTAGGAGTGA
1 TTATGATTAGGAGTGA
21294 TT
1 TT
21296 GTAACCTATC
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:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (16 bp):
TTATGATTAGGAGTGA
Found at i:23772 original size:16 final size:18
Alignment explanation
Indices: 23751--23786 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
23741 AAATTAATCG
23751 TAAAATTAA-AC-AAATT
1 TAAAATTAACACTAAATT
23767 TAAAATTAACACTAAATT
1 TAAAATTAACACTAAATT
23785 TA
1 TA
23787 TTCTATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATTAACACTAAATT
Found at i:30333 original size:14 final size:14
Alignment explanation
Indices: 30314--30341 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30304 TGTATTTTGC
30314 AAATCATAATAGGA
1 AAATCATAATAGGA
30328 AAATCATAATAGGA
1 AAATCATAATAGGA
30342 TTTAAACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
AAATCATAATAGGA
Found at i:37187 original size:2 final size:2
Alignment explanation
Indices: 37180--37205 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37170 TGGTGGTGAG
37180 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
37206 TTGTTCATTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:51779 original size:2 final size:2
Alignment explanation
Indices: 51772--51805 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
51762 ATCTTTTCCT
51772 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
51806 ACTTCATGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:65354 original size:25 final size:24
Alignment explanation
Indices: 65326--65375 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
65316 AACCCATGAC
*
65326 TTCTAAAGCTATGATTAGATTTTTT
1 TTCTAAA-CTATGATTAGATATTTT
* *
65351 TTCTGAATTATGATTAGATATTTT
1 TTCTAAACTATGATTAGATATTTT
65375 T
1 T
65376 AACTCGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (24 bp):
TTCTAAACTATGATTAGATATTTT
Found at i:65384 original size:26 final size:24
Alignment explanation
Indices: 65335--65384 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
65325 CTTCTAAAGC
**
65335 TATGATTAGATTTTTTTTCTGAAT
1 TATGATTAGATTTTTTAACTGAAT
65359 TATGATTAGATATTTTTAACTCGAAT
1 TATGATTAGAT-TTTTTAACT-GAAT
65385 AGATGGGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 7 0.32
26 4 0.18
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (24 bp):
TATGATTAGATTTTTTAACTGAAT
Found at i:66771 original size:17 final size:16
Alignment explanation
Indices: 66749--66783 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
66739 GTTTATTTGT
66749 TTACTAATTCTAAGTGA
1 TTACTAATT-TAAGTGA
*
66766 TTACTAATTTAATTGA
1 TTACTAATTTAAGTGA
66782 TT
1 TT
66784 CAACCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (16 bp):
TTACTAATTTAAGTGA
Found at i:80029 original size:16 final size:16
Alignment explanation
Indices: 79995--80029 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
79985 GATTAAAAAG
*
79995 AAATCAAGAATACATC
1 AAATCAAGAATACAAC
*
80011 AAATCAAGAATTCAAC
1 AAATCAAGAATACAAC
80027 AAA
1 AAA
80030 ATCAGAGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.17, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATCAAGAATACAAC
Found at i:89478 original size:22 final size:23
Alignment explanation
Indices: 89446--89489 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
89436 AAGAATTCAC
**
89446 CAATAAACATATTAAAAAAAAAT
1 CAATAAACATAAAAAAAAAAAAT
89469 CAAT-AACATAAAAAAAAAAAA
1 CAATAAACATAAAAAAAAAAAA
89490 AAGAGCACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (23 bp):
CAATAAACATAAAAAAAAAAAAT
Found at i:94355 original size:21 final size:21
Alignment explanation
Indices: 94331--94421 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 21
94321 TGTCCGTTAT
*
94331 CCACCTCCACCGGTTAAGTCA
1 CCACCACCACCGGTTAAGTCA
* * * *
94352 CCACCACCACCAGTTTACTCC
1 CCACCACCACCGGTTAAGTCA
* * ** * *
94373 CCTCCACCACCTGTCCATTCT
1 CCACCACCACCGGTTAAGTCA
94394 CCACCACCACCGGTTAAGTCA
1 CCACCACCACCGGTTAAGTCA
*
94415 CCGCCAC
1 CCACCAC
94422 TACGACCTAC
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.22, C:0.49, G:0.10, T:0.19
Consensus pattern (21 bp):
CCACCACCACCGGTTAAGTCA
Found at i:97958 original size:20 final size:21
Alignment explanation
Indices: 97918--97959 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
97908 AAGATTTGGA
*
97918 ATTTGAATGACTTATTGATTG
1 ATTTGAATGACATATTGATTG
*
97939 ATTTGGATGACATA-TGATTG
1 ATTTGAATGACATATTGATTG
97959 A
1 A
97960 AAGCATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
ATTTGAATGACATATTGATTG
Found at i:100710 original size:31 final size:31
Alignment explanation
Indices: 100675--100733 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
100665 TGAATTATAC
*
100675 ATTTTAAAGAGAG-TAAAATATAATTTTATCA
1 ATTTTAAAGAG-GTTAAAATATAAATTTATCA
* *
100706 ATTTTAGAGAGGTTAAATTATAAATTTA
1 ATTTTAAAGAGGTTAAAATATAAATTTA
100734 CCATTATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.41
Consensus pattern (31 bp):
ATTTTAAAGAGGTTAAAATATAAATTTATCA
Found at i:102289 original size:29 final size:30
Alignment explanation
Indices: 102222--102291 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
102212 GTTAACGATT
*
102222 AAAT-CTAAATTTTAAAATATGAGAAGTAA
1 AAATACTAAATTCTAAAATATGAGAAGTAA
* * *
102251 AAAGATTAAATTCCTAAAA-AT-AGAAGTAC
1 AAATACTAAATT-CTAAAATATGAGAAGTAA
102280 AAATACTAAATT
1 AAATACTAAATT
102292 AATTTTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 20 0.61
30 8 0.24
31 5 0.15
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29
Consensus pattern (30 bp):
AAATACTAAATTCTAAAATATGAGAAGTAA
Found at i:102709 original size:21 final size:21
Alignment explanation
Indices: 102668--102720 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
102658 ATATTTATTT
* *
102668 TATATATTATA-AATTATAAA
1 TATATATTAAATAATTAAAAA
*
102688 TATATTTTAAATAATTAAAAA
1 TATATATTAAATAATTAAAAA
*
102709 TCTATATTAAAT
1 TATATATTAAAT
102721 TAAGTAGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATATATTAAATAATTAAAAA
Found at i:104218 original size:19 final size:21
Alignment explanation
Indices: 104172--104225 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
104162 TTACAAAAAA
* *
104172 ATAATAATTTAAAATAATCTT
1 ATAAAAATTCAAAATAATCTT
104193 A-AAAAATTCAAAAT-AT-TT
1 ATAAAAATTCAAAATAATCTT
104211 ATAAAAATTTCAAAA
1 ATAAAAA-TTCAAAA
104226 ATTATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 7 0.24
20 18 0.62
21 1 0.03
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAAATTCAAAATAATCTT
Found at i:104907 original size:24 final size:23
Alignment explanation
Indices: 104856--104954 Score: 68
Period size: 23 Copynumber: 4.5 Consensus size: 23
104846 TTTAAAATAT
104856 ATATTTATATTATATTATTTTTA
1 ATATTTATATTATATTATTTTTA
*
104879 ATATTTA-ATTTTA-TATTTTT-
1 ATATTTATATTATATTATTTTTA
* * *
104899 TTATTTAT-TGA-A-AATTTTTA
1 ATATTTATATTATATTATTTTTA
* * *
104919 TATAGTCATCTTAATATTA-TTTTA
1 -ATATTTATATT-ATATTATTTTTA
104943 ATATTTATATTA
1 ATATTTATATTA
104955 GAATAATATT
Statistics
Matches: 56, Mismatches: 13, Indels: 15
0.67 0.15 0.18
Matches are distributed among these distances:
19 7 0.12
20 7 0.12
21 12 0.21
22 7 0.12
23 16 0.29
24 6 0.11
25 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
ATATTTATATTATATTATTTTTA
Found at i:106584 original size:31 final size:31
Alignment explanation
Indices: 106549--106611 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
106539 TATATAATGA
*
106549 TCATTGAACTATTT-AAAAGTTTTCGTTTAAG
1 TCATTGAACTATTTGAAAA-TTTTCATTTAAG
*
106580 TCATTGAACTATTTGAAAATTTTTATTTAAG
1 TCATTGAACTATTTGAAAATTTTCATTTAAG
106611 T
1 T
106612 TATTCGGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (31 bp):
TCATTGAACTATTTGAAAATTTTCATTTAAG
Found at i:110193 original size:4 final size:4
Alignment explanation
Indices: 110182--110215 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
110172 GAGGAATATA
110182 TATG -ATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
110216 AATCTTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:112266 original size:2 final size:2
Alignment explanation
Indices: 112259--112283 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
112249 TTTTTAATGT
112259 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 T
112284 GAATGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:114176 original size:64 final size:64
Alignment explanation
Indices: 114071--114196 Score: 171
Period size: 64 Copynumber: 2.0 Consensus size: 64
114061 TATTTTTTTA
* * * * *
114071 GCATGAAGTAAACCTGCTCATGAATCGGGCCACCCACCCAGGCCCGAAGGTTTGCCCGAAAATG
1 GCATGAAGCAAACCTGCTAATGAATCGAGCCACCCACCCAGGCCCGAAAGCTTGCCCGAAAATG
** * *
114135 GCATGAAGCAAACCTGCTAATGGGTCGAGCCACCCATCCAGGCCCGAAAGCTTGCCTGAAAA
1 GCATGAAGCAAACCTGCTAATGAATCGAGCCACCCACCCAGGCCCGAAAGCTTGCCCGAAAA
114197 CGGAAGGGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15
Consensus pattern (64 bp):
GCATGAAGCAAACCTGCTAATGAATCGAGCCACCCACCCAGGCCCGAAAGCTTGCCCGAAAATG
Found at i:114380 original size:29 final size:29
Alignment explanation
Indices: 114327--114391 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
114317 ACCGACCCAA
*
114327 ATTTATA-ATGTTAAAAAAATTATTATATT
1 ATTTATATATGTTAAAAAAATAATTATA-T
*
114356 ATTTATATATGTT-AAATAATAATTATAT
1 ATTTATATATGTTAAAAAAATAATTATAT
114384 ATTTATAT
1 ATTTATAT
114392 TTATATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 9 0.27
29 19 0.58
30 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTTATATATGTTAAAAAAATAATTATAT
Found at i:117818 original size:2 final size:2
Alignment explanation
Indices: 117811--117837 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
117801 ATCAATCTTT
117811 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
117838 TCTGCTGAGC
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:121310 original size:31 final size:31
Alignment explanation
Indices: 121273--121339 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
121263 TTAACAACCT
* *
121273 AATGACTTGAATAAAAACTTTTGAATAGTTG
1 AATGACTTAAATAAAAACTTTCGAATAGTTG
*
121304 AATGACTTAAATAAAAACTTTCGAATAGTTT
1 AATGACTTAAATAAAAACTTTCGAATAGTTG
121335 AATGA
1 AATGA
121340 TCATTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.34
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCGAATAGTTG
Found at i:121532 original size:15 final size:14
Alignment explanation
Indices: 121505--121534 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
121495 TACATGTTTT
121505 TAATATTTATATTA
1 TAATATTTATATTA
121519 TAATATTATATATTA
1 TAATATT-TATATTA
121534 T
1 T
121535 TATAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTTATATTA
Found at i:128790 original size:15 final size:15
Alignment explanation
Indices: 128739--128790 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
128729 ATTGTAACAA
*
128739 GATTTTCACTCGGTTT
1 GATTTT-ACTCGATTT
* *
128755 GACTTAACTCGAATTT
1 GATTTTACTCG-ATTT
*
128771 CATTTTACTCGATTT
1 GATTTTACTCGATTT
128786 GATTT
1 GATTT
128791 GAAAAAATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.48
Consensus pattern (15 bp):
GATTTTACTCGATTT
Found at i:130660 original size:22 final size:21
Alignment explanation
Indices: 130635--130682 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
130625 ATTTGTTATT
*
130635 TTTACATGTTATTTAAAAAAAA
1 TTTACATGTTAGTT-AAAAAAA
* *
130657 TTTAAGATGTTAGTTAAATAAA
1 TTT-ACATGTTAGTTAAAAAAA
130679 TTTA
1 TTTA
130683 AAGGTTATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 12 0.55
23 9 0.41
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (21 bp):
TTTACATGTTAGTTAAAAAAA
Found at i:130683 original size:22 final size:23
Alignment explanation
Indices: 130640--130683 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
130630 TTATTTTTAC
*
130640 ATGTTATTTAAAAAAAATTTAAG
1 ATGTTAGTTAAAAAAAATTTAAG
*
130663 ATGTTAGTT-AAATAAATTTAA
1 ATGTTAGTTAAAAAAAATTTAA
130684 AGGTTATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (23 bp):
ATGTTAGTTAAAAAAAATTTAAG
Found at i:131528 original size:9 final size:9
Alignment explanation
Indices: 131514--131565 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 9
131504 TGGAAGATGG
131514 ATAAATAAA
1 ATAAATAAA
131523 ATAAAT-AA
1 ATAAATAAA
131531 ATAAATAAA
1 ATAAATAAA
131540 ATAGAATATAA
1 ATA-AATA-AA
131551 ATAAGATAAA
1 ATAA-ATAAA
131561 GATAA
1 -ATAA
131566 GGTAGGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.21
9 11 0.29
10 7 0.18
11 12 0.32
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (9 bp):
ATAAATAAA
Found at i:131982 original size:17 final size:18
Alignment explanation
Indices: 131950--131983 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
131940 CAATAATTTA
*
131950 ATAAATAATTAAAAATTC
1 ATAAATAATAAAAAATTC
131968 ATAAA-AATAAAAAATT
1 ATAAATAATAAAAAATT
131984 TTATCAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATAATAAAAAATTC
Found at i:133636 original size:2 final size:2
Alignment explanation
Indices: 133631--133657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
133621 TTCCACACAT
133631 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
133658 GTGAACTTGC
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:136038 original size:4 final size:4
Alignment explanation
Indices: 136029--136058 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
136019 TACAGCTAAT
136029 TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
136059 AGCATGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:137496 original size:2 final size:2
Alignment explanation
Indices: 137489--137515 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
137479 CAAAATTACA
137489 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
137516 AAATAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:139026 original size:11 final size:11
Alignment explanation
Indices: 139010--139147 Score: 59
Period size: 10 Copynumber: 13.0 Consensus size: 11
139000 CTCTAACATA
139010 AATATTAAAAT
1 AATATTAAAAT
*
139021 AATATTAAGAT
1 AATATTAAAAT
*
139032 GAT-TATATAAA-
1 AATAT-TA-AAAT
*
139043 AA-ATT-AATT
1 AATATTAAAAT
139052 AATATATAATATAT
1 AATAT-TAA-A-AT
*
139066 AATATTATAA-
1 AATATTAAAAT
139076 AATATTAAAAT
1 AATATTAAAAT
139087 AA-ATTAAAAT
1 AATATTAAAAT
139097 CAA-A-T-AAAT
1 -AATATTAAAAT
* *
139106 ATTTTTAAAA-
1 AATATTAAAAT
139116 AAT-TTAAAA-
1 AATATTAAAAT
139125 AATATTAAAAGT
1 AATATTAAAA-T
139137 AA-ATTTAAAAT
1 AATA-TTAAAAT
139148 GAACATGAGT
Statistics
Matches: 98, Mismatches: 11, Indels: 36
0.68 0.08 0.25
Matches are distributed among these distances:
8 3 0.03
9 15 0.15
10 31 0.32
11 28 0.29
12 12 0.12
13 3 0.03
14 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:146976 original size:97 final size:97
Alignment explanation
Indices: 146801--146994 Score: 270
Period size: 97 Copynumber: 2.0 Consensus size: 97
146791 AACTTTGGAA
146801 AAGGATATTCGATTATCTCGATTTGAAAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* *
146866 GAATCAGAGAT-AAAGAAACATTGCCTCGATTT
66 AAATCAGAAATAAAAG-AACATTGCCTCGATTT
* *
146898 AAGGGTATTCGATTAT-TCCGATTTGAAGAAAAA-TCGCGCCTAGTAAGTTAAGGCACAAATTTT
1 AAGGATATTCGATTATCT-CGATTTGAA-AAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTT
* *
146961 CAAAACTC-GAAATAAAAGAATATTGCCTTGATTT
64 CAAAA-TCAGAAATAAAAGAACATTGCCTCGATTT
146995 TAAAGTTTTC
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
96 1 0.01
97 75 0.86
98 11 0.13
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAATCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:147425 original size:30 final size:28
Alignment explanation
Indices: 147332--147438 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 28
147322 ATCTAGGTCA
147332 AAAAT-GAATTTTTT-GAAGTTTGAGGGT
1 AAAATGGAATTTTTTGGAAG-TTGAGGGT
* *
147359 AAAATGGTAATTTCTTGGAAAAATTG-GGGT
1 AAAATGG-AATTTTTTGG--AAGTTGAGGGT
*
147389 CTAAATGGAATTTTTTTGGAAGTTCGAGGGT
1 -AAAATGGAA-TTTTTTGGAAGTT-GAGGGT
*
147420 AAAATGGTATTTTTTGGAA
1 AAAATGGAATTTTTTGGAA
147439 AAAAAAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
27 5 0.08
28 1 0.02
29 21 0.33
30 15 0.23
31 20 0.31
32 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (28 bp):
AAAATGGAATTTTTTGGAAGTTGAGGGT
Found at i:147434 original size:31 final size:29
Alignment explanation
Indices: 147340--147438 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 29
147330 CAAAAATGAA
*
147340 TTTTTT-GAAGTTTGAGGGTAAAATGGTAA
1 TTTTTTGGAAG-TTGAGGGTAAAATGGTAT
* * * *
147369 TTTCTTGGAAAAATTG-GGGTCTAAATGGAAT
1 TTTTTTGG--AAGTTGAGGGT-AAAATGGTAT
147400 TTTTTTGGAAGTTCGAGGGTAAAATGGTA-
1 TTTTTTGGAAGTT-GAGGGTAAAATGGTAT
147429 TTTTTTGGAA
1 TTTTTTGGAA
147439 AAAAAAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
29 19 0.35
30 13 0.24
31 21 0.38
32 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.27, T:0.40
Consensus pattern (29 bp):
TTTTTTGGAAGTTGAGGGTAAAATGGTAT
Found at i:147485 original size:29 final size:29
Alignment explanation
Indices: 147453--147542 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 29
147443 AAAAAATCGA
*
147453 GGTCAAAATGTAATTTTTAAAAAGTTTAG
1 GGTCAAAATGTAATTTTTGAAAAGTTTAG
* *
147482 GGTCAAAAATGAAATTTTGGAAAAGTTTAG
1 GGTC-AAAATGTAATTTTTGAAAAGTTTAG
* * * *
147512 GTTCAAAATATGATTTTTGAACAGTTTAG
1 GGTCAAAATGTAATTTTTGAAAAGTTTAG
147541 GG
1 GG
147543 ACCTCTAGGG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 25 0.50
30 25 0.50
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (29 bp):
GGTCAAAATGTAATTTTTGAAAAGTTTAG
Found at i:147491 original size:30 final size:29
Alignment explanation
Indices: 147453--147542 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 29
147443 AAAAAATCGA
*
147453 GGTC-AAAATGTAATTTTTAAAAAGTTTAG
1 GGTCAAAAATG-AATTTTTGAAAAGTTTAG
*
147482 GGTCAAAAATGAAATTTTGGAAAAGTTTAG
1 GGTCAAAAATG-AATTTTTGAAAAGTTTAG
* *
147512 GTTCAAAATATG-ATTTTTGAACAGTTTAG
1 GGTCAAAA-ATGAATTTTTGAAAAGTTTAG
147541 GG
1 GG
147543 ACCTCTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.38
30 29 0.56
31 3 0.06
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (29 bp):
GGTCAAAAATGAATTTTTGAAAAGTTTAG
Found at i:148595 original size:22 final size:22
Alignment explanation
Indices: 148567--148650 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
148557 TTTTATTCAA
148567 TATTAATATTAATTATTAATAT
1 TATTAATATTAATTATTAATAT
* *
148589 TATTAATATT-TTTATTAATGTT
1 TATTAATATTAATTATTAAT-AT
* * * * *
148611 TATTAATGTCATTTATTACTAC
1 TATTAATATTAATTATTAATAT
148633 TATTTAATATTAA-TATTA
1 TA-TTAATATTAATTATTA
148651 TCATTAATAT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
21 8 0.16
22 26 0.53
23 15 0.31
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTAATATTAATTATTAATAT
Found at i:152533 original size:16 final size:17
Alignment explanation
Indices: 152512--152543 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
152502 GAATCAATAT
152512 AAATTATT-ATAATTTA
1 AAATTATTAATAATTTA
152528 AAATTATTAATAATTT
1 AAATTATTAATAATTT
152544 CATAAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTATTAATAATTTA
Found at i:157146 original size:261 final size:261
Alignment explanation
Indices: 156682--157204 Score: 1019
Period size: 261 Copynumber: 2.0 Consensus size: 261
156672 TTACAAAATG
156682 GGTTCTCATTGTTTCCCCCTTTCAGATTTCAAAATATAGATTCAAGGGCGAAGCTGAAAACTTTT
1 GGTTCTCATTGTTTCCCCCTTTCAGATTTCAAAATATAGATTCAAGGGCGAAGCTGAAAACTTTT
*
156747 TCGGGGATTAAGATTAAGTTATATATTTTTATGAGAAATAAAATACAATTTCACCAATTTATTGA
66 TCGGAGATTAAGATTAAGTTATATATTTTTATGAGAAATAAAATACAATTTCACCAATTTATTGA
*
156812 CATTTTTATAGTTTTTAGAAAGGTCAAATCAAAATGCATCATTTTTAGGGATTAGGCTATAATTT
131 CATTTTTATAGTTTTTAGAAAGGTCAAATCAAAATGCATCATTTTTAGGGATTAAGCTATAATTT
156877 TATCATATATTTACTTAAAATTTCATAAACTTTTAATAGGATAAAACTGAAAATTTTTATTTTAA
196 TATCATATATTTACTTAAAATTTCATAAACTTTTAATAGGATAAAACTGAAAATTTTTATTTTAA
156942 A
261 A
156943 GGTTCTCATTGTTTCCCCCTTTCAGATTTCAAAATATAGATTCAAGGGCGAAGCTGAAAACTTTT
1 GGTTCTCATTGTTTCCCCCTTTCAGATTTCAAAATATAGATTCAAGGGCGAAGCTGAAAACTTTT
*
157008 TCGGAGATTAAGATTAAGTTATATATTTTTATGAGAAATAAAATATAATTTCACCAATTTATTGA
66 TCGGAGATTAAGATTAAGTTATATATTTTTATGAGAAATAAAATACAATTTCACCAATTTATTGA
157073 CATTTTTATAGTTTTTAGAAAGGTCAAATCAAAATGCATCATTTTTAGGGATTAAGCTATAATTT
131 CATTTTTATAGTTTTTAGAAAGGTCAAATCAAAATGCATCATTTTTAGGGATTAAGCTATAATTT
157138 TATCATATATTTACTTAAAATTTCATAAACTTTTAATAGGATAAAACTGAAAATTTTTATTTTAA
196 TATCATATATTTACTTAAAATTTCATAAACTTTTAATAGGATAAAACTGAAAATTTTTATTTTAA
157203 A
261 A
157204 G
1 G
157205 AAGACCAAGC
Statistics
Matches: 259, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
261 259 1.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (261 bp):
GGTTCTCATTGTTTCCCCCTTTCAGATTTCAAAATATAGATTCAAGGGCGAAGCTGAAAACTTTT
TCGGAGATTAAGATTAAGTTATATATTTTTATGAGAAATAAAATACAATTTCACCAATTTATTGA
CATTTTTATAGTTTTTAGAAAGGTCAAATCAAAATGCATCATTTTTAGGGATTAAGCTATAATTT
TATCATATATTTACTTAAAATTTCATAAACTTTTAATAGGATAAAACTGAAAATTTTTATTTTAA
A
Found at i:163951 original size:6 final size:6
Alignment explanation
Indices: 163940--163964 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
163930 CGCTTGCAAA
163940 ACTAGC ACTAGC ACTAGC ACTAGC A
1 ACTAGC ACTAGC ACTAGC ACTAGC A
163965 ATGACAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
ACTAGC
Found at i:166465 original size:29 final size:29
Alignment explanation
Indices: 166422--166523 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
166412 ATATCATTTT
*
166422 TTTTCTTTTAAAAATCGACTAATTGATCAA
1 TTTTC-TTTATAAATCGACTAATTGATCAA
* * *
166452 TTTTCTTTATAAAT--AATATAAT-ATCAT
1 TTTTCTTTATAAATCGACTA-ATTGATCAA
*
166479 TTTGTCTTT-TAAAGATCGACTAATCGATCAA
1 TTT-TCTTTAT-AA-ATCGACTAATTGATCAA
166510 TTTTCTTTATAAAT
1 TTTTCTTTATAAAT
166524 AAAATAATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
27 11 0.20
28 9 0.16
29 12 0.21
30 13 0.23
31 11 0.20
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (29 bp):
TTTTCTTTATAAATCGACTAATTGATCAA
Found at i:166491 original size:27 final size:27
Alignment explanation
Indices: 166447--166549 Score: 86
Period size: 27 Copynumber: 3.7 Consensus size: 27
166437 CGACTAATTG
166447 ATCAATTTTCTTTATAAATAATATAAT
1 ATCAATTTTCTTTATAAATAATATAAT
* *
166474 ATCATTTTGTCTTT-TAAA-GATCGACTAAT
1 ATCAATTT-TCTTTATAAATAAT--A-TAAT
*
166503 CGATCAATTTTCTTTATAAATAAAATAAT
1 --ATCAATTTTCTTTATAAATAATATAAT
*
166532 ATCATTTTGTCTTT-TAAA
1 ATCAATTT-TCTTTATAAA
166550 GATCGATCGA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
26 2 0.03
27 22 0.36
28 11 0.18
29 8 0.13
30 6 0.10
31 11 0.18
32 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.47
Consensus pattern (27 bp):
ATCAATTTTCTTTATAAATAATATAAT
Found at i:166514 original size:58 final size:58
Alignment explanation
Indices: 166387--166555 Score: 250
Period size: 58 Copynumber: 2.9 Consensus size: 58
166377 AAAAAGATAT
* * * * *
166387 ATCAATTTACTTTACAAAT-ATGATAATATCATTTTTTTTCTTTTAAAAATCGACTAATTG
1 ATCAATTTTCTTTATAAATAAT-ATAATATCA--TTTTGTCTTTTAAAGATCGACTAATCG
166447 ATCAATTTTCTTTATAAATAATATAATATCATTTTGTCTTTTAAAGATCGACTAATCG
1 ATCAATTTTCTTTATAAATAATATAATATCATTTTGTCTTTTAAAGATCGACTAATCG
*
166505 ATCAATTTTCTTTATAAATAAAATAATATCATTTTGTCTTTTAAAGATCGA
1 ATCAATTTTCTTTATAAATAATATAATATCATTTTGTCTTTTAAAGATCGA
166556 TCGATCGACC
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
58 74 0.73
60 26 0.25
61 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (58 bp):
ATCAATTTTCTTTATAAATAATATAATATCATTTTGTCTTTTAAAGATCGACTAATCG
Found at i:166562 original size:66 final size:64
Alignment explanation
Indices: 166492--166621 Score: 145
Period size: 66 Copynumber: 2.0 Consensus size: 64
166482 GTCTTTTAAA
* * *
166492 GATCGACTAATCGATCAATTT-TCTTTATAAATAAAATAATATCATTTTGTCTTTTAAAGATCGA
1 GATCGACCAATCGATCAATTTAT-TTTA-AAATAAAATAATATCATTTTATC-TTTAAAAATCGA
166556 TC
63 TC
* * ** *
166558 GATCGACCGATTGATCAATTTAGTTTTAAAATATGATAATATGATTTTATCTTTAAAAATCGAT
1 GATCGACCAATCGATCAATTTA-TTTTAAAATAAAATAATATCATTTTATCTTTAAAAATCGAT
166622 GCAATTTATG
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
65 12 0.22
66 37 0.69
67 4 0.07
68 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (64 bp):
GATCGACCAATCGATCAATTTATTTTAAAATAAAATAATATCATTTTATCTTTAAAAATCGATC
Found at i:176434 original size:27 final size:27
Alignment explanation
Indices: 176349--176434 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
176339 TTTATTTTGC
* *
176349 AATACGATAATATCATTTAGACTTTTA
1 AATATGATAATATCATTTTGACTTTTA
* * *
176376 AAGATCGACATATGATCAATTT-ACTTTATA
1 AATAT-GATA-AT-ATCATTTTGACTTT-TA
*
176406 AATATGATAATATCATTTTGTCTTTTA
1 AATATGATAATATCATTTTGACTTTTA
176433 AA
1 AA
176435 GATCGACCGA
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
27 14 0.31
28 9 0.20
29 10 0.22
30 12 0.27
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (27 bp):
AATATGATAATATCATTTTGACTTTTA
Found at i:176471 original size:54 final size:55
Alignment explanation
Indices: 176336--176484 Score: 178
Period size: 57 Copynumber: 2.7 Consensus size: 55
176326 AAAGACCGGC
* * * *
176336 CAATTTATTTTGC-AATACGATAATATCATTTAGACTTTTAAAGATCGACATATGAT
1 CAATTTATTTTTCAAATATGATAATATCATTTAGTCTTTTAAAGATCGAC--ACGAT
* *
176392 CAATTTACTTTAT-AAATATGATAATATCATTTTGTCTTTTAAAGATCGAC-CGAT
1 CAATTTA-TTTTTCAAATATGATAATATCATTTAGTCTTTTAAAGATCGACACGAT
* *
176446 CAATTTATTTTTCAAATATGATAATATAATTTCGTCTTT
1 CAATTTATTTTTCAAATATGATAATATCATTTAGTCTTT
176485 AAAAATTGAC
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
53 4 0.05
54 34 0.42
56 7 0.09
57 36 0.44
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (55 bp):
CAATTTATTTTTCAAATATGATAATATCATTTAGTCTTTTAAAGATCGACACGAT
Found at i:180273 original size:13 final size:13
Alignment explanation
Indices: 180255--180280 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
180245 CGATATGAAA
180255 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
180268 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
180281 AAAATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:182607 original size:14 final size:14
Alignment explanation
Indices: 182575--182604 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
182565 GGACTTGGAC
182575 TTTATTTTATTTCA
1 TTTATTTTATTTCA
182589 TTTATTTTATTT-A
1 TTTATTTTATTTCA
182602 TTT
1 TTT
182605 TATAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTCA
Found at i:185014 original size:41 final size:40
Alignment explanation
Indices: 184967--185066 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 40
184957 CGACCTTAAG
** *
184967 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGA
1 TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGA
**
185007 TTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGATAGA
1 -TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGA
*
185045 CCGATGAGACACTGGGTGTCAC
1 TCGATGAGACACTGGGTGTCAC
185067 TTTATTGCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
37 10 0.21
38 19 0.40
39 4 0.08
40 4 0.08
41 11 0.23
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGA
Found at i:185059 original size:37 final size:38
Alignment explanation
Indices: 184992--185070 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
184982 GTGTCATTAT
* **
184992 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
**
185030 TTTACTTCGGATAGA-CCGATGAGACACTGGGTGTCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
185067 TTTA
1 TTTA
185071 TTGCTTCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 21 0.58
38 15 0.42
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (38 bp):
TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
Found at i:189705 original size:14 final size:13
Alignment explanation
Indices: 189684--189713 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
189674 TTATTTTATA
189684 AAATAAATAAAAT
1 AAATAAATAAAAT
189697 AAATGAAATAAAAT
1 AAAT-AAATAAAAT
189711 AAA
1 AAA
189714 GTCCAAGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:190910 original size:34 final size:35
Alignment explanation
Indices: 190847--190919 Score: 80
Period size: 34 Copynumber: 2.1 Consensus size: 35
190837 AATGTTCATA
* * *
190847 TTATTTTATTCATTATTTATTTTATTTA-TTGCTT
1 TTATTTTATTCATTATTTATCTTAGTTATTTACTT
190881 TTATTTTATTCATTAATTT-TGCTT-GTTATTTACTT
1 TTATTTTATTCATT-ATTTAT-CTTAGTTATTTACTT
190916 TTAT
1 TTAT
190920 GAAATTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (35 bp):
TTATTTTATTCATTATTTATCTTAGTTATTTACTT
Found at i:192026 original size:13 final size:13
Alignment explanation
Indices: 192008--192033 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
191998 TTTTTATTTT
192008 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
192021 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
192034 TTTCATATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Found at i:193830 original size:23 final size:23
Alignment explanation
Indices: 193761--193830 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
193751 TCATTAACAT
* *
193761 TGTTCGTGAACGTGTTCAATTCTA
1 TGTTCGTGAACATGTTCAATT-AA
* **
193785 TGTTCATGAACATGTTCTTTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
193808 TGTTCGTGAACATGTTCCATTAA
1 TGTTCGTGAACATGTTCAATTAA
193831 GTTAAATGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 21 0.55
24 17 0.45
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:196378 original size:29 final size:29
Alignment explanation
Indices: 196345--196408 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
196335 AAGGTTAGAC
*
196345 ATAATATGAATACAATTTCAAATACAGAT
1 ATAATATGAATACAATTTCAAATACAAAT
* * * * *
196374 ATAATATGGATATAGTTTCAGATGCAAAT
1 ATAATATGAATACAATTTCAAATACAAAT
196403 ATAATA
1 ATAATA
196409 CATATACAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (29 bp):
ATAATATGAATACAATTTCAAATACAAAT
Found at i:196419 original size:29 final size:29
Alignment explanation
Indices: 196387--196455 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
196377 ATATGGATAT
*
196387 AGTTTCAGATGCAAATATAATACATATAC
1 AGTTACAGATGCAAATATAATACATATAC
* ** *
196416 AGTTACAGATACGGATATAATACATATAT
1 AGTTACAGATGCAAATATAATACATATAC
196445 AGTTACAGATG
1 AGTTACAGATG
196456 TAGATTCCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (29 bp):
AGTTACAGATGCAAATATAATACATATAC
Found at i:198330 original size:3 final size:3
Alignment explanation
Indices: 198322--198389 Score: 82
Period size: 3 Copynumber: 22.7 Consensus size: 3
198312 ATAAATGAAA
* * *
198322 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
198370 GAT AAT AAT GAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
198390 AAATGTAACC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:200288 original size:101 final size:100
Alignment explanation
Indices: 200164--200436 Score: 320
Period size: 101 Copynumber: 2.7 Consensus size: 100
200154 TTGCAACTTC
200164 AGGGATATAAGATTTTGTGTTGTAGCTTCATCTTGCTCTACTGAAACTTCAGAGAGATAAAGATT
1 AGGGATATAAGATTTT-TGTTGTAGCTTCATCTTGCTCTACTGAAACTTCAGAGAGATAAAGATT
* * *
200229 TGCTATCGTAATTTTGATTCGATCCACTGTAA-CCA
65 TGCTATCGTAATTTCGATCCGATCCACTGCAATCCA
* * * * * *
200264 TAGGGGTATAAGATTTGTTATTGTAGCTTCATCTTGCTCTATTGCAACTTCAAAGAGACAAAGAT
1 -AGGGATATAAGATTT-TTGTTGTAGCTTCATCTTGCTCTACTGAAACTTCAGAGAGATAAAGAT
* *
200329 TTGCTATCGTAATTTCGATCCGATCCATTGCAATTTCA
64 TTGCTATCGTAATTTCGATCCGATCCACTGCAA-TCCA
* * *
200367 A-GAATAT-AGAATTTAATGTTGTAGCTTCATATTGCTCTACT-ACAACTTCAGAGAGATAAAGA
1 AGGGATATAAG-ATTT-TTGTTGTAGCTTCATCTTGCTCTACTGA-AACTTCAGAGAGATAAAGA
*
200429 TTTACTAT
63 TTTGCTAT
200437 TGTAGCTTTA
Statistics
Matches: 145, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
100 2 0.01
101 139 0.96
102 2 0.01
103 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (100 bp):
AGGGATATAAGATTTTTGTTGTAGCTTCATCTTGCTCTACTGAAACTTCAGAGAGATAAAGATTT
GCTATCGTAATTTCGATCCGATCCACTGCAATCCA
Found at i:200361 original size:51 final size:51
Alignment explanation
Indices: 200208--200367 Score: 128
Period size: 51 Copynumber: 3.2 Consensus size: 51
200198 GCTCTACTGA
* * * * *
200208 AACTTCAGAGAGATAAAGATTTGCTATCGTAATTTTGATTCGATCCACTGT
1 AACTTCAAAGAGATAAAGATTTGCTATCGTAATTTCGATCCGATCCATTGC
* * * * * ** * * *
200259 AAC--CATAGGGGTATAAGATTTGTTATTGTAGCTTC-ATCTTGCTCTATTGC
1 AACTTCAAAGAGATA-AAGATTTGCTATCGTAATTTCGATC-CGATCCATTGC
*
200309 AACTTCAAAGAGACAAAGATTTGCTATCGTAATTTCGATCCGATCCATTGC
1 AACTTCAAAGAGATAAAGATTTGCTATCGTAATTTCGATCCGATCCATTGC
*
200360 AATTTCAA
1 AACTTCAA
200368 GAATATAGAA
Statistics
Matches: 78, Mismatches: 26, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
49 9 0.12
50 25 0.32
51 35 0.45
52 9 0.12
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (51 bp):
AACTTCAAAGAGATAAAGATTTGCTATCGTAATTTCGATCCGATCCATTGC
Found at i:200468 original size:101 final size:101
Alignment explanation
Indices: 200148--200476 Score: 314
Period size: 101 Copynumber: 3.3 Consensus size: 101
200138 GTTTCAGTCT
* * * **
200148 GATCCATTGCAACTTCAGGGATATA-AGATTTTGTGTTGTAGCTTCATCTTGCTCTACTGA-AAC
1 GATCCACTGTAACTTCAAGGATATAGAGATTTAATGTTGTAGCTTCATCTTGCTCTACT-ACAAC
*
200211 TTCAGAGAGATAAAGATTTGCTATCGTAATTTTGA-TTC
65 TTCAGAGAGATAAAGATTTGCTATCGTAA-TTT-ACTCC
* ** * * *
200249 GATCCACTGTAAC--CATAGGGGTATA-AGATTTGTTATTGTAGCTTCATCTTGCTCTATTGCAA
1 GATCCACTGTAACTTCA-A-GGATATAGAGATTTAATGTTGTAGCTTCATCTTGCTCTACTACAA
* *
200311 CTTCAAAGAGACAAAGATTTGCTATCGTAATTT-CGATCC
64 CTTCAGAGAGATAAAGATTTGCTATCGTAATTTAC--TCC
* * * * *
200350 GATCCATTGCAATTTCAAGAATATAGA-ATTTAATGTTGTAGCTTCATATTGCTCTACTACAACT
1 GATCCACTGTAACTTCAAGGATATAGAGATTTAATGTTGTAGCTTCATCTTGCTCTACTACAACT
* * *
200414 TCAGAGAGATAAAGATTTACTATTGTAGCTTTACTCC
66 TCAGAGAGATAAAGATTTGCTATCGTA-ATTTACTCC
* *
200451 AATCCACTATAACTTCAAGGATATAG
1 GATCCACTGTAACTTCAAGGATATAG
200477 GAGTTATTGT
Statistics
Matches: 183, Mismatches: 34, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
99 2 0.01
100 3 0.02
101 170 0.93
102 5 0.03
103 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (101 bp):
GATCCACTGTAACTTCAAGGATATAGAGATTTAATGTTGTAGCTTCATCTTGCTCTACTACAACT
TCAGAGAGATAAAGATTTGCTATCGTAATTTACTCC
Found at i:205307 original size:24 final size:25
Alignment explanation
Indices: 205264--205314 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
205254 CAAGTTCTTT
205264 TTCTTCTTTCTCTTTTTCCTT-TCC
1 TTCTTCTTTCTCTTTTTCCTTCTCC
205288 TTCTTC-TTCT-TTTTGATCCTTCTCC
1 TTCTTCTTTCTCTTTT--TCCTTCTCC
205313 TT
1 TT
205315 TAACTAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 4 0.17
24 11 0.46
25 5 0.21
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (25 bp):
TTCTTCTTTCTCTTTTTCCTTCTCC
Found at i:225286 original size:39 final size:39
Alignment explanation
Indices: 225243--225374 Score: 113
Period size: 39 Copynumber: 3.3 Consensus size: 39
225233 CCGACCATGG
* *
225243 GGCAGATTGAAGTCATCCAATTTTTTACCCTAATTAGAA
1 GGCAGATTGAAGTCATCCAATCTTTTACCCTAATCAGAA
* * * ** * *
225282 GGCAGATTAAAGATACCATCTAATCTCTTACCCCGACCATG-G
1 GGCAGATTGAAG-T--CATCCAATCTTTTACCCTAATCA-GAA
* *
225324 GGCAGATTGAAGCCATTCAATCTTTTACCCTAATCAGAA
1 GGCAGATTGAAGTCATCCAATCTTTTACCCTAATCAGAA
*
225363 GGCAAATTGAAG
1 GGCAGATTGAAG
225375 ACACCATCCA
Statistics
Matches: 69, Mismatches: 19, Indels: 10
0.70 0.19 0.10
Matches are distributed among these distances:
38 1 0.01
39 39 0.57
40 1 0.01
42 27 0.39
43 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (39 bp):
GGCAGATTGAAGTCATCCAATCTTTTACCCTAATCAGAA
Found at i:225328 original size:42 final size:41
Alignment explanation
Indices: 225209--225331 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 41
225199 TAAGCAAGGC
225209 AAAGCTACCATCTAATCTCTTACCCCGACCATGGGGCAGATT
1 AAAG-TACCATCTAATCTCTTACCCCGACCATGGGGCAGATT
* * * * ** ** *
225251 GAAGT--CATCCAATTTTTTACCCTAATTA-GAAGGCAGATT
1 AAAGTACCATCTAATCTCTTACCCCGACCATG-GGGCAGATT
225290 AAAGATACCATCTAATCTCTTACCCCGACCATGGGGCAGATT
1 AAAG-TACCATCTAATCTCTTACCCCGACCATGGGGCAGATT
225332 GAAGCCATTC
Statistics
Matches: 58, Mismatches: 18, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
38 1 0.02
39 27 0.47
40 1 0.02
41 1 0.02
42 27 0.47
43 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (41 bp):
AAAGTACCATCTAATCTCTTACCCCGACCATGGGGCAGATT
Found at i:225350 original size:81 final size:81
Alignment explanation
Indices: 225209--225382 Score: 276
Period size: 81 Copynumber: 2.1 Consensus size: 81
225199 TAAGCAAGGC
* * *
225209 AAAGCTACCATCTAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATTTTTTACCCT
1 AAAGATACCATCTAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCT
* *
225274 AATTAGAAGGCAGATT
66 AATCAGAAGGCAAATT
*
225290 AAAGATACCATCTAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATTCAATCTTTTACCCT
1 AAAGATACCATCTAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCT
225355 AATCAGAAGGCAAATT
66 AATCAGAAGGCAAATT
* *
225371 GAAGACACCATC
1 AAAGATACCATC
225383 CATGGGGCAA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (81 bp):
AAAGATACCATCTAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCT
AATCAGAAGGCAAATT
Found at i:225419 original size:64 final size:64
Alignment explanation
Indices: 225318--225448 Score: 183
Period size: 64 Copynumber: 2.0 Consensus size: 64
225308 CTTACCCCGA
* * * *
225318 CCATGGGGCAGATTGAAGCCATTCAATCTTTTACCCTAA-TCAGAAGGCAAATTGAAGACACCAT
1 CCATGGGGCAAATTAAAGCCATCCAATCTTTTACCCTAACT-AGAAGGCAAATTAAAGACACCAT
* * *
225382 CCATGGGGCAAATTAAAGTCATCCAATCTTTTACCCTAACTAGAGGGCAGATTAAAGACACCAT
1 CCATGGGGCAAATTAAAGCCATCCAATCTTTTACCCTAACTAGAAGGCAAATTAAAGACACCAT
225446 CCA
1 CCA
225449 ATCTCTTATC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 58 0.98
65 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (64 bp):
CCATGGGGCAAATTAAAGCCATCCAATCTTTTACCCTAACTAGAAGGCAAATTAAAGACACCAT
Found at i:225500 original size:145 final size:145
Alignment explanation
Indices: 225237--225527 Score: 431
Period size: 145 Copynumber: 2.0 Consensus size: 145
225227 CTTACCCCGA
* * * * *
225237 CCATGGGGCAGATTGAAGTCATCCAATTTTTTACCCTAATTAGAAGGCAGATTAAAGATACCATC
1 CCATGGGGCAAATTAAAGTCATCCAATCTTTTACCCTAACTAGAAGGCAGATTAAAGACACCATC
* * *
225302 TAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATTCAATCTTTTACCCTAATCAGAAGGCA
66 CAATCTCTTACCCCGACCATGGGGCAGATTAAAGCCATTCAATCTCTTACCCTAATCAGAAGGCA
225367 AATTGAAGACACCAT
131 AATTGAAGACACCAT
*
225382 CCATGGGGCAAATTAAAGTCATCCAATCTTTTACCCTAACTAGAGGGCAGATTAAAGACACCATC
1 CCATGGGGCAAATTAAAGTCATCCAATCTTTTACCCTAACTAGAAGGCAGATTAAAGACACCATC
* * * * *
225447 CAATCTCTTATCCTGACCATGGGGCAGATTAAAGCCA-TCTAATCTCTTACCCTAATTAGAGGGT
66 CAATCTCTTACCCCGACCATGGGGCAGATTAAAGCCATTC-AATCTCTTACCCTAATCAGAAGGC
*
225511 AGATTGAAGACACCAT
130 AAATTGAAGACACCAT
225527 C
1 C
225528 TTATCTCTTA
Statistics
Matches: 130, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
144 2 0.02
145 128 0.98
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (145 bp):
CCATGGGGCAAATTAAAGTCATCCAATCTTTTACCCTAACTAGAAGGCAGATTAAAGACACCATC
CAATCTCTTACCCCGACCATGGGGCAGATTAAAGCCATTCAATCTCTTACCCTAATCAGAAGGCA
AATTGAAGACACCAT
Found at i:225521 original size:81 final size:81
Alignment explanation
Indices: 225382--226048 Score: 735
Period size: 81 Copynumber: 8.2 Consensus size: 81
225372 AAGACACCAT
* * * *
225382 CCATGGGGCAAATTAAAGTCATCCAATCTTTTACCCTAACTAGAGGGCAGATTAAAGACACCATC
1 CCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACCATC
*
225447 CAATCTCTTATCCTGA
66 CAATCTCTTACCCTGA
* * ** *
225463 CCATGGGGCAGATTAAAGCCATCTAATCTCTTACCCTAATTAGAGGGTAGATTGAAGACACCATC
1 CCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACCATC
** *
225528 TTATCTCTTACTCTGA
66 CAATCTCTTACCCTGA
* * * * * *
225544 CCATGGAGTAGATTGAAGCCATCCAATCTTCTACCCTAACTAGAGGGCAGATTGAAGACACCGTC
1 CCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACCATC
*
225609 TAATCTCTTA-CCTCGA
66 CAATCTCTTACCCT-GA
** * * * * * * * * *
225625 CCATGATGTAGATTGAAGTCATCCAATCTTTTACCCTAACCAAAGGGTAGATTAAAGATACTATA
1 CCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACCATC
* **
225690 AAATCTCTTACCCCAA
66 CAATCTCTTACCCTGA
* * * * ** * *
225706 CCATAGGGTAGATTTAAGTCATCCAATCTTTTACGTTAACCAAAAGGCAGATTGAAGACACCATC
1 CCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACCATC
* *
225771 CAATCTCGTACCCCGA
66 CAATCTCTTACCCTGA
* * * *
225787 CCATGGGGCAGATTAAAGTCATCCAATCTTTTACCCTAATC-GAAGGGCAAATTGAAGAGACCAT
1 CCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACCAG-AGGGCAGATTGAAGACACCAT
* *
225851 CCAATCTTTTACCCCGA
65 CCAATCTCTTACCCTGA
* ** * * *
225868 CCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAAAGCAAATTGAAGAGATCATC
1 CCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACCATC
225933 CAATCTCTTACCCTGA
66 CAATCTCTTACCCTGA
* * * * * *
225949 CCATGGAGCAAATTGAAGCCATCAAATCTTTTACCCTAACCAGAGGGCAAATTAAAGACACCATC
1 CCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACCATC
*
226014 CAATCTCATACCCTGA
66 CAATCTCTTACCCTGA
226030 CCATGGGGCAGATTAAAGC
1 CCATGGGGCAGATTAAAGC
226049 TACCATCTCA
Statistics
Matches: 496, Mismatches: 86, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
80 2 0.00
81 491 0.99
82 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (81 bp):
CCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACCATC
CAATCTCTTACCCTGA
Found at i:229508 original size:36 final size:36
Alignment explanation
Indices: 229461--229532 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
229451 CGGAGGCAAG
229461 ATAGCATGAAAAAGGAGACAGTTTGTTAGAGGGAAT
1 ATAGCATGAAAAAGGAGACAGTTTGTTAGAGGGAAT
*
229497 ATAGCGTGAAAAAGGAGACAGTTTGTTAGAGGGAAT
1 ATAGCATGAAAAAGGAGACAGTTTGTTAGAGGGAAT
229533 GTATCAGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.06, G:0.32, T:0.22
Consensus pattern (36 bp):
ATAGCATGAAAAAGGAGACAGTTTGTTAGAGGGAAT
Found at i:239294 original size:42 final size:41
Alignment explanation
Indices: 239247--239798 Score: 388
Period size: 42 Copynumber: 13.6 Consensus size: 41
239237 TAGAGGTCAA
*
239247 ATTGAAGAAACCATCCAATCTCTTACCCCGACCATGGGGCAT
1 ATTGAAG-AACCATCCAATCTCTTACCCCGACCATGGGGCAG
* * ** ** *
239289 ATTGAAG--TCATCCAATCTTTTACCCTAATTATAGGGCAG
1 ATTGAAGAACCATCCAATCTCTTACCCCGACCATGGGGCAG
*
239328 ATTGAAGACACCATCCAATCTCTTACCCCGACCATGTGGCAG
1 ATTGAAGA-ACCATCCAATCTCTTACCCCGACCATGGGGCAG
*** * ** * *
239370 ATT-AA-AGTTATCCAATCTTTTACCCTAATCA-GAAGGCAG
1 ATTGAAGAACCATCCAATCTCTTACCCCGACCATG-GGGCAG
*
239409 ATTGAAGACACCATCCAATCTCTTACCCCGATCATGGGGCAG
1 ATTGAAGA-ACCATCCAATCTCTTACCCCGACCATGGGGCAG
* * * **
239451 ATTGAAG--TCATCCAATCTTTTTTCCCTAACCA-GAGGGCAG
1 ATTGAAGAACCATCCAATC-TCTTACCCCGACCATG-GGGCAG
* * *
239491 ATTGAAGACACCATTCAATCTCTTACTCCGACCATGAGGCAG
1 ATTGAAGA-ACCATCCAATCTCTTACCCCGACCATGGGGCAG
* * * ** * *
239533 ATTGAAG--TCATCAAATCTCTTA-CCCTAATAAGAGGGCAA
1 ATTGAAGAACCATCCAATCTCTTACCCCGACCATG-GGGCAG
*
239572 ATTGAAAACACCATCCAATCTCTTACCCCGACCATGGGGCAG
1 ATTGAAGA-ACCATCCAATCTCTTACCCCGACCATGGGGCAG
* * ** * * *
239614 A-TG-A-ATCCATCCAATCTTTTA-CCAAAACAAGAGGGTAG
1 ATTGAAGAACCATCCAATCTCTTACCCCGACCATG-GGGCAG
*
239652 ATTGAAGACACCATCCAATCTCTTACCTCGACCATGGGGCAG
1 ATTGAAGA-ACCATCCAATCTCTTACCCCGACCATGGGGCAG
* ** ** *
239694 ATTGAAG-A-CATTCAATCTCTTACCCTAATTA-GAGGGCAT
1 ATTGAAGAACCATCCAATCTCTTACCCCGACCATG-GGGCAG
* *
239733 ATTGAAGACACCATCTAATCTCTTACCCTGACCATGGGGCAG
1 ATTGAAGA-ACCATCCAATCTCTTACCCCGACCATGGGGCAG
*
239775 ATTGAAG--CCATCCAATCTTTTACC
1 ATTGAAGAACCATCCAATCTCTTACC
239799 TTAACTAGAG
Statistics
Matches: 387, Mismatches: 93, Indels: 63
0.71 0.17 0.12
Matches are distributed among these distances:
37 6 0.02
38 27 0.07
39 136 0.35
40 28 0.07
41 7 0.02
42 161 0.42
43 22 0.06
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (41 bp):
ATTGAAGAACCATCCAATCTCTTACCCCGACCATGGGGCAG
Found at i:239332 original size:81 final size:81
Alignment explanation
Indices: 239181--239992 Score: 945
Period size: 81 Copynumber: 10.2 Consensus size: 81
239171 AGCTACTATT
* * * * * * *
239181 CAATCTCTTACCTCGACCGTGGGGCAGATTGAAGGCATACAATTTTTTACCTTAACTAGAGGTCA
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAGAGGGCA
* *
239246 AATTGAAGAAACCATC
66 GATTGAAGACACCATC
* * *
239262 CAATCTCTTACCCCGACCATGGGGCATATTGAAGTCATCCAATCTTTTACCCTAATTATAGGGCA
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAGAGGGCA
239327 GATTGAAGACACCATC
66 GATTGAAGACACCATC
* * * *
239343 CAATCTCTTACCCCGACCATGTGGCAGATTAAAGTTATCCAATCTTTTACCCTAA-TCAGAAGGC
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACT-AGAGGGC
239407 AGATTGAAGACACCATC
65 AGATTGAAGACACCATC
* * *
239424 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGTCATCCAATCTTTTTTCCCTAACCAGAGGGC
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATC-TTTTACCCTAACTAGAGGGC
*
239489 AGATTGAAGACACCATT
65 AGATTGAAGACACCATC
* * * *
239506 CAATCTCTTACTCCGACCATGAGGCAGATTGAAGTCATCAAATCTCTTACCCTAA-TAAGAGGGC
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACT-AGAGGGC
* *
239570 AAATTGAAAACACCATC
65 AGATTGAAGACACCATC
** * *
239587 CAATCTCTTACCCCGACCATGGGGCAGA-TGAA-TCCATCCAATCTTTTACCAAAACAAGAGGGT
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGT-CATCCAATCTTTTACCCTAACTAGAGGGC
239650 AGATTGAAGACACCATC
65 AGATTGAAGACACCATC
* * * * *
239667 CAATCTCTTACCTCGACCATGGGGCAGATTGAAGACATTCAATCTCTTACCCTAATTAGAGGGCA
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAGAGGGCA
*
239732 TATTGAAGACACCATC
66 GATTGAAGACACCATC
* * * *
239748 TAATCTCTTACCCTGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCTTAACTAGAGGGCA
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAGAGGGCA
239813 GATT---G-----A--
66 GATTGAAGACACCATC
* * * * * *
239819 -AATCTCTTACCCCGACCATGGGACAAATTGAAGCCATCAAATCATTTACCCTAATTAGAGGGCA
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAGAGGGCA
* *
239883 AATTGAAGACATCATC
66 GATTGAAGACACCATC
* ** * * * * *
239899 CAATCTCTTACCCCAATTATGGGGCATATTAAAGTCATCTAATTTTTTACCCTAACTAGAAGGCA
1 CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAGAGGGCA
* *
239964 AATTGATA-AAACCATC
66 GATTGA-AGACACCATC
239980 CAATCTCTTACCC
1 CAATCTCTTACCC
239993 TAATTATGGG
Statistics
Matches: 624, Mismatches: 87, Indels: 40
0.83 0.12 0.05
Matches are distributed among these distances:
70 60 0.10
73 2 0.00
78 2 0.00
79 1 0.00
80 69 0.11
81 417 0.67
82 73 0.12
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (81 bp):
CAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATCCAATCTTTTACCCTAACTAGAGGGCA
GATTGAAGACACCATC
Found at i:239867 original size:70 final size:70
Alignment explanation
Indices: 239749--239889 Score: 210
Period size: 70 Copynumber: 2.0 Consensus size: 70
239739 GACACCATCT
* * * * * * *
239749 AATCTCTTACCCTGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCTTAACTAGAGGGCAG
1 AATCTCTTACCCCGACCATGGGACAAATTGAAGCCATCAAATCATTTACCCTAACTAGAGGGCAA
239814 ATTGA
66 ATTGA
*
239819 AATCTCTTACCCCGACCATGGGACAAATTGAAGCCATCAAATCATTTACCCTAATTAGAGGGCAA
1 AATCTCTTACCCCGACCATGGGACAAATTGAAGCCATCAAATCATTTACCCTAACTAGAGGGCAA
239884 ATTGA
66 ATTGA
239889 A
1 A
239890 GACATCATCC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (70 bp):
AATCTCTTACCCCGACCATGGGACAAATTGAAGCCATCAAATCATTTACCCTAACTAGAGGGCAA
ATTGA
Found at i:239885 original size:39 final size:38
Alignment explanation
Indices: 239842--239998 Score: 109
Period size: 42 Copynumber: 3.9 Consensus size: 38
239832 GACCATGGGA
239842 CAAATTGAAGCCATCAAATCATTTACCCTAATTAGAGGG
1 CAAATTGAAGCCATCAAATC-TTTACCCTAATTAGAGGG
* *
239881 CAAATTGAAGACATCATCCAATCTCTTACCCCAATTATG-GGG
1 CAAATTGAAG-C--CATCAAATCT-TTACCCTAATTA-GAGGG
* * * * * * *
239923 CATATTAAAGTCATCTAATTTTTTACCCTAACTAGAAGG
1 CAAATTGAAGCCATC-AAATCTTTACCCTAATTAGAGGG
* *
239962 CAAATTGATAAAACCATCCAATCTCTTACCCTAATTA
1 CAAATTG---AAGCCATCAAATCT-TTACCCTAATTA
239999 TGGGCCACGT
Statistics
Matches: 88, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
38 1 0.01
39 31 0.35
40 4 0.05
41 4 0.05
42 47 0.53
43 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (38 bp):
CAAATTGAAGCCATCAAATCTTTACCCTAATTAGAGGG
Found at i:239924 original size:42 final size:41
Alignment explanation
Indices: 239864--240002 Score: 124
Period size: 42 Copynumber: 3.4 Consensus size: 41
239854 ATCAAATCAT
239864 TTACCCTAATTA-GAGGGCAAATTGAAGACATCATCCAATCTC
1 TTACCCTAATTATG-GGGCAAATTGAA-ACATCATCCAATCTC
* * * * * *
239906 TTACCCCAATTATGGGGCATATT-AAA-GTCATCTAATTTT
1 TTACCCTAATTATGGGGCAAATTGAAACATCATCCAATCTC
* * * *
239945 TTACCCTAACTA-GAAGGCAAATTGATAAAACCATCCAATCTC
1 TTACCCTAATTATG-GGGCAAATTGA-AACATCATCCAATCTC
239987 TTACCCTAATTATGGG
1 TTACCCTAATTATGGG
240003 CCACGTCAAC
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
38 1 0.01
39 26 0.35
40 2 0.03
41 4 0.05
42 39 0.53
43 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (41 bp):
TTACCCTAATTATGGGGCAAATTGAAACATCATCCAATCTC
Found at i:239947 original size:151 final size:151
Alignment explanation
Indices: 239668--239969 Score: 401
Period size: 151 Copynumber: 2.0 Consensus size: 151
239658 GACACCATCC
* * * *
239668 AATCTCTTACCTCGACCATGGGGCAGATTGAAGACATTCAATCTCTTACCCTAATTAGAGGGCAT
1 AATCTCTTACCCCGACCATGGGACAAATTGAAGACATTCAATCTCTTACCCTAATTAGAGGGCAA
* ** *
239733 ATTGAAGACACCATCTAATCTCTTACCCTGACCATGGGGCAGATTGAAGCCATCCAATCTTTTAC
66 ATTGAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATTAAAGCCATCCAATCTTTTAC
* * *
239798 CTTAACTAGAGGGCAGATTGA
131 CCTAACTAGAAGGCAAATTGA
*
239819 AATCTCTTACCCCGACCATGGGACAAATTGAAGCCA-TCAAATCAT-TTACCCTAATTAGAGGGC
1 AATCTCTTACCCCGACCATGGGACAAATTGAAGACATTC-AATC-TCTTACCCTAATTAGAGGGC
* ** * * * *
239882 AAATTGAAGACATCATCCAATCTCTTACCCCAATTATGGGGCATATTAAAGTCATCTAATTTTTT
64 AAATTGAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATTAAAGCCATCCAATCTTTT
239947 ACCCTAACTAGAAGGCAAATTGA
129 ACCCTAACTAGAAGGCAAATTGA
239970 TAAAACCATC
Statistics
Matches: 130, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
150 2 0.02
151 127 0.98
152 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (151 bp):
AATCTCTTACCCCGACCATGGGACAAATTGAAGACATTCAATCTCTTACCCTAATTAGAGGGCAA
ATTGAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATTAAAGCCATCCAATCTTTTAC
CCTAACTAGAAGGCAAATTGA
Found at i:241042 original size:12 final size:12
Alignment explanation
Indices: 241025--241065 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
241015 CAAATATTCC
*
241025 ATTTTTTTTTTA
1 ATTTTTATTTTA
* *
241037 ATTTTTACTTGA
1 ATTTTTATTTTA
241049 ATTTTTATTTTA
1 ATTTTTATTTTA
241061 ATTTT
1 ATTTT
241066 ACCCTTCAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:241569 original size:108 final size:109
Alignment explanation
Indices: 241374--241581 Score: 265
Period size: 108 Copynumber: 1.9 Consensus size: 109
241364 ATGTTTTTAT
* * * * * *
241374 TTTTATTTTAGGGAATTAGAGAAATTGTGCTCTAACGTATTGGGTATGGTTTTTCTTTGAATCTA
1 TTTTATTTTAGGGAACTAGAGAAATTGTGCTCAAACGTACTGGATATGATTTTTCTTTGAACCTA
** ***
241439 AATAATCGAGTATCGTTTTTAAAATAAATAAATGTTCGATGTTC
66 AATAATCGAACATCCCATTTAAAATAAATAAATGTTCGATGTTC
*
241483 TTTTA-TTTAGGGAACTCGAGAAATTGTGCTCAAACGTACTGGATATGATTTTTCTTTGAACCTA
1 TTTTATTTTAGGGAACTAGAGAAATTGTGCTCAAACGTACTGGATATGATTTTTCTTTGAACCTA
** * *
241547 TGTAATTGAACATCCCATTTAAAATCAATAAATGT
66 AATAATCGAACATCCCATTTAAAATAAATAAATGT
241582 CCTTTGTCGT
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
108 78 0.94
109 5 0.06
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (109 bp):
TTTTATTTTAGGGAACTAGAGAAATTGTGCTCAAACGTACTGGATATGATTTTTCTTTGAACCTA
AATAATCGAACATCCCATTTAAAATAAATAAATGTTCGATGTTC
Found at i:253487 original size:29 final size:30
Alignment explanation
Indices: 253454--253512 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
253444 ATGTTTAATA
*
253454 TACAATTGTATACAT-GAATTTTGATTTTG
1 TACAATTGTATACATAAAATTTTGATTTTG
* *
253483 TACAATTTTATATATAAAATTTTGATTTTG
1 TACAATTGTATACATAAAATTTTGATTTTG
253513 ATTCAATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (30 bp):
TACAATTGTATACATAAAATTTTGATTTTG
Found at i:254142 original size:15 final size:16
Alignment explanation
Indices: 254122--254165 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
254112 ATTTAACATT
*
254122 ATAAAATAATTTTTAA
1 ATAAAATAATTTATAA
254138 A-AAAATATATTTATAA
1 ATAAAATA-ATTTATAA
254154 ATAAAGATAATT
1 ATAAA-ATAATT
254166 AGAATGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.25
16 9 0.38
17 6 0.25
18 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
ATAAAATAATTTATAA
Found at i:261794 original size:15 final size:15
Alignment explanation
Indices: 261776--261806 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
261766 TTCAAGTAAG
261776 TGTATTATTTTCTTA
1 TGTATTATTTTCTTA
*
261791 TGTATTATTTTTTTA
1 TGTATTATTTTCTTA
261806 T
1 T
261807 ATATATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.71
Consensus pattern (15 bp):
TGTATTATTTTCTTA
Found at i:262499 original size:9 final size:8
Alignment explanation
Indices: 262483--262520 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
262473 AATTTTATCC
*
262483 TTAAAATT
1 TTAAAAAT
262491 TTAAAAAT
1 TTAAAAAT
262499 TTAAAAAT
1 TTAAAAAT
262507 TTAAAGAAT
1 TTAAA-AAT
262516 TTAAA
1 TTAAA
262521 TGAAAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
TTAAAAAT
Found at i:265600 original size:23 final size:23
Alignment explanation
Indices: 265584--265646 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
265574 TTGTACAGAA
265584 AAAATACAGTGAGTTGTACAACG
1 AAAATACAGTGAGTTGTACAACG
265607 AAAATACAGTGAGTTGTACAACG
1 AAAATACAGTGAGTTGTACAACG
*
265630 AAAATTCAGTGAGTTGT
1 AAAATACAGTGAGTTGT
265647 GGTTTAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.25
Consensus pattern (23 bp):
AAAATACAGTGAGTTGTACAACG
Found at i:265782 original size:23 final size:23
Alignment explanation
Indices: 265698--265782 Score: 59
Period size: 23 Copynumber: 3.7 Consensus size: 23
265688 TTGTATTCTG
* * * *
265698 AAAATACCGCAAACTGTATTGGA
1 AAAATACTGCGAACTGGATTGCA
*
265721 AAAATAATGCGAACAAT-G-TTGCA
1 AAAATACTGCGAAC--TGGATTGCA
* *
265744 AAAGTACTGC-AGACTGGATTGTA
1 AAAATACTGCGA-ACTGGATTGCA
265767 AAAATACTGCGAACTG
1 AAAATACTGCGAACTG
265783 TACTAAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
21 1 0.02
22 2 0.04
23 42 0.89
24 1 0.02
25 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.22
Consensus pattern (23 bp):
AAAATACTGCGAACTGGATTGCA
Found at i:265905 original size:52 final size:54
Alignment explanation
Indices: 265840--266000 Score: 177
Period size: 54 Copynumber: 3.0 Consensus size: 54
265830 ATTACATGAG
* * *
265840 AAAGTTGCAATCTTAAATCAGC-AACTACAAGATAT-G-GAAATCTTGTAAGTAT
1 AAAGTTGCGATCTTAAATCAGCGAACCACAAGAT-TCGAAAAATCTTGTAAGTAT
* * * *
265892 AAAGTTACGATCTTAAATCGGCGAGCCACAAGATTCGAAAAATCTTGTAAGTGT
1 AAAGTTGCGATCTTAAATCAGCGAACCACAAGATTCGAAAAATCTTGTAAGTAT
* * ** *
265946 AAGGTTGCGATCTTAAATCGGTAAACCACAAGATTC-AAAAATCTTTTAAGTAT
1 AAAGTTGCGATCTTAAATCAGCGAACCACAAGATTCGAAAAATCTTGTAAGTAT
265999 AA
1 AA
266001 GGCTATGATC
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
52 20 0.22
53 27 0.29
54 45 0.49
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (54 bp):
AAAGTTGCGATCTTAAATCAGCGAACCACAAGATTCGAAAAATCTTGTAAGTAT
Found at i:266033 original size:53 final size:54
Alignment explanation
Indices: 265877--266025 Score: 201
Period size: 54 Copynumber: 2.8 Consensus size: 54
265867 CAAGATATGG
* *
265877 AAATCTTGTAAGTATAAAGTTACGATCTTAAATCGGCGAGCCACAAGATTCGAA
1 AAATCTTGTAAGTATAAGGTTACGATCTTAAATCGGTGAGCCACAAGATTCGAA
* * * *
265931 AAATCTTGTAAGTGTAAGGTTGCGATCTTAAATCGGTAAACCACAAGATTC-AA
1 AAATCTTGTAAGTATAAGGTTACGATCTTAAATCGGTGAGCCACAAGATTCGAA
* * * *
265984 AAATCTTTTAAGTATAAGGCTATGATCTTAAATTGGTGAGCC
1 AAATCTTGTAAGTATAAGGTTACGATCTTAAATCGGTGAGCC
266026 GTAAGATTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
53 36 0.44
54 45 0.56
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (54 bp):
AAATCTTGTAAGTATAAGGTTACGATCTTAAATCGGTGAGCCACAAGATTCGAA
Found at i:266111 original size:71 final size:71
Alignment explanation
Indices: 265995--266136 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
265985 AATCTTTTAA
265995 GTATAAGGCTATGATCTTAAATTGGTGAGCCGTAAGATTTGAACAAAAATCGGCAAACTACAAGA
1 GTATAAGGCTATGATCTTAAATTGGTGAGCCGTAAGATTTGAACAAAAATCGGCAAACTACAAGA
266060 TTTTCC
66 TTTTCC
266066 GTATAAGGCTATGATCTTAAATTGGTGAGCCGTAAGATTTGAACAAAAATCGGCAAACTACAAGA
1 GTATAAGGCTATGATCTTAAATTGGTGAGCCGTAAGATTTGAACAAAAATCGGCAAACTACAAGA
266131 TTTTCC
66 TTTTCC
266137 AAATCTTGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (71 bp):
GTATAAGGCTATGATCTTAAATTGGTGAGCCGTAAGATTTGAACAAAAATCGGCAAACTACAAGA
TTTTCC
Found at i:266195 original size:54 final size:54
Alignment explanation
Indices: 266137--266363 Score: 251
Period size: 54 Copynumber: 4.2 Consensus size: 54
266127 AAGATTTTCC
** *
266137 AAATCTTGTAAGTATAAGGCTGCGATATTAAATCGGCAAGCCACAAGATTCAAA
1 AAATCTTGTAAGTATAAGGCTATGATCTTAAATCGGCAAGCCACAAGATTCAAA
* * ** * * *
266191 AAATCTGGTAAGTATAAGGTTATGATCTTAAATAAGCAAACCGCAAGATTCGAA
1 AAATCTTGTAAGTATAAGGCTATGATCTTAAATCGGCAAGCCACAAGATTCAAA
* * * * *
266245 AAATCTTGTAAGTATAAGGCTATAATCTTAAATTGACAAGCCATAAGATTCGAA
1 AAATCTTGTAAGTATAAGGCTATGATCTTAAATCGGCAAGCCACAAGATTCAAA
* **
266299 AAATCTTGTAAGTATAAGGCTGTGATCTTAAATCAAGG--AGCCGTAAGATTCAAA
1 AAATCTTGTAAGTATAAGGCTATGATCTTAAATC--GGCAAGCCACAAGATTCAAA
*
266353 ATATCTTGTAA
1 AAATCTTGTAA
266364 TTAGTAAATT
Statistics
Matches: 145, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
54 144 0.99
56 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (54 bp):
AAATCTTGTAAGTATAAGGCTATGATCTTAAATCGGCAAGCCACAAGATTCAAA
Found at i:266310 original size:108 final size:107
Alignment explanation
Indices: 266137--266363 Score: 294
Period size: 108 Copynumber: 2.1 Consensus size: 107
266127 AAGATTTTCC
* * *
266137 AAATCTTGTAAGTATAAGGCTGCGATATTAAATCGGCAAGCCACAAGATTCAAAAAATCTGGTAA
1 AAATCTTGTAAGTATAAGGCTACAATATTAAATCGACAAGCCACAAGATTCAAAAAATCTGGTAA
*
266202 GTATAAGGTTATGATCTTAAAT-AAGCAAACCGCAAGATTCGAA
66 GTATAAGGCTATGATCTTAAATCAAG-AAACCGCAAGATTC-AA
* * * * * *
266245 AAATCTTGTAAGTATAAGGCTATAATCTTAAATTGACAAGCCATAAGATTCGAAAAATCTTGTAA
1 AAATCTTGTAAGTATAAGGCTACAATATTAAATCGACAAGCCACAAGATTCAAAAAATCTGGTAA
* * * *
266310 GTATAAGGCTGTGATCTTAAATCAAGGAGCCGTAAGATTCAA
66 GTATAAGGCTATGATCTTAAATCAAGAAACCGCAAGATTCAA
266352 AATATCTTGTAA
1 AA-ATCTTGTAA
266364 TTAGTAAATT
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
107 4 0.04
108 96 0.93
109 3 0.03
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (107 bp):
AAATCTTGTAAGTATAAGGCTACAATATTAAATCGACAAGCCACAAGATTCAAAAAATCTGGTAA
GTATAAGGCTATGATCTTAAATCAAGAAACCGCAAGATTCAA
Found at i:266987 original size:21 final size:21
Alignment explanation
Indices: 266943--266994 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
266933 GGGTAGATTT
*
266943 CTACCGATACAAGTGAGACAA
1 CTACCGATACAAGTCAGACAA
* * *
266964 CTATCGATACAAGTCATACTA
1 CTACCGATACAAGTCAGACAA
266985 CTACCGATAC
1 CTACCGATAC
266995 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (21 bp):
CTACCGATACAAGTCAGACAA
Found at i:267725 original size:36 final size:37
Alignment explanation
Indices: 267655--267756 Score: 127
Period size: 36 Copynumber: 2.8 Consensus size: 37
267645 ATCATTATTC
* * *
267655 TTTTACTCTCTATTGACCCTAAGGGTCATGATGCTC-G
1 TTTTACTCTTTGTTGACCC-AAAGGTCATGATGCTCAG
* *
267692 TTTTACTCTTTGTTGACCCAAAGGTCATTATGCTCAT
1 TTTTACTCTTTGTTGACCCAAAGGTCATGATGCTCAG
*
267729 TTTTA-TCCTTGTTGACCCAAAGGTCATG
1 TTTTACTCTTTGTTGACCCAAAGGTCATG
267757 CTTGTTACCA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
36 35 0.61
37 22 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (37 bp):
TTTTACTCTTTGTTGACCCAAAGGTCATGATGCTCAG
Found at i:275027 original size:36 final size:36
Alignment explanation
Indices: 274962--275064 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 36
274952 ATTGTTATTT
* *
274962 GTTTTACTTCCTGTTGACCCCAAGGGTCATGATGCTC
1 GTTTTACTCCCTGTTGA-CCCAAAGGTCATGATGCTC
* *
274999 GTTTTACTCCCTATTGACCCAAAGGTCATTATGCTC
1 GTTTTACTCCCTGTTGACCCAAAGGTCATGATGCTC
* * * * *
275035 ATTTTTCTCTCTGTTGGCCTAAAGGTCATG
1 GTTTTACTCCCTGTTGACCCAAAGGTCATG
275065 CCTGCTATGA
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
36 40 0.73
37 15 0.27
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (36 bp):
GTTTTACTCCCTGTTGACCCAAAGGTCATGATGCTC
Found at i:278606 original size:13 final size:13
Alignment explanation
Indices: 278588--278613 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
278578 TAGTTTACCG
278588 AAATTATTATAAT
1 AAATTATTATAAT
278601 AAATTATTATAAT
1 AAATTATTATAAT
278614 TATGATTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTATAAT
Found at i:283362 original size:40 final size:39
Alignment explanation
Indices: 283307--283489 Score: 235
Period size: 40 Copynumber: 4.6 Consensus size: 39
283297 TTCCCTGGTG
* * *
283307 TTTATCAGGCTTAGTGCCTAGTAGGCTTAGTACCTGTGTA
1 TTTATCGGGCTTAGTGCCTAGCAGGCTTAGTGCC-GTGTA
* * *
283347 TTTATCGGGCTTAGTGTCTATCAGGCTTCA-TGCCG-GTG
1 TTTATCGGGCTTAGTGCCTAGCAGGCTT-AGTGCCGTGTA
* *
283385 TTTATCGGGCTTAGTGCCTAGCAAGCTTAGTGTCAGTGTA
1 TTTATCGGGCTTAGTGCCTAGCAGGCTTAGTG-CCGTGTA
283425 TTTATCGGGCTTAGTGCCTAGCAGGCTTAGTGCCGATGTA
1 TTTATCGGGCTTAGTGCCTAGCAGGCTTAGTGCCG-TGTA
*
283465 TTCATCGGGCTTAGTGCCTAGCAGG
1 TTTATCGGGCTTAGTGCCTAGCAGG
283490 TAACTTGTAC
Statistics
Matches: 124, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
37 1 0.01
38 29 0.23
39 5 0.04
40 88 0.71
41 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.34
Consensus pattern (39 bp):
TTTATCGGGCTTAGTGCCTAGCAGGCTTAGTGCCGTGTA
Found at i:283432 original size:78 final size:78
Alignment explanation
Indices: 283303--283487 Score: 255
Period size: 78 Copynumber: 2.3 Consensus size: 78
283293 TAAATTCCCT
* * * * * *
283303 GGTGTTTATCAGGCTTAGTGCCTAGTAGGCTTAGTACCTGTGTATTTATCGGGCTTAGTGTCTAT
1 GGTGTTTATCGGGCTTAGTGCCTAGCAAGCTTAGTACCAGTGTATTTATCGGGCTTAGTGCCTAG
283368 CAGGCTTCA-TGCC
66 CAGGCTT-AGTGCC
**
283381 GGTGTTTATCGGGCTTAGTGCCTAGCAAGCTTAGTGTCAGTGTATTTATCGGGCTTAGTGCCTAG
1 GGTGTTTATCGGGCTTAGTGCCTAGCAAGCTTAGTACCAGTGTATTTATCGGGCTTAGTGCCTAG
283446 CAGGCTTAGTGCC
66 CAGGCTTAGTGCC
*
283459 GATGTATTCATCGGGCTTAGTGCCTAGCA
1 GGTGT-TT-ATCGGGCTTAGTGCCTAGCA
283488 GGTAACTTGT
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
77 1 0.01
78 72 0.76
79 2 0.02
80 20 0.21
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (78 bp):
GGTGTTTATCGGGCTTAGTGCCTAGCAAGCTTAGTACCAGTGTATTTATCGGGCTTAGTGCCTAG
CAGGCTTAGTGCC
Found at i:283867 original size:25 final size:25
Alignment explanation
Indices: 283820--283867 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
283810 TTATATGAAA
* *
283820 ATAATGGATATGGATATATGTATGT
1 ATAATGGATATAGATATAGGTATGT
283845 ATAATGGATGATAGATA-AGGTAT
1 ATAATGGAT-ATAGATATAGGTAT
283868 AAATACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (25 bp):
ATAATGGATATAGATATAGGTATGT
Found at i:286781 original size:22 final size:22
Alignment explanation
Indices: 286752--286809 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
286742 TTTTATATGG
*
286752 AATT-TTGAATTGAAGAATTTT
1 AATTATTGAATTAAAGAATTTT
*
286773 AGTTATTGAATTAAAGAATTTT
1 AATTATTGAATTAAAGAATTTT
286795 AATTATTGAATTAAA
1 AATTATTGAATTAAA
286810 AGTTAGTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 3 0.09
22 30 0.91
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (22 bp):
AATTATTGAATTAAAGAATTTT
Found at i:287988 original size:16 final size:16
Alignment explanation
Indices: 287967--287998 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
287957 AGTAAATTTT
*
287967 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
287983 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
287999 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:289494 original size:21 final size:21
Alignment explanation
Indices: 289470--289509 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
289460 TAGAAGTGTG
* *
289470 ACTTGTATTGGTAGTATCCAT
1 ACTTGTATTGATAGAATCCAT
289491 ACTTGTATTGATAGAATCC
1 ACTTGTATTGATAGAATCC
289510 TTCCAACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
ACTTGTATTGATAGAATCCAT
Found at i:298395 original size:20 final size:20
Alignment explanation
Indices: 298370--298410 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
298360 ATTTTACAAA
298370 ACTGATACG-TAGGTATCGAT
1 ACTGATA-GATAGGTATCGAT
*
298390 ACTGATAGATTGGTATCGAT
1 ACTGATAGATAGGTATCGAT
298410 A
1 A
298411 TTTCTCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (20 bp):
ACTGATAGATAGGTATCGAT
Found at i:298552 original size:28 final size:28
Alignment explanation
Indices: 298512--298570 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
298502 TGATGAAGTA
298512 TCGATAATTTCATCCCAAGTATCGATAC
1 TCGATAATTTCATCCCAAGTATCGATAC
298540 TCGATAATTTCATCCCAAGTATCGATAC
1 TCGATAATTTCATCCCAAGTATCGATAC
298568 TCG
1 TCG
298571 TGATAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (28 bp):
TCGATAATTTCATCCCAAGTATCGATAC
Found at i:301100 original size:11 final size:11
Alignment explanation
Indices: 301086--301131 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
301076 TTTTGGGCCA
*
301086 TTTTATTGTTG
1 TTTTGTTGTTG
*
301097 TTTTGTAGTTG
1 TTTTGTTGTTG
301108 -TTT-TTGTTG
1 TTTTGTTGTTG
*
301117 TTTTGTTGTCG
1 TTTTGTTGTTG
301128 TTTT
1 TTTT
301132 TAATATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 5 0.17
10 6 0.21
11 18 0.62
ACGTcount: A:0.04, C:0.02, G:0.22, T:0.72
Consensus pattern (11 bp):
TTTTGTTGTTG
Found at i:301116 original size:20 final size:20
Alignment explanation
Indices: 301091--301132 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
301081 GGCCATTTTA
*
301091 TTGTTGTTTTGTAGTTGTTT
1 TTGTTGTTTTGTAGTCGTTT
*
301111 TTGTTGTTTTGTTGTCGTTT
1 TTGTTGTTTTGTAGTCGTTT
301131 TT
1 TT
301133 AATATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.02, G:0.24, T:0.71
Consensus pattern (20 bp):
TTGTTGTTTTGTAGTCGTTT
Found at i:310498 original size:22 final size:22
Alignment explanation
Indices: 310470--310518 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
310460 AAGAAAGAAA
310470 GAAAAAAGAAGATAAAA-GGTTT
1 GAAAAAAGAAGA-AAAAGGGTTT
*
310492 GAAAAAAGATGAAAAAGGGTTT
1 GAAAAAAGAAGAAAAAGGGTTT
310514 -AAAAA
1 GAAAAA
310519 CCCTACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (22 bp):
GAAAAAAGAAGAAAAAGGGTTT
Found at i:337284 original size:17 final size:16
Alignment explanation
Indices: 337262--337308 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
337252 CAATCACTTG
**
337262 AAAAAAAAAATGAGAA
1 AAAAAAAAAAAAAGAA
337278 AAAAAAAAAAGAAAGAA
1 AAAAAAAAAA-AAAGAA
337295 AAAAGAAAAAAAAA
1 AAAA-AAAAAAAAA
337309 TAAATTGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 10 0.37
17 11 0.41
18 6 0.22
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAA
Found at i:337296 original size:11 final size:10
Alignment explanation
Indices: 337279--337308 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
337269 AAATGAGAAA
337279 AAAAAAAAAG
1 AAAAAAAAAG
337289 AAAGAAAAAAG
1 AAA-AAAAAAG
337300 AAAAAAAAA
1 AAAAAAAAA
337309 TAAATTGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:338058 original size:6 final size:6
Alignment explanation
Indices: 338047--338071 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
338037 TATAACTGCA
338047 AGATCT AGATCT AGATCT AGATCT A
1 AGATCT AGATCT AGATCT AGATCT A
338072 AGAATGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
AGATCT
Found at i:338324 original size:21 final size:21
Alignment explanation
Indices: 338300--338342 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
338290 AGGTTAGAGA
338300 TAGTAAGCTTCGTTGTACTCT
1 TAGTAAGCTTCGTTGTACTCT
338321 TAGTAAGCTTCGTTGTACTCT
1 TAGTAAGCTTCGTTGTACTCT
338342 T
1 T
338343 TAATTCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (21 bp):
TAGTAAGCTTCGTTGTACTCT
Found at i:344390 original size:25 final size:25
Alignment explanation
Indices: 344360--344407 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
344350 GAAAAGAAGG
*
344360 GAGACTGCAAAATTGCAGAAAAAAC
1 GAGACTGCAAAAGTGCAGAAAAAAC
**
344385 GAGACTGTGAAAGTGCAGAAAAA
1 GAGACTGCAAAAGTGCAGAAAAA
344408 TGAGTCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (25 bp):
GAGACTGCAAAAGTGCAGAAAAAAC
Done.