Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010266.1 Kokia drynarioides strain JFW-HI SEQ_125105, 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: 23668
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:2025 original size:16 final size:16
Alignment explanation
Indices: 2001--2038 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1991 AATCTTTTAA
2001 AAAATAAAT-AAAATTT
1 AAAA-AAATAAAAATTT
2017 CAAAAAAATAAAAATTT
1 -AAAAAAATAAAAATTT
2034 AAAAA
1 AAAAA
2039 TATACCCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAAATAAAAATTT
Found at i:5584 original size:16 final size:16
Alignment explanation
Indices: 5563--5593 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5553 TTTGTTGTAA
5563 AACGAATGTTCATAAC
1 AACGAATGTTCATAAC
5579 AACGAATGTTCATAA
1 AACGAATGTTCATAA
5594 TTCTCGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (16 bp):
AACGAATGTTCATAAC
Found at i:6315 original size:3 final size:3
Alignment explanation
Indices: 6307--6350 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
6297 AAAATTAAAC
6307 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
6351 GAAAGATCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6460 original size:18 final size:17
Alignment explanation
Indices: 6434--6491 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
6424 CATCATCGGT
*
6434 TAATAATTAATCAAATA
1 TAATTATTAATCAAATA
6451 TAAGTTATTAAT--AATA
1 TAA-TTATTAATCAAATA
6467 -AA-TATTTAATCAAATA
1 TAATTA-TTAATCAAATA
6483 TAAATTATT
1 T-AATTATT
6492 TATGTTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
13 2 0.06
14 5 0.15
15 2 0.06
16 8 0.24
17 3 0.09
18 11 0.33
19 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (17 bp):
TAATTATTAATCAAATA
Found at i:7659 original size:43 final size:43
Alignment explanation
Indices: 7608--7707 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
7598 TGTTATTCAT
*
7608 TGACATGTTATTAAATTATATTACTTGACTCGTGTTAATATAG
1 TGACATGTTATTAAATTATATTACTTGACTCGTATTAATATAG
* * * *
7651 TGGCATGTTACTAAATTATATTACTTGACTCTTATTAATATCG
1 TGACATGTTATTAAATTATATTACTTGACTCGTATTAATATAG
7694 TGACATGTTATTAA
1 TGACATGTTATTAA
7708 TTGTGCAGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (43 bp):
TGACATGTTATTAAATTATATTACTTGACTCGTATTAATATAG
Found at i:8567 original size:6 final size:6
Alignment explanation
Indices: 8536--8613 Score: 79
Period size: 6 Copynumber: 13.0 Consensus size: 6
8526 CATTAAACCC
* **
8536 AATTCTA AATTTTA AATTTT AA-TTA AATTTA AATTTA AATTTA TTTTTA
1 AATT-TA AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *
8585 AGTTTA AATTT- ATTTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA
8614 TTTTGAGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
5 8 0.14
6 43 0.73
7 6 0.10
8 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (6 bp):
AATTTA
Found at i:8568 original size:17 final size:18
Alignment explanation
Indices: 8541--8639 Score: 87
Period size: 17 Copynumber: 5.6 Consensus size: 18
8531 AACCCAATTC
*
8541 TAAATTTTAAATTTTAAT
1 TAAATTTTAAATTTAAAT
8559 TAAA-TTTAAATTTAAAT
1 TAAATTTTAAATTTAAAT
* * *
8576 TTATTTTTAAGTTTAAAT
1 TAAATTTTAAATTTAAAT
*
8594 T-TATTTTAAATTTAAAT
1 TAAATTTTAAATTTAAAT
* * *
8611 T-TATTTTGAGTTTAAAAT
1 TAAATTTTAAATTT-AAAT
*
8629 TAAAATTTAAA
1 TAAATTTTAAA
8640 ATGTCCAAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
17 38 0.58
18 22 0.34
19 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAAATTTTAAATTTAAAT
Found at i:8584 original size:35 final size:35
Alignment explanation
Indices: 8545--8639 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
8535 CAATTCTAAA
*
8545 TTTTAAATTTTAATTAAATTTAAATTTAAATTTAT
1 TTTTAAATTTAAATTAAATTTAAATTTAAATTTAT
* * *
8580 TTTTAAGTTTAAATTTATTTTAAATTTAAATTTA-
1 TTTTAAATTTAAATTAAATTTAAATTTAAATTTAT
* *
8614 TTTTGAGTTTAAAATTAAAATTTAAA
1 TTTTAAATTT-AAATT-AAATTTAAA
8640 ATGTCCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 9 0.18
35 35 0.69
36 7 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTTAAATTTAAATTAAATTTAAATTTAAATTTAT
Found at i:9627 original size:30 final size:30
Alignment explanation
Indices: 9550--9720 Score: 178
Period size: 29 Copynumber: 5.9 Consensus size: 30
9540 CCCAGAATTC
*
9550 CCAAAAATCACATTTTTATCCCT-AAACTT
1 CCAAAAATCACATTTTTACCCCTAAAACTT
*
9579 CCAAAAATTC-CA-TTTTACCCCTCAAACTT
1 CCAAAAA-TCACATTTTTACCCCTAAAACTT
**
9608 -CAAAAATTCACATTTTTACCCC-CGAACTT
1 CCAAAAA-TCACATTTTTACCCCTAAAACTT
*
9637 CCAAAAATCACATTTTTA-CCCTAAAATTT
1 CCAAAAATCACATTTTTACCCCTAAAACTT
* *
9666 CCCAAAATGACATTTTTACCCCTAAAACTTT
1 CCAAAAATCACATTTTTACCCCTAAAAC-TT
* *
9697 CC-AAAATTACA-TTTTAACCCTAAA
1 CCAAAAATCACATTTTTACCCCTAAA
9721 CTCTCAGAAA
Statistics
Matches: 124, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
28 21 0.17
29 66 0.53
30 33 0.27
31 4 0.03
ACGTcount: A:0.38, C:0.29, G:0.01, T:0.32
Consensus pattern (30 bp):
CCAAAAATCACATTTTTACCCCTAAAACTT
Found at i:10154 original size:97 final size:97
Alignment explanation
Indices: 9978--10163 Score: 277
Period size: 97 Copynumber: 1.9 Consensus size: 97
9968 TTTAAAATCA
* *
9978 AGGCAATATTCCTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTATTAGGCGCAATTTTTCT
1 AGGCAATATTCCTTTATATCGAGTTTTGAAAATTTGTGCCTTAACTTATTAGGCGCAACTTTTCT
*
10043 TCAAACCGGGATAATCGAATACCCCTAAGTCT
66 TCAAACCGGAATAATCGAATACCCCTAAGTCT
* *
10075 AGGCAATGTTTCTTTATATCTG-GTTTTGAAAATTTGTGCCTTAACTTATTAGGCG-AGACTTTT
1 AGGCAATATTCCTTTATATC-GAGTTTTGAAAATTTGTGCCTTAACTTATTAGGCGCA-ACTTTT
* *
10138 CTTTAAATCGGAATAATCGAATACCC
64 CTTCAAACCGGAATAATCGAATACCC
10164 TTTTCCAAGG
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 1 0.01
97 78 0.98
98 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (97 bp):
AGGCAATATTCCTTTATATCGAGTTTTGAAAATTTGTGCCTTAACTTATTAGGCGCAACTTTTCT
TCAAACCGGAATAATCGAATACCCCTAAGTCT
Found at i:12802 original size:36 final size:36
Alignment explanation
Indices: 12755--12827 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
12745 GAAGAAAGAC
12755 TATAAAAAGCTTCACTTGTCAATGAGGACTGCCGAT
1 TATAAAAAGCTTCACTTGTCAATGAGGACTGCCGAT
12791 TATAAAAAGCTTCACTTGTCAATGAGGACTGCCGAT
1 TATAAAAAGCTTCACTTGTCAATGAGGACTGCCGAT
12827 T
1 T
12828 TAGGTAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (36 bp):
TATAAAAAGCTTCACTTGTCAATGAGGACTGCCGAT
Found at i:21973 original size:209 final size:210
Alignment explanation
Indices: 21613--22123 Score: 636
Period size: 209 Copynumber: 2.4 Consensus size: 210
21603 AGAGAAGTTT
* * * *
21613 GAAACTTCGAACCTCAGCTTCCT-ATTGAGGTACTGAGAAGCAAGTCAAAGCAATAAAATTGTCG
1 GAAACTTCGAACCTCAGCTTCCTGA-TGAGGTACTGAGAAGTAGGTCGAAGCAATAAAATGGTCG
* * * *
21677 TCTTCCTGATAAGATACAGAGAAGTGGATCAAATTTGTCTTCCTGATGAGATACAGAGAAGTGGA
65 ACTTCCTGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAAAAGTGGA
* * * *
21742 TTAAAACAAGTGATGCGGTCATCTTCCTGATAAGATACAGAGAAGTATACGAAATCAA-TGAAAC
130 TTAAAACAAATGAGGCGGTCATCTTCCTGATAAGATACAAAGAAGTAGACGAAATCAAGTGAAAC
*
21806 AAGGCTCAACAT-GAGC
195 AAAG-TCAACATCGAGC
21822 GAAACTTCGAACCTCAGCTTCCTGATGAGGTACTGAGAAGTAGGTCGAAGCAATAAAATGGTCGA
1 GAAACTTCGAACCTCAGCTTCCTGATGAGGTACTGAGAAGTAGGTCGAAGCAATAAAATGGTCGA
*
21887 CTTCCTGATGAGATACAGAGAAGTGGACCAAATCTT-TCTTCCTGATGGGATACAGAAAAGTGGA
66 CTTCCTGATGAGATACAGAGAAGTGGACCAAAT-TTGTCTTCCTGATGAGATACAGAAAAGTGGA
* * *
21951 TTAAAACAAATGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGTAGACTAAATCAAGTGAAAT
130 TTAAAACAAATGAGGCGGTCATCTTCCTGATAAGATACAAAGAAGTAGACGAAATCAAGTGAAAC
** * *
22016 AAAGTTTAGATGCGAGT
195 AAAGTCAACAT-CGAGC
* * * * * * * **
22033 GAAGCTTCAAACCCCTATCTTCCTGATGAGATACAGAGAAGTAGGTCGAAGCGATAAAGCGGTC-
1 GAAACTTCGAACCTC-AGCTTCCTGATGAGGTACTGAGAAGTAGGTCGAAGCAATAAAATGGTCG
* *
22097 ATCTTCCTAATGATATAACAGAGAAGT
65 A-CTTCCTGATGAGAT-ACAGAGAAGT
22124 CAACCGAGAG
Statistics
Matches: 262, Mismatches: 32, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
209 171 0.65
210 11 0.04
211 16 0.06
212 54 0.21
213 10 0.04
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (210 bp):
GAAACTTCGAACCTCAGCTTCCTGATGAGGTACTGAGAAGTAGGTCGAAGCAATAAAATGGTCGA
CTTCCTGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAAAAGTGGAT
TAAAACAAATGAGGCGGTCATCTTCCTGATAAGATACAAAGAAGTAGACGAAATCAAGTGAAACA
AAGTCAACATCGAGC
Found at i:22507 original size:7 final size:7
Alignment explanation
Indices: 22492--22540 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
22482 CATTCAACCC
*
22492 AATTCTA
1 AATTTTA
22499 AATTTTA
1 AATTTTA
22506 AATTTTA
1 AATTTTA
22513 AATTTT-
1 AATTTTA
22519 AA--TTA
1 AATTTTA
22524 AA-TTTA
1 AATTTTA
22530 AA-TTTA
1 AATTTTA
22536 AATTT
1 AATTT
22541 ACTTTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 13 0.34
7 21 0.55
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTTA
Found at i:22526 original size:11 final size:12
Alignment explanation
Indices: 22492--22569 Score: 81
Period size: 11 Copynumber: 6.5 Consensus size: 12
22482 CATTCAACCC
22492 AATTCTAAATTTTA
1 AATT-TAAA-TTTA
*
22506 AATTTTAAATTTT
1 AA-TTTAAATTTA
22519 AA-TTAAATTTA
1 AATTTAAATTTA
22530 AATTTAAATTT-
1 AATTTAAATTTA
*
22541 ACTTTAAATTT-
1 AATTTAAATTTA
*
22552 ATTTTAAATTTA
1 AATTTAAATTTA
22564 AATTTA
1 AATTTA
22570 TTTTGAGTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
11 30 0.54
12 13 0.23
13 5 0.09
14 6 0.11
15 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (12 bp):
AATTTAAATTTA
Found at i:22530 original size:6 final size:6
Alignment explanation
Indices: 22492--22569 Score: 81
Period size: 6 Copynumber: 13.0 Consensus size: 6
22482 CATTCAACCC
*
22492 AATTCTA AATTTTA AATTTTA AATTTT AA-TTA AATTTA AATTTA AATTT-
1 AATT-TA AA-TTTA AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *
22541 ACTTTA AATTT- ATTTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA
22570 TTTTGAGTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
5 12 0.20
6 34 0.56
7 13 0.21
8 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:22582 original size:17 final size:17
Alignment explanation
Indices: 22500--22573 Score: 80
Period size: 17 Copynumber: 4.3 Consensus size: 17
22490 CCAATTCTAA
22500 ATTTTAAATTTTAAATTT
1 ATTTTAAA-TTTAAATTT
*
22518 -TAATTAAATTTAAATTT
1 AT-TTTAAATTTAAATTT
* *
22535 AAATTT-ACTTTAAATTT
1 -ATTTTAAATTTAAATTT
22552 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
22569 ATTTT
1 ATTTT
22574 GAGTTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 4 0.09
17 35 0.76
18 7 0.15
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:23319 original size:15 final size:15
Alignment explanation
Indices: 23301--23342 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
23291 ATAATAATGG
23301 TAATAATAAATATAT
1 TAATAATAAATATAT
23316 TAATAATAACA-ATAT
1 TAATAATAA-ATATAT
*
23331 TAGTAATAAATA
1 TAATAATAAATA
23343 ATAAGAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
TAATAATAAATATAT
Found at i:23324 original size:18 final size:19
Alignment explanation
Indices: 23301--23346 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
23291 ATAATAATGG
*
23301 TAATAATAAATA-TATTAA
1 TAATAATAAATATTAGTAA
*
23319 TAATAA-CAATATTAGTAA
1 TAATAATAAATATTAGTAA
23337 TAAATAATAA
1 T-AATAATAA
23347 GAATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 5 0.23
20 1 0.05
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TAATAATAAATATTAGTAA
Done.