Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013270.1 Kokia drynarioides strain JFW-HI SEQ_128291, 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: 40978
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:505 original size:29 final size:29
Alignment explanation
Indices: 471--534 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
461 AAATGAGACT
* *
471 TTTTGGA-TACTCGGGGGGCAAAATGGTAA
1 TTTTGGACT-CTCAGGGAGCAAAATGGTAA
500 TTTTGGACTCTCAGGGAGCAAAATGGTAA
1 TTTTGGACTCTCAGGGAGCAAAATGGTAA
529 TTTTGG
1 TTTTGG
535 GAAAATTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.31
Consensus pattern (29 bp):
TTTTGGACTCTCAGGGAGCAAAATGGTAA
Found at i:597 original size:58 final size:57
Alignment explanation
Indices: 519--770 Score: 215
Period size: 58 Copynumber: 4.3 Consensus size: 57
509 CTCAGGGAGC
* * * *
519 AAAATGGTAATTTTGGGAAAATTTGGAGTTAAAAATGAAATTTTAGATATTCCGAGGT
1 AAAATGGTAATTTT-TGAAAATTTGGAGTCAAAAATGAAATTTTGGATATTCCGGGGT
* ** * **
577 AAAACGGTAATTTTTAGAAAAATCAGGA-TCAAAAATGGAATTTTTGGATATTTGGGGGT
1 AAAATGGTAATTTTT-G-AAAATTTGGAGTCAAAAAT-GAAATTTTGGATATTCCGGGGT
* * * * * *
636 AAAATGGTAACTTTTGAAAGTTTGGGGTAAAAAATGAAGCTTTTGGACA-TCCGGGGGT
1 AAAATGGTAATTTTTGAAAATTTGGAGTCAAAAATGAA-ATTTTGGATATTCC-GGGGT
* * * *
694 AAAATGGTAATTTTTTAAAGTTTCGAGGTCAAAAATGAAATTTTGGA-AGTGT-AGGGGT
1 AAAATGGTAATTTTTGAAAATTTGGA-GTCAAAAATGAAATTTTGGATA-T-TCCGGGGT
752 AAAATGGTAATTTTTGAAA
1 AAAATGGTAATTTTTGAAA
771 GTTTTAGGGG
Statistics
Matches: 155, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
57 11 0.07
58 94 0.61
59 49 0.32
60 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTTGAAAATTTGGAGTCAAAAATGAAATTTTGGATATTCCGGGGT
Found at i:639 original size:29 final size:29
Alignment explanation
Indices: 607--983 Score: 293
Period size: 29 Copynumber: 12.8 Consensus size: 29
597 AATCAGGATC
607 AAAAATGGAATTTTTGGATA-TTTGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTGGGGGT
* *
636 -AAAATGGTAACTTTTGAAAGTTT-GGGGT
1 AAAAATGG-AATTTTTGGAAGTTTGGGGGT
* **
664 AAAAAAT-GAAGCTTTTGGACA-TCCGGGGGT
1 -AAAAATGGAA-TTTTTGGA-AGTTTGGGGGT
** * *
694 -AAAATGGTAATTTTTTAAAGTTTCGAGGT
1 AAAAATGG-AATTTTTGGAAGTTTGGGGGT
* * *
723 CAAAAAT-GAAATTTTGGAAGTGTAGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
752 -AAAATGGTAATTTTTGAAAGTTTTAGGGGTT
1 AAAAATGG-AATTTTTGGAAG-TTT-GGGGGT
**
783 AAAAATGGAATTTTTGGAAGTTTAAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * *
812 AAAAATGTAATTTTTGGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAAG-TTTGGGGGT
* *
842 AAGAATGGAATTTTTGGAAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * *
871 AAAAATGTAATTTTTTGAATTTTTGGGGGTT
1 AAAAATGGAATTTTTGGAA-GTTTGGGGG-T
* * *
902 AAAAATGGAATTTTAGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* **
931 AAAAATGTAATTTTTGGAAGTTTCAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
*
960 CAAAATGGAATTTTTGGATAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
984 AGGGACTTCC
Statistics
Matches: 277, Mismatches: 50, Indels: 41
0.75 0.14 0.11
Matches are distributed among these distances:
27 5 0.02
28 22 0.08
29 144 0.52
30 62 0.22
31 37 0.13
32 7 0.03
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGGT
Found at i:645 original size:59 final size:58
Alignment explanation
Indices: 574--987 Score: 342
Period size: 59 Copynumber: 7.0 Consensus size: 58
564 GATATTCCGA
* ** * * *
574 GGTAAAACGGTAATTTTTAGAAAAATCAGGATCAAAAATGGAATTTTTGGATA-TTTGGG
1 GGTAAAATGGTAATTTTT-GAAATTTTAGGGTCAAAAATGGAATTTTTGGA-AGTTTAGG
* * * * * ***
633 GGTAAAATGGTAACTTTTGAAAGTTTGGGGTAAAAAAT-GAAGCTTTTGGACA-TCCGGG
1 GGTAAAATGGTAATTTTTGAAATTTTAGGGTCAAAAATGGAA-TTTTTGGA-AGTTTAGG
* * * * *
691 GGTAAAATGGTAATTTTTTAAAGTTTCGAGGTCAAAAAT-GAAATTTTGGAAGTGTAGG
1 GGTAAAATGGTAATTTTTGAAATTTTAG-GGTCAAAAATGGAATTTTTGGAAGTTTAGG
* *
749 GGTAAAATGGTAATTTTTGAAAGTTTTAGGGGTTAAAAATGGAATTTTTGGAAGTTTAAG
1 GGTAAAATGGTAATTTTTGAAA-TTTTA-GGGTCAAAAATGGAATTTTTGGAAGTTTAGG
* * *
809 GGTAAAAAT-GTAATTTTTGGAAGTTTTAGGGTTAAGAATGGAATTTTTGGAAGTTTAGG
1 GGT-AAAATGGTAATTTTT-GAAATTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGG
* * * * *
868 GGTAAAAAT-GTAATTTTTTGAATTTTTGGGGGTTAAAAATGGAATTTTAGGAAG-TTCGAG
1 GGT-AAAATGGTAA-TTTTTGAAATTTT-AGGGTCAAAAATGGAATTTTTGGAAGTTTAG-G
* *
928 GGTAAAAAT-GTAATTTTTGGAAGTTTCAGGGTC-AAAATGGAATTTTTGGATAGTTTAGG
1 GGT-AAAATGGTAATTTTT-GAAATTTTAGGGTCAAAAATGGAATTTTTGGA-AGTTTAGG
987 G
1 G
988 ACTTCCAAGG
Statistics
Matches: 300, Mismatches: 41, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
57 4 0.01
58 98 0.33
59 105 0.35
60 85 0.28
61 8 0.03
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTTGAAATTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGG
Found at i:767 original size:116 final size:116
Alignment explanation
Indices: 519--796 Score: 296
Period size: 116 Copynumber: 2.4 Consensus size: 116
509 CTCAGGGAGC
* * * *
519 AAAATGGTAATTTTGGGAAAATTTGGAGTTAAAAATGAAATTTTAGATATTCCGAGGTAAAACGG
1 AAAATGGTAATTTT-TGAAAGTTTGGGGTTAAAAATGAAATTTTAGACATTCCGAGGTAAAACGG
* * *
584 TAATTTTTAGAAAAATCAGGATCAAAAATGGAATTTTTGGATATTTGGGGGT
65 TAATTTTTAGAAAAATCAGGATCAAAAATGGAAATTTTGGATATGTAGGGGT
* * * * * *
636 AAAATGGTAACTTTTGAAAGTTTGGGGTAAAAAATGAAGCTTTTGGACA-TCCGGGGGTAAAATG
1 AAAATGGTAATTTTTGAAAGTTTGGGGTTAAAAATGAA-ATTTTAGACATTCC-GAGGTAAAACG
***
700 GTAATTTTTTA-AAGTTTCGAGG-TCAAAAAT-GAAATTTTGGA-AGTGTAGGGGT
64 GTAA-TTTTTAGAAAAATC-AGGATCAAAAATGGAAATTTTGGATA-TGTAGGGGT
*
752 AAAATGGTAATTTTTGAAAGTTTTAGGGGTTAAAAATGGAATTTT
1 AAAATGGTAATTTTTGAAAG-TTT-GGGGTTAAAAATGAAATTTT
797 TGGAAGTTTA
Statistics
Matches: 134, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
115 1 0.01
116 59 0.44
117 52 0.39
118 22 0.16
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (116 bp):
AAAATGGTAATTTTTGAAAGTTTGGGGTTAAAAATGAAATTTTAGACATTCCGAGGTAAAACGGT
AATTTTTAGAAAAATCAGGATCAAAAATGGAAATTTTGGATATGTAGGGGT
Found at i:900 original size:119 final size:118
Alignment explanation
Indices: 599--987 Score: 431
Period size: 119 Copynumber: 3.3 Consensus size: 118
589 TTTAGAAAAA
* * *
599 TCAGGATCAAAAATGGAATTTTTGGATA-TTTGGGGGTAAAATGGTAACTTTTGAAAG-TTT-GG
1 TCAGGGTC-AAAATGGAATTTTTGGA-AGTTTAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGG
* * ** **
661 GGTAAAAAAT-GAAGCTTTT-GGACA-TCCGGGGGT-AAAATGGTAATTTTTTAAAGTT
64 GGTTAAAAATGGAA--TTTTAGGA-AGTTCAAGGGTAAAAAT-GTAATTTTTGGAAGTT
* *
716 TC-GAGGTCAAAAAT-GAAATTTTGGAAGTGTAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGG
1 TCAG-GGTC-AAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGG
* *
779 GGTTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGGAAGTT
64 GGTTAAAAATGGAATTTTAGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTT
* * * *
834 TTAGGGTTAAGAATGGAATTTTTGGAAGTTTAGGGGTAAAAAT-GTAATTTTTTG-AATTTTTGG
1 TCAGGGTCAA-AATGGAATTTTTGGAAGTTTAGGGGT-AAAATGGTAA-TTTTTGAAAGTTTTAG
*
897 GGGTTAAAAATGGAATTTTAGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTT
63 GGGTTAAAAATGGAATTTTAGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTT
953 TCAGGGTCAAAATGGAATTTTTGGATAGTTTAGGG
1 TCAGGGTCAAAATGGAATTTTTGGA-AGTTTAGGG
988 ACTTCCAAGG
Statistics
Matches: 235, Mismatches: 23, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
115 1 0.00
116 37 0.16
117 21 0.09
118 55 0.23
119 110 0.47
120 11 0.05
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (118 bp):
TCAGGGTCAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGG
TTAAAAATGGAATTTTAGGAAGTTCAAGGGTAAAAATGTAATTTTTGGAAGTT
Found at i:1001 original size:60 final size:58
Alignment explanation
Indices: 690--987 Score: 336
Period size: 60 Copynumber: 5.1 Consensus size: 58
680 GGACATCCGG
** * * * *
690 GGGT-AAAATGGTAATTTTTTAAAG-TTTCGAGGTCAAAAAT-GAAATTTTGGAAGTGTA
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTTAG-GGTTAAAAATGGAATTTTTGGAAGTTTA
*
747 GGGGT-AAAATGGTAATTTTTGAAAGTTTTAGGGGTTAAAAATGGAATTTTTGGAAGTTTAA
1 -GGGTAAAAAT-GTAATTTTTGGAAGTTTTA-GGGTTAAAAATGGAATTTTTGGAAGTTT-A
*
808 GGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAGAATGGAATTTTTGGAAGTTTA
1 GGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTTTA
* * * * *
866 GGGGTAAAAATGTAATTTTTTGAATTTTTGGGGGTTAAAAATGGAATTTTAGGAAGTTCGA
1 -GGGTAAAAATGTAATTTTTGGAAGTTTT-AGGGTTAAAAATGGAATTTTTGGAAGTT-TA
* *
927 GGGTAAAAATGTAATTTTTGGAAGTTTCAGGG-TCAAAATGGAATTTTTGGATAGTTTA
1 GGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTTGGA-AGTTTA
985 GGG
1 GGG
988 ACTTCCAAGG
Statistics
Matches: 211, Mismatches: 20, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
58 45 0.21
59 72 0.34
60 87 0.41
61 7 0.03
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.37
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTTTA
Found at i:1998 original size:24 final size:24
Alignment explanation
Indices: 1971--2061 Score: 68
Period size: 24 Copynumber: 3.8 Consensus size: 24
1961 ATTTTAATAT
*
1971 TAAATATTTATTTATTATTATTAA
1 TAAATATTTATTTACTATTATTAA
*
1995 TAAAT-TCATTA-TTACTGTTATTAA
1 TAAATAT--TTATTTACTATTATTAA
2019 T-AATATTTA-TTAC-ATTA-TAA
1 TAAATATTTATTTACTATTATTAA
*
2039 CTAATATATATATATTACTATTA
1 -TAA-ATATTTAT-TTACTATTA
2062 ATGCTTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
20 3 0.06
21 4 0.07
22 8 0.15
23 10 0.19
24 18 0.33
25 7 0.13
26 4 0.07
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (24 bp):
TAAATATTTATTTACTATTATTAA
Found at i:2823 original size:17 final size:17
Alignment explanation
Indices: 2798--2882 Score: 82
Period size: 17 Copynumber: 4.9 Consensus size: 17
2788 TTCTAAAATT
2798 ATTTCAAATTTAAATTAA
1 ATTT-AAATTTAAATTAA
* **
2816 ATTGAAATTTAAAACAA
1 ATTTAAATTTAAATTAA
* *
2833 ATTTAAATTTAAAAATGA
1 ATTTAAATTT-AAATTAA
2851 ATTTAAATTTAAATTTAA
1 ATTTAAATTTAAA-TTAA
*
2869 A-GTAAATTTAAATT
1 ATTTAAATTTAAATT
2883 TAGAAATAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
16 2 0.04
17 33 0.59
18 21 0.38
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAATTAA
Found at i:2857 original size:41 final size:41
Alignment explanation
Indices: 2808--2898 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
2798 ATTTCAAATT
2808 TAAA-TTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
1 TAAATTTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
* * ** *
2848 TGAATTTAAATTTAAATTTAAAGTAAATTTAAATTTAGAAA
1 TAAATTTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
*
2889 TAAATCTAAA
1 TAAATTTAAA
2899 ATAATTTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 3 0.07
41 40 0.93
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.37
Consensus pattern (41 bp):
TAAATTTAAATTGAAATTTAAAACAAATTTAAATTTAAAAA
Found at i:2883 original size:6 final size:6
Alignment explanation
Indices: 2767--2884 Score: 84
Period size: 6 Copynumber: 20.0 Consensus size: 6
2757 ATGAACTTTG
* * *
2767 AATTTA ATTTTA AAGTTTA AGTTCTA AAATT- -ATTTCA AATTTA AA-TTA
1 AATTTA AATTTA AA-TTTA AATT-TA AATTTA AATTT-A AATTTA AATTTA
* ** ** *
2815 AATTGA AATTTA AA-ACA AATTTA AATTTA AAAATG AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
2862 AATTTA AA-GTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA
2885 GAAATAAATC
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
4 3 0.04
5 12 0.14
6 56 0.67
7 13 0.15
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:5330 original size:30 final size:29
Alignment explanation
Indices: 5193--5420 Score: 182
Period size: 29 Copynumber: 7.8 Consensus size: 29
5183 ATCGGGATAA
* * *
5193 AAAACGGAATTTTTGGAA-ATCCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTC
* *
5221 AAAAGGGTAATTTTT-GAGAGTTTCTGGGTC
1 AAAATGG-AATTTTTGGA-AGTTTCGGGGTC
*
5251 AAAATGGAATTTTTGGAAGTTTAGGGGT-
1 AAAATGGAATTTTTGGAAGTTTCGGGGTC
***
5279 AAAATGGTAATTTTCAAAAGTTTCGGGGTC
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTC
*
5309 AAAATCAGG-ATTTTTGGAAG-TTCGTGGTC
1 AAAAT--GGAATTTTTGGAAGTTTCGGGGTC
* **
5338 ACAAATGGAATTTTTAGAAGTTTCGAAGTC
1 A-AAATGGAATTTTTGGAAGTTTCGGGGTC
*
5368 AAAAATGGAATTTTTGGAAG-TTCGAGGGTA
1 -AAAATGGAATTTTTGGAAGTTTCG-GGGTC
*
5398 AAAATGTAATTTTTGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
5421 AGGGACCTCT
Statistics
Matches: 161, Mismatches: 23, Indels: 29
0.76 0.11 0.14
Matches are distributed among these distances:
28 17 0.11
29 84 0.52
30 55 0.34
31 3 0.02
32 2 0.01
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTC
Found at i:5350 original size:59 final size:58
Alignment explanation
Indices: 5198--5410 Score: 202
Period size: 59 Copynumber: 3.6 Consensus size: 58
5188 GATAAAAAAC
* * * ** * *
5198 GGAATTTTTGGAAATCCGAGGGTAAAAGGGTAATTTTTGAGAGTTTCTGGGTCAAAAT-
1 GGAATTTTTGGAAGTTCG-GGGTAAAATGGTAATTTTCAAAAGTTTCGGGGTCAAAATA
*
5256 GGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTCAAAAGTTTCGGGGTCAAAATCA
1 GGAATTTTTGGAAG-TTCGGGGTAAAATGGTAATTTTCAAAAGTTTCGGGGTCAAAAT-A
* * * **
5316 GG-ATTTTTGGAAGTTCGTGGTCACAAATGG-AATTTTTAGAAGTTTCGAAGTCAAAA-A
1 GGAATTTTTGGAAGTTCGGGGT-A-AAATGGTAATTTTCAAAAGTTTCGGGGTCAAAATA
5373 TGGAATTTTTGGAAGTTCGAGGGTAAAAAT-GTAATTTT
1 -GGAATTTTTGGAAGTTCG-GGGT-AAAATGGTAATTTT
5411 TGGATAGTTT
Statistics
Matches: 130, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
57 1 0.01
58 56 0.43
59 61 0.47
60 12 0.09
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (58 bp):
GGAATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTCAAAAGTTTCGGGGTCAAAATA
Found at i:6519 original size:18 final size:17
Alignment explanation
Indices: 6484--6540 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
6474 TCTCTCTTTT
* *
6484 TTATTA-TTAATTATTA
1 TTATTATTTAATAAATA
6500 TTAATTATTTAATAAATA
1 TT-ATTATTTAATAAATA
*
6518 TTATCA-TTAATAAA-A
1 TTATTATTTAATAAATA
6533 TTATTATT
1 TTATTATT
6541 ATTATCATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 6 0.18
16 11 0.32
17 7 0.21
18 10 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTATTTAATAAATA
Found at i:6543 original size:24 final size:24
Alignment explanation
Indices: 6516--6561 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
6506 ATTTAATAAA
6516 TATTATCATTAATAAAATTATTAT
1 TATTATCATTAATAAAATTATTAT
*
6540 TATTATCATTAATGAAATTATT
1 TATTATCATTAATAAAATTATT
6562 TAATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTATCATTAATAAAATTATTAT
Found at i:7385 original size:17 final size:18
Alignment explanation
Indices: 7360--7403 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
7350 TTTCAAATGT
7360 AAACTAAATTGAAATTTA
1 AAACTAAATTGAAATTTA
*
7378 AAAC-AAATTTAAATTTA
1 AAACTAAATTGAAATTTA
7395 GAAA-TAAAT
1 -AAACTAAAT
7404 CTAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
AAACTAAATTGAAATTTA
Found at i:17152 original size:35 final size:38
Alignment explanation
Indices: 17082--17161 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 38
17072 GCATGCTGGT
*
17082 TTCTATATAAACCAAAGTTGCAGTCTTGCTGTGCTGTGCC
1 TTCTATATAAACCAAAATTGCAG--TTGCTGTGCTGTGCC
17122 TTCTATATAAACCAAAATTGCAG-T-CT-TGCTGTGCC
1 TTCTATATAAACCAAAATTGCAGTTGCTGTGCTGTGCC
17157 TTCTA
1 TTCTA
17162 GATAGAGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
35 14 0.36
36 2 0.05
37 1 0.03
40 22 0.56
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (38 bp):
TTCTATATAAACCAAAATTGCAGTTGCTGTGCTGTGCC
Found at i:21866 original size:23 final size:23
Alignment explanation
Indices: 21813--21869 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
21803 CACTTGACCT
*
21813 ATTGACTTTGATCGAATCGAACC
1 ATTGACTTTGATCGAACCGAACC
* * * *
21836 GTTAACTTTGATTGAACCGAATC
1 ATTGACTTTGATCGAACCGAACC
21859 ATTGACTTTGA
1 ATTGACTTTGA
21870 CCAACCGTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (23 bp):
ATTGACTTTGATCGAACCGAACC
Found at i:22544 original size:12 final size:12
Alignment explanation
Indices: 22527--22556 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
22517 TGTAATATCA
*
22527 TGAGATTAAGAT
1 TGAGATTAAAAT
22539 TGAGATTAAAAT
1 TGAGATTAAAAT
22551 TGAGAT
1 TGAGAT
22557 ATACATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (12 bp):
TGAGATTAAAAT
Found at i:24022 original size:30 final size:29
Alignment explanation
Indices: 23988--24051 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
23978 CAACTTAACA
* *
23988 AACAAATACTTCTAAAATAGTAACAAAATT
1 AACAAATACCTCTAAAATAAT-ACAAAATT
* *
24018 AACAAATGCCTCTAAAATAATTCAAAATT
1 AACAAATACCTCTAAAATAATACAAAATT
24047 AACAA
1 AACAA
24052 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (29 bp):
AACAAATACCTCTAAAATAATACAAAATT
Found at i:30682 original size:21 final size:23
Alignment explanation
Indices: 30658--30707 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
30648 CGAAAATTTG
30658 AAAAATATCAATTC-AAAT-AAT
1 AAAAATATCAATTCTAAATAAAT
**
30679 AAAAA-ATTGATTCTAAATAAAT
1 AAAAATATCAATTCTAAATAAAT
30701 AAAAATA
1 AAAAATA
30708 GGAAAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 6 0.25
21 9 0.38
22 8 0.33
23 1 0.04
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAATATCAATTCTAAATAAAT
Done.