Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011343.1 Kokia drynarioides strain JFW-HI SEQ_126323, 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: 56972
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:9536 original size:19 final size:20
Alignment explanation
Indices: 9502--9540 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9492 TATTATACTA
*
9502 ATAAAAAATATGTAAAATTG
1 ATAAAAAAAATGTAAAATTG
9522 ATAAAAAAAAT-TAAAATTG
1 ATAAAAAAAATGTAAAATTG
9541 TGATTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (20 bp):
ATAAAAAAAATGTAAAATTG
Found at i:13235 original size:21 final size:22
Alignment explanation
Indices: 13202--13255 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
13192 ATAATATTCA
*
13202 TATTT-AATATTAAATCTATTT
1 TATTTAAATATTAAATATATTT
*
13223 TATTTAAAT-TTAATTATATTT
1 TATTTAAATATTAAATATATTT
13244 T-TTTAAAATATT
1 TATTT-AAATATT
13256 TTAAAAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 3 0.11
21 20 0.71
22 5 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTAAATATTAAATATATTT
Found at i:14358 original size:11 final size:11
Alignment explanation
Indices: 14344--14380 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
14334 AAATGACTGC
14344 AAAACAACGAG
1 AAAACAACGAG
14355 AAAACAACGAG
1 AAAACAACGAG
*
14366 AAAACAACAAG
1 AAAACAACGAG
14377 AAAA
1 AAAA
14381 TAATAGCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.70, C:0.16, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAACAACGAG
Found at i:14391 original size:22 final size:22
Alignment explanation
Indices: 14342--14407 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
14332 TAAAATGACT
* *
14342 GCAAAACAACGAGAAAACAACGA
1 GCAAAACAACAAGAAAACAA-TA
*
14365 G-AAAACAACAAGAAAATAATA
1 GCAAAACAACAAGAAAACAATA
*
14386 GCAAAATAACAAGAAAACAATA
1 GCAAAACAACAAGAAAACAATA
14408 ATTAATTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.05
22 34 0.92
23 1 0.03
ACGTcount: A:0.67, C:0.15, G:0.12, T:0.06
Consensus pattern (22 bp):
GCAAAACAACAAGAAAACAATA
Found at i:14402 original size:11 final size:11
Alignment explanation
Indices: 14344--14405 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
14334 AAATGACTGC
*
14344 AAAACAACGAG
1 AAAACAACAAG
*
14355 AAAACAACGAG
1 AAAACAACAAG
14366 AAAACAACAAG
1 AAAACAACAAG
* *
14377 AAAATAA-TAG
1 AAAACAACAAG
*
14387 CAAAATAACAAG
1 -AAAACAACAAG
14399 AAAACAA
1 AAAACAA
14406 TAATTAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
10 2 0.05
11 40 0.91
12 2 0.05
ACGTcount: A:0.69, C:0.15, G:0.11, T:0.05
Consensus pattern (11 bp):
AAAACAACAAG
Found at i:21921 original size:16 final size:18
Alignment explanation
Indices: 21902--21941 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
21892 TAGTCGTATT
21902 TTATAACAA-T-ATTTTA
1 TTATAACAATTAATTTTA
21918 TTATAACAATTAATTTTA
1 TTATAACAATTAATTTTA
21936 TTATAA
1 TTATAA
21942 AATCGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.41
17 1 0.05
18 12 0.55
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATAACAATTAATTTTA
Found at i:25136 original size:3 final size:3
Alignment explanation
Indices: 25128--25155 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25118 ATGCAGAAAA
25128 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
25156 TGATGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:26674 original size:17 final size:18
Alignment explanation
Indices: 26649--26685 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
26639 TTATTTAAAA
26649 ATTATAAAT-ATATAAATT
1 ATTATAAATAATA-AAATT
26667 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
26684 AT
1 AT
26686 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:55408 original size:22 final size:22
Alignment explanation
Indices: 55383--55443 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
55373 CGATCTAAGG
* *
55383 AAAAATCAAAGAAAA-AGGATT
1 AAAAATAAAAGAAAATAGAATT
55404 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
55426 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
55444 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.40
22 20 0.57
23 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:55436 original size:15 final size:16
Alignment explanation
Indices: 55409--55438 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55399 GGATTAAAAA
55409 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
55425 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
55439 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:56773 original size:23 final size:23
Alignment explanation
Indices: 56699--56880 Score: 90
Period size: 23 Copynumber: 8.5 Consensus size: 23
56689 TAAACGGAAC
* * *
56699 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
56721 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
56743 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
56769 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* *
56789 --AC--TGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
56808 AATCAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* *
56828 --AC--TGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
56847 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
56870 AAACAAAGAGC
1 AAACAGAGAGC
56881 GCGCTAGTGT
Statistics
Matches: 117, Mismatches: 24, Indels: 37
0.66 0.13 0.21
Matches are distributed among these distances:
16 18 0.15
18 5 0.04
19 2 0.02
20 2 0.02
21 4 0.03
22 18 0.15
23 48 0.41
25 13 0.11
26 7 0.06
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:56807 original size:39 final size:39
Alignment explanation
Indices: 56753--56866 Score: 192
Period size: 39 Copynumber: 2.9 Consensus size: 39
56743 GGGCAACAGA
* *
56753 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACACAGTGCTAATCAGAGAGTACACAAAGTACT
56792 GAGCACACACAGTGCTAATCAGAGAGTACACAAAGTACT
1 GAGCACACACAGTGCTAATCAGAGAGTACACAAAGTACT
* *
56831 GAGCACACACAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACACAGTGCTAATCAGAGAGTACACAAAGT
56867 GCTAAACAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.13
Consensus pattern (39 bp):
GAGCACACACAGTGCTAATCAGAGAGTACACAAAGTACT
Done.