Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010777.1 Kokia drynarioides strain JFW-HI SEQ_125741, 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: 8564
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1285 original size:30 final size:30
Alignment explanation
Indices: 1251--1307 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1241 CTAAAAATAC
*
1251 AATTTAACCTCCAAACTTTCCAAAAATTTT
1 AATTTAACCCCCAAACTTTCCAAAAATTTT
* * *
1281 AATTTGACCCCCAATCTTTCCCAAAAT
1 AATTTAACCCCCAAACTTTCCAAAAAT
1308 CACATATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (30 bp):
AATTTAACCCCCAAACTTTCCAAAAATTTT
Found at i:1359 original size:30 final size:30
Alignment explanation
Indices: 1318--1587 Score: 168
Period size: 30 Copynumber: 9.1 Consensus size: 30
1308 CACATATTAA
1318 CCTTAAACTTCACAAAAATTACATTTTTAC
1 CCTTAAACTTCACAAAAATTACATTTTTAC
* *
1348 CCTTGAACTTCACAAAAATTATATTTTTAC
1 CCTTAAACTTCACAAAAATTACATTTTTAC
** * * *
1378 CCTCGAATTTC-CAGAATTTACCA-TTTTA-
1 CCTTAAACTTCACAAAAATTA-CATTTTTAC
* * * *
1406 CCTCCAAATTTC-CAAAAATTCCATTTTTGC
1 CCT-TAAACTTCACAAAAATTACATTTTTAC
* *
1436 CCTTAAACTTTAAAAAAATTAGCA-TTTTAC
1 CCTTAAACTTCACAAAAATTA-CATTTTTAC
* * *
1466 CCTTAGA--TGACAAAAAATTCCATTTTTAAC
1 CCTTAAACTTCAC-AAAAATTACATTTTT-AC
* *
1496 CC-TAAACTTACAAAAAAATTATATTTTTAC
1 CCTTAAACTT-CACAAAAATTACATTTTTAC
* * *
1526 CCCTAAACTAC-CAAAAATTCCCATTTTTATC
1 CCTTAAACTTCACAAAAATT-ACATTTTTA-C
* *
1557 CC-TAAAATT-TCAAAAATTACCA-TTTTAC
1 CCTTAAACTTCACAAAAATTA-CATTTTTAC
1585 CCT
1 CCT
1588 CGAACTTTTA
Statistics
Matches: 188, Mismatches: 34, Indels: 37
0.73 0.13 0.14
Matches are distributed among these distances:
28 12 0.06
29 60 0.32
30 90 0.48
31 25 0.13
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
CCTTAAACTTCACAAAAATTACATTTTTAC
Found at i:1464 original size:59 final size:57
Alignment explanation
Indices: 1399--1586 Score: 173
Period size: 59 Copynumber: 3.2 Consensus size: 57
1389 CAGAATTTAC
* *
1399 CATTTTACCTCCAAATTTCCAAAAATTCCATTTTT-GCCCTTAAACTTTAAAAAAATTA
1 CATTTTACC-CCAAATTACCAAAAATTCCATTTTTAACCC-TAAACTTTAAAAAAATTA
* * * * *
1457 GCATTTTACCCTTAGATGACAAAAAATTCCATTTTTAACCCTAAACTTACAAAAAAATTA
1 -CATTTTACCC-CAAATTACCAAAAATTCCATTTTTAACCCTAAACTT-TAAAAAAATTA
* * * * *
1517 TATTTTTACCCCTAAACTACCAAAAATTCCCATTTTTATCCCTAAAATTT-CAAAAATTA
1 CA-TTTTACCCC-AAATTACCAAAAATT-CCATTTTTAACCCTAAACTTTAAAAAAATTA
1576 CCATTTTACCC
1 -CATTTTACCC
1587 TCGAACTTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
58 1 0.01
59 52 0.50
60 33 0.32
61 18 0.17
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (57 bp):
CATTTTACCCCAAATTACCAAAAATTCCATTTTTAACCCTAAACTTTAAAAAAATTA
Found at i:1646 original size:29 final size:29
Alignment explanation
Indices: 1520--1648 Score: 86
Period size: 29 Copynumber: 4.4 Consensus size: 29
1510 AAAATTATAT
* *
1520 TTTTACCCCTAAACTAC-CAAAAATTCCCA
1 TTTTACCCCTAAA-TCCTCAAAAATTACCA
* *
1549 TTTTTATCCCTAAAAT-TTCAAAAATTACCA
1 -TTTTACCCCT-AAATCCTCAAAAATTACCA
* * * * *
1579 TTTTACCCTCGAACT-TTTAAAAA-TATCA
1 TTTTACCC-CTAAATCCTCAAAAATTACCA
* *
1607 TTTTAAACCCTAAATCCTCTAAAATTACCA
1 TTTT-ACCCCTAAATCCTCAAAAATTACCA
1637 TTTTACCCCTAA
1 TTTTACCCCTAA
1649 GGTTCTAGAA
Statistics
Matches: 77, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
28 12 0.16
29 32 0.42
30 30 0.39
31 3 0.04
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (29 bp):
TTTTACCCCTAAATCCTCAAAAATTACCA
Found at i:5813 original size:5 final size:5
Alignment explanation
Indices: 5803--5836 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
5793 TTTTTTATTA
5803 TTTAT TTTAT TTTATT ATTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTA-T -TTTAT TTTAT TTTAT TT
5837 ACATTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 21 0.78
6 2 0.07
7 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:5817 original size:17 final size:17
Alignment explanation
Indices: 5795--5835 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
5785 TTAGCCATTT
5795 TTTTATTATTTATTTTA
1 TTTTATTATTTATTTTA
5812 TTTTATTATTTATTTTA
1 TTTTATTATTTATTTTA
5829 TTTTATT
1 TTTTATT
5836 TACATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTATTTATTTTA
Found at i:5845 original size:22 final size:21
Alignment explanation
Indices: 5794--5850 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
5784 TTTAGCCATT
*
5794 TTTTTATTATTTATTTTATTTTA
1 TTTTTA-T-TTTATTTTATTTCA
5817 TTATTTATTTTATTTTATTTACA
1 TT-TTTATTTTATTTTATTT-CA
*
5840 TTTTTAATTTA
1 TTTTTATTTTA
5851 AATTTTCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 20 0.67
23 6 0.20
24 4 0.13
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTATTTTATTTTATTTCA
Found at i:5863 original size:14 final size:13
Alignment explanation
Indices: 5829--5870 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5819 ATTTATTTTA
*
5829 TTTT-ATTTACAT
1 TTTTAATTTAAAT
5841 TTTTAATTTAAAT
1 TTTTAATTTAAAT
5854 TTTCTAATTT-AAT
1 TTT-TAATTTAAAT
5867 TTTT
1 TTTT
5871 TCCCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 5 0.19
13 16 0.59
14 6 0.22
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTAATTTAAAT
Done.