Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009012.1 Kokia drynarioides strain JFW-HI SEQ_123710, 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: 18257
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:202 original size:60 final size:59
Alignment explanation
Indices: 119--453 Score: 293
Period size: 60 Copynumber: 5.6 Consensus size: 59
109 AGAGAAAGTT
* * *
119 GGTGTC-AGCCATTGCATGACCAACACTAAAAAATTTGATTTTTTTTATCAGATAAATAAG
1 GGTGTCGA-CCATGGCATGGCCAACACAAAAAAATTTGA-TTTTTTTATCAGATAAATAAG
** ** * *
179 GGTGTCGGTCATGGCATGGCCAACACCCAAAAATTTAATTTTTTTATTCAGATAAAAAAAGG
1 GGTGTCGACCATGGCATGGCCAACACAAAAAAATTTGATTTTTTTA-TCAGAT-AAATAA-G
* * * **
241 GGTGTCGATCATGGCATGGCTAACACAAAAAAAATTTGAAAATTTTTTATTTGATAAAT-AG
1 GGTGTCGACCATGGCATGGCCAACAC-AAAAAAATTTG--ATTTTTTTATCAGATAAATAAG
* * * * * * *
302 GGTTGTTGACCACGGCATGGTCAACACCAAAAAAA-TTGAATTTTTTATCTGACAAAAAAGG
1 GG-TGTCGACCATGGCATGGCCAACA-CAAAAAAATTTGATTTTTTTATCAGATAAATAA-G
* * * *
363 GGTGTC-AGCCATTGCATAGACAACACAAAAAAATTTGATTTTTTTATCA-ATAAATAGG
1 GGTGTCGA-CCATGGCATGGCCAACACAAAAAAATTTGATTTTTTTATCAGATAAATAAG
*
421 GGTGTCGACCATCGCATGGCCAACACAAAAAAA
1 GGTGTCGACCATGGCATGGCCAACACAAAAAAA
454 ATTAAAATTT
Statistics
Matches: 223, Mismatches: 38, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
58 29 0.13
59 39 0.17
60 66 0.30
61 14 0.06
62 51 0.23
63 12 0.05
64 4 0.02
65 8 0.04
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (59 bp):
GGTGTCGACCATGGCATGGCCAACACAAAAAAATTTGATTTTTTTATCAGATAAATAAG
Found at i:485 original size:60 final size:59
Alignment explanation
Indices: 160--481 Score: 218
Period size: 62 Copynumber: 5.4 Consensus size: 59
150 AATTTGATTT
* * * ** * ** * **
160 TTTTTATCAGATAAATAAGGGTGTCGGTCATGGCATGGCCAACACCCAAAAATTTAATT
1 TTTTTATCTGACAAATAGGGGTGTCGACCATCGCATGGCCAACACAAAAAAAATTAAAA
* * * * * *
219 TTTTTATTCAGATAAAAAAAGGGGTGTCGATCATGGCATGGCTAACACAAAAAAAATTTGAAAA
1 TTTTTA-TCTG--ACAAATAGGGGTGTCGACCATCGCATGGCCAACACAAAAAAAA-TT-AAAA
* * * * * * * *
283 TTTTTTATTTGATAAATAGGGTTGTTGACCA-CGGCATGGTCAACACCAAAAAAATTGAAT
1 -TTTTTATCTGACAAATAGGGGTGTCGACCATC-GCATGGCCAACACAAAAAAAATTAAAA
* * * * * * **
343 TTTTTATCTGACAAAAAAGGGGTGTC-AGCCATTGCATAGACAACACAAAAAAATTTGATT
1 TTTTTATCTGAC-AAATAGGGGTGTCGA-CCATCGCATGGCCAACACAAAAAAAATTAAAA
* *
403 TTTTTATC-AATAAATAGGGGTGTCGACCATCGCATGGCCAACACAAAAAAAATTAAAA
1 TTTTTATCTGACAAATAGGGGTGTCGACCATCGCATGGCCAACACAAAAAAAATTAAAA
*
461 TTTTCATCTGACAAATAGGGG
1 TTTTTATCTGACAAATAGGGG
482 GTGTTGGCAA
Statistics
Matches: 204, Mismatches: 47, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
58 44 0.22
59 29 0.14
60 49 0.24
61 2 0.01
62 68 0.33
63 2 0.01
64 4 0.02
65 6 0.03
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (59 bp):
TTTTTATCTGACAAATAGGGGTGTCGACCATCGCATGGCCAACACAAAAAAAATTAAAA
Found at i:1116 original size:24 final size:24
Alignment explanation
Indices: 1089--1135 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1079 GAGTTAATGT
*
1089 GTTAAA-AATATTAATTAAAAAAAA
1 GTTAAACAATA-TAAATAAAAAAAA
1113 GTTAAAGCAATATAAATAAAAAA
1 GTTAAA-CAATATAAATAAAAAA
1136 TAAAAAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 10 0.50
26 4 0.20
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (24 bp):
GTTAAACAATATAAATAAAAAAAA
Found at i:1414 original size:29 final size:29
Alignment explanation
Indices: 1350--1414 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
1340 TTTAGCTAAA
*
1350 ATTAAAATCGACATAATCTGATAAATTTT
1 ATTAAAATCGACATAATCTGATAAATTTG
** **
1379 AAAAAAATCGATTTAATCTGAT-AATTATG
1 ATTAAAATCGACATAATCTGATAAATT-TG
1408 ATTAAAA
1 ATTAAAA
1415 ATCAACATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (29 bp):
ATTAAAATCGACATAATCTGATAAATTTG
Found at i:3426 original size:7 final size:7
Alignment explanation
Indices: 3414--3466 Score: 97
Period size: 7 Copynumber: 7.6 Consensus size: 7
3404 GTTTAAGATT
3414 CGAGGTA
1 CGAGGTA
3421 CGAGGTA
1 CGAGGTA
3428 CGAGGTA
1 CGAGGTA
3435 CGAGGTA
1 CGAGGTA
3442 CGAGGTA
1 CGAGGTA
3449 CGAGGTA
1 CGAGGTA
*
3456 CGAGGTT
1 CGAGGTA
3463 CGAG
1 CGAG
3467 ATTTAGAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.26, C:0.15, G:0.43, T:0.15
Consensus pattern (7 bp):
CGAGGTA
Found at i:6431 original size:19 final size:19
Alignment explanation
Indices: 6407--6443 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6397 TTATTCCGCT
6407 CTACTTTAATTTAATTTTA
1 CTACTTTAATTTAATTTTA
**
6426 CTACTTTTCTTTAATTTT
1 CTACTTTAATTTAATTTT
6444 TTCAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (19 bp):
CTACTTTAATTTAATTTTA
Found at i:9572 original size:12 final size:12
Alignment explanation
Indices: 9555--9579 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9545 TGCTCTTTTA
9555 AAAAAAAAAAAG
1 AAAAAAAAAAAG
9567 AAAAAAAAAAAG
1 AAAAAAAAAAAG
9579 A
1 A
9580 CTAGTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Done.