Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014832.1 Kokia drynarioides strain JFW-HI SEQ_129874, 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: 75861
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:199 original size:84 final size:84
Alignment explanation
Indices: 1--155 Score: 240
Period size: 84 Copynumber: 1.9 Consensus size: 84
* * * * *
1 TTAAAA-TTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATA
1 TTAAAATTTGATAAATATTGTATTATCAAATTAACACAATATTTGATAAAAATTGTAATATAATA
65 ATAATTTGTACTTTAAATA
66 ATAATTTGTACTTTAAATA
* *
84 TTAAAATTTGATAAATATTGTATTATCAAATTAACACAATATTTTATATAAATTGTAATATAATA
1 TTAAAATTTGATAAATATTGTATTATCAAATTAACACAATATTTGATAAAAATTGTAATATAATA
149 ATAATTT
66 ATAATTT
156 TTTATTTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 6 0.09
84 58 0.91
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (84 bp):
TTAAAATTTGATAAATATTGTATTATCAAATTAACACAATATTTGATAAAAATTGTAATATAATA
ATAATTTGTACTTTAAATA
Found at i:297 original size:12 final size:12
Alignment explanation
Indices: 280--327 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
270 AAACATGTTC
280 ATTAATTTCCAA
1 ATTAATTTCCAA
292 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
*
308 ATTAATTTTCAA
1 ATTAATTTCCAA
320 ATTAATTT
1 ATTAATTT
328 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:326 original size:16 final size:16
Alignment explanation
Indices: 290--324 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
280 ATTAATTTCC
*
290 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
306 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
323 AA
1 AA
325 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:337 original size:28 final size:28
Alignment explanation
Indices: 280--337 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
270 AAACATGTTC
**
280 ATTAATTTCCAAATTAATTTCAACTTAA
1 ATTAATTTCCAAATTAATTTCAACACAA
* **
308 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTCCAAATTAATTTCAACACAA
336 AT
1 AT
338 ATTCTTCGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTTCCAAATTAATTTCAACACAA
Found at i:4444 original size:117 final size:117
Alignment explanation
Indices: 4217--4686 Score: 696
Period size: 117 Copynumber: 4.0 Consensus size: 117
4207 AAAAATTGAA
*
4217 CTCAAAAAGCGA-GTGTCGGCCATGCAATGGCCAACACCCAAAAATGCAATTTTTTTTTCTGAAA
1 CTCAAAAAG-GAGGTGTCGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTTCTGAAA
* *
4281 AAGGAGGTGTCGACAATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTTT
65 AAGG-GGTGTCGGCCATTGCATGACCAACACCAAAAAATTTTGAAA-TTTTTTTT
* *
4336 CTCAAAAAGGGGGTGTCGGCCATGTAATGGCCAACACCCAAAAATGTAA-TTTTTTTT-TGAAAA
1 CTCAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTTCTGAAAA
4399 AGGGGATGTCGGCCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTT
66 AGGGG-TGTCGGCCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTT
* *
4452 CTCAAAAAGGAGGTGTCGACCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTTTCTAAAA
1 CTCAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACCCAAAAATGTAA-TTTTTTTTTCTGAAA
* *
4517 AAGGGGGTGTCAGCCATTGCATGACCAACACCAAAAAATTTTGAAATTGTTTTT
65 AA-GGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTT
* * * * *
4571 CTCAAAAA-GAGTTGTCGGCCATGCAATGGTCAACACCTAAAAATATAATTTTTTTTTTTGAAAA
1 CTCAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTTCTGAAAA
* * *
4635 AGCGGGTGTCGGCCATTGCGTGACCAACACAAAAAAAATTTGAAATTTTTTT
66 AG-GGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTT
4687 CTTAAAATGG
Statistics
Matches: 321, Mismatches: 23, Indels: 16
0.89 0.06 0.04
Matches are distributed among these distances:
116 57 0.18
117 105 0.33
118 52 0.16
119 103 0.32
120 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (117 bp):
CTCAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTTCTGAAAA
AGGGGTGTCGGCCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTT
Found at i:4507 original size:59 final size:58
Alignment explanation
Indices: 4217--4650 Score: 418
Period size: 59 Copynumber: 7.4 Consensus size: 58
4207 AAAAATTGAA
* *
4217 CTCAAAAAGCGA-GTGTCGGCCATGCAATGGCCAACACCCAAAAATGCAATTTTTTTTT
1 CTCAAAAAG-GAGGTGTCGGCCATGCAATGGCCAACACCAAAAAATGTAATTTTTTTTT
* * * * *
4275 CTGAAAAAGGAGGTGTCGACAATTGC-ATGACCAACACCAAAAAATTTTGAAATTTTTTTTT
1 CTCAAAAAGGAGGTGTCGGCCA-TGCAATGGCCAACACCAAAAAA---TGTAATTTTTTTTT
* * *
4336 CTCAAAAAGGGGGTGTCGGCCATGTAATGGCCAACACCCAAAAATGTAA-TTTTTTTT
1 CTCAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACCAAAAAATGTAATTTTTTTTT
* * * *
4393 -TGAAAAAGG-GGATGTCGGCCATTGC-ATGACCAACACCAAAAAATTTTGAAATTTTTTTT
1 CTCAAAAAGGAGG-TGTCGGCCA-TGCAATGGCCAACACCAAAAAA-TGT-AATTTTTTTTT
* *
4452 CTCAAAAAGGAGGTGTCGACCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTTT
1 CTCAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACCAAAAAATGTAA-TTTTTTTTT
* * * * * * *
4511 CTAAAAAAGGGGGTGTCAGCCATTGC-ATGACCAACACCAAAAAATTTTGAAATTGTTTTT
1 CTCAAAAAGGAGGTGTCGGCCA-TGCAATGGCCAACACCAAAAAA-TGT-AATTTTTTTTT
* * * *
4571 CTCAAAAA-GAGTTGTCGGCCATGCAATGGTCAACACCTAAAAATATAATTTTTTTTT
1 CTCAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACCAAAAAATGTAATTTTTTTTT
* *
4628 TTGAAAAAGCG-GGTGTCGGCCAT
1 CTCAAAAAG-GAGGTGTCGGCCAT
4651 TGCGTGACCA
Statistics
Matches: 308, Mismatches: 47, Indels: 42
0.78 0.12 0.11
Matches are distributed among these distances:
55 2 0.01
56 33 0.11
57 29 0.09
58 56 0.18
59 84 0.27
60 53 0.17
61 51 0.17
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (58 bp):
CTCAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACCAAAAAATGTAATTTTTTTTT
Found at i:4560 original size:236 final size:234
Alignment explanation
Indices: 4217--4686 Score: 714
Period size: 236 Copynumber: 2.0 Consensus size: 234
4207 AAAAATTGAA
* *
4217 CTCAAAAAGCGAGTGTCGGCCATGCAATGGCCAACACCCAAAAATGCAATTTTTTTTTCTGAAAA
1 CTCAAAAAGCGAGTGTCGACCATGCAATGGCCAACACCCAAAAATGCAATTTTTTTTTCTAAAAA
* *
4282 AGGAGGTGTCGACAATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTTTCTCAAAAAGGG
66 AGGAGGTGTCGACAATTGCATGACCAACACCAAAAAATTTTGAAA-TTGTTTTTCTCAAAAA-GA
* *
4347 GGTGTCGGCCATGTAATGGCCAACACCCAAAAATGTAA-TTTTTTTTTGAAAAAG-GGGATGTCG
129 GGTGTCGGCCATGCAATGGCCAACACCCAAAAATATAATTTTTTTTTTGAAAAAGCGGG-TGTCG
* *
4410 GCCATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTT
193 GCCATTGCATGACCAACACAAAAAAAATTTGAAATTTTTTTT
*
4452 CTCAAAAAG-GAGGTGTCGACCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTTTCTAAA
1 CTCAAAAAGCGA-GTGTCGACCATGCAATGGCCAACACCCAAAAATGCAA-TTTTTTTTTCTAAA
* *
4516 AAAGGGGGTGTC-AGCCATTGCATGACCAACACCAAAAAATTTTGAAATTGTTTTTCTCAAAAAG
64 AAAGGAGGTGTCGA-CAATTGCATGACCAACACCAAAAAATTTTGAAATTGTTTTTCTCAAAAAG
* * *
4580 AGTTGTCGGCCATGCAATGGTCAACACCTAAAAATATAATTTTTTTTTTTGAAAAAGCGGGTGTC
128 AGGTGTCGGCCATGCAATGGCCAACACCCAAAAATATAA-TTTTTTTTTTGAAAAAGCGGGTGTC
*
4645 GGCCATTGCGTGACCAACACAAAAAAAATTTGAAATTTTTTT
192 GGCCATTGCATGACCAACACAAAAAAAATTTGAAATTTTTTT
4687 CTTAAAATGG
Statistics
Matches: 214, Mismatches: 15, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
234 36 0.17
235 60 0.28
236 115 0.54
237 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (234 bp):
CTCAAAAAGCGAGTGTCGACCATGCAATGGCCAACACCCAAAAATGCAATTTTTTTTTCTAAAAA
AGGAGGTGTCGACAATTGCATGACCAACACCAAAAAATTTTGAAATTGTTTTTCTCAAAAAGAGG
TGTCGGCCATGCAATGGCCAACACCCAAAAATATAATTTTTTTTTTGAAAAAGCGGGTGTCGGCC
ATTGCATGACCAACACAAAAAAAATTTGAAATTTTTTTT
Found at i:4757 original size:55 final size:57
Alignment explanation
Indices: 4693--4823 Score: 151
Period size: 59 Copynumber: 2.3 Consensus size: 57
4683 TTTTCTTAAA
*
4693 ATGGCCAACACCCAAAAATGCAA-TTTTTA-AA-AAAAAAAGAGATGTCGATCCTTGC
1 ATGGCCAACACCCAAAAATGCAATTTTTTATAACAAAAAAAG-GATGTCGATCATTGC
* * ** * *
4748 ATGGGCAACACCAAAAAATTTAATTTTTTATCTAACAAAAAAAGGGTGTCGGTCATTGC
1 ATGGCCAACACCCAAAAATGCAATTTTTTA--TAACAAAAAAAGGATGTCGATCATTGC
4807 ATGGCCAACACCCAAAA
1 ATGGCCAACACCCAAAA
4824 TTGTTTTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
55 19 0.31
56 6 0.10
59 29 0.47
60 8 0.13
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (57 bp):
ATGGCCAACACCCAAAAATGCAATTTTTTATAACAAAAAAAGGATGTCGATCATTGC
Found at i:9390 original size:18 final size:16
Alignment explanation
Indices: 9364--9427 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
9354 AAACATTTTT
9364 AAAATTAAAAATTACTA
1 AAAATTAAAAATTA-TA
*
9381 AAAATATAAATATTATA
1 AAAAT-TAAAAATTATA
*
9398 AAAATT-TAAATATATGA
1 AAAATTAAAAAT-TAT-A
9415 AAAATTGAAAAAT
1 AAAATT-AAAAAT
9428 AAAATATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 3 0.08
16 4 0.11
17 19 0.50
18 8 0.21
19 4 0.11
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATTAAAAATTATA
Found at i:9417 original size:16 final size:17
Alignment explanation
Indices: 9364--9419 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
9354 AAACATTTTT
*
9364 AAAAT-TAAAAATTACTA
1 AAAATATAAATATTA-TA
9381 AAAATATAAATATTATA
1 AAAATATAAATATTATA
*
9398 AAAATTTAAATA-TATGA
1 AAAATATAAATATTAT-A
9415 AAAAT
1 AAAAT
9420 TGAAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 3 0.09
17 24 0.69
18 8 0.23
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAATATAAATATTATA
Found at i:11065 original size:29 final size:29
Alignment explanation
Indices: 11023--11081 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
11013 TCAAGGAGAA
11023 TGTTAATTTATGAATTTCATAGTAATCAG
1 TGTTAATTTATGAATTTCATAGTAATCAG
*
11052 TGTTAGTTTATGAATTTCATAGTAATCAG
1 TGTTAATTTATGAATTTCATAGTAATCAG
11081 T
1 T
11082 TTTTTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (29 bp):
TGTTAATTTATGAATTTCATAGTAATCAG
Found at i:22260 original size:21 final size:21
Alignment explanation
Indices: 22236--22285 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
22226 CATTGATTGG
*
22236 TTTAAAAATTATTAAA-AATTA
1 TTTAAAAATTA-TAAATAAATA
22257 TTTAAAAATTATAAATAAATA
1 TTTAAAAATTATAAATAAATA
*
22278 CTTAAAAA
1 TTTAAAAA
22286 ATGAAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAAAATTATAAATAAATA
Found at i:22261 original size:11 final size:11
Alignment explanation
Indices: 22236--22268 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
22226 CATTGATTGG
22236 TTTAAAAATTA
1 TTTAAAAATTA
22247 -TTAAAAATTA
1 TTTAAAAATTA
22257 TTTAAAAATTA
1 TTTAAAAATTA
22268 T
1 T
22269 AAATAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTAAAAATTA
Found at i:22287 original size:11 final size:10
Alignment explanation
Indices: 22237--22268 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
22227 ATTGATTGGT
22237 TTAAAAATTA
1 TTAAAAATTA
22247 TTAAAAATTA
1 TTAAAAATTA
22257 TTTAAAAATTA
1 -TTAAAAATTA
22268 T
1 T
22269 AAATAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:22384 original size:20 final size:20
Alignment explanation
Indices: 22344--22396 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
22334 AAAATAGTAA
22344 AAAACTTGTAAAAATTCATTT
1 AAAA-TTGTAAAAATTCATTT
22365 AAAAGTTGTAAAAATT-ATTT
1 AAAA-TTGTAAAAATTCATTT
*
22385 TAAATT-TAAAAA
1 AAAATTGTAAAAA
22397 ATTAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 6 0.20
19 2 0.07
20 7 0.23
21 15 0.50
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.38
Consensus pattern (20 bp):
AAAATTGTAAAAATTCATTT
Found at i:22908 original size:14 final size:15
Alignment explanation
Indices: 22874--22907 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
22864 AACTTTAATG
22874 AAAAATTTAAACAAA
1 AAAAATTTAAACAAA
*
22889 AAAAATTTAAATAAA
1 AAAAATTTAAACAAA
22904 AAAA
1 AAAA
22908 TATAAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATTTAAACAAA
Found at i:22956 original size:14 final size:14
Alignment explanation
Indices: 22904--22949 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
22894 TTTAAATAAA
22904 AAAATATAAAAACTT
1 AAAATATAAAAA-TT
22919 AATAACT-T-AAAATT
1 AA-AA-TATAAAAATT
22933 AAAATATAAAAATT
1 AAAATATAAAAATT
22947 AAA
1 AAA
22950 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
12 1 0.04
13 3 0.11
14 13 0.48
15 6 0.22
16 3 0.11
17 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:23516 original size:4 final size:4
Alignment explanation
Indices: 23507--23541 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
23497 AATGAAGGAA
*
23507 AAAG AAAG AAAA AAGAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AA
23542 GAAGGAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:23517 original size:21 final size:21
Alignment explanation
Indices: 23493--23551 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
23483 GGGAACCAAC
23493 GAAAAATGAAGGAA-AAAGAAA
1 GAAAAA-GAAGGAAGAAAGAAA
*
23514 GAAAAA-AGAGAAAGAAAGAAA
1 GAAAAAGA-AGGAAGAAAGAAA
23535 GAAAGAAGAAGGAAGAA
1 GAAA-AAGAAGGAAGAA
23552 GGAGAAGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 17 0.53
22 9 0.28
23 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (21 bp):
GAAAAAGAAGGAAGAAAGAAA
Found at i:23550 original size:18 final size:17
Alignment explanation
Indices: 23507--23569 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 17
23497 AATGAAGGAA
23507 AAAGAAAGAAAAAAGAG
1 AAAGAAAGAAAAAAGAG
*
23524 AAAGAAAGAAAGAA-AG
1 AAAGAAAGAAAAAAGAG
* * *
23540 -AAGAAGGAAGAAGGAG
1 AAAGAAAGAAAAAAGAG
*
23556 AAGGAAA-AAAAAAG
1 AAAGAAAGAAAAAAG
23570 GTAATGTGTT
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
15 9 0.26
16 9 0.26
17 17 0.49
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAG
Found at i:23557 original size:32 final size:31
Alignment explanation
Indices: 23504--23569 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 31
23494 AAAAATGAAG
23504 GAAA-AAGAAAGAAAAAAGAGAAAGAAAGAAA
1 GAAAGAAGAAAGAAAAAAGAGAAAGAAA-AAA
* * * *
23535 GAAAGAAGAAGGAAGAAGGAGAAGGAAAAAA
1 GAAAGAAGAAAGAAAAAAGAGAAAGAAAAAA
23566 -AAAG
1 GAAAG
23570 GTAATGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 4 0.13
31 7 0.23
32 19 0.63
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (31 bp):
GAAAGAAGAAAGAAAAAAGAGAAAGAAAAAA
Found at i:23947 original size:20 final size:21
Alignment explanation
Indices: 23906--23948 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
23896 TAATTTACTT
23906 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
23927 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
23947 TA
1 TA
23949 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:25945 original size:997 final size:987
Alignment explanation
Indices: 24013--25996 Score: 3878
Period size: 997 Copynumber: 2.0 Consensus size: 987
24003 NNNNNNNNNN
24013 TCATATATACATAATCATGTATTTTTCACCTTTATTTGCTCAAAGGCTTACACAATATCACCATT
1 TCATATATACATAATCATGTATTTTTCACCTTTATTTGCTCAAAGGCTTACACAATATCACCATT
24078 TTATCATATAATCAATATTCATAATTAAACACATAATATTTCACATATATATTGTTCATCACATA
66 TTATCATATAATCAATATTCATAATTAAACACATAATATTTCACATATATATTGTTCATCACATA
24143 TGTATCATCATATATATCTTTACTCTTATTTTCACATTAATTTTCAAAGCTGTCCACTTGCGTCA
131 TGTATCATCATATATATCTTTACTCTTATTTTCACATTAATTTTCAAAGCTGTCCACTTGCGTCA
24208 CAGTCACTAAATTATTTATATCTTGGGCTACAGAATTCGAAATTATAAACCCCTTGATGTTTCTG
196 CAGTCACTAAATTATTTATATCTTGGGCTACAGAATTCGAAATTATAAACCCCTTGATGTTTCTG
24273 AAACTAGACTCAATCATCTTCTTACCATAAAATTTCCAGAATTTTTAATTTAGCCAACTTGTAAA
261 AAACTAGACTCAATCATCTTCTTACCATAAAATTTCCAGAATTTTTAATTTAGCCAACTTGTAAA
24338 GTAAATTCTTTCAATTTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTTCTTCACTAAAAATT
326 GTAAATTCTTTCAATTTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTTCTTCACTAAAAATT
24403 ATCTATCTTTTAGTAAAAACATAAAATGATGTTTTCGTCTATTTCTATTGAAAATAGACTCATTA
391 ATCTATCTTTTAGTAAAAACATAAAATGATGTTTTCGTCTATTTCTATTGAAAATAGACTCATTA
24468 AAGATTCATCAATATAAATTTCAGTCTCTAATAATTTTTCTACATTTTTCTATAATTTTTCAAAG
456 AAGATTCATCAATATAAATTTCAGTCTCTAATAATTTTTCTACATTTTTCTATAATTTTTCAAAG
24533 TCAGAACAGGGGAACTCGAATCTACTCTGACCTTATTACACTAAAACTAGTATATCTCGAAATAT
521 TCAGAACAGGGGAACTCGAATCTACTCTGACCTTATTACACTAAAACTAGTATATCTCGAAATAT
24598 GCAGTTCCTTTTCTTTCACTGTTTCTTCCATATGAAACTAAACTCAATAAGCTTTAATTACATAT
586 GCAGTTCCTTTTCTTTCACTGTTTCTTCCATATGAAACTAAACTCAATAAGCTTTAATTACATAT
24663 ATAATTCGACCCTTAACTCATTATATACAATTTTTGGTGAATTTTCGAAGTTAGTCCCCTGTTAC
651 ATAATTCGACCCTTAACTCATTATATACAATTTTTGGTGAATTTTCGAAGTTAGTCCCCTGTTAC
24728 TGTCCAAACTGTTTTGAAGTGAATTTTTCCCTTCTCATATTTCCTTTGCACTAAATTTCATTTAA
716 TGTCCAAACTGTTTTGAAGTGAATTTTTCCCTTCTCATATTTCCTTTGCACTAAATTTCATTTAA
24793 TCACACCTAATCACCATATTTATAACTAAACATATCATTTTACTAATTTTTATCACAATGAATTA
781 TCACACCTAATCACCATATTTATAACTAAACATATCATTTTACTAATTTTTATCACAATGAATTA
24858 TATACTTTAAAGAGAATAAATCTTCAATTTAAAATCTTGTAGTACTTACAACTCTAGTAGAAAAC
846 TATACTTTAAAGAGAATAAATCTTCAATTTAAAATCTTGTAGTACTTACAACTCTAGTAGAAAAC
24923 TTCCTTTTCCTCTTTGATCTTCTCTTTTCCTTTCTCTTCAATTGAGTCATTCTCCTTCTTTTCTT
911 TTCCTTTTCCTCTTTGATCTTCTCTTTTCCTTTCTCTTCAATTGAGTCATTCTCCTTCTTTTCTT
24988 TCTCTTCAATTC
976 TCTCTTCAATTC
25000 NNNNNNNNNNTCATATATACATAATCATGTATTTTTCACCTTTATTTGCTCAAAGGCTTACACAA
1 ----------TCATATATACATAATCATGTATTTTTCACCTTTATTTGCTCAAAGGCTTACACAA
25065 TATCACCATTTTATCATATAATCAATATTCATAATTAAACACATAATATTTCACATATATATTGT
56 TATCACCATTTTATCATATAATCAATATTCATAATTAAACACATAATATTTCACATATATATTGT
25130 TCATCACATATGTATCATCATATATATCTTTACTCTTATTTTCACATTAATTTTCAAAGCTGTCC
121 TCATCACATATGTATCATCATATATATCTTTACTCTTATTTTCACATTAATTTTCAAAGCTGTCC
25195 ACTTGCGTCACAGTCACTAAATTATTTATATCTTGGGCTACAGAATTCGAAATTATAAACCCCTT
186 ACTTGCGTCACAGTCACTAAATTATTTATATCTTGGGCTACAGAATTCGAAATTATAAACCCCTT
25260 GATGTTTCTGAAACTAGACTCAATCATCTTCTTACCATAAAATTTCCAGAATTTTTAATTTAGCC
251 GATGTTTCTGAAACTAGACTCAATCATCTTCTTACCATAAAATTTCCAGAATTTTTAATTTAGCC
25325 AACTTGTAAAGTAAATTCTTTCAATTTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTTCTTC
316 AACTTGTAAAGTAAATTCTTTCAATTTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTTCTTC
25390 ACTAAAAATTATCTATCTTTTAGTAAAAACATAAAATGATGTTTTCGTCTATTTCTATTGAAAAT
381 ACTAAAAATTATCTATCTTTTAGTAAAAACATAAAATGATGTTTTCGTCTATTTCTATTGAAAAT
25455 AGACTCATTAAAGATTCATCAATATAAATTTCAGTCTCTAATAATTTTTCTACATTTTTCTATAA
446 AGACTCATTAAAGATTCATCAATATAAATTTCAGTCTCTAATAATTTTTCTACATTTTTCTATAA
25520 TTTTTCAAAGTCAGAACAGGGGAACTCGAATCTACTCTGACCTTATTACACTAAAACTAGTATAT
511 TTTTTCAAAGTCAGAACAGGGGAACTCGAATCTACTCTGACCTTATTACACTAAAACTAGTATAT
25585 CTCGAAATATGCAGTTCCTTTTCTTTCACTGTTTCTTCCATATGAAACTAAACTCAATAAGCTTT
576 CTCGAAATATGCAGTTCCTTTTCTTTCACTGTTTCTTCCATATGAAACTAAACTCAATAAGCTTT
25650 AATTACATATATAATTCGACCCTTAACTCATTATATACAATTTTTGGTGAATTTTCGAAGTTAGT
641 AATTACATATATAATTCGACCCTTAACTCATTATATACAATTTTTGGTGAATTTTCGAAGTTAGT
25715 CCCCTGTTACTGTCCAAACTGTTTTGAAGTGAATTTTTCCCTTCTCATATTTCCTTTGCACTAAA
706 CCCCTGTTACTGTCCAAACTGTTTTGAAGTGAATTTTTCCCTTCTCATATTTCCTTTGCACTAAA
25780 TTTCATTTAATCACACCTAATCACCATATTTATAACTAAACATATCATTTTACTAATTTTTATCA
771 TTTCATTTAATCACACCTAATCACCATATTTATAACTAAACATATCATTTTACTAATTTTTATCA
25845 CAATGAATTATATACTTTAAAGAGAATAAATCTTCAATTTAAAATCTTGTAGTACTTACAACTCT
836 CAATGAATTATATACTTTAAAGAGAATAAATCTTCAATTTAAAATCTTGTAGTACTTACAACTCT
25910 AGTAGAAAACTTCCTTTTCCTCTTTGATCTTCTCTTTTCCTTTCTCTTCAATTGAGTCATTCTCC
901 AGTAGAAAACTTCCTTTTCCTCTTTGATCTTCTCTTTTCCTTTCTCTTCAATTGAGTCATTCTCC
25975 TTCTTTTCTTTCTCTTCAATTC
966 TTCTTTTCTTTCTCTTCAATTC
25997 NNNNNNNNNN
Statistics
Matches: 987, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
997 987 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (987 bp):
TCATATATACATAATCATGTATTTTTCACCTTTATTTGCTCAAAGGCTTACACAATATCACCATT
TTATCATATAATCAATATTCATAATTAAACACATAATATTTCACATATATATTGTTCATCACATA
TGTATCATCATATATATCTTTACTCTTATTTTCACATTAATTTTCAAAGCTGTCCACTTGCGTCA
CAGTCACTAAATTATTTATATCTTGGGCTACAGAATTCGAAATTATAAACCCCTTGATGTTTCTG
AAACTAGACTCAATCATCTTCTTACCATAAAATTTCCAGAATTTTTAATTTAGCCAACTTGTAAA
GTAAATTCTTTCAATTTACCCCTTCGCTGCTGCCTGACAGTTTCGACCTTTCTTCACTAAAAATT
ATCTATCTTTTAGTAAAAACATAAAATGATGTTTTCGTCTATTTCTATTGAAAATAGACTCATTA
AAGATTCATCAATATAAATTTCAGTCTCTAATAATTTTTCTACATTTTTCTATAATTTTTCAAAG
TCAGAACAGGGGAACTCGAATCTACTCTGACCTTATTACACTAAAACTAGTATATCTCGAAATAT
GCAGTTCCTTTTCTTTCACTGTTTCTTCCATATGAAACTAAACTCAATAAGCTTTAATTACATAT
ATAATTCGACCCTTAACTCATTATATACAATTTTTGGTGAATTTTCGAAGTTAGTCCCCTGTTAC
TGTCCAAACTGTTTTGAAGTGAATTTTTCCCTTCTCATATTTCCTTTGCACTAAATTTCATTTAA
TCACACCTAATCACCATATTTATAACTAAACATATCATTTTACTAATTTTTATCACAATGAATTA
TATACTTTAAAGAGAATAAATCTTCAATTTAAAATCTTGTAGTACTTACAACTCTAGTAGAAAAC
TTCCTTTTCCTCTTTGATCTTCTCTTTTCCTTTCTCTTCAATTGAGTCATTCTCCTTCTTTTCTT
TCTCTTCAATTC
Found at i:26429 original size:225 final size:215
Alignment explanation
Indices: 26038--26477 Score: 790
Period size: 225 Copynumber: 2.0 Consensus size: 215
26028 NNNNNNNNNN
26038 TATCATAATCTATGTTTCTAAACCAAAACTAACATGTATTTAAAGAGGAGTTTAGCTTTCTTACC
1 TATCATAATCTATGTTTCTAAACCAAAACTAACATGTATTTAAAGAGGAGTTTAGCTTTCTTACC
26103 TTAATCACTTGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTATGGTTGCATT
66 TTAATCACTTGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTATGGTTGCATT
26168 TCTTTTAAAAATTGGATAGCTACTACACTTCTCTATCAATTTTATTCACTAATCTTGAAGAAATT
131 TCTTTTAAAAATTGGATAGCTACTACACTTCTCTATCAATTTTATTCACTAATCTTGAAGAAATT
26233 TGGAAGAAACTAGCTTAATT
196 TGGAAGAAACTAGCTTAATT
26253 NNNNNNNNNNTATCATAATCTATGTTTCTAAACCAAAACTAACATGTATTTAAAGAGGAGTTTAG
1 ----------TATCATAATCTATGTTTCTAAACCAAAACTAACATGTATTTAAAGAGGAGTTTAG
26318 CTTTCTTACCTTAATCACTTGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTA
56 CTTTCTTACCTTAATCACTTGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTA
26383 TGGTTGCATTTCTTTTAAAAATTGGATAGCTACTACACTTCTCTATCAATTTTATTCACTAATCT
121 TGGTTGCATTTCTTTTAAAAATTGGATAGCTACTACACTTCTCTATCAATTTTATTCACTAATCT
26448 TGAAGAAATTTGGAAGAAACTAGCTTAATT
186 TGAAGAAATTTGGAAGAAACTAGCTTAATT
26478 GGTTTGTATT
Statistics
Matches: 215, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 215 1.00
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.38
Consensus pattern (215 bp):
TATCATAATCTATGTTTCTAAACCAAAACTAACATGTATTTAAAGAGGAGTTTAGCTTTCTTACC
TTAATCACTTGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTATGGTTGCATT
TCTTTTAAAAATTGGATAGCTACTACACTTCTCTATCAATTTTATTCACTAATCTTGAAGAAATT
TGGAAGAAACTAGCTTAATT
Found at i:27247 original size:21 final size:21
Alignment explanation
Indices: 27221--27273 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
27211 TACAAATTTC
* *
27221 TACCGATACAAGTGATTGTTA
1 TACCGATACAAGTGACTCTTA
*
27242 TACCGATACAAGTGACTCTTC
1 TACCGATACAAGTGACTCTTA
27263 TACCGATACAA
1 TACCGATACAA
27274 ATTTCACCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
TACCGATACAAGTGACTCTTA
Found at i:28104 original size:52 final size:52
Alignment explanation
Indices: 28048--28184 Score: 213
Period size: 52 Copynumber: 2.6 Consensus size: 52
28038 GTATTGAGAA
*
28048 TCATATACTCACGATGACACATAGTCATTGGACCTCATAATCCATAAAGGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAT
* **
28100 TCATATACTCACGATGACTA-ATAGTCATCAGACCTCATAATCTGTAAAGGAT
1 TCATATACTCACGATGAC-ACATAGTCATCGGACCTCATAATCCATAAAGGAT
*
28152 TCATATACTCACAATGACACATAGTCATCGGAC
1 TCATATACTCACGATGACACATAGTCATCGGAC
28185 GTATTACATT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
51 1 0.01
52 75 0.97
53 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
TCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAT
Found at i:36893 original size:35 final size:34
Alignment explanation
Indices: 36854--37021 Score: 100
Period size: 35 Copynumber: 5.0 Consensus size: 34
36844 TATATGATAG
*
36854 ATAAATATTCTATTAATTTAATAATTATCTTATAA
1 ATAAATATTTTATTAATTTAATAATTAT-TTATAA
* * * *
36889 ATAAACATTTTATTAAATTAATAA-AATTTA-AT
1 ATAAATATTTTATTAATTTAATAATTATTTATAA
* * * *
36921 ATTAA-A---TA-TAATTTAAT-ATCGATCTTGTAG
1 ATAAATATTTTATTAATTTAATAAT-TAT-TTATAA
* * * *
36951 ATAAATATTGTCTTAATTTAATAATTATTTTGTAC
1 ATAAATATTTTATTAATTTAATAATTA-TTTATAA
* *
36986 ATAAATATTTTATTAAATTAATATAATATTTATAA
1 ATAAATATTTTATTAATTTAATA-ATTATTTATAA
37021 A
1 A
37022 GAGAGGCTTG
Statistics
Matches: 101, Mismatches: 20, Indels: 24
0.70 0.14 0.17
Matches are distributed among these distances:
26 1 0.01
27 8 0.08
28 4 0.04
29 2 0.02
30 5 0.05
31 2 0.02
32 5 0.05
33 3 0.03
34 3 0.03
35 62 0.61
36 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (34 bp):
ATAAATATTTTATTAATTTAATAATTATTTATAA
Found at i:42282 original size:5 final size:5
Alignment explanation
Indices: 42272--42298 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
42262 TTATTTACAA
42272 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
42299 TTATTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:43542 original size:26 final size:26
Alignment explanation
Indices: 43506--43555 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
43496 GGTTCAATTC
43506 TCAATTCTCAATTATTCTTTTAAGGT
1 TCAATTCTCAATTATTCTTTTAAGGT
43532 TCAATTCTCAATTATTCTTTTAAG
1 TCAATTCTCAATTATTCTTTTAAG
43556 TGTTATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (26 bp):
TCAATTCTCAATTATTCTTTTAAGGT
Found at i:54327 original size:145 final size:145
Alignment explanation
Indices: 54064--54351 Score: 513
Period size: 145 Copynumber: 2.0 Consensus size: 145
54054 TGCTGAATAT
* *
54064 ATATCTGTATTCAAAGTCCTGAAAGAAATACATTCAACAATTTTTATTATTTTTTGGCAAAATTA
1 ATATCTGTATCCAAAGTCCTGAAAGAAATACATTCAACAATTTTTATTATATTTTGGCAAAATTA
*
54129 TTCAATTTTATCAATTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGCATG
66 TTCAATTTTATCAATTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGCATA
54194 CATGAGGTTGGTGAA
131 CATGAGGTTGGTGAA
* *
54209 ATATCTGTATCCAAAGTGCTGAAAGAAATACATTCAACATTTTTTATTATATTTTGGCAAAATTA
1 ATATCTGTATCCAAAGTCCTGAAAGAAATACATTCAACAATTTTTATTATATTTTGGCAAAATTA
* *
54274 TTTAATTTTATCACTTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGCATA
66 TTCAATTTTATCAATTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGCATA
54339 CATGAGGTTGGTG
131 CATGAGGTTGGTG
54352 TACATGAGAC
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 136 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (145 bp):
ATATCTGTATCCAAAGTCCTGAAAGAAATACATTCAACAATTTTTATTATATTTTGGCAAAATTA
TTCAATTTTATCAATTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGCATA
CATGAGGTTGGTGAA
Found at i:59658 original size:19 final size:20
Alignment explanation
Indices: 59636--59673 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
59626 AAATAAATAA
59636 AAATATTAAAAA-ATTCAAC
1 AAATATTAAAAAGATTCAAC
*
59655 AAATTTTAAAAAGATTCAA
1 AAATATTAAAAAGATTCAA
59674 AAACATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.29
Consensus pattern (20 bp):
AAATATTAAAAAGATTCAAC
Found at i:60022 original size:22 final size:23
Alignment explanation
Indices: 59988--60033 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
59978 TGACTCTCAA
**
59988 TTTTAAATTTTAATTAAATTAATT
1 TTTTAAA-TTTAAAAAAATTAATT
60012 TTTTAAA-TTAAAAAAATTAATT
1 TTTTAAATTTAAAAAAATTAATT
60034 AAACCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTAAATTTAAAAAAATTAATT
Found at i:60990 original size:20 final size:19
Alignment explanation
Indices: 60949--60991 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
60939 TAATTCATGA
*
60949 AATTTAAAAAAAAAATCTT
1 AATTTAAAAAAAAAATCGT
60968 AATTTAAAGAAAATAAA-CGT
1 AATTTAAA-AAAA-AAATCGT
60988 AATT
1 AATT
60992 ATCTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 10 0.48
21 3 0.14
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
AATTTAAAAAAAAAATCGT
Found at i:61897 original size:138 final size:140
Alignment explanation
Indices: 61747--62010 Score: 354
Period size: 141 Copynumber: 1.9 Consensus size: 140
61737 TCTTACTTAC
* * *
61747 ATTTGTTTTTTTTAATTTCATGTTACTTCAAGCTTTTTAAAATTTT-ATTAA-TTTTTTAACACA
1 ATTTGTATTTTTTAATTTCATCTTACTTCAAGATTTTTAAAATTTTAATTAAGTTTTTTAACACA
61810 TTAGTCCT-TTGATTAGATGGGCAGATAGTTGCAATTACATCTTTGAGTCTCGAGTTTGATAACT
66 TTAGT-CTATTGATTAGATGGGCAGATAGTTGCAATTACATCTTTGAGTCTCGAGTTTGATAACT
61874 CTTCCACTCAT
130 CTTCCACTCAT
* * * * * *
61885 ATTTGTATTTTTTTATTTCATCTTGCTTTAAGATTTTTAAATTTTTAATTAATGTTTTTTAATAT
1 ATTTGTATTTTTTAATTTCATCTTACTTCAAGATTTTTAAAATTTTAATTAA-GTTTTTTAACAC
* * * ** *
61950 TTTTGTCTATTGGTTAGATGGTTAGATAGTTGTAATTACATCTTTGAGTCTCGAGTTTGAT
65 ATTAGTCTATTGATTAGATGGGCAGATAGTTGCAATTACATCTTTGAGTCTCGAGTTTGAT
62011 TCATCTACTA
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
138 39 0.36
139 5 0.05
140 2 0.02
141 61 0.57
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (140 bp):
ATTTGTATTTTTTAATTTCATCTTACTTCAAGATTTTTAAAATTTTAATTAAGTTTTTTAACACA
TTAGTCTATTGATTAGATGGGCAGATAGTTGCAATTACATCTTTGAGTCTCGAGTTTGATAACTC
TTCCACTCAT
Found at i:62272 original size:3 final size:3
Alignment explanation
Indices: 62264--62303 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
62254 TGAAAATGCC
62264 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
62304 TGCTTATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:69753 original size:23 final size:22
Alignment explanation
Indices: 69714--69760 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
69704 AAATTGATCG
69714 ATTAAGTGTTAAATTAAGTAAA
1 ATTAAGTGTTAAATTAAGTAAA
*
69736 ATTAA-TGTTCAAGATTAATTAAA
1 ATTAAGTGTT-AA-ATTAAGTAAA
69759 AT
1 AT
69761 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 7 0.32
23 11 0.50
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (22 bp):
ATTAAGTGTTAAATTAAGTAAA
Found at i:70378 original size:14 final size:14
Alignment explanation
Indices: 70359--70406 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
70349 GATATTTTAT
*
70359 TTTTATTTTATAAA
1 TTTTATTTTATATA
*
70373 TTTTATCCTTTATATT
1 TTTTAT--TTTATATA
*
70389 TTTTATTATATATA
1 TTTTATTTTATATA
70403 TTTT
1 TTTT
70407 CTGTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 16 0.57
16 12 0.43
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTTATATA
Found at i:72450 original size:19 final size:19
Alignment explanation
Indices: 72417--72468 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
72407 CACATTGGAT
*
72417 AGGATGTGATAGTTGAAACC
1 AGGA-GTGATGGTTGAAACC
72437 AGGAGTGATGGTTGAAACC
1 AGGAGTGATGGTTGAAACC
72456 AGGAGTGATGGTT
1 AGGAGTGATGGTT
72469 AATAAGTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 27 0.87
20 4 0.13
ACGTcount: A:0.31, C:0.08, G:0.37, T:0.25
Consensus pattern (19 bp):
AGGAGTGATGGTTGAAACC
Found at i:75562 original size:30 final size:30
Alignment explanation
Indices: 75525--75797 Score: 193
Period size: 30 Copynumber: 9.1 Consensus size: 30
75515 CTAAAGAGGT
*
75525 CCCTAAACTTTTCAAAAATCATATTTTGAC
1 CCCTAAACTTTTCAAAAATTATATTTTGAC
* ** *
75555 CCTTAAACTTTTTTAAAATTATATTTTAAC
1 CCCTAAACTTTTCAAAAATTATATTTTGAC
* *
75585 CCCTAAAATGTTCCAAAAATTATATTTTGAC
1 CCCTAAACT-TTTCAAAAATTATATTTTGAC
* * *
75616 CCCT-CA-TTTTCCCAAAATTATATTTTGGC
1 CCCTAAACTTTT-CAAAAATTATATTTTGAC
* * * *
75645 CCCTAAATTTTTCTAAAATCACATTTTGA-
1 CCCTAAACTTTTCAAAAATTATATTTTGAC
** *
75674 CCCTAAACTTCCCCAAAATTATATTTTGAC
1 CCCTAAACTTTTCAAAAATTATATTTTGAC
* ***
75704 CCCCAAAC-TTTCATAAAAATTGCCTTTTGAC
1 CCCTAAACTTTTC--AAAAATTATATTTTGAC
* * *
75735 CCCTAAA-TTCTCCCAAAATTATATTTTAAC
1 CCCTAAACTT-TTCAAAAATTATATTTTGAC
* *
75765 CTC-AAA-TTCTTCAAAACTTCAT-TTTTGAC
1 CCCTAAACTT-TTCAAAAATT-ATATTTTGAC
75794 CCCT
1 CCCT
75798 TTATTATTAT
Statistics
Matches: 186, Mismatches: 46, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
28 2 0.01
29 67 0.36
30 70 0.38
31 45 0.24
32 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTTTCAAAAATTATATTTTGAC
Found at i:75637 original size:29 final size:30
Alignment explanation
Indices: 75525--75761 Score: 194
Period size: 30 Copynumber: 7.9 Consensus size: 30
75515 CTAAAGAGGT
* *
75525 CCCTAAACTTTT-CAAAAATCATATTTTGAC
1 CCCTAAA-TTTTCCCAAAATTATATTTTGAC
* ** *
75555 CCTTAAACTTTT-TTAAAATTATATTTTAAC
1 CCCTAAA-TTTTCCCAAAATTATATTTTGAC
* *
75585 CCCTAAAATGTTCCAAAAATTATATTTTGAC
1 CCCT-AAATTTTCCCAAAATTATATTTTGAC
* *
75616 CCCT-CATTTTCCCAAAATTATATTTTGGC
1 CCCTAAATTTTCCCAAAATTATATTTTGAC
* * * *
75645 CCCTAAATTTTTCTAAAATCACATTTTGA-
1 CCCTAAATTTTCCCAAAATTATATTTTGAC
* *
75674 CCCTAAACTTCCCCAAAATTATATTTTGAC
1 CCCTAAATTTTCCCAAAATTATATTTTGAC
* * ** ***
75704 CCCCAAACTTTCATAAAAATTGCCTTTTGAC
1 CCCTAAATTTTC-CCAAAATTATATTTTGAC
*
75735 CCCTAAATTCTCCCAAAATTATATTTT
1 CCCTAAATTTTCCCAAAATTATATTTT
75762 AACCTCAAAT
Statistics
Matches: 161, Mismatches: 41, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
29 48 0.30
30 69 0.43
31 44 0.27
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (30 bp):
CCCTAAATTTTCCCAAAATTATATTTTGAC
Found at i:75640 original size:60 final size:60
Alignment explanation
Indices: 75525--75765 Score: 218
Period size: 59 Copynumber: 4.0 Consensus size: 60
75515 CTAAAGAGGT
* * * * * **
75525 CCCTAAACTTTTCAAAAATCATATTTTGACCCTTAAACTTTT-TTAAAATTATATTTTAAC
1 CCCTAAAATTTCCAAAAATTACATTTTGACCCCTAAA-TTTTCCCAAAATTATATTTTAAC
* * **
75585 CCCTAAAATGTTCCAAAAATTATATTTTGACCCCT-CATTTTCCCAAAATTATATTTTGGC
1 CCCTAAAAT-TTCCAAAAATTACATTTTGACCCCTAAATTTTCCCAAAATTATATTTTAAC
* * * * * * *
75645 CCCTAAATTTTTCTAAAATCACATTTTGA-CCCTAAACTTCCCCAAAATTATATTTTGAC
1 CCCTAAAATTTCCAAAAATTACATTTTGACCCCTAAATTTTCCCAAAATTATATTTTAAC
* * * * * *
75704 CCCCAAACTTTCATAAAAATTGCCTTTTGACCCCTAAATTCTCCCAAAATTATATTTTAAC
1 CCCTAAAATTTC-CAAAAATTACATTTTGACCCCTAAATTTTCCCAAAATTATATTTTAAC
75765 C
1 C
75766 TCAAATTCTT
Statistics
Matches: 146, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
58 4 0.03
59 50 0.34
60 43 0.29
61 49 0.34
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (60 bp):
CCCTAAAATTTCCAAAAATTACATTTTGACCCCTAAATTTTCCCAAAATTATATTTTAAC
Found at i:75723 original size:90 final size:89
Alignment explanation
Indices: 75531--75743 Score: 216
Period size: 90 Copynumber: 2.4 Consensus size: 89
75521 AGGTCCCTAA
* * * * *
75531 ACTTTTCAAAAATCATATTTTGACCCTTAAACTTTTTTAAAATTATATTTTAACCCCTAAAATGT
1 ACTTTCCAAAAATTATATTTTGACCCCTAAA-TTTTTTAAAATCACATTTTAACCCCTAAAATGT
*
75596 TCCAAAAATTATATTTTGACCCCTC
65 CCCAAAAATTATATTTTGACCCCTC
* * * * *
75621 ATTTTCCCAAAATTATATTTTGGCCCCTAAATTTTTCTAAAATCACATTTTGA-CCCTAAACT-T
1 ACTTTCCAAAAATTATATTTTGACCCCTAAATTTTT-TAAAATCACATTTTAACCCCTAAAATGT
*
75684 CCCCAAAATTATATTTTGACCCC-C
65 CCCAAAAATTATATTTTGACCCCTC
* ***
75708 AAACTTTCATAAAAATTGCCTTTTGACCCCTAAATT
1 --ACTTTC-CAAAAATTATATTTTGACCCCTAAATT
75744 CTCCCAAAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
87 1 0.01
88 22 0.22
89 18 0.18
90 59 0.59
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (89 bp):
ACTTTCCAAAAATTATATTTTGACCCCTAAATTTTTTAAAATCACATTTTAACCCCTAAAATGTC
CCAAAAATTATATTTTGACCCCTC
Found at i:75806 original size:3 final size:3
Alignment explanation
Indices: 75798--75861 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
75788 TTTGACCCCT
75798 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
75846 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.