Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010599.1 Kokia drynarioides strain JFW-HI SEQ_125530, 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, 898
Length: 1497
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Found at i:445 original size:25 final size:24
Alignment explanation
Indices: 415--494 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 24
405 GGGTTAATTG
415 ATTTGGGCCTATTTGGGCCATTGTA
1 ATTTGGGCCTATTTGGG-CATTGTA
**
440 ATTTGGGTTTAGTTTGGGTCATT-TGA
1 ATTTGGGCCTA-TTTGGG-CATTGT-A
* * *
466 ATTTGGGCCCAATTGGGCTTTGTA
1 ATTTGGGCCTATTTGGGCATTGTA
490 ATTTG
1 ATTTG
495 ACATTTTGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
24 9 0.20
25 16 0.36
26 19 0.43
ACGTcount: A:0.16, C:0.11, G:0.29, T:0.44
Consensus pattern (24 bp):
ATTTGGGCCTATTTGGGCATTGTA
Found at i:542 original size:17 final size:17
Alignment explanation
Indices: 521--628 Score: 128
Period size: 17 Copynumber: 6.2 Consensus size: 17
511 CTTTATTTTT
* * *
521 TTTAAATTTATAGTAAT
1 TTTAAATTTAAAATAAA
538 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
556 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
573 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
590 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
608 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
625 TTTA
1 TTTA
629 TAATGAGTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.01
17 51 0.65
18 26 0.33
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:566 original size:6 final size:6
Alignment explanation
Indices: 538--598 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
528 TTATAGTAAT
* *
538 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
585 -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
599 TAAAACAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
5 12 0.26
6 31 0.67
7 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:577 original size:11 final size:11
Alignment explanation
Indices: 539--597 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
529 TATAGTAATT
539 TTAAATTTGAAA
1 TTAAATTT-AAA
*
551 ATAAATTTAAA
1 TTAAATTTAAA
562 CTTAAA-TTAAA
1 -TTAAATTTAAA
573 TTTAAATTTAAA
1 -TTAAATTTAAA
*
585 ATAAATTTAAA
1 TTAAATTTAAA
596 TT
1 TT
598 TTAAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:577 original size:35 final size:35
Alignment explanation
Indices: 538--628 Score: 123
Period size: 35 Copynumber: 2.6 Consensus size: 35
528 TTATAGTAAT
**
538 TTTAAATTTGAAAATAAATTTAAA-CTTAAATTAAA
1 TTTAAATTT-AAAATAAATTTAAATCTTAAAACAAA
*
573 TTTAAATTTAAAATAAATTTAAATTTTAAAACAAA
1 TTTAAATTTAAAATAAATTTAAATCTTAAAACAAA
608 TTT-AATCTTAAAATAAATTTA
1 TTTAAAT-TTAAAATAAATTTA
629 TAATGAGTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
34 17 0.33
35 34 0.67
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (35 bp):
TTTAAATTTAAAATAAATTTAAATCTTAAAACAAA
Found at i:579 original size:52 final size:52
Alignment explanation
Indices: 521--628 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 52
511 CTTTATTTTT
* * * * *
521 TTTAAATTTATAGTAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
* *
573 TTTAAATTTAAAATAAATTTAAATTTTAAAACAAATTTAATCTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
625 TTTA
1 TTTA
629 TAATGAGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
Found at i:1317 original size:206 final size:206
Alignment explanation
Indices: 958--1497 Score: 755
Period size: 206 Copynumber: 2.6 Consensus size: 206
948 TTTGTTTTCA
* * * * ** *
958 TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGGTGACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCTCATCATTTGTTTCAATCCGCTT
* * * * * * *
1023 CTCTGTGT-ATCATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCA-AGGAGTTAACC
66 CTCTGTATCA-CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAGA-AAGCTAACC
* *
1086 ACTTTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTAGGG-TTCGAAGATTTGCTCA
129 ACTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCT-GGGATTCGAAGATTTGCTCA
*
1150 CATCGAGCGTGGGT
193 CATCGAGCATGGGT
* * * *
1164 TTGATTTGGTCTTCTTCTCAGTATCTTATTAGAAAGATGACCTCATCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCTCATCATTTGTTTCAATCCGCTT
*
1229 CTCTGTATCACATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAGAAAGCTAACCAT
66 CTCTGTATCACATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAGAAAGCTAACCAC
*
1294 TTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCATAT
131 TTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAT
1359 CGAGCATGGGT
196 CGAGCATGGGT
**
1370 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA-CTGTGTCATTTGTTTCAATCCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCT-CATCATTTGTTTCAATCCGCT
* * * *
1434 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCAATATCTTATCAGGAAGCTAACC
65 TCTCTGTATCACATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAGAAAGCTAACC
Statistics
Matches: 297, Mismatches: 33, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
205 5 0.02
206 290 0.98
207 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCTCATCATTTGTTTCAATCCGCTT
CTCTGTATCACATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAGAAAGCTAACCAC
TTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAT
CGAGCATGGGT
Done.