Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013537.1 Kokia drynarioides strain JFW-HI SEQ_128563, 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: 32035
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:2452 original size:30 final size:30
Alignment explanation
Indices: 2418--2780 Score: 300
Period size: 29 Copynumber: 12.3 Consensus size: 30
2408 TGAAACGATA
* * *
2418 ATTTTGGGAAAATTCGGGGTCAAAAATGAG
1 ATTTTTGGAAATTTCGGGGTCAAAAATGGG
*
2448 ATTTTT-GAAAGTTTTGGGGT-AAAAATGGG
1 ATTTTTGGAAA-TTTCGGGGTCAAAAATGGG
* *
2477 ATTTTTGGAAGTTTTGGGGTCAAAAATGGG
1 ATTTTTGGAAATTTCGGGGTCAAAAATGGG
* *
2507 ATTTTTGG-AAGTTCAGGGGT-AAAAATGAG
1 ATTTTTGGAAATTTC-GGGGTCAAAAATGGG
* * *
2536 ATTTTTGGAAGTTTCGAGGCCAAAAATGGG
1 ATTTTTGGAAATTTCGGGGTCAAAAATGGG
* *
2566 ATTTTTGG-AAGTTCGGGGGT-AAAAATGGA
1 ATTTTTGGAAATTTC-GGGGTCAAAAATGGG
* *
2595 ATTTTTGGAAGTTTTGGGGTCAAAAATGGG
1 ATTTTTGGAAATTTCGGGGTCAAAAATGGG
* * *
2625 ATTTTTTG-AAGTTCGGGGGT-AAAAATAGG
1 ATTTTTGGAAATTTC-GGGGTCAAAAATGGG
* * *
2654 ATTTTTGGAAGTTTTGGGGTTAAAAATGGG
1 ATTTTTGGAAATTTCGGGGTCAAAAATGGG
* ** * *
2684 ATTTTTGGAAGTTTAAGGGT-AAAAACGGA
1 ATTTTTGGAAATTTCGGGGTCAAAAATGGG
* **
2713 ATTTTTGGAAGTTTCAAGGT-AAAAATTGGG
1 ATTTTTGGAAATTTCGGGGTCAAAAA-TGGG
* * *
2743 ATTTTTGG-AAGTTCGGGGGT-AAAAATAGA
1 ATTTTTGGAAATTTC-GGGGTCAAAAATGGG
2772 ATTTTTGGA
1 ATTTTTGGA
2781 CAGTTTAGGG
Statistics
Matches: 271, Mismatches: 47, Indels: 30
0.78 0.14 0.09
Matches are distributed among these distances:
29 141 0.52
30 130 0.48
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (30 bp):
ATTTTTGGAAATTTCGGGGTCAAAAATGGG
Found at i:2481 original size:59 final size:59
Alignment explanation
Indices: 2430--2786 Score: 473
Period size: 59 Copynumber: 6.0 Consensus size: 59
2420 TTTGGGAAAA
* * **
2430 TTCGGGGTCAAAAATGAGATTTTTGAAAGTTTTGGGGTAAAAATGGGATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGT
* * *
2489 TTTGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAAATGAGATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGT
* * *
2548 TTCGAGGCCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGT
* * *
2607 TTTGGGGTCAAAAATGGGATTTTTTGAAGTTCGGGGGTAAAAATAGGATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGT
* * *** * *
2666 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTAAGGGTAAAAACGGAATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGT
** * *
2725 TTCAAGGT-AAAAATTGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGGACAGT
1 TTCGGGGTCAAAAA-TGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGA-AGT
2785 TT
1 TT
2787 AGGGACCTTC
Statistics
Matches: 262, Mismatches: 34, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
58 5 0.02
59 252 0.96
60 5 0.02
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (59 bp):
TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGT
Found at i:3858 original size:17 final size:16
Alignment explanation
Indices: 3836--3877 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
3826 TGTCATTAAT
3836 AATATTATTATTAAGAA
1 AATATTATTATTAA-AA
*
3853 AATATTTATTATTAATA
1 AATA-TTATTATTAAAA
3870 AATATTAT
1 AATATTAT
3878 GAAAACCGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 9 0.39
18 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATATTATTATTAAAA
Found at i:4637 original size:6 final size:6
Alignment explanation
Indices: 4623--4686 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
4613 ATTTGGAAAA
* *
4623 TAAATT TAAACT TAAA-T TAAATT TAAATT CGAAA-- TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT TAAATT
*
4669 T-AATA TAAATT TAAATT T
1 TAAATT TAAATT TAAATT T
4687 CTACACAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 33 0.69
7 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:4686 original size:17 final size:16
Alignment explanation
Indices: 4591--4686 Score: 95
Period size: 17 Copynumber: 5.6 Consensus size: 16
4581 CCTTATTTAT
4591 TTTAAATTTATAAT-AA
1 TTTAAATTTA-AATAAA
4607 TCTTAAATTTGGAAAATAAA
1 T-TTAAATTT---AAATAAA
*
4627 TTTAAACTTAAATTAAA
1 TTTAAATTTAAA-TAAA
*
4644 TTTAAATTCGAAATAAA
1 TTTAAATT-TAAATAAA
4661 TTTAAATTTAATATAAA
1 TTTAAATTTAA-ATAAA
4678 TTTAAATTT
1 TTTAAATTT
4687 CTACACAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
16 6 0.09
17 45 0.66
18 3 0.04
19 10 0.15
20 4 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:17064 original size:25 final size:25
Alignment explanation
Indices: 17036--17100 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
17026 TTTTTTTCTG
* *
17036 TTTTAGTTGCTATTTTGGTGCT-TT
1 TTTTTGTTGCTATTTTGATGCTGTT
* *
17060 TTTTTTTTACTATTTTGATGCTGTT
1 TTTTTGTTGCTATTTTGATGCTGTT
*
17085 TTTTTGTTGTTATTTT
1 TTTTTGTTGCTATTTT
17101 TGTTGTTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.69
Consensus pattern (25 bp):
TTTTTGTTGCTATTTTGATGCTGTT
Found at i:17322 original size:29 final size:27
Alignment explanation
Indices: 17266--17323 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
17256 TATAAAAAAA
*
17266 TTTTAATGTATTTTAAATTTTTTTATT
1 TTTTAATGTATTTTAAATTTTTTAATT
* *
17293 TTTTAATGTTTGTTTTAATATTTTTAATT
1 TTTTAATGTAT-TTTAAAT-TTTTTAATT
17322 TT
1 TT
17324 ATTTGATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 10 0.38
28 6 0.23
29 10 0.38
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (27 bp):
TTTTAATGTATTTTAAATTTTTTAATT
Found at i:17323 original size:27 final size:26
Alignment explanation
Indices: 17264--17347 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 26
17254 AATATAAAAA
*
17264 AATTTTAATGTATTTTAAATTTTTTT
1 AATTTTAATGTATTTTAAATATTTTT
* * *
17290 ATTTTTTAATGTTTGTTTTAATATTTTT
1 A-ATTTTAATGTAT-TTTAAATATTTTT
* * *
17318 AATTTTATTTGATATATTATATATTTTT
1 AATTTTA-ATG-TATTTTAAATATTTTT
17346 AA
1 AA
17348 AATTATTGTA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
26 1 0.02
27 15 0.34
28 26 0.59
29 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (26 bp):
AATTTTAATGTATTTTAAATATTTTT
Found at i:17334 original size:21 final size:21
Alignment explanation
Indices: 17292--17335 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17282 ATTTTTTTAT
* *
17292 TTTTTAATGTTTGTTTTAATA
1 TTTTTAATGTTTATTTGAATA
17313 TTTTTAAT-TTTATTTGATATA
1 TTTTTAATGTTTATTTGA-ATA
17334 TT
1 TT
17336 ATATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTTTAATGTTTATTTGAATA
Found at i:17762 original size:22 final size:22
Alignment explanation
Indices: 17734--17776 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17724 ATTTTCTAAT
17734 AGATTTAATGAATAAATTCAAA
1 AGATTTAATGAATAAATTCAAA
17756 AGATTTAATGAATAAATTCAA
1 AGATTTAATGAATAAATTCAA
17777 GGTTTCAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (22 bp):
AGATTTAATGAATAAATTCAAA
Found at i:22131 original size:37 final size:37
Alignment explanation
Indices: 22081--22181 Score: 202
Period size: 37 Copynumber: 2.7 Consensus size: 37
22071 TTCTTTCATA
22081 TCACTATGCATAGCTAGCATATGATTTATGTATGGGG
1 TCACTATGCATAGCTAGCATATGATTTATGTATGGGG
22118 TCACTATGCATAGCTAGCATATGATTTATGTATGGGG
1 TCACTATGCATAGCTAGCATATGATTTATGTATGGGG
22155 TCACTATGCATAGCTAGCATATGATTT
1 TCACTATGCATAGCTAGCATATGATTT
22182 TGGGACCTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.36
Consensus pattern (37 bp):
TCACTATGCATAGCTAGCATATGATTTATGTATGGGG
Found at i:22641 original size:20 final size:20
Alignment explanation
Indices: 22616--22655 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
22606 ATTAAATATG
22616 ATTAAAAACTAATGTTCATA
1 ATTAAAAACTAATGTTCATA
22636 ATTAAAAACTAATGTTCATA
1 ATTAAAAACTAATGTTCATA
22656 CAAGAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTAAAAACTAATGTTCATA
Found at i:22663 original size:21 final size:20
Alignment explanation
Indices: 22619--22663 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
22609 AAATATGATT
**
22619 AAAAACTAATGTTCATAATT
1 AAAAACTAATGTTCATAAAG
22639 AAAAACTAATGTTCATACAAG
1 AAAAACTAATGTTCATA-AAG
22660 AAAA
1 AAAA
22664 CTCAAGATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAAACTAATGTTCATAAAG
Found at i:23080 original size:19 final size:20
Alignment explanation
Indices: 23030--23087 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
23020 TCACTTTGTC
** *
23030 TATTTTTTCTATTTTTATAT
1 TATTTTTTGAATTTTTATAG
23050 TATTTCTTTGAATTTTTAT-G
1 TATTT-TTTGAATTTTTATAG
23070 TATTTTTTGAATTATTTA
1 TATTTTTTGAATT-TTTA
23088 AGAAATTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 8 0.24
20 14 0.42
21 11 0.33
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.69
Consensus pattern (20 bp):
TATTTTTTGAATTTTTATAG
Found at i:26626 original size:2 final size:2
Alignment explanation
Indices: 26621--26647 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26611 TATATATATA
26621 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
26648 ATGATGTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:29667 original size:86 final size:87
Alignment explanation
Indices: 29504--29675 Score: 310
Period size: 86 Copynumber: 2.0 Consensus size: 87
29494 TCGAGTTATG
*
29504 ACTTAATCGACAATATAAACACATTTTTAATAACTTTTTTAACTATTATTTAACTTTGTATAGTT
1 ACTTAATCGACAATATAAACACATTTTTAATAAC-TTTTTAACTATTATTTAACTTTGTATAATT
*
29569 TTAATATTATATCATTAAATGCA
65 CTAATATTATATCATTAAATGCA
29592 ACTTAATCGACAATATAAACACATTTTTAATAAC-TTTTAACTATTATTTAACTTTGTATAATTC
1 ACTTAATCGACAATATAAACACATTTTTAATAACTTTTTAACTATTATTTAACTTTGTATAATTC
29656 TAATATTATATCATTAAATG
66 TAATATTATATCATTAAATG
29676 TCACTTTTTA
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
86 48 0.59
88 34 0.41
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.45
Consensus pattern (87 bp):
ACTTAATCGACAATATAAACACATTTTTAATAACTTTTTAACTATTATTTAACTTTGTATAATTC
TAATATTATATCATTAAATGCA
Found at i:31201 original size:29 final size:29
Alignment explanation
Indices: 31169--31465 Score: 170
Period size: 29 Copynumber: 10.1 Consensus size: 29
31159 GTTCGGAATC
*
31169 AAAAATAGGATTTTTGGAAGTTTGAGGGT
1 AAAAATAGGATTTTTGGAAGTTCGAGGGT
*
31198 -AAAAT-GGTAATTTTTGGAAATTCGA-GG-
1 AAAAATAGG--ATTTTTGGAAGTTCGAGGGT
* * **
31225 AAAAATAGTAATTTTTGGAAGATTCAAGGCC
1 AAAAATAG-GATTTTTGGAAG-TTCGAGGGT
* * * *
31256 AAAAATGGGATTGTTGGAAGTTTGGGGGT
1 AAAAATAGGATTTTTGGAAGTTCGAGGGT
** *
31285 -AAAAT-GGTAATTTTAAGAAGGTTTG-GGGTT
1 AAAAATAGG--ATTTTTGGAA-GTTCGAGGG-T
*
31315 AAAAATGGGATTTTTGGAAGTTC-AGCGGT
1 AAAAATAGGATTTTTGGAAGTTCGAG-GGT
* * *
31344 -AAAATAGTAATTTTTGTAAGGTTCG-GGAT
1 AAAAATAG-GATTTTTGGAA-GTTCGAGGGT
* *
31373 AAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 -AAAAATAGGATTTTTGGAAGTTCGAGGGT
*
31403 -AAAATAGTAATTTTTGGAAGATTCG-GGGT
1 AAAAATAG-GATTTTTGGAAG-TTCGAGGGT
*
31432 CAAAAAT-GAGATTTTTGGAAGTTCGGGGGT
1 -AAAAATAG-GATTTTTGGAAGTTCGAGGGT
31462 AAAA
1 AAAA
31466 TAGTAAAATA
Statistics
Matches: 209, Mismatches: 32, Indels: 54
0.71 0.11 0.18
Matches are distributed among these distances:
27 4 0.02
28 39 0.19
29 77 0.37
30 64 0.31
31 23 0.11
32 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (29 bp):
AAAAATAGGATTTTTGGAAGTTCGAGGGT
Found at i:31261 original size:59 final size:59
Alignment explanation
Indices: 31170--31551 Score: 396
Period size: 59 Copynumber: 6.4 Consensus size: 59
31160 TTCGGAATCA
* * * * * *
31170 AAAATAG-GATTTTTGGAAG-TTTGAGGGT--AAAATGGTAATTTTTGGAAATTC-GAGGA
1 AAAATAGTAATTTTTGGAAGATTCG-GGGTCAAAAATGG-GATTTTTGGAAGTTCGGGGGT
** * * *
31226 AAAATAGTAATTTTTGGAAGATTCAAGGCCAAAAATGGGATTGTTGGAAGTTTGGGGGT
1 AAAATAGTAATTTTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* ** * * * * *
31285 AAAATGGTAATTTTAAGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCAGCGGT
1 AAAATAGTAATTTTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
31344 AAAATAGTAATTTTTGTAAGGTTCGGGATAAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATAGTAATTTTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
*
31403 AAAATAGTAATTTTTGGAAGATTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATA
1 AAAATAGTAATTTTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-GGGG-------
31468 GT
58 GT
* * *
31470 AAAATAGTAATTTTTAGAAGATTCGGGGTTAAAAATGGGATTTTTGGAAGTTAGGGGGT
1 AAAATAGTAATTTTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
31529 AAAATAGTAATTTTTGGAAGATT
1 AAAATAGTAATTTTTGGAAGATT
31552 TAGGGACCTC
Statistics
Matches: 270, Mismatches: 43, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
56 7 0.03
57 13 0.05
58 13 0.05
59 178 0.66
60 4 0.01
66 4 0.01
67 51 0.19
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAATAGTAATTTTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:31389 original size:30 final size:29
Alignment explanation
Indices: 31150--31532 Score: 179
Period size: 30 Copynumber: 12.7 Consensus size: 29
31140 AGAATGGTAG
** * *
31150 TTTTGGAATGTTCGGAATCAAAAATAGGAT
1 TTTTGGAA-GTTCGGGGTAAAAAATGGGAT
* *
31180 TTTTGGAAGTTTGAGGGT--AAAATGGTAAT
1 TTTTGGAAGTTCG-GGGTAAAAAATGG-GAT
* * **
31209 TTTTGGAAATTCGAGG--AAAAATAGTAAT
1 TTTTGGAAGTTCGGGGTAAAAAAT-GGGAT
** **
31237 TTTTGGAAGATTCAAGGCCAAAAATGGGAT
1 TTTTGGAAG-TTCGGGGTAAAAAATGGGAT
* * *
31267 TGTTGGAAGTTTGGGGGT--AAAATGGTAAT
1 TTTTGGAAG-TTCGGGGTAAAAAATGG-GAT
** * *
31296 TTTAAGAAGGTTTGGGGTTAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGTAAAAAATGGGAT
* * **
31326 TTTTGGAAGTTCAGCGGTAAAATA-GTAAT
1 TTTTGGAAGTTC-GGGGTAAAAAATGGGAT
* *
31355 TTTTGTAAGGTTCGGGATAAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGTAAAAAATGGGAT
* **
31385 TTTTGGAAGTTCGGGGGTAAAATA-GTAAT
1 TTTTGGAAGTTC-GGGGTAAAAAATGGGAT
* *
31414 TTTTGGAAGATTCGGGGTCAAAAATGAGAT
1 TTTTGGAAG-TTCGGGGTAAAAAATGGGAT
**
31444 TTTTGGAAGTTCGGGGGTAAAATAGTAAAATAGTAAT
1 TTTTGGAAGTTC-GGGGT---A-A--AAAAT-GGGAT
* *
31481 TTTTAGAAGATTCGGGGTTAAAAATGGGAT
1 TTTTGGAAG-TTCGGGGTAAAAAATGGGAT
*
31511 TTTTGGAAGTTAGGGGGTAAAA
1 TTTTGGAAGTT-CGGGGTAAAA
31533 TAGTAATTTT
Statistics
Matches: 268, Mismatches: 58, Indels: 54
0.71 0.15 0.14
Matches are distributed among these distances:
28 31 0.12
29 89 0.33
30 104 0.39
31 18 0.07
33 1 0.00
34 1 0.00
36 5 0.02
37 16 0.06
38 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
TTTTGGAAGTTCGGGGTAAAAAATGGGAT
Found at i:31512 original size:67 final size:67
Alignment explanation
Indices: 31401--31538 Score: 240
Period size: 67 Copynumber: 2.1 Consensus size: 67
31391 AAGTTCGGGG
* *
31401 GTAAAATAGTAATTTTTGGAAGATTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAA
1 GTAAAATAGTAATTTTTAGAAGATTCGGGGTCAAAAATGAGATTTTTGGAAGTTAGGGGGTAAAA
31466 TA
66 TA
* *
31468 GTAAAATAGTAATTTTTAGAAGATTCGGGGTTAAAAATGGGATTTTTGGAAGTTAGGGGGTAAAA
1 GTAAAATAGTAATTTTTAGAAGATTCGGGGTCAAAAATGAGATTTTTGGAAGTTAGGGGGTAAAA
31533 TA
66 TA
31535 GTAA
1 GTAA
31539 TTTTTGGAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (67 bp):
GTAAAATAGTAATTTTTAGAAGATTCGGGGTCAAAAATGAGATTTTTGGAAGTTAGGGGGTAAAA
TA
Found at i:31541 original size:29 final size:30
Alignment explanation
Indices: 31468--31556 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 30
31458 GGGTAAAATA
* *
31468 GTAAAATAGTAATTTTTAGAAGATTCGGGG
1 GTAAAATAGTAATTTTTGGAAGATTAGGGG
* **
31498 TTAAAA-ATGGGATTTTTGGAAG-TTAGGGG
1 GTAAAATA-GTAATTTTTGGAAGATTAGGGG
31527 GTAAAATAGTAATTTTTGGAAGATTTAGGG
1 GTAAAATAGTAATTTTTGGAAGA-TTAGGG
31557 ACCTCCGGGG
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
29 24 0.51
30 17 0.36
31 6 0.13
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.35
Consensus pattern (30 bp):
GTAAAATAGTAATTTTTGGAAGATTAGGGG
Done.