Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013657.1 Kokia drynarioides strain JFW-HI SEQ_128685, 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: 38761
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:556 original size:10 final size:10
Alignment explanation
Indices: 541--582 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
531 TCATGTCTTT
541 AAAAAATTAA
1 AAAAAATTAA
551 AAAAAATTAA
1 AAAAAATTAA
**
561 AAATTATT-A
1 AAAAAATTAA
570 AAAAAATTAA
1 AAAAAATTAA
580 AAA
1 AAA
583 TTCAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:594 original size:19 final size:19
Alignment explanation
Indices: 539--597 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
529 TTTCATGTCT
*
539 TTAAAAAAT-TAAAAAAAA
1 TTAAAAATTATAAAAAAAA
*
557 TTAAAAATTATTAAAAAAA
1 TTAAAAATTATAAAAAAAA
576 TTAAAAATTCA-AAAAAAAA
1 TTAAAAATT-ATAAAAAAAA
595 TTA
1 TTA
598 GTATGTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.22
19 27 0.75
20 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAAAAATTATAAAAAAAA
Found at i:623 original size:12 final size:10
Alignment explanation
Indices: 603--651 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 10
593 AATTAGTATG
603 TTTATTTTCAT
1 TTTATTTT-AT
614 TTTCATTTTCATT
1 TTT-ATTTT-A-T
627 TTTAGTTTTAT
1 TTTA-TTTTAT
638 TTTATTTTAT
1 TTTATTTTAT
648 TTTA
1 TTTA
652 ATTATGCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.29
11 8 0.23
12 9 0.26
13 8 0.23
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:642 original size:5 final size:5
Alignment explanation
Indices: 603--651 Score: 53
Period size: 6 Copynumber: 8.8 Consensus size: 5
593 AATTAGTATG
603 TTTAT TTTCAT TTTCAT TTTCATT TTTAGT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTT-AT TTT-AT TTT-A-T TTTA-T TTTAT TTTAT TTTAT TTTA
652 ATTATGCAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
5 18 0.44
6 19 0.46
7 4 0.10
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:2664 original size:23 final size:25
Alignment explanation
Indices: 2638--2683 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2628 CCAATTAGAG
2638 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
2661 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
2684 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:3101 original size:15 final size:15
Alignment explanation
Indices: 3064--3102 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
3054 TTATGTGTGC
*
3064 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
3079 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
3093 TTAATTCTTG
1 TTAATTCTTG
3103 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:11117 original size:21 final size:20
Alignment explanation
Indices: 11076--11117 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11066 TAATCAACTA
*
11076 ATTTTAATGCATCCAAACAT
1 ATTTTAATGCATCAAAACAT
*
11096 ATTTTAATGCATGAATAACAT
1 ATTTTAATGCATCAA-AACAT
11117 A
1 A
11118 AATGATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (20 bp):
ATTTTAATGCATCAAAACAT
Found at i:21662 original size:11 final size:12
Alignment explanation
Indices: 21631--21672 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
21621 TGTGGATGAC
*
21631 AAAATTATATAAA
1 AAAATT-TATATA
21644 AAATATTTAT-TA
1 AAA-ATTTATATA
21656 AAAATTTATATA
1 AAAATTTATATA
21668 AAAAT
1 AAAAT
21673 CAAATTAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 6 0.23
12 11 0.42
13 6 0.23
14 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTTATATA
Found at i:23013 original size:2 final size:2
Alignment explanation
Indices: 23006--23042 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
22996 TTTGAGTTCA
* *
23006 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23043 CTATTTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23689 original size:2 final size:2
Alignment explanation
Indices: 23684--23714 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23674 CATGTATATA
23684 TG TG 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 TG TG T
23715 AATGTGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:30373 original size:15 final size:15
Alignment explanation
Indices: 30355--30468 Score: 54
Period size: 15 Copynumber: 7.3 Consensus size: 15
30345 GTATTGATAT
30355 TAAAAATATATAATA
1 TAAAAATATATAATA
*
30370 TAAAAATATGTAATA
1 TAAAAATATATAATA
* * * *
30385 TGAATATCATTATATTTG
1 TAAAAAT-A-TATA-ATA
30403 TAAAAATATATAAATA
1 TAAAAATATAT-AATA
* *
30419 TTTTTAATAATATAAAATA
1 ----TAAAAATATATAATA
30438 TAAAAATAT-TAAT-
1 TAAAAATATATAATA
* *
30451 TATAAATAAATAA-A
1 TAAAAATATATAATA
30465 TAAA
1 TAAA
30469 TTTCAAATTT
Statistics
Matches: 72, Mismatches: 17, Indels: 21
0.65 0.15 0.19
Matches are distributed among these distances:
13 7 0.10
14 9 0.12
15 27 0.38
16 5 0.07
17 5 0.07
18 6 0.08
19 4 0.06
20 9 0.12
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAAAATATATAATA
Found at i:30419 original size:20 final size:19
Alignment explanation
Indices: 30396--30438 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
30386 GAATATCATT
30396 ATATTTGTAAAAATATATAA
1 ATATTTGTAAAAATATA-AA
* *
30416 ATATTTTTAATAATATAAA
1 ATATTTGTAAAAATATAAA
30435 ATAT
1 ATAT
30439 AAAAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATATTTGTAAAAATATAAA
Found at i:30462 original size:25 final size:27
Alignment explanation
Indices: 30405--30460 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
30395 TATATTTGTA
* *
30405 AAAATATATAAATATTTTTAATAATAT
1 AAAATATAAAAATATTATTAATAATAT
30432 AAAATATAAAAATATTAATT-ATAA-AT
1 AAAATATAAAAATATT-ATTAATAATAT
30458 AAA
1 AAA
30461 TAAATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.19
27 19 0.73
28 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAATATAAAAATATTATTAATAATAT
Found at i:30469 original size:25 final size:27
Alignment explanation
Indices: 30405--30469 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
30395 TATATTTGTA
* *
30405 AAAATATATAAATATTTTTAATAATAT
1 AAAATAAATAAATATTATTAATAATAT
30432 AAAATATAA-AAATATTAATT-ATAA-AT
1 AAAATA-AATAAATATT-ATTAATAATAT
30458 -AAATAAATAAAT
1 AAAATAAATAAAT
30470 TTCAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 2 0.06
25 9 0.27
26 2 0.06
27 17 0.52
28 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAATAAATAAATATTATTAATAATAT
Found at i:31905 original size:3 final size:3
Alignment explanation
Indices: 31899--31939 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31889 CTAATTTTTT
31899 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31940 GGGTTAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:38303 original size:21 final size:20
Alignment explanation
Indices: 38265--38437 Score: 76
Period size: 23 Copynumber: 7.5 Consensus size: 20
38255 ATACGGAACA
* *
38265 AACAGAGAGTACCAAAGTACT
1 AACAGAGAGCA-CAAAGTGCT
*
38286 AACAGAGAGCACATAAGTGGT
1 AACAGAGAGCACA-AAGTGCT
*
38307 GGGCAACAAAGAGCACACACAGTGCT
1 ----AACAGAGAGCACA-A-AGTGCT
*
38333 AAACAGAGAGTACACAAAGTACT
1 -AACAGAGAG--CACAAAGTGCT
38356 AATCAGAGAGCACACACAGTGCT
1 AA-CAGAGAGCACA-A-AGTGCT
*
38379 AATCAGAGAGCATACACAGTGCTAAT
1 AA-CAGAGAGC--ACAAAGTGC---T
*
38405 AACAGAGAGCACAAGACATGCT
1 AACAGAGAGCACAA-A-GTGCT
38427 AAACAGAGAGC
1 -AACAGAGAGC
38438 GCGCTAGTGT
Statistics
Matches: 120, Mismatches: 13, Indels: 36
0.71 0.08 0.21
Matches are distributed among these distances:
20 2 0.02
21 19 0.16
22 4 0.03
23 54 0.45
24 2 0.02
25 31 0.26
26 8 0.07
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
AACAGAGAGCACAAAGTGCT
Found at i:38342 original size:23 final size:23
Alignment explanation
Indices: 38311--38437 Score: 148
Period size: 23 Copynumber: 5.4 Consensus size: 23
38301 AGTGGTGGGC
*
38311 AACAAAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
38334 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
*
38357 ATCAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
38380 ATCAGAGAGCATACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
38404 TAACAGAGAGCACAAGACA-TGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
38428 AACAGAGAGC
1 AACAGAGAGC
38438 GCGCTAGTGT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 69 0.78
24 2 0.02
25 14 0.16
26 4 0.04
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:38389 original size:69 final size:67
Alignment explanation
Indices: 38264--38413 Score: 178
Period size: 69 Copynumber: 2.1 Consensus size: 67
38254 TATACGGAAC
* *
38264 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGGTGGGCAACAAAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAGTGCT--G-AACAAAGAGCACACACAG
38329 TGCT-
63 TGCTA
* *
38333 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCT-AATCAGAGAGCATACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACACA-AGTGCTGAA-CAAAGAGCACACACA
38397 GTGCTA
62 GTGCTA
38403 ATAACAGAGAG
1 A-AACAGAGAG
38414 CACAAGACAT
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
68 2 0.03
69 31 0.44
70 12 0.17
71 21 0.30
72 5 0.07
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACACAAGTGCTGAACAAAGAGCACACACAGTGC
TA
Done.