Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009502.1 Kokia drynarioides strain JFW-HI SEQ_124213, 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: 124508
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:3681 original size:19 final size:19
Alignment explanation
Indices: 3648--3692 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3638 ACCCACATAA
3648 TATTTTT-TTTATTTTT-T
1 TATTTTTCTTTATTTTTCT
3665 TATTTTTCTTGTATTTTTCT
1 TATTTTTCTT-TATTTTTCT
3685 T-TTTTTCT
1 TATTTTTCT
3693 CTACTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
19 14 0.56
20 2 0.08
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.82
Consensus pattern (19 bp):
TATTTTTCTTTATTTTTCT
Found at i:10034 original size:24 final size:24
Alignment explanation
Indices: 9998--10048 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
9988 GTATACTGGT
* *
9998 TAACTATTTTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
10022 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
10046 TAA
1 TAA
10049 AGTTATCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGC
Found at i:12969 original size:91 final size:91
Alignment explanation
Indices: 12872--13060 Score: 315
Period size: 91 Copynumber: 2.1 Consensus size: 91
12862 TTTATTTGTG
* *
12872 ATGTTAAGTTTCTGGTTTTTTTAATGGATTTATGGGTGTTCTAAGTTTGAATTTTTTTTTCTAAT
1 ATGTTAAGTTTCTGGTTTTTTTAATGGATTGATGGGTGTTCTAAGTCTGAATTTTTTTTTCTAAT
*
12937 GGGTGTTCTAAGTTTGGATGTTTGAT
66 GAGTGTTCTAAGTTTGGATGTTTGAT
* * *
12963 ATGTTAAGTTTTTGGTTTTTTTAATGGATTGATGGGTGTTTTAAGTCTGGATTTTTTTTTCTAAT
1 ATGTTAAGTTTCTGGTTTTTTTAATGGATTGATGGGTGTTCTAAGTCTGAATTTTTTTTTCTAAT
*
13028 GAGTGTTTTAAGTTTGGATGTTTGAT
66 GAGTGTTCTAAGTTTGGATGTTTGAT
13054 ATGTTAA
1 ATGTTAA
13061 TTTTTAGGGT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (91 bp):
ATGTTAAGTTTCTGGTTTTTTTAATGGATTGATGGGTGTTCTAAGTCTGAATTTTTTTTTCTAAT
GAGTGTTCTAAGTTTGGATGTTTGAT
Found at i:13183 original size:117 final size:117
Alignment explanation
Indices: 12963--13275 Score: 554
Period size: 117 Copynumber: 2.7 Consensus size: 117
12953 GATGTTTGAT
* *
12963 ATGTTAAGTTTTTGGTTTTTTTAATGGATTGATGGGTGTTTTAAGTCTGGATTTTTTTTTCTAAT
1 ATGTTAAGCTTTTGGTTTTTTTAATGGATTGATGGGTGTTCTAAGTCTGGA-TTTTTTTTCTAAT
* *
13028 GAGTGTTTTAAGTTTGGATGTTTGATATGTTAATTTTTAGGGTTTTATTTGTG
65 GGGTGTTCTAAGTTTGGATGTTTGATATGTTAATTTTTAGGGTTTTATTTGTG
* *
13081 ATGTTAAGCTTTTGGTTTTTTTAATGGATTGATGGGTGTTCTAAGTCCGGATTTTTTTCCTAATG
1 ATGTTAAGCTTTTGGTTTTTTTAATGGATTGATGGGTGTTCTAAGTCTGGATTTTTTTTCTAATG
13146 GGTGTTCTAAGTTTGGATGTTTGATATGTTAATTTTTAGGGTTTTATTTGTG
66 GGTGTTCTAAGTTTGGATGTTTGATATGTTAATTTTTAGGGTTTTATTTGTG
*
13198 ATGTTAAGCTTTTGGTTTTTTTAATGGATTGATGGGTGTTCTAAGTCTGAATTTTTTTTCTAATG
1 ATGTTAAGCTTTTGGTTTTTTTAATGGATTGATGGGTGTTCTAAGTCTGGATTTTTTTTCTAATG
13263 GGTGTTCTAAGTT
66 GGTGTTCTAAGTT
13276 CGGGTTTCAA
Statistics
Matches: 186, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
117 138 0.74
118 48 0.26
ACGTcount: A:0.19, C:0.04, G:0.24, T:0.53
Consensus pattern (117 bp):
ATGTTAAGCTTTTGGTTTTTTTAATGGATTGATGGGTGTTCTAAGTCTGGATTTTTTTTCTAATG
GGTGTTCTAAGTTTGGATGTTTGATATGTTAATTTTTAGGGTTTTATTTGTG
Found at i:13451 original size:24 final size:23
Alignment explanation
Indices: 13408--13456 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
13398 CAAAGGAAAA
13408 AAAGAAAGGAAAAAATTTGCAGT
1 AAAGAAAGGAAAAAATTTGCAGT
13431 AAAGAAATGGAAAAGAA-TTGCAGT
1 AAAGAAA-GGAAAA-AATTTGCAGT
13455 AA
1 AA
13457 CCAAAAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.29
24 15 0.62
25 2 0.08
ACGTcount: A:0.57, C:0.04, G:0.22, T:0.16
Consensus pattern (23 bp):
AAAGAAAGGAAAAAATTTGCAGT
Found at i:13469 original size:25 final size:25
Alignment explanation
Indices: 13412--13472 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
13402 GGAAAAAAAG
*
13412 AAAGGAAAA-AATTTGCAGTAAAGA
1 AAAGGAAAAGAATTTGCAGTAAACA
* *
13436 AATGGAAAAGAA-TTGCAGTAACCA
1 AAAGGAAAAGAATTTGCAGTAAACA
13460 AAAGGTAAAAGAA
1 AAAGG-AAAAGAA
13473 AAGGATGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.15
Consensus pattern (25 bp):
AAAGGAAAAGAATTTGCAGTAAACA
Found at i:16820 original size:31 final size:31
Alignment explanation
Indices: 16785--16854 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
16775 CCAGAAGAAT
16785 GAACTGGAAAGGTTAACCAAAGAAATGCTTC
1 GAACTGGAAAGGTTAACCAAAGAAATGCTTC
16816 GAACTGGAAAGGTTAACCAAAGAAATGCTTC
1 GAACTGGAAAGGTTAACCAAAGAAATGCTTC
*
16847 AAACTGGA
1 GAACTGGA
16855 GTAATAAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.19
Consensus pattern (31 bp):
GAACTGGAAAGGTTAACCAAAGAAATGCTTC
Found at i:22619 original size:50 final size:50
Alignment explanation
Indices: 22413--22612 Score: 237
Period size: 50 Copynumber: 4.1 Consensus size: 50
22403 TTAAATTGAA
* * * * * * *
22413 TAAACGCATATTTAAGCTGACGAGCATAAACGTGTGCAAGTTAGCTAGCA
1 TAAATGCATAATTAAGCTAACGAGCATAAACGTGTGCAAGCTGGCGAGCG
* * *
22463 TAAATGCATAATTAAGCTAACGATCGTAAACGTGTGCAACCTGGCGAGCG
1 TAAATGCATAATTAAGCTAACGAGCATAAACGTGTGCAAGCTGGCGAGCG
* *
22513 TAAATGCATAATTAAGCTAACGAGCGT-AA---GTGAAAGCTGGCGAGCG
1 TAAATGCATAATTAAGCTAACGAGCATAAACGTGTGCAAGCTGGCGAGCG
* * *
22559 TAAACGCATAATTGAGCTGACGAGCATAAACGTGTGCAAGCTGGCGAGCG
1 TAAATGCATAATTAAGCTAACGAGCATAAACGTGTGCAAGCTGGCGAGCG
22609 TAAA
1 TAAA
22613 GACATAAATA
Statistics
Matches: 128, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
46 38 0.30
47 2 0.02
49 2 0.02
50 86 0.67
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (50 bp):
TAAATGCATAATTAAGCTAACGAGCATAAACGTGTGCAAGCTGGCGAGCG
Found at i:29546 original size:74 final size:74
Alignment explanation
Indices: 29424--29599 Score: 210
Period size: 74 Copynumber: 2.4 Consensus size: 74
29414 TTGGCGAGCG
* * * ** * *
29424 TAAACATGTGCAAGTTGGCGAGCGTAAACATGTGCAAGTTGGCGAGCGTAAATGCATAGTTAATC
1 TAAACATGTGCAAGCTGGCGAGCGTAAACATGTGCAAGCTGGCAAGCGTAAACACATAATTAAGC
*
29489 TGTCAAGCA
66 TGACAAGCA
*
29498 TAAACTTGTGCAAGCTGAG-GAGCGTAAACATGTGCAAGCTGGCAAGCGTAAACACATAATTAAG
1 TAAACATGTGCAAGCTG-GCGAGCGTAAACATGTGCAAGCTGGCAAGCGTAAACACATAATTAAG
* *
29562 CTGACGAGCG
65 CTGACAAGCA
* * *
29572 TAAACGTGTGCAAGCTAGCAAGCGTAAA
1 TAAACATGTGCAAGCTGGCGAGCGTAAA
29600 AGCATAATTG
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
73 1 0.01
74 84 0.98
75 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.21
Consensus pattern (74 bp):
TAAACATGTGCAAGCTGGCGAGCGTAAACATGTGCAAGCTGGCAAGCGTAAACACATAATTAAGC
TGACAAGCA
Found at i:29546 original size:98 final size:98
Alignment explanation
Indices: 29374--29551 Score: 268
Period size: 98 Copynumber: 1.8 Consensus size: 98
29364 TTAAATTGAA
* * * *
29374 TAAATGCATATTTAAGCTGACGAGCATAAACGTGTGCAAGTTGGCGAGCGTAAACATGTGCAAGT
1 TAAATGCATAGTTAAGCTGACAAGCATAAACGTGTGCAAGCTGGCGAGCGTAAACATGTGCAAGC
*
29439 TGGCGAGCGTAAACATGTGCAAGTTGGCGAGCG
66 TGGCAAGCGTAAACATGTGCAAGTTGGCGAGCG
* * *
29472 TAAATGCATAGTTAATCTGTCAAGCATAAACTTGTGCAAGCTGAG-GAGCGTAAACATGTGCAAG
1 TAAATGCATAGTTAAGCTGACAAGCATAAACGTGTGCAAGCTG-GCGAGCGTAAACATGTGCAAG
29536 CTGGCAAGCGTAAACA
65 CTGGCAAGCGTAAACA
29552 CATAATTAAG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 70 0.99
99 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (98 bp):
TAAATGCATAGTTAAGCTGACAAGCATAAACGTGTGCAAGCTGGCGAGCGTAAACATGTGCAAGC
TGGCAAGCGTAAACATGTGCAAGTTGGCGAGCG
Found at i:29563 original size:50 final size:50
Alignment explanation
Indices: 29509--29656 Score: 219
Period size: 50 Copynumber: 3.0 Consensus size: 50
29499 AAACTTGTGC
* *
29509 AAGCTGAGGAGCGTAAACATGTGCAAGCTGGCAAGCGTAAACA-CATAATT
1 AAGCTGACGAGCGTAAACATGTGCAAGCTAGCAAGCGTAAA-AGCATAATT
*
29559 AAGCTGACGAGCGTAAACGTGTGCAAGCTAGCAAGCGTAAAAGCATAATT
1 AAGCTGACGAGCGTAAACATGTGCAAGCTAGCAAGCGTAAAAGCATAATT
* * *
29609 GAGCTGACGAGCGTAAACATGTGCAAGCTAGCGAG-GTAAAGGCATAAT
1 AAGCTGACGAGCGTAAACATGTGCAAGCTAGCAAGCGTAAAAGCATAAT
29657 ATGATGAAGA
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 13 0.14
50 77 0.86
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.18
Consensus pattern (50 bp):
AAGCTGACGAGCGTAAACATGTGCAAGCTAGCAAGCGTAAAAGCATAATT
Found at i:29595 original size:24 final size:24
Alignment explanation
Indices: 29387--29648 Score: 185
Period size: 24 Copynumber: 10.7 Consensus size: 24
29377 ATGCATATTT
* * *
29387 AAGCTGACGAGCATAAACGTGTGC
1 AAGCTGGCGAGCGTAAACATGTGC
*
29411 AAGTTGGCGAGCGTAAACATGTGC
1 AAGCTGGCGAGCGTAAACATGTGC
*
29435 AAGTTGGCGAGCGTAAACATGTGC
1 AAGCTGGCGAGCGTAAACATGTGC
* *
29459 AAGTTGGCGAGCGTAAATGCATAGT-T
1 AAGCTGGCGAGCGTAAA--CAT-GTGC
* * * * *
29485 AATCTGTCAAGCATAAACTTGTGC
1 AAGCTGGCGAGCGTAAACATGTGC
29509 AAGCTGAG-GAGCGTAAACATGTGC
1 AAGCTG-GCGAGCGTAAACATGTGC
* * *
29533 AAGCTGGCAAGCGTAAACACATAAT-T
1 AAGCTGGCGAGCGT-AA-ACAT-GTGC
* *
29559 AAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGGCGAGCGTAAACATGTGC
* * *
29583 AAGCTAGCAAGCGTAAAAGCATAATTG-
1 AAGCTGGCGAGCGT-AAA-CAT--GTGC
*
29610 -AGCTGACGAGCGTAAACATGTGC
1 AAGCTGGCGAGCGTAAACATGTGC
*
29633 AAGCTAGCGAG-GTAAA
1 AAGCTGGCGAGCGTAAA
29649 GGCATAATAT
Statistics
Matches: 186, Mismatches: 36, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
22 2 0.01
23 9 0.05
24 117 0.63
25 10 0.05
26 43 0.23
27 3 0.02
28 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (24 bp):
AAGCTGGCGAGCGTAAACATGTGC
Found at i:36591 original size:50 final size:50
Alignment explanation
Indices: 36498--36783 Score: 338
Period size: 50 Copynumber: 5.7 Consensus size: 50
36488 TTAAATTGAA
* ** *
36498 TAAACGCATATTTAAGCTGACGAGCGTAAACGTGTTTATGCTGGCGAGCG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCG
* * * * ** *
36548 TAAATGCATAATTAAGTTGACGAGCATAAATGTGTGCAAGCTGGTAATCG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCG
* * * ** *
36598 TAAACGCATAATTAAGCTGACGAGTGTAAACGTGTGCAATCTAGTAAGCA
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCG
* *
36648 TAAACGCATAATTAAGCTAACGAGCGTAAACGTGTGCAAGTTGGCGAGCG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCG
**
36698 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTAACGAGCG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCG
* ** * *
36748 TAAATGTTTAATTAAGCTGACAAGCATAAACGTGTG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTG
36784 ACATAGCAGT
Statistics
Matches: 199, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 199 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (50 bp):
TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCG
Found at i:36744 original size:24 final size:24
Alignment explanation
Indices: 36661--36751 Score: 94
Period size: 24 Copynumber: 3.7 Consensus size: 24
36651 ACGCATAATT
36661 AAGCTAACGAGCGTAAACGTGTGC
1 AAGCTAACGAGCGTAAACGTGTGC
* ** * *
36685 AAGTTGGCGAGCGTAAACGCATAAT-T
1 AAGCTAACGAGCGTAAACG--T-GTGC
*
36711 AAGCTGACGAGCGTAAACGTGTGC
1 AAGCTAACGAGCGTAAACGTGTGC
36735 AAGCTAACGAGCGTAAA
1 AAGCTAACGAGCGTAAA
36752 TGTTTAATTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.02
24 33 0.62
26 18 0.34
27 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.18
Consensus pattern (24 bp):
AAGCTAACGAGCGTAAACGTGTGC
Found at i:36768 original size:150 final size:150
Alignment explanation
Indices: 36497--36783 Score: 385
Period size: 150 Copynumber: 1.9 Consensus size: 150
36487 ATTAAATTGA
* * ** * *
36497 ATAAACGCATATTTAAGCTGACGAGCGTAAACGTGTTTATGCTGGCGAGCGTAAATGCATAATTA
1 ATAAACGCATAATTAAGCTAACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTA
* * *** * * **
36562 AGTTGACGAGCATAAATGTGTGCAAGCTGGTAATCGTAAACGCATAATTAAGCTGACGAGTGTAA
66 AGCTGACGAGCATAAACGTGTGCAAGCTAACAAGCGTAAACGCATAATTAAGCTGACAAGCATAA
36627 ACGTGTGCAATCTAGTAAGC
131 ACGTGTGCAATCTAGTAAGC
*
36647 ATAAACGCATAATTAAGCTAACGAGCGTAAACGTGTGCAAGTTGGCGAGCGTAAACGCATAATTA
1 ATAAACGCATAATTAAGCTAACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTA
* * * **
36712 AGCTGACGAGCGTAAACGTGTGCAAGCTAACGAGCGTAAATGTTTAATTAAGCTGACAAGCATAA
66 AGCTGACGAGCATAAACGTGTGCAAGCTAACAAGCGTAAACGCATAATTAAGCTGACAAGCATAA
36777 ACGTGTG
131 ACGTGTG
36784 ACATAGCAGT
Statistics
Matches: 116, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
150 116 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (150 bp):
ATAAACGCATAATTAAGCTAACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAATTA
AGCTGACGAGCATAAACGTGTGCAAGCTAACAAGCGTAAACGCATAATTAAGCTGACAAGCATAA
ACGTGTGCAATCTAGTAAGC
Found at i:38404 original size:21 final size:21
Alignment explanation
Indices: 38375--38415 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38365 ACGTGGCAAA
38375 TTAACTGGCCACATCAGCTAG
1 TTAACTGGCCACATCAGCTAG
* *
38396 TTAATTGGCCACGTCAGCTA
1 TTAACTGGCCACATCAGCTA
38416 TTCCGTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (21 bp):
TTAACTGGCCACATCAGCTAG
Found at i:45997 original size:13 final size:14
Alignment explanation
Indices: 45963--46001 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
45953 TATCTCTTTT
*
45963 TCTTCCTTTTCATC
1 TCTTTCTTTTCATC
*
45977 TTTTTCTTTTC-TC
1 TCTTTCTTTTCATC
45990 TCTTTCTTTTCA
1 TCTTTCTTTTCA
46002 CTTTCTTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTCTTTTCATC
Found at i:46016 original size:31 final size:28
Alignment explanation
Indices: 45981--46037 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
45971 TTCATCTTTT
*
45981 TCTTTTCTCTCTTTCTTTTCACTTTCTTTGC
1 TCTTTTCTCTC-AT-TTTTC-CTTTCTTTGC
46012 TCTTTTCTCTCATTTTTCCTTTCTTT
1 TCTTTTCTCTCATTTTTCCTTTCTTT
46038 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 5 0.20
30 1 0.04
31 11 0.44
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.67
Consensus pattern (28 bp):
TCTTTTCTCTCATTTTTCCTTTCTTTGC
Found at i:46038 original size:21 final size:20
Alignment explanation
Indices: 46012--46060 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
46002 CTTTCTTTGC
*
46012 TCTTTTCTCTCATTTTTCCTT
1 TCTTTT-TCTCAATTTTCCTT
* *
46033 TCTTTTTTTCAATTTTCTTT
1 TCTTTTTCTCAATTTTCCTT
46053 TCTTTTTC
1 TCTTTTTC
46061 ATTCTCATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTTTTCTCAATTTTCCTT
Found at i:50002 original size:59 final size:59
Alignment explanation
Indices: 49844--50169 Score: 313
Period size: 59 Copynumber: 5.5 Consensus size: 59
49834 CAAAAAAAAT
* * ** *
49844 ATTTTTTATCAGATAAATAGGTGGTGTCTG-TCATGCAATAGGAAAGATCAAAAAATTTG
1 ATTTTTTATCAGATAAAAAGGTGGTGTC-GACCATGCAATAGCCAACATCAAAAAATTTG
* * *
49903 ATTTTTTTTTATAAGATAAAAAGGTGGTGTC-AGCCTTGCAATTGCCAACATCAAAAAATTTG
1 A---TTTTTTATCAGATAAAAAGGTGGTGTCGA-CCATGCAATAGCCAACATCAAAAAATTTG
* * * **
49965 ATTTTTTATCAGATAAATAGGGGGTGTCGACCATGCAATAGCCAACACCAAAAAAAAT-
1 ATTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATAGCCAACATCAAAAAATTTG
* * * * *
50023 ATTTTTTATC--TTACAAAAGGGGTGTGTCGACCATACAATGGCTAACAT-AAAAAATTTG
1 ATTTTTTATCAGATA-AAAAGGTG-GTGTCGACCATGCAATAGCCAACATCAAAAAATTTG
* * * * *
50081 ATTTTTTACCAGCTAAAAAAGGTGGTGTCGACCATGCAATAGTCAACACCAAAAAAATTG
1 ATTTTTTATCAGAT-AAAAAGGTGGTGTCGACCATGCAATAGCCAACATCAAAAAATTTG
*
50141 ATTTTTTATCAGATAAAAAAAGTGGTGTC
1 ATTTTTTATCAGAT-AAAAAGGTGGTGTC
50170 AATCAATGCA
Statistics
Matches: 218, Mismatches: 36, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
56 2 0.01
57 14 0.06
58 40 0.18
59 68 0.31
60 44 0.20
61 1 0.00
62 49 0.22
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (59 bp):
ATTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATAGCCAACATCAAAAAATTTG
Found at i:55299 original size:24 final size:24
Alignment explanation
Indices: 55214--55287 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
55204 AGAAATAATC
* *
55214 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTATTTATTTG
*
55238 TTTCAATTAAACT-TGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
*
55261 TATCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
55285 TTT
1 TTT
55288 GAGTCAAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 20 0.47
24 23 0.53
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:61768 original size:20 final size:21
Alignment explanation
Indices: 61727--61781 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
61717 AGTGGATTGG
*
61727 AATGGTTTATATTAAGTGTAAA
1 AATGATTTA-ATTAAGTGTAAA
*
61749 TA-GATTTAATTAAGAT-TAAA
1 AATGATTTAATTAAG-TGTAAA
61769 AATGA-TTAATTAA
1 AATGATTTAATTAA
61782 AGCTTAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 19 0.68
21 8 0.29
22 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (21 bp):
AATGATTTAATTAAGTGTAAA
Found at i:64413 original size:16 final size:16
Alignment explanation
Indices: 64392--64437 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
64382 GTTTGGTTTG
*
64392 CTGTAATGGAATAGAA
1 CTGTAATGTAATAGAA
*
64408 CTGTAATGTAATATAA
1 CTGTAATGTAATAGAA
64424 CTGTAATGTAATAG
1 CTGTAATGTAATAG
64438 GGCTATAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.33
Consensus pattern (16 bp):
CTGTAATGTAATAGAA
Found at i:64703 original size:60 final size:60
Alignment explanation
Indices: 64605--64780 Score: 195
Period size: 60 Copynumber: 3.0 Consensus size: 60
64595 GATTATTGTT
* *
64605 ATTAAATTTTAATA-AATTTATTATTAAATATAATTTAATAAAAAAATAATAAATAATTTA
1 ATTAAATTTTAATATAA-TTATTATTAAATACAATTTAATAAAAAAATAATATATAATTTA
* *
64665 ATTATATTTTAACATAATTATTATTAAATACAATTTAAT----AAATAATATATAATTTA
1 ATTAAATTTTAATATAATTATTATTAAATACAATTTAATAAAAAAATAATATATAATTTA
* *
64721 A-TAACATTTTTAATATAATTATTATTAAAATATGAA-TTAATAAAAATCATAATATATAAT
1 ATTAA-A-TTTTAATATAATTATTATT-AAATA-CAATTTAATAAAAA-AATAATATATAAT
64781 ATTAGAAAAA
Statistics
Matches: 98, Mismatches: 8, Indels: 17
0.80 0.07 0.14
Matches are distributed among these distances:
55 2 0.02
56 18 0.18
57 18 0.18
58 10 0.10
59 2 0.02
60 33 0.34
61 2 0.02
62 1 0.01
63 12 0.12
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (60 bp):
ATTAAATTTTAATATAATTATTATTAAATACAATTTAATAAAAAAATAATATATAATTTA
Found at i:64752 original size:29 final size:27
Alignment explanation
Indices: 64670--64749 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 27
64660 ATTTAATTAT
*
64670 ATTTTAACATAATTATTATTAAAT-AC
1 ATTTTAATATAATTATTATTAAATAAC
* * *
64696 AATTTAATAAATAATATATAATTTAATAAC
1 ATTTTAAT--ATAAT-TATTATTAAATAAC
64726 ATTTTTAATATAATTATTATTAAA
1 A-TTTTAATATAATTATTATTAAA
64750 ATATGAATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
26 6 0.14
28 13 0.31
29 14 0.33
30 3 0.07
31 6 0.14
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTTTAATATAATTATTATTAAATAAC
Found at i:72511 original size:20 final size:21
Alignment explanation
Indices: 72475--72524 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
72465 ATTGACATGG
*
72475 TTTATATTAAGTGTAAATAT-A
1 TTTA-ATTAAGTGTAAAAATGA
72496 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
72517 -TTAATTAA
1 TTTAATTAA
72525 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:79022 original size:12 final size:12
Alignment explanation
Indices: 79007--79032 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
78997 ATTCTCCGAC
79007 TTTTTCTAGAGG
1 TTTTTCTAGAGG
79019 TTTTTCTAGAGG
1 TTTTTCTAGAGG
79031 TT
1 TT
79033 GTTTACCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (12 bp):
TTTTTCTAGAGG
Found at i:84121 original size:30 final size:31
Alignment explanation
Indices: 84068--84141 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 31
84058 AAAGTTGAAA
*
84068 TACCAATTTAAAAAAAAGATGTCAAATTTAAG
1 TACCAAATT-AAAAAAAGATGTCAAATTTAAG
84100 TACCAAATTAAAAAAAG-TGTCAAATTTAAG
1 TACCAAATTAAAAAAAGATGTCAAATTTAAG
*
84130 TATCAAATTAAA
1 TACCAAATTAAA
84142 TCATAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 24 0.60
31 8 0.20
32 8 0.20
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.28
Consensus pattern (31 bp):
TACCAAATTAAAAAAAGATGTCAAATTTAAG
Found at i:91423 original size:30 final size:29
Alignment explanation
Indices: 91369--91447 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
91359 TATGGTTTAA
* * *
91369 TATGTAATTGTATACA-TGAATTTTGAATT
1 TATGCAATTTTATACATTAAATTTTG-ATT
91398 TATGCAATTTTATACATTAAATTTTGATT
1 TATGCAATTTTATACATTAAATTTTGATT
* *
91427 TGATTCAATTATTATAAATTA
1 T-ATGCAATT-TTATACATTA
91448 TTAACACGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 18 0.43
30 15 0.36
31 9 0.21
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (29 bp):
TATGCAATTTTATACATTAAATTTTGATT
Found at i:91622 original size:33 final size:32
Alignment explanation
Indices: 91551--91622 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
91541 TATTTCTTTA
*
91551 AATGTATATAATTAAATCAAAATTACAGTTTC
1 AATGTATATAATTAAACCAAAATTACAGTTTC
* * * *
91583 AA-GTATATATTTGAACCATAATTAGAGTTTC
1 AATGTATATAATTAAACCAAAATTACAGTTTC
91614 ACATGTATA
1 A-ATGTATA
91623 ATTGCATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 25 0.76
32 3 0.09
33 5 0.15
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (32 bp):
AATGTATATAATTAAACCAAAATTACAGTTTC
Found at i:92277 original size:24 final size:24
Alignment explanation
Indices: 92230--92282 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
92220 TTTTTCAATG
* * *
92230 GTTTATTTGCAAATTAGGGCTTAA
1 GTTTATTTACAAATTAAGACTTAA
*
92254 GTTTATTTACAAATTAAGATTTAA
1 GTTTATTTACAAATTAAGACTTAA
*
92278 ATTTA
1 GTTTA
92283 AGAGTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (24 bp):
GTTTATTTACAAATTAAGACTTAA
Found at i:96605 original size:21 final size:21
Alignment explanation
Indices: 96555--96607 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
96545 AAAAATTATA
96555 TTGTTGTTTTGGTACTATTTT
1 TTGTTGTTTTGGTACTATTTT
*
96576 TT-TACTGTTTTGGTTGCT-TTTT
1 TTGT--TGTTTTGG-TACTATTTT
96598 TTGTTGTTTT
1 TTGTTGTTTT
96608 TTACTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
20 1 0.04
21 8 0.30
22 14 0.52
23 4 0.15
ACGTcount: A:0.06, C:0.06, G:0.19, T:0.70
Consensus pattern (21 bp):
TTGTTGTTTTGGTACTATTTT
Found at i:96624 original size:30 final size:32
Alignment explanation
Indices: 96573--96638 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
96563 TTGGTACTAT
*
96573 TTTTTTACTGTTTTGGTTGC-TTTTTTTGTTG
1 TTTTTTACTGTTTTGGTTGCTTTTTTTTATTG
96604 TTTTTTACTGTTTTGG-TGCTTTTTTTTATTG
1 TTTTTTACTGTTTTGGTTGCTTTTTTTTATTG
96635 TTTT
1 TTTT
96639 GGTTGCTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 3 0.09
31 30 0.91
ACGTcount: A:0.05, C:0.06, G:0.17, T:0.73
Consensus pattern (32 bp):
TTTTTTACTGTTTTGGTTGCTTTTTTTTATTG
Found at i:96628 original size:21 final size:22
Alignment explanation
Indices: 96602--96650 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
96592 CTTTTTTTGT
96602 TGTTTTTTACTGTTTTGG-TGC
1 TGTTTTTTACTGTTTTGGTTGC
* *
96623 TTTTTTTTATTGTTTTGGTTGC
1 TGTTTTTTACTGTTTTGGTTGC
96645 TGTTTT
1 TGTTTT
96651 CATGTTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.04, C:0.06, G:0.20, T:0.69
Consensus pattern (22 bp):
TGTTTTTTACTGTTTTGGTTGC
Found at i:96639 original size:52 final size:55
Alignment explanation
Indices: 96559--96661 Score: 158
Period size: 52 Copynumber: 1.9 Consensus size: 55
96549 ATTATATTGT
*
96559 TGTTTTGGTACTATTTTTTTACTGTTTTGGTTGCT-TTTT-TTGTTGTTTTTTAC
1 TGTTTTGGTACTATTTTTTTACTGTTTTGGTTGCTGTTTTCATGTTGTTTTTTAC
* *
96612 TGTTTTGGTGCT-TTTTTTTATTGTTTTGGTTGCTGTTTTCATGTTGTTTT
1 TGTTTTGGTACTATTTTTTTACTGTTTTGGTTGCTGTTTTCATGTTGTTTT
96662 ACTATTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 21 0.47
53 15 0.33
54 9 0.20
ACGTcount: A:0.06, C:0.07, G:0.19, T:0.68
Consensus pattern (55 bp):
TGTTTTGGTACTATTTTTTTACTGTTTTGGTTGCTGTTTTCATGTTGTTTTTTAC
Found at i:96690 original size:32 final size:30
Alignment explanation
Indices: 96626--96718 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 30
96616 TTGGTGCTTT
* * *
96626 TTTTTATTGTTTTGGTTGCTGTTTTCATGTTG
1 TTTTTATTTTTTTTGTTGCTATTTT--TGTTG
96658 TTTTACTATTTTTTTTGTTGCTATTTTTGTTG
1 TTTT--TATTTTTTTTGTTGCTATTTTTGTTG
* *
96690 TTTTTAATGTTGTTTTGTTGTTATTTTTG
1 TTTTT-AT-TTTTTTTGTTGCTATTTTTG
96719 CTGCTATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 2 0.04
32 31 0.60
34 18 0.35
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (30 bp):
TTTTTATTTTTTTTGTTGCTATTTTTGTTG
Found at i:96717 original size:12 final size:12
Alignment explanation
Indices: 96669--96747 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
96659 TTTACTATTT
*
96669 TTTTTGTTGCTA
1 TTTTTGTTGTTA
96681 TTTTTGTTGTT-
1 TTTTTGTTGTTA
*
96692 TTTAATGTTG---
1 TTT-TTGTTGTTA
96702 -TTTTGTTGTTA
1 TTTTTGTTGTTA
* *
96713 TTTTTGCTGCTA
1 TTTTTGTTGTTA
*
96725 -TTTTGATTATTA
1 TTTTTG-TTGTTA
96737 TTTTTGTTGTT
1 TTTTTGTTGTT
96748 TGGATATTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
8 5 0.10
9 2 0.04
11 8 0.16
12 31 0.61
13 5 0.10
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:98328 original size:17 final size:17
Alignment explanation
Indices: 98303--98368 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
98293 AACCCAATCG
*
98303 TTAATTTTAAATTTATT
1 TTAAATTTAAATTTATT
*
98320 TTAAATTTAAATTTATC
1 TTAAATTTAAATTTATT
98337 TTAAATTTAAAATTT-TT
1 TTAAATTT-AAATTTATT
* *
98354 CTAAATTTAACTTTA
1 TTAAATTTAAATTTA
98369 AATTTAGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 5 0.12
17 31 0.74
18 6 0.14
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATTTAAATTTATT
Found at i:99040 original size:23 final size:22
Alignment explanation
Indices: 99000--99046 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
98990 GCATTTATTG
*
99000 TATATTAAGTATAATAAATAAA
1 TATATTAAATATAATAAATAAA
99022 TATATTAAATAATAATAAATAAA
1 TATATTAAAT-ATAATAAATAAA
99045 TA
1 TA
99047 AAAGGAGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
TATATTAAATATAATAAATAAA
Found at i:100173 original size:30 final size:29
Alignment explanation
Indices: 100093--100339 Score: 237
Period size: 30 Copynumber: 8.4 Consensus size: 29
100083 GTCCATGAAT
* * * * *
100093 TTCTCTAAAATGATATTTTGACCCGAAAC
1 TTCTCCAAAATTACATTTTAACCCTAAAC
*
100122 TTTTCCAAAATTACA-TTTAACCGCTAAAC
1 TTCTCCAAAATTACATTTTAACC-CTAAAC
100151 TTCTCCAAAATTACATTTTAACCCTTAAAC
1 TTCTCCAAAATTACATTTTAACCC-TAAAC
* * *
100181 TTTTCTAAAATTACATTTTACCCCTAAAC
1 TTCTCCAAAATTACATTTTAACCCTAAAC
* *
100210 TTCTCTAAAAATTACATTTTAAACCTTAAAC
1 TTCTC-CAAAATTACATTTT-AACCCTAAAC
* *
100241 TT-TTCAAAATTACATTTTAAAGCCTAAAC
1 TTCTCCAAAATTACATTTT-AACCCTAAAC
* * *
100270 TTCTCTAAAATTACATTTTGACCCCTAAAT
1 TTCTCCAAAATTACATTTT-AACCCTAAAC
* ** * *
100300 TTCTCTAAAATCCCATTTTGACCCCAAAC
1 TTCTCCAAAATTACATTTTAACCCTAAAC
100329 TTCTCCAAAAT
1 TTCTCCAAAAT
100340 CATGATTTTG
Statistics
Matches: 181, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
28 6 0.03
29 80 0.44
30 85 0.47
31 10 0.06
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
TTCTCCAAAATTACATTTTAACCCTAAAC
Found at i:100192 original size:59 final size:60
Alignment explanation
Indices: 100118--100339 Score: 267
Period size: 59 Copynumber: 3.8 Consensus size: 60
100108 TTTTGACCCG
*
100118 AAACTTTTCCAAAATTACA-TTTAACCGCTAAACTTCTCCAAAATTACATTTTAACCCTT
1 AAACTTTTCTAAAATTACATTTTAACCGCTAAACTTCTCCAAAATTACATTTTAACCCTT
* * *
100177 AAACTTTTCTAAAATTACATTTT-ACCCCTAAACTTCTCTAAAAATTACATTTTAAACCTT
1 AAACTTTTCTAAAATTACATTTTAACCGCTAAACTTCTC-CAAAATTACATTTTAACCCTT
* * * *
100237 AAACTTTTC-AAAATTACATTTTAA-AGCCTAAACTTCTCTAAAATTACATTTTGACCCCT
1 AAACTTTTCTAAAATTACATTTTAACCG-CTAAACTTCTCCAAAATTACATTTTAACCCTT
** * *
100296 AAA-TTTCTCTAAAATCCCATTTTGACC-CCAAACTTCTCCAAAAT
1 AAACTTT-TCTAAAATTACATTTTAACCGCTAAACTTCTCCAAAAT
100340 CATGATTTTG
Statistics
Matches: 140, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
58 3 0.02
59 82 0.59
60 55 0.39
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.36
Consensus pattern (60 bp):
AAACTTTTCTAAAATTACATTTTAACCGCTAAACTTCTCCAAAATTACATTTTAACCCTT
Found at i:100317 original size:89 final size:90
Alignment explanation
Indices: 100146--100339 Score: 261
Period size: 89 Copynumber: 2.2 Consensus size: 90
100136 ATTTAACCGC
*
100146 TAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTACCCCTAAACT
1 TAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTCTCTAAAATTACATTTTACCCCTAAACT
*
100211 TCTCTAAAAATTACATTTTAAACCT
66 TCTCTAAAAATCACATTTTAAACCT
* *
100236 TAAACTT-TTCAAAATTACATTTTAAAGCC-TAAACTTCTCTAAAATTACATTTTGACCCCTAAA
1 TAAACTTCTCCAAAATTACATTTT-AACCCTTAAACTTCTCTAAAATTACATTTT-ACCCCTAAA
* * * *
100299 TTTCTCT-AAAATCCCATTTT-GACCC
64 CTTCTCTAAAAATCACATTTTAAACCT
*
100324 CAAACTTCTCCAAAAT
1 TAAACTTCTCCAAAAT
100340 CATGATTTTG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
88 9 0.10
89 56 0.62
90 26 0.29
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (90 bp):
TAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTCTCTAAAATTACATTTTACCCCTAAACT
TCTCTAAAAATCACATTTTAAACCT
Found at i:100349 original size:30 final size:30
Alignment explanation
Indices: 100093--100341 Score: 211
Period size: 29 Copynumber: 8.4 Consensus size: 30
100083 GTCCATGAAT
* * *
100093 TTCTCTAAAATGATATTTTGA-CCCGAAAC
1 TTCTCTAAAATCACATTTTGACCCCTAAAC
* * * * *
100122 TTTTCCAAAATTACA-TTTAACCGCTAAAC
1 TTCTCTAAAATCACATTTTGACCCCTAAAC
* * * *
100151 TTCTCCAAAATTACATTTTAACCCTTAAAC
1 TTCTCTAAAATCACATTTTGACCCCTAAAC
* *
100181 TTTTCTAAAATTACATTTT-ACCCCTAAAC
1 TTCTCTAAAATCACATTTTGACCCCTAAAC
* * * *
100210 TTCTCTAAAAATTACATTTTAAACCTTAAAC
1 TTCTCT-AAAATCACATTTTGACCCCTAAAC
* * * **
100241 TTTTC-AAAATTACATTTTAAAGCCTAAAC
1 TTCTCTAAAATCACATTTTGACCCCTAAAC
* *
100270 TTCTCTAAAATTACATTTTGACCCCTAAAT
1 TTCTCTAAAATCACATTTTGACCCCTAAAC
*
100300 TTCTCTAAAATCCCATTTTGACCCC-AAAC
1 TTCTCTAAAATCACATTTTGACCCCTAAAC
*
100329 TTCTCCAAAATCA
1 TTCTCTAAAATCA
100342 TGATTTTGCC
Statistics
Matches: 186, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
28 4 0.02
29 85 0.46
30 85 0.46
31 12 0.06
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (30 bp):
TTCTCTAAAATCACATTTTGACCCCTAAAC
Found at i:100367 original size:29 final size:29
Alignment explanation
Indices: 100345--100455 Score: 145
Period size: 29 Copynumber: 3.8 Consensus size: 29
100335 AAAATCATGA
**
100345 TTTTGCCCTTGAAC-ATCCAAAAATTACCA
1 TTTTGCCCTT-AACTATCCAAAAATTACTG
*
100374 TTTTTCCCTTGAAC-ATCCAAAAATTACTG
1 TTTTGCCCTT-AACTATCCAAAAATTACTG
*
100403 TTTTGCCCTTAACTTTCCAAAAATTACTG
1 TTTTGCCCTTAACTATCCAAAAATTACTG
*
100432 TTTTGCCCTTAACTTTCCAAAAAT
1 TTTTGCCCTTAACTATCCAAAAAT
100456 CACATTTTCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 3 0.04
29 73 0.96
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (29 bp):
TTTTGCCCTTAACTATCCAAAAATTACTG
Found at i:105223 original size:17 final size:17
Alignment explanation
Indices: 105191--105237 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
105181 ATATATATGG
* *
105191 AAATGCAATGATAATAT
1 AAATGCAATGACAATAA
* *
105208 AGATGCAGTGACAATAA
1 AAATGCAATGACAATAA
105225 AAATGCAATGACA
1 AAATGCAATGACA
105238 TTCATACTGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:110356 original size:15 final size:16
Alignment explanation
Indices: 110338--110367 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
110328 AAGAATAACT
110338 AAATCAAGT-TGAAAG
1 AAATCAAGTATGAAAG
110353 AAATCAAGTATGAAA
1 AAATCAAGTATGAAA
110368 TCTTGTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (16 bp):
AAATCAAGTATGAAAG
Found at i:111870 original size:2 final size:2
Alignment explanation
Indices: 111863--111887 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111853 ATGTTTTGTG
111863 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
111888 TACTTGATTT
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:112628 original size:18 final size:18
Alignment explanation
Indices: 112551--112628 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 18
112541 ATATATACAC
*
112551 TATACATATATACTATT-T
1 TATATATATATA-TATTGT
* * *
112569 TATATTTACATATATTAT
1 TATATATATATATATTGT
* * *
112587 TTTTTAAATATATATTGAT
1 TATATATATATATATTG-T
112606 CTATATATATATATATTGT
1 -TATATATATATATATTGT
112625 TATA
1 TATA
112629 CAATTCTTTT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
17 4 0.09
18 25 0.56
19 2 0.04
20 14 0.31
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
TATATATATATATATTGT
Found at i:117009 original size:18 final size:18
Alignment explanation
Indices: 116994--117041 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
116984 TAATGCTCTT
116994 ACGAGCTAGTATGCTCAA
1 ACGAGCTAGTATGCTCAA
* * *
117012 ATGAGCCAATATGCTCAA
1 ACGAGCTAGTATGCTCAA
117030 ACGAGCTAGTAT
1 ACGAGCTAGTAT
117042 ACTCTTCCTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (18 bp):
ACGAGCTAGTATGCTCAA
Found at i:122162 original size:68 final size:68
Alignment explanation
Indices: 122063--122234 Score: 227
Period size: 68 Copynumber: 2.5 Consensus size: 68
122053 TGCAACATCT
* * * *
122063 ATTGAAACATGTATTTTAATCTAACCTAATGACATGGAATTGTCTAACTTTTGACAACAACTAAC
1 ATTGAAACATG-ATTTTAATCCAACCAAATGACATGGAATTGTCTAACTTTGGACAACAAATAAC
122128 TTCA
65 TTCA
* * * **
122132 ATTGAAACATGATTTTAATCCAGCCAAATGACATTGAATTGTCTAGCTTTGGGTAACAAATAACT
1 ATTGAAACATGATTTTAATCCAACCAAATGACATGGAATTGTCTAACTTTGGACAACAAATAACT
*
122197 TCC
66 TCA
* *
122200 CTTGAAACATGATTTTAATCCAACCGAATGACATG
1 ATTGAAACATGATTTTAATCCAACCAAATGACATG
122235 CATTTAACTT
Statistics
Matches: 89, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
68 78 0.88
69 11 0.12
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (68 bp):
ATTGAAACATGATTTTAATCCAACCAAATGACATGGAATTGTCTAACTTTGGACAACAAATAACT
TCA
Found at i:123582 original size:68 final size:68
Alignment explanation
Indices: 123455--123626 Score: 211
Period size: 68 Copynumber: 2.5 Consensus size: 68
123445 TGCAACATCT
* * *
123455 ATTGGAACATGTATTTTAGTCTAACCTAATGACATGGAACTGTCCAACTTCTGACAACAACTAAC
1 ATTGAAACATG-ATTTTAATCTAACCAAATGACATGGAACTGTCCAACTTCTGACAACAACTAAC
123520 TTCA
65 TTCA
* * * * **
123524 ATTGAAACATGATTTTAATCTAGCCAAATGACATGGAATTGTCTAGCTT-TGGGTAACAACTAAC
1 ATTGAAACATGATTTTAATCTAACCAAATGACATGGAACTGTCCAACTTCT-GACAACAACTAAC
*
123588 TTCC
65 TTCA
* *
123592 ATTGAAACAAGATTTTAATCTAACCGAATGACATG
1 ATTGAAACATGATTTTAATCTAACCAAATGACATG
123627 CATTTAACTT
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
67 1 0.01
68 78 0.88
69 10 0.11
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (68 bp):
ATTGAAACATGATTTTAATCTAACCAAATGACATGGAACTGTCCAACTTCTGACAACAACTAACT
TCA
Done.