Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014716.1 Kokia drynarioides strain JFW-HI SEQ_129755, 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: 29072
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:266 original size:22 final size:22
Alignment explanation
Indices: 227--290 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
217 GTAAGCACAC
227 ACAGTGCAATCCAGTAGGCGCAA
1 ACAGTGCAAT-CAGTAGGCGCAA
*
250 ACAGTGCAATCAGTAGGCGCAC
1 ACAGTGCAATCAGTAGGCGCAA
* *
272 ATAGCGCAAATCAGTAGGC
1 ACAGTGC-AATCAGTAGGC
291 ACACGAAGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.34, C:0.25, G:0.27, T:0.14
Consensus pattern (22 bp):
ACAGTGCAATCAGTAGGCGCAA
Found at i:310 original size:23 final size:23
Alignment explanation
Indices: 279--336 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
269 CACATAGCGC
*
279 AAATCAGTAGGCACACGAAGTGCG
1 AAAT-AGTAAGCACACGAAGTGCG
*
303 AAATAGTAAGCACACGATGTGCG
1 AAATAGTAAGCACACGAAGTGCG
*
326 AAACAGTAAGC
1 AAATAGTAAGC
337 GCACTAGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (23 bp):
AAATAGTAAGCACACGAAGTGCG
Found at i:7508 original size:22 final size:22
Alignment explanation
Indices: 7457--7536 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 22
7447 GCTGGAGAAA
*
7457 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
7479 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
7502 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
7525 CAGTAGGCACAC
1 CAGTAGGCACAC
7537 GAAGTGTGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 16 0.31
23 35 0.69
ACGTcount: A:0.36, C:0.29, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:7551 original size:23 final size:23
Alignment explanation
Indices: 7429--7578 Score: 89
Period size: 23 Copynumber: 6.4 Consensus size: 23
7419 CGAAGTACTT
7429 AACAGTAAGCACAC-AAGTGCTGGAGA
1 AACAGTAAGCACACGAAGTGC----GA
7455 AACAGTAAGCACAC-ACAGTGC-A
1 AACAGTAAGCACACGA-AGTGCGA
* *
7477 ATCCAGTAGGCACAC-ACAGTGC-A
1 A-ACAGTAAGCACACGA-AGTGCGA
* * * *
7500 ATCAGTAGGCGCAC-ATAGCGC-A
1 AACAGTAAGCACACGA-AGTGCGA
* *
7522 AATCAGTAGGCACACGAAGTGTGA
1 AA-CAGTAAGCACACGAAGTGCGA
*
7546 AACAGTAAGCACACGATGTGCGA
1 AACAGTAAGCACACGAAGTGCGA
7569 AACAGTAAGC
1 AACAGTAAGC
7579 GCACTAGCGT
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
22 20 0.19
23 62 0.58
24 4 0.04
26 15 0.14
27 5 0.05
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (23 bp):
AACAGTAAGCACACGAAGTGCGA
Found at i:14794 original size:6 final size:6
Alignment explanation
Indices: 14769--14813 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
14759 ACAATTCATA
* * *
14769 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
14814 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:20557 original size:21 final size:21
Alignment explanation
Indices: 20519--20558 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20509 TTTTAAAAGG
*
20519 TTTTTTACCAAATCTTTTTTT
1 TTTTTTACCAAATATTTTTTT
**
20540 TTTTTTACTTAATATTTTT
1 TTTTTTACCAAATATTTTT
20559 GTCAAGCCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTACCAAATATTTTTTT
Found at i:25451 original size:21 final size:23
Alignment explanation
Indices: 25427--25476 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
25417 AAAATTCGAA
*
25427 AAATAATTTAA-AT-TTTGAGTT
1 AAATAATTCAAGATATTTGAGTT
*
25448 AAATAATTCAAGTTATTTGAGTT
1 AAATAATTCAAGATATTTGAGTT
25471 AAATAA
1 AAATAA
25477 GTTATTCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 1 0.04
23 14 0.56
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (23 bp):
AAATAATTCAAGATATTTGAGTT
Done.