Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012769.1 Kokia drynarioides strain JFW-HI SEQ_127781, 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: 47845
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:313 original size:29 final size:28
Alignment explanation
Indices: 277--647 Score: 299
Period size: 29 Copynumber: 12.8 Consensus size: 28
267 CGGATGCACA
* *
277 GGGG-CAAAATGGTAGTTTTGGAAGATTC
1 GGGGTCAAAATGGGATTTTTGGAAG-TTC
*
305 GGAGTCAAAAATGGGATTTTTGGAAGTTC
1 GGGGTC-AAAATGGGATTTTTGGAAGTTC
** * *
334 GAGGGT-AAAATGATAATTTTCGAAAGGTTC
1 G-GGGTCAAAATG-GGATTTTTGGAA-GTTC
*
364 GGGGTCAAAATGGGATTTTTGGAAGTTT
1 GGGGTCAAAATGGGATTTTTGGAAGTTC
**
392 GAGGGT-AAAATGATAATTTTTGGAAGGTTC
1 G-GGGTCAAAATG-GGATTTTTGGAA-GTTC
422 GGGGTCAAATATGGGATTTTTGGAAGTTC
1 GGGGTCAAA-ATGGGATTTTTGGAAGTTC
* * * *
451 GGGAGT-AAAATGGTAATTTTCGAAAGGTTT
1 GGG-GTCAAAATGG-GATTTTTGGAA-GTTC
481 GGGGTCAAAAATGGGATTTTTGGAAGTTC
1 GGGGTC-AAAATGGGATTTTTGGAAGTTC
* *
510 GGGGGT-AAAATGGTAATTTTTAGAAGGTTC
1 -GGGGTCAAAATGG-GATTTTTGGAA-GTTC
540 GGGGTCAAAATTGGGATTTTTGGAAGTTC
1 GGGGTCAAAA-TGGGATTTTTGGAAGTTC
* *
569 GGGGGT-ATAATGGTGATTTTTAGAAGGTTC
1 -GGGGTCAAAATGG-GATTTTTGGAA-GTTC
* *
599 GAGGTC-AAATGGGATTTTTGGAAGTTT
1 GGGGTCAAAATGGGATTTTTGGAAGTTC
*
626 GGGGAT-AAAATGGTAATTTTTG
1 GGGG-TCAAAATGG-GATTTTTG
648 AAAAGTTTAG
Statistics
Matches: 277, Mismatches: 38, Indels: 55
0.75 0.10 0.15
Matches are distributed among these distances:
27 6 0.02
28 50 0.18
29 113 0.41
30 95 0.34
31 13 0.05
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (28 bp):
GGGGTCAAAATGGGATTTTTGGAAGTTC
Found at i:468 original size:59 final size:57
Alignment explanation
Indices: 277--647 Score: 476
Period size: 59 Copynumber: 6.4 Consensus size: 57
267 CGGATGCACA
* * * *
277 GGGGCAAAATGGT-AGTTTTGGAAGATTCGGAGTCAAAAATGGGATTTTTGGAAGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTC-AAAATGGGATTTTTGGAAGTTC
* * * *
334 GAGGGTAAAATGATAATTTTCGAAAGGTTCGGGGTCAAAATGGGATTTTTGGAAGTTT
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAATGGGATTTTTGGAAGTTC
*
392 GAGGGTAAAATGATAATTTTTGGAAGGTTCGGGGTCAAATATGGGATTTTTGGAAGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAA-ATGGGATTTTTGGAAGTTC
* * *
451 GGGAGTAAAATGGTAATTTTCGAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTC
1 GGG-GTAAAATGGTAATTTTTGGAAGGTTCGGGGTC-AAAATGGGATTTTTGGAAGTTC
*
510 GGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAATTGGGATTTTTGGAAGTTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAA-TGGGATTTTTGGAAGTTC
* * * * *
569 GGGGGTATAATGGTGATTTTTAGAAGGTTCGAGGTC-AAATGGGATTTTTGGAAGTTT
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAATGGGATTTTTGGAAGTTC
626 GGGGATAAAATGGTAATTTTTG
1 GGGG-TAAAATGGTAATTTTTG
648 AAAAGTTTAG
Statistics
Matches: 280, Mismatches: 26, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
56 4 0.01
57 32 0.11
58 77 0.28
59 161 0.57
60 6 0.02
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAATGGGATTTTTGGAAGTTC
Found at i:2449 original size:10 final size:10
Alignment explanation
Indices: 2417--2449 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2407 TAGGCTAAAG
2417 TTTGGGCC-T
1 TTTGGGCCAT
2426 ATTTGGGCCAT
1 -TTTGGGCCAT
2437 TTTGGGCCAT
1 TTTGGGCCAT
2447 TTT
1 TTT
2450 AGTTTAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 21 0.95
11 1 0.05
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.45
Consensus pattern (10 bp):
TTTGGGCCAT
Found at i:2561 original size:18 final size:17
Alignment explanation
Indices: 2524--2613 Score: 83
Period size: 17 Copynumber: 5.2 Consensus size: 17
2514 GAACTTTACC
* *
2524 TTAAATTTATAATAATT
1 TTAAATTTAAAATAAAT
2541 TTAAATTTGAAAATAAAT
1 TTAAATTT-AAAATAAAT
* *
2559 TTAAATTTAAATTTAAT
1 TTAAATTTAAAATAAAT
** **
2576 TTAAATTTTTAACGAAT
1 TTAAATTTAAAATAAAT
2593 TT-AATCTTAAAATAAAT
1 TTAAAT-TTAAAATAAAT
2610 TTAA
1 TTAA
2614 GAGGGAGTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
16 3 0.05
17 38 0.67
18 16 0.28
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:2569 original size:12 final size:12
Alignment explanation
Indices: 2540--2583 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
2530 TTATAATAAT
2540 TTTAAATTTGAAA
1 TTTAAATTT-AAA
*
2553 -ATAAATTTAAA
1 TTTAAATTTAAA
2564 TTTAAATTT-AA
1 TTTAAATTTAAA
2575 TTTAAATTT
1 TTTAAATTT
2584 TTAACGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.50
12 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:2578 original size:5 final size:6
Alignment explanation
Indices: 2540--2583 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
2530 TTATAATAAT
*
2540 TTTAAA TTTGAAA -ATAAA TTTAAA TTTAAA TTT-AA TTTAAA TTT
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
2584 TTAACGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 8 0.24
6 22 0.67
7 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:5427 original size:20 final size:19
Alignment explanation
Indices: 5402--5441 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5392 TTTTCTAATC
5402 TTTAATAATATTTATTAAAT
1 TTTAATAATATTTA-TAAAT
* *
5422 TTTAATCATTTTTATAAAT
1 TTTAATAATATTTATAAAT
5441 T
1 T
5442 AAAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATAATATTTATAAAT
Found at i:8490 original size:14 final size:14
Alignment explanation
Indices: 8473--8508 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
8463 AAAGTTATAA
*
8473 AAAAAAAGAAAAAT
1 AAAAAAAGAAAAAG
8487 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
8501 AAAAAAAG
1 AAAAAAAG
8509 GGGGGGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:12130 original size:29 final size:30
Alignment explanation
Indices: 12075--12131 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
12065 TATTATGCCA
*
12075 TAAAAATAAGTTAAAATATATTAGAAAAAT
1 TAAAAATAAGTTAAAATAGATTAGAAAAAT
*
12105 TAAATAATAA-TT-AAATAGATTGGAAAA
1 TAAA-AATAAGTTAAAATAGATTAGAAAA
12132 TAAAAGTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.54
30 6 0.25
31 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (30 bp):
TAAAAATAAGTTAAAATAGATTAGAAAAAT
Found at i:13271 original size:273 final size:272
Alignment explanation
Indices: 12802--13347 Score: 819
Period size: 273 Copynumber: 2.0 Consensus size: 272
12792 TTTTCCATAC
* * * *
12802 GAGGAAAAGTACTTTTGAAAAGTTAAAAATTTCTTTCAAAAATTGATTGTTTAGCATTGCTTTTA
1 GAGGAAAAATACTTTTGAAAAATTAAAAATTTCTTTCAAAAATTGATTGTTTAGCACTACTTTTA
* * *
12867 GCCAAAAAGCACTTTTACAGTAAAAAATATTTTTTGGAAGCATTGGTGAATAGGGCCAAACACGG
66 GCCAAAAAACACTTTTACAGTAAAAAATACTTTTTGAAAGCATTGGTGAATAGGGCCAAACACGG
* *
12932 GCTCCTCTAGAGACTATAATTTTTTTATTTTTCTTTCTTTTATTTTCCTTAATTTATGCCATGGT
131 ACTCCTCTAGAGACTATAATTTTTTTATTTTTCTTTCTTTTATTTTCCTTAATTTATGCAATGGT
*
12997 CTCCATCCCCAAACTCAATTCGAAATTGAGGTTGAAATTTTTTTTTGTTGGCCAGCGAAAATTTT
196 CTCCATCCCCAAACTCAATTCGAAATTGAGGTTGAAA-TTTTTTTTGTTGGCCAGCGAAAATTTA
13062 GATCGAAAAAATT
260 GATCGAAAAAATT
*
13075 GAGGAAAAATACTTTTGAAAAATTAAAAATTTCTTTCAAAAGTTGATTG-TTAGCACTACTTTTA
1 GAGGAAAAATACTTTTGAAAAATTAAAAATTTCTTTCAAAAATTGATTGTTTAGCACTACTTTTA
* * * * *
13139 GTCAAAAGAACACTTTTACAGTGAAAAATGCTTTTTGAAAGCATTGGTGAAT-GGAGCCTAACAT
66 GCCAAAA-AACACTTTTACAGTAAAAAATACTTTTTGAAAGCATTGGTGAATAGG-GCCAAACAC
* * * *
13203 GGACTCCTCTAGATACTATAATATTTTTTATTTTT-TTTCTTTTCTTTTCCTTTATTTATGTAAT
129 GGACTCCTCTAGAGACTATAAT-TTTTTTATTTTTCTTTCTTTTATTTTCCTTAATTTATGCAAT
* * *
13267 GGTCTCCATCCCCAAACTCAGTTTGAAATTGAGGTTGAAATTTTTTTTGTTGGTCAGCGAAAATT
193 GGTCTCCATCCCCAAACTCAATTCGAAATTGAGGTTGAAATTTTTTTTGTTGGCCAGCGAAAATT
*
13332 TAGATCGGAAAAATT
258 TAGATCGAAAAAATT
13347 G
1 G
13348 GTTTGTGTTG
Statistics
Matches: 246, Mismatches: 24, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
272 59 0.24
273 175 0.71
274 12 0.05
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (272 bp):
GAGGAAAAATACTTTTGAAAAATTAAAAATTTCTTTCAAAAATTGATTGTTTAGCACTACTTTTA
GCCAAAAAACACTTTTACAGTAAAAAATACTTTTTGAAAGCATTGGTGAATAGGGCCAAACACGG
ACTCCTCTAGAGACTATAATTTTTTTATTTTTCTTTCTTTTATTTTCCTTAATTTATGCAATGGT
CTCCATCCCCAAACTCAATTCGAAATTGAGGTTGAAATTTTTTTTGTTGGCCAGCGAAAATTTAG
ATCGAAAAAATT
Found at i:13620 original size:139 final size:139
Alignment explanation
Indices: 13450--13728 Score: 454
Period size: 139 Copynumber: 2.0 Consensus size: 139
13440 TATTGTTAAT
*
13450 TTTAGATTTAATATTAAGATTATATTGTTGTTAG-TAAAGATTGTATTTGTGTTTAAGGTGTAAG
1 TTTAGATTTAATATTAAGATTATATTGTTGTTAGTTAAAG-TTATATTTGTGTTTAAGGTGTAAG
* *
13514 GATAGATTAAGATAGTTTTAATGTA-TGTTTTTTTAGTTTGTAATAATAATTTTTATATTATAAT
65 GATAGATTAAGATAGTTTTAATATATTGTTTTTTTAGTTTGTAATAATAATTTGTATATTATAAT
13578 ATTTTACATA
130 ATTTTACATA
* * * * *
13588 TTTAGATTTAATATTTAAGATTTTATTTTTGTTTGTTAAAGTTATATTTGTGTTTAAGTTGTAGG
1 TTTAGATTTAATA-TTAAGATTATATTGTTGTTAGTTAAAGTTATATTTGTGTTTAAGGTGTAAG
13653 GATAGATTAAGATAGTTTTAATATATTGTTTTTTTAGTTTGTAATAATAATTTGTATATTATAAT
65 GATAGATTAAGATAGTTTTAATATATTGTTTTTTTAGTTTGTAATAATAATTTGTATATTATAAT
13718 ATTTTACATA
130 ATTTTACATA
13728 T
1 T
13729 AATTTTTAGA
Statistics
Matches: 130, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
138 13 0.10
139 63 0.48
140 54 0.42
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (139 bp):
TTTAGATTTAATATTAAGATTATATTGTTGTTAGTTAAAGTTATATTTGTGTTTAAGGTGTAAGG
ATAGATTAAGATAGTTTTAATATATTGTTTTTTTAGTTTGTAATAATAATTTGTATATTATAATA
TTTTACATA
Found at i:16483 original size:14 final size:14
Alignment explanation
Indices: 16466--16501 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
16456 AAAGTTATAA
*
16466 AAAAAAAGAAAAAT
1 AAAAAAAGAAAAAG
16480 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
16494 AAAAAAAG
1 AAAAAAAG
16502 GGGGGGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:20123 original size:29 final size:30
Alignment explanation
Indices: 20068--20124 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
20058 TATTATGCCA
*
20068 TAAAAATAAGTTAAAATATATTAGAAAAAT
1 TAAAAATAAGTTAAAATAGATTAGAAAAAT
*
20098 TAAATAATAA-TT-AAATAGATTGGAAAA
1 TAAA-AATAAGTTAAAATAGATTAGAAAA
20125 TAAAAGTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.54
30 6 0.25
31 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (30 bp):
TAAAAATAAGTTAAAATAGATTAGAAAAAT
Found at i:21264 original size:273 final size:272
Alignment explanation
Indices: 20795--21340 Score: 819
Period size: 273 Copynumber: 2.0 Consensus size: 272
20785 TTTTCCATAC
* * * *
20795 GAGGAAAAGTACTTTTGAAAAGTTAAAAATTTCTTTCAAAAATTGATTGTTTAGCATTGCTTTTA
1 GAGGAAAAATACTTTTGAAAAATTAAAAATTTCTTTCAAAAATTGATTGTTTAGCACTACTTTTA
* * *
20860 GCCAAAAAGCACTTTTACAGTAAAAAATATTTTTTGGAAGCATTGGTGAATAGGGCCAAACACGG
66 GCCAAAAAACACTTTTACAGTAAAAAATACTTTTTGAAAGCATTGGTGAATAGGGCCAAACACGG
* *
20925 GCTCCTCTAGAGACTATAATTTTTTTATTTTTCTTTCTTTTATTTTCCTTAATTTATGCCATGGT
131 ACTCCTCTAGAGACTATAATTTTTTTATTTTTCTTTCTTTTATTTTCCTTAATTTATGCAATGGT
*
20990 CTCCATCCCCAAACTCAATTCGAAATTGAGGTTGAAATTTTTTTTTGTTGGCCAGCGAAAATTTT
196 CTCCATCCCCAAACTCAATTCGAAATTGAGGTTGAAA-TTTTTTTTGTTGGCCAGCGAAAATTTA
21055 GATCGAAAAAATT
260 GATCGAAAAAATT
*
21068 GAGGAAAAATACTTTTGAAAAATTAAAAATTTCTTTCAAAAGTTGATTG-TTAGCACTACTTTTA
1 GAGGAAAAATACTTTTGAAAAATTAAAAATTTCTTTCAAAAATTGATTGTTTAGCACTACTTTTA
* * * * *
21132 GTCAAAAGAACACTTTTACAGTGAAAAATGCTTTTTGAAAGCATTGGTGAAT-GGAGCCTAACAT
66 GCCAAAA-AACACTTTTACAGTAAAAAATACTTTTTGAAAGCATTGGTGAATAGG-GCCAAACAC
* * * *
21196 GGACTCCTCTAGATACTATAATATTTTTTATTTTT-TTTCTTTTCTTTTCCTTTATTTATGTAAT
129 GGACTCCTCTAGAGACTATAAT-TTTTTTATTTTTCTTTCTTTTATTTTCCTTAATTTATGCAAT
* * *
21260 GGTCTCCATCCCCAAACTCAGTTTGAAATTGAGGTTGAAATTTTTTTTGTTGGTCAGCGAAAATT
193 GGTCTCCATCCCCAAACTCAATTCGAAATTGAGGTTGAAATTTTTTTTGTTGGCCAGCGAAAATT
*
21325 TAGATCGGAAAAATT
258 TAGATCGAAAAAATT
21340 G
1 G
21341 GTTTGTGTTG
Statistics
Matches: 246, Mismatches: 24, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
272 59 0.24
273 175 0.71
274 12 0.05
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (272 bp):
GAGGAAAAATACTTTTGAAAAATTAAAAATTTCTTTCAAAAATTGATTGTTTAGCACTACTTTTA
GCCAAAAAACACTTTTACAGTAAAAAATACTTTTTGAAAGCATTGGTGAATAGGGCCAAACACGG
ACTCCTCTAGAGACTATAATTTTTTTATTTTTCTTTCTTTTATTTTCCTTAATTTATGCAATGGT
CTCCATCCCCAAACTCAATTCGAAATTGAGGTTGAAATTTTTTTTGTTGGCCAGCGAAAATTTAG
ATCGAAAAAATT
Found at i:21613 original size:139 final size:139
Alignment explanation
Indices: 21443--21721 Score: 454
Period size: 139 Copynumber: 2.0 Consensus size: 139
21433 TATTGTTAAT
*
21443 TTTAGATTTAATATTAAGATTATATTGTTGTTAG-TAAAGATTGTATTTGTGTTTAAGGTGTAAG
1 TTTAGATTTAATATTAAGATTATATTGTTGTTAGTTAAAG-TTATATTTGTGTTTAAGGTGTAAG
* *
21507 GATAGATTAAGATAGTTTTAATGTA-TGTTTTTTTAGTTTGTAATAATAATTTTTATATTATAAT
65 GATAGATTAAGATAGTTTTAATATATTGTTTTTTTAGTTTGTAATAATAATTTGTATATTATAAT
21571 ATTTTACATA
130 ATTTTACATA
* * * * *
21581 TTTAGATTTAATATTTAAGATTTTATTTTTGTTTGTTAAAGTTATATTTGTGTTTAAGTTGTAGG
1 TTTAGATTTAATA-TTAAGATTATATTGTTGTTAGTTAAAGTTATATTTGTGTTTAAGGTGTAAG
21646 GATAGATTAAGATAGTTTTAATATATTGTTTTTTTAGTTTGTAATAATAATTTGTATATTATAAT
65 GATAGATTAAGATAGTTTTAATATATTGTTTTTTTAGTTTGTAATAATAATTTGTATATTATAAT
21711 ATTTTACATA
130 ATTTTACATA
21721 T
1 T
21722 AATTTTTAGA
Statistics
Matches: 130, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
138 13 0.10
139 63 0.48
140 54 0.42
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (139 bp):
TTTAGATTTAATATTAAGATTATATTGTTGTTAGTTAAAGTTATATTTGTGTTTAAGGTGTAAGG
ATAGATTAAGATAGTTTTAATATATTGTTTTTTTAGTTTGTAATAATAATTTGTATATTATAATA
TTTTACATA
Found at i:26243 original size:74 final size:74
Alignment explanation
Indices: 26162--26310 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
26152 AGATGATGCT
26162 TATGTTTCTTTATTTTGTTTTTATCTTTTAATGCTATTATAACATATATTTAATTTTAAAATAAA
1 TATGTTTCTTTATTTTGTTTTTATCTTTTAATGCTATTATAACATATATTTAATTTTAAAATAAA
26227 ACATTTTAA
66 ACATTTTAA
26236 TATGTTTCTTTATTTTGTTTTTATCTTTTAATGCTATTATAACATATATTTAATTTTAAAATAAA
1 TATGTTTCTTTATTTTGTTTTTATCTTTTAATGCTATTATAACATATATTTAATTTTAAAATAAA
26301 ACATTTTAA
66 ACATTTTAA
26310 T
1 T
26311 CATATAATTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.56
Consensus pattern (74 bp):
TATGTTTCTTTATTTTGTTTTTATCTTTTAATGCTATTATAACATATATTTAATTTTAAAATAAA
ACATTTTAA
Found at i:28218 original size:17 final size:17
Alignment explanation
Indices: 28184--28218 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28174 ACAATTAAAG
* *
28184 AAAAAAATTAATATATT
1 AAAAAAATTAAAAAATT
28201 AAAAAAATTAAAAAATT
1 AAAAAAATTAAAAAATT
28218 A
1 A
28219 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAAATTAAAAAATT
Found at i:28226 original size:20 final size:20
Alignment explanation
Indices: 28202--28240 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28192 TAATATATTA
28202 AAAAAATTAAAAAATTATAAT
1 AAAAAA-TAAAAAATTATAAT
*
28223 AAAAAATAAAATATTATA
1 AAAAAATAAAAAATTATA
28241 GCTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAATAAAAAATTATAAT
Found at i:29630 original size:5 final size:5
Alignment explanation
Indices: 29620--29654 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
29610 AAGGGACAGG
29620 GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA
1 GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA
29655 CCGAAGTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.60, T:0.00
Consensus pattern (5 bp):
GGGCA
Found at i:32774 original size:30 final size:27
Alignment explanation
Indices: 32733--32790 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
32723 GCATAAAATA
32733 AATGCACAAATAGGTCAAATTTCTATGATT
1 AATGCACAAATAGGT--AATTTCT-TGATT
* *
32763 AATGGACAAATATGTAATTTCTTGATT
1 AATGCACAAATAGGTAATTTCTTGATT
32790 A
1 A
32791 TAATTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 7 0.27
30 13 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (27 bp):
AATGCACAAATAGGTAATTTCTTGATT
Found at i:40253 original size:15 final size:15
Alignment explanation
Indices: 40208--40254 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
40198 CTCCTATTAT
*
40208 ATTTTAGTTATTTAT
1 ATTTTAGTTATTTAC
* * *
40223 ATTTGAATT-GTTAC
1 ATTTTAGTTATTTAC
40237 ATTTTAGTTATTTAC
1 ATTTTAGTTATTTAC
40252 ATT
1 ATT
40255 ATCTTTATGT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.60
Consensus pattern (15 bp):
ATTTTAGTTATTTAC
Found at i:40405 original size:18 final size:18
Alignment explanation
Indices: 40382--40421 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
40372 TAATAGATTT
40382 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
40400 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
40418 TTAA
1 TTAA
40422 ATACACCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Done.