Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004704.1 Kokia drynarioides strain JFW-HI SEQ_118269, 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: 59851
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:6422 original size:29 final size:30
Alignment explanation
Indices: 6380--6458 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
6370 TAAATGATTT
*
6380 TAAATTTATTAAAATTATTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTAAAATAA
*
6409 TAAAATTATTAAAATTATTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAATAA
*
6439 TTAAATTATT-AAA-TATTTTT
1 TAAAATTATTAAAATTATTTTT
6459 AATTTCCAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.15
29 29 0.63
30 10 0.22
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAATAA
Found at i:7574 original size:22 final size:22
Alignment explanation
Indices: 7531--7574 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
7521 AAAATTATTT
*
7531 AATAATTTTATTATTTCAAAAA
1 AATAATTTTATAATTTCAAAAA
*
7553 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATAATTTCAAAA
7575 TCATTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTATAATTTCAAAAA
Found at i:10868 original size:17 final size:17
Alignment explanation
Indices: 10846--10882 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
10836 TCATTATAAT
10846 AATATTATTATTCAAAA
1 AATATTATTATTCAAAA
10863 AATATTATTATTCAAAA
1 AATATTATTATTCAAAA
10880 AAT
1 AAT
10883 TTAAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATTATTATTCAAAA
Found at i:18837 original size:2 final size:2
Alignment explanation
Indices: 18830--18855 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18820 TTTTACCCCC
18830 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
18856 GTATGAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19313 original size:29 final size:29
Alignment explanation
Indices: 19281--19356 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 29
19271 CTGTCCATAT
19281 TATTTTTTTATTT-T-TTTAATAAATATTTA
1 TATTTTTTTATTTATATTTAAT-AAT-TTTA
* *
19310 TATTATATTATTTTAATATTTAATAATTTTA
1 TATTTTTTTA-TTT-ATATTTAATAATTTTA
19341 TATATTTTTTATTTAT
1 TAT-TTTTTTATTTAT
19357 TGAATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
29 8 0.21
30 5 0.13
31 10 0.26
32 9 0.24
33 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
TATTTTTTTATTTATATTTAATAATTTTA
Found at i:19345 original size:28 final size:28
Alignment explanation
Indices: 19313--19387 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
19303 ATATTTATAT
19313 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTTAATAATTTTA
* * **
19341 TATATT-TTTTATTTATTGAATTTTTTTA
1 TATATTATTTTA-ATATTTAATAATTTTA
* *
19369 TATAGTCATTTTAACATTT
1 TATA-TTATTTTAATATTT
19388 TCAATGTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
27 5 0.14
28 22 0.61
29 4 0.11
30 5 0.14
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (28 bp):
TATATTATTTTAATATTTAATAATTTTA
Found at i:30046 original size:14 final size:14
Alignment explanation
Indices: 30019--30053 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
30009 TATAAAGGGC
30019 TAAAAATGATTTTT
1 TAAAAATGATTTTT
30033 TATAAAAT-ATTTTT
1 TA-AAAATGATTTTT
30047 TAAAAAT
1 TAAAAAT
30054 TTCAATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TAAAAATGATTTTT
Found at i:30434 original size:30 final size:29
Alignment explanation
Indices: 30400--30459 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
30390 TTGTTAATAG
*
30400 TAATTAATACCAAGTAAAATATAAAATATA
1 TAATTAATACAAAGTAAAA-ATAAAATATA
* *
30430 TAATTAATATAAATTAAAAATAAAATATA
1 TAATTAATACAAAGTAAAAATAAAATATA
30459 T
1 T
30460 TATTGCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (29 bp):
TAATTAATACAAAGTAAAAATAAAATATA
Found at i:30821 original size:18 final size:19
Alignment explanation
Indices: 30806--30841 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30796 TATTATAATT
30806 AATAATAATA-AAATAAAA
1 AATAATAATATAAATAAAA
*
30824 AATAATTATATAAATAAA
1 AATAATAATATAAATAAA
30842 TGTGATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAATAATATAAATAAAA
Found at i:31621 original size:30 final size:30
Alignment explanation
Indices: 31585--31679 Score: 163
Period size: 30 Copynumber: 3.2 Consensus size: 30
31575 CAACTTAACA
31585 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
* *
31615 AACAAATGCCTCTAAAATAATAATAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
*
31645 AACAAACGTCTCTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAACAAAATT
31675 AACAA
1 AACAA
31680 TACAATAAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (30 bp):
AACAAATGTCTCTAAAATAATAACAAAATT
Found at i:35372 original size:57 final size:57
Alignment explanation
Indices: 35304--35418 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
35294 TGCCGTTTCA
35304 GATGCTAATTTCAACTTTGGAACTACTGAGGTAAGAATTATTTACTTAGCTTTTTAT
1 GATGCTAATTTCAACTTTGGAACTACTGAGGTAAGAATTATTTACTTAGCTTTTTAT
35361 GATGCTAATTTCAACTTTGGAACTACTGAGGTAAGAATTATTTACTTAGCTTTTTAT
1 GATGCTAATTTCAACTTTGGAACTACTGAGGTAAGAATTATTTACTTAGCTTTTTAT
35418 G
1 G
35419 TGTGTATATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (57 bp):
GATGCTAATTTCAACTTTGGAACTACTGAGGTAAGAATTATTTACTTAGCTTTTTAT
Found at i:38821 original size:23 final size:23
Alignment explanation
Indices: 38782--38835 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
38772 ACAAATTGTT
*
38782 TTATATTAAATTTAATTATAATA
1 TTATATTAAATTAAATTATAATA
* *
38805 TTATATT-AATATAAATTTTAATT
1 TTATATTAAAT-TAAATTATAATA
38828 TTAATATT
1 TT-ATATT
38836 TTGACATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 18 0.69
24 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATATTAAATTAAATTATAATA
Found at i:38962 original size:17 final size:18
Alignment explanation
Indices: 38920--38962 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
38910 AGCTGCGTTT
38920 TTTTAAAAGTGTTTTTCA
1 TTTTAAAAGTGTTTTTCA
** *
38938 TTCAAAAAGT-TTTTTGA
1 TTTTAAAAGTGTTTTTCA
38955 TTTTAAAA
1 TTTTAAAA
38963 CATTACTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (18 bp):
TTTTAAAAGTGTTTTTCA
Found at i:40613 original size:22 final size:23
Alignment explanation
Indices: 40581--40630 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
40571 AATTTTAGTT
*
40581 ATTTTATTTTTTG-AATTTGTAA
1 ATTTTAATTTTTGTAATTTGTAA
* *
40603 ATTTTAATTTTTGTATTTTTTAA
1 ATTTTAATTTTTGTAATTTGTAA
40626 ATTTT
1 ATTTT
40631 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (23 bp):
ATTTTAATTTTTGTAATTTGTAA
Found at i:40620 original size:31 final size:31
Alignment explanation
Indices: 40571--40641 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
40561 TTATCTGACT
* *
40571 AATTTTAGTTATTTTATTTTTTGAATTTGTA
1 AATTTTAATTATTTTATTTTTTAAATTTGTA
*
40602 AATTTTAATT-TTTGTATTTTTTAAATTTTTA
1 AATTTTAATTATTT-TATTTTTTAAATTTGTA
40633 AATTTTAAT
1 AATTTTAAT
40642 CTTGGTCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 3 0.08
31 33 0.92
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (31 bp):
AATTTTAATTATTTTATTTTTTAAATTTGTA
Found at i:42909 original size:41 final size:39
Alignment explanation
Indices: 42863--42952 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
42853 TTAAAAATAT
* *
42863 TTATATTAAAAAACACTACCATAAATATAGTAAATGTTTTA
1 TTATATTAAAAAACAC-A-AATAAATATAGTAAATATTTTA
* *
42904 TTATATTAAAAAGCGCAAATAAATATAGTAAATATTTTA
1 TTATATTAAAAAACACAAATAAATATAGTAAATATTTTA
*
42943 TTGTATTAAA
1 TTATATTAAA
42953 TATAAATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 29 0.66
40 1 0.02
41 14 0.32
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (39 bp):
TTATATTAAAAAACACAAATAAATATAGTAAATATTTTA
Found at i:48140 original size:3 final size:3
Alignment explanation
Indices: 48132--48160 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
48122 ATTCTTATGC
48132 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
48161 TGCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:53457 original size:28 final size:29
Alignment explanation
Indices: 53426--53485 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
53416 AAAATGAGAC
53426 TTTTTGGA-TACCCGAGGCAAAATGGTAA
1 TTTTTGGATTACCCGAGGCAAAATGGTAA
** *
53454 -TTTTGGATTTTCGGAGGCAAAATGGTAA
1 TTTTTGGATTACCCGAGGCAAAATGGTAA
53482 TTTT
1 TTTT
53486 GGGAAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.26
28 17 0.63
29 3 0.11
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTTTGGATTACCCGAGGCAAAATGGTAA
Found at i:53568 original size:58 final size:57
Alignment explanation
Indices: 53503--53720 Score: 176
Period size: 59 Copynumber: 3.7 Consensus size: 57
53493 TTCAGGGTTA
*
53503 AAAATGGAATTTTTAGACATTCGGGGGTAAAAGGGTAA-TTTCAAGAGTTTCGAGGTC
1 AAAATGGAATTTTTGGACATTCGGGGGTAAAAGGGTAATTTTCAA-AGTTTCGAGGTC
* * * * * *
53560 GAAAATGGAGTTTTTGGACGTTC-GGGGAAAAATGGTAATTTTTGAAAGTTTCGGGGTC
1 -AAAATGGAATTTTTGGACATTCGGGGGTAAAAGGGTAA-TTTTCAAAGTTTCGAGGTC
* * * * *
53618 AAAATGGTAATTTTTGGA-AGTTCGAGGGTAAAAATGG-AATTTTTGAAAGTTTCGAGATAA
1 AAAATGG-AATTTTTGGACA-TTCGGGGGT-AAAAGGGTAA-TTTTCAAAGTTTCGAGGT-C
* **
53678 AAAATGGAATTTTTGGA-AGTTCGAGAGGTAAAAATGTAATTTT
1 AAAATGGAATTTTTGGACA-TTCG-GGGGTAAAAGGGTAATTTT
53721 TGGATAGTTT
Statistics
Matches: 133, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
57 20 0.15
58 42 0.32
59 52 0.39
60 19 0.14
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.33
Consensus pattern (57 bp):
AAAATGGAATTTTTGGACATTCGGGGGTAAAAGGGTAATTTTCAAAGTTTCGAGGTC
Found at i:53613 original size:29 final size:30
Alignment explanation
Indices: 53472--53722 Score: 181
Period size: 30 Copynumber: 8.5 Consensus size: 30
53462 TTTCGGAGGC
* *
53472 AAAATGGTAATTTTGGGAAAATTC-AGGGTTA
1 AAAATGGTAATTTT-TGAAAGTTCGAGGG-TA
* *
53503 AAAATGG-AATTTTTAGACA-TTCGGGGGT-
1 AAAATGGTAATTTTT-GAAAGTTCGAGGGTA
* * *
53531 AAAAGGGTAA--TTTCAAGAGTTTCGA-GGTCG
1 AAAATGGTAATTTTTGAA-AG-TTCGAGGGT-A
* * *
53561 AAAATGG-AGTTTTTGGACGTTCG-GGG-A
1 AAAATGGTAATTTTTGAAAGTTCGAGGGTA
*
53588 AAAATGGTAATTTTTGAAAGTTTCG-GGGTC
1 AAAATGGTAATTTTTGAAAG-TTCGAGGGTA
*
53618 AAAATGGTAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGTAATTTTTGAAAGTTCGAGGGTA
*
53648 AAAATGG-AATTTTTGAAAGTTTCGA-GATAA
1 AAAATGGTAATTTTTGAAAG-TTCGAGGGT-A
*
53678 AAAATGG-AATTTTTGGAAGTTCGAGAGGTA
1 AAAATGGTAATTTTTGAAAGTTCGAG-GGTA
53708 AAAAT-GTAATTTTTG
1 AAAATGGTAATTTTTG
53723 GATAGTTTAG
Statistics
Matches: 177, Mismatches: 23, Indels: 41
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.01
27 11 0.06
28 18 0.10
29 47 0.27
30 87 0.49
31 13 0.07
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (30 bp):
AAAATGGTAATTTTTGAAAGTTCGAGGGTA
Found at i:53670 original size:59 final size:58
Alignment explanation
Indices: 53548--53722 Score: 237
Period size: 59 Copynumber: 3.0 Consensus size: 58
53538 TAATTTCAAG
* *
53548 AGTTTCGAGGTCGAAAATGGAGTTTTTGGACGTTCG-GGG-AAAAATGGTAATTTTTGAA
1 AGTTTCGAGGTC-AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGG-AATTTTTGAA
*
53606 AGTTTCGGGGTCAAAATGGTAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAA
1 AGTTTCGAGGTCAAAATGG-AATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAA
* * *
53665 AGTTTCGAGATAAAAAATGGAATTTTTGGAAGTTCGAGAGGTAAAAATGTAATTTTTG
1 AGTTTCGAGGT-CAAAATGGAATTTTTGGAAGTTCGAG-GGTAAAAATGGAATTTTTG
53723 GATAGTTTAG
Statistics
Matches: 105, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
57 7 0.07
58 25 0.24
59 40 0.38
60 33 0.31
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (58 bp):
AGTTTCGAGGTCAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAA
Found at i:53723 original size:30 final size:29
Alignment explanation
Indices: 53561--53729 Score: 184
Period size: 30 Copynumber: 5.7 Consensus size: 29
53551 TTCGAGGTCG
* *
53561 AAAATGGAGTTTTTGGACGTTCG-GGG-A
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
53588 AAAATGGTAATTTTTGAAAGTTTCG-GGGTC
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGTA
53618 AAAATGGTAATTTTTGGAAGTTCGAGGGTA
1 AAAATGG-AATTTTTGGAAGTTCGAGGGTA
* *
53648 AAAATGGAATTTTTGAAAGTTTCGA-GATAA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
53678 AAAATGGAATTTTTGGAAGTTCGAGAGGTA
1 AAAATGGAATTTTTGGAAGTTCGAG-GGTA
*
53708 AAAATGTAATTTTTGGATAGTT
1 AAAATGGAATTTTTGGA-AGTT
53730 TAGGGACCTC
Statistics
Matches: 122, Mismatches: 11, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.06
28 9 0.07
29 29 0.24
30 71 0.58
31 6 0.05
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:54423 original size:2 final size:2
Alignment explanation
Indices: 54411--54441 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
54401 ATGTATTTGT
*
54411 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54442 TTTAAATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:54684 original size:99 final size:99
Alignment explanation
Indices: 54507--54694 Score: 227
Period size: 99 Copynumber: 1.9 Consensus size: 99
54497 TAAAGGCTAA
* * * *
54507 AACTATCCATAGCCTCTCTGCAACCCATAAATAAGAGAATAATATGTTTTAGCGCACTTGAAACC
1 AACTATCCATAGCCTCTCTGCAACCCATAAATAAGAGAATAATATGTTTCAACGAACTCGAAACC
** *
54572 ACATCATTTTGTATTGGCAACAATGCCTAGAACT
66 ACATCATCCTGTATTGACAACAATGCCTAGAACT
* * * * *
54606 AACTATCCATAGCCTCTCT-CTAACCCATAAATAGGAGGATAATGTGTTTCAATGAACTCGAACC
1 AACTATCCATAGCCTCTCTGC-AACCCATAAATAAGAGAATAATATGTTTCAACGAACTCGAAAC
*
54670 CACGTTC-TCCTGTATTGACAACAAT
65 CAC-ATCATCCTGTATTGACAACAAT
54695 ACTTATGCCA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
98 1 0.01
99 71 0.96
100 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.28
Consensus pattern (99 bp):
AACTATCCATAGCCTCTCTGCAACCCATAAATAAGAGAATAATATGTTTCAACGAACTCGAAACC
ACATCATCCTGTATTGACAACAATGCCTAGAACT
Found at i:54811 original size:24 final size:24
Alignment explanation
Indices: 54766--54813 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
54756 ATGGATGTTC
*
54766 AACCTTACATCTCCCTTGACCTTT
1 AACCTTACATCTCCCTTAACCTTT
* * *
54790 AACCTTCCATCTTCTTTAACCTTT
1 AACCTTACATCTCCCTTAACCTTT
54814 CATATCCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.35, G:0.02, T:0.42
Consensus pattern (24 bp):
AACCTTACATCTCCCTTAACCTTT
Found at i:54823 original size:17 final size:17
Alignment explanation
Indices: 54785--54823 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
54775 TCTCCCTTGA
*
54785 CCTTTAACCTTCCATCT
1 CCTTTAACCTTCCATAT
* *
54802 TCTTTAACCTTTCATAT
1 CCTTTAACCTTCCATAT
54819 CCTTT
1 CCTTT
54824 TAACTACTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (17 bp):
CCTTTAACCTTCCATAT
Done.