Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011609.1 Kokia drynarioides strain JFW-HI SEQ_126599, 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: 2285
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:392 original size:15 final size:15
Alignment explanation
Indices: 372--417 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
362 AAATGTTTTG
372 ATATTAATAATAATA
1 ATATTAATAATAATA
* *
387 ATATTAATAATTATT
1 ATATTAATAATAATA
402 A-ATTAATAATTAATA
1 ATATTAATAA-TAATA
417 A
1 A
418 AAAAAAGGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTAATAATAATA
Found at i:404 original size:7 final size:7
Alignment explanation
Indices: 379--417 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
369 TTGATATTAA
379 TAATAA-
1 TAATAAT
385 TAAT-AT
1 TAATAAT
391 TAATAAT
1 TAATAAT
*
398 TATTAAT
1 TAATAAT
405 TAATAAT
1 TAATAAT
412 TAATAA
1 TAATAA
418 AAAAAAGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.03
6 8 0.28
7 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:1406 original size:59 final size:58
Alignment explanation
Indices: 1311--2010 Score: 725
Period size: 59 Copynumber: 11.9 Consensus size: 58
1301 TACCTAAACA
* * * **
1311 TTCCAAAAATTACCA-TTTT-ACCCCTGAGCTTCCAAAAATTACCATTTTACCCCTAAAC
1 TTCCAAAAA-TCCCATTTTTGA-CCCTGAACTTTCAAAAATTACCATTTTACCCCCGAAC
* * *
1369 TTCGAAAAATCTCATTTTTGACCCTGAACATTTCAAAAATTACCATTTTACCCTCGAAC
1 TTCCAAAAATCCCATTTTTGACCCTGAAC-TTTCAAAAATTACCATTTTACCCCCGAAC
* * ** ** *
1428 TCCCAAAAATCCCATTTTTAACCCCAAACCATCTTAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCTGAACTTTC-AAAAATTACCATTTTACCCCCGAAC
1487 TTCCAAAAATCCCATTTTTGA-CCTCGAACTTTCCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCT-GAACTTT-CAAAAATTACCATTTTACCCCCGAAC
* * * *
1546 TTCCAAAAATCCCATTTTTTACCTTAAAATTTCCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCTGAACTTT-CAAAAATTACCATTTTACCCCCGAAC
* * *
1605 -TCCAAAAAATCCCATTTTT-AACCTCGAACCTTCTAAAAATTACCATTTTACCCTCGAAC
1 TTCC-AAAAATCCCATTTTTGACCCT-GAACTTTC-AAAAATTACCATTTTACCCCCGAAC
* *
1664 TTCCAAAAATCCCATTTTTGACCATAAACTTTCCAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCTGAACTTT-CAAAAATTACCATTTTACCCCCGAAC
* * * * * **
1723 TCCCAAAAATCCCATTTTTAACCCCGAACCTTCTAAAAATTACCATTTTAACCCTAAAC
1 TTCCAAAAATCCCATTTTTGACCCTGAACTTTC-AAAAATTACCATTTTACCCCCGAAC
* * * *
1782 AT-CTAAAATCCCATTTTTAACCCTAAACTTTCAAAAAATTACCATTTTACCCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCTGAACTTTC-AAAAATTACCATTTTACCCCCGAAC
* * * * * *
1840 TTCCATAAATTCTATTTTTGA-CCTCAAACCTTCTAAAAATTACCATTTTAGCCCCGAAC
1 TTCCAAAAATCCCATTTTTGACCCT-GAACTTTC-AAAAATTACCATTTTACCCCCGAAC
* * ** *
1899 TTCTAAAAATCCCATTTTTGATCC-GAACCTTTTGAAAATTACCATTTTACCCTCGAAC
1 TTCCAAAAATCCCATTTTTGACCCTGAA-CTTTCAAAAATTACCATTTTACCCCCGAAC
* * * * *
1957 TTCCAAAAATCCCATTTTTGATTCC-GAACCTTCCAAAACTACCATTTTGCCCCC
1 TTCCAAAAATCCCATTTTTGA-CCCTGAACTTTCAAAAATTACCATTTTACCCCC
2011 CCGTGCATCC
Statistics
Matches: 538, Mismatches: 85, Indels: 38
0.81 0.13 0.06
Matches are distributed among these distances:
57 3 0.01
58 147 0.27
59 376 0.70
60 12 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (58 bp):
TTCCAAAAATCCCATTTTTGACCCTGAACTTTCAAAAATTACCATTTTACCCCCGAAC
Found at i:1538 original size:118 final size:118
Alignment explanation
Indices: 1340--2004 Score: 833
Period size: 118 Copynumber: 5.7 Consensus size: 118
1330 ACCCCTGAGC
** * * * *
1340 TTCCAAAAATTACCATTTTACCCCTAAACTTCGAAAAATCTCATTTTTGACC-CTGAACATTTCA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC-GAACCTTCCA
* * *
1404 AAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAACC
65 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAACT
* ** *
1458 ATCTTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACTTTCCAA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCAA
* * * *
1523 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCTTAAAAT
66 AAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAACT
* *
1576 TTCCAAAAATTACCATTTTACCCCCGAAC-TCCAAAAAATCCCATTTTTAACCTCGAACCTTCTA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCC-AAAAATCCCATTTTTGACCTCGAACCTTCCA
* *
1640 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCATAAACT
65 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAACT
* * * *
1694 TTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCGAACCTTCTAA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCAA
* * *
1759 AAATTACCATTTTAACCCT-AAACAT-CTAAAATCCCATTTTTAACCCTAAACT
66 AAATTACCATTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAACT
* * * * * *
1811 TTCAAAAAATTACCATTTTACCCCCGAACTTCCATAAATTCTATTTTTGACCTCAAACCTTCTAA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCAA
* * * * *
1876 AAATTACCATTTTAGCCC-CGAACTTCTAAAAATCCCATTTTTGATCCGAACCT
66 AAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAACT
** * *
1929 TT-TGAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA-TTCCGAACCTTCC-
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCT-CGAACCTTCCA
*
1991 AAAACTACCATTTT
65 AAAATTACCATTTT
2005 GCCCCCCCGT
Statistics
Matches: 480, Mismatches: 59, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
116 15 0.03
117 153 0.32
118 304 0.63
119 8 0.02
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (118 bp):
TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCAA
AAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAACT
Found at i:1540 original size:177 final size:177
Alignment explanation
Indices: 1340--2010 Score: 854
Period size: 177 Copynumber: 3.8 Consensus size: 177
1330 ACCCCTGAGC
** * *
1340 TTCCAAAAATTACCATTTTACCCCTAAACTTCGAAAAATCTCATTTTTGACCCTGAACATTTCAA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACATTTCAA
* *
1405 AAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCATCTTAAAATTA
66 AAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCTAAAAATTA
*
1470 CCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACT
131 CCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCAAACT
* * *
1517 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTA-CCTTAAAATTTCCA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACATTT-CA
* * * *
1581 AAAATTACCATTTTACCCCCGAACTCCAAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAATT
65 AAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCTAAAAATT
*
1646 ACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCAT-AAACT
130 ACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC-TCAAACT
* * * *
1694 TTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCGAAC-CTTCTA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACATTTC-A
* * * * *
1758 AAAATTACCATTTTAACCCT-AAACAT--CTAAAATCCCATTTTTAACCCTAAACTTTCAAAAAA
65 AAAATTACCATTTT-ACCCTCGAAC-TCCCAAAAATCCCATTTTTAACCCCAAACCTTCTAAAAA
* * * *
1820 TTACCATTTTACCCCCGAACTTCCATAAATTCTATTTTTGACCTCAAACC
128 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCAAACT
* * * * * **
1870 TTCTAAAAATTACCATTTTAGCCCCGAACTTCTAAAAATCCCATTTTTGATCC-GAACCTTTTGA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACATTTCAA
* * ** * * *
1934 AAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGATTCCGAACCTTC-CAAAACTA
66 AAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCTAAAAATTA
*
1998 CCATTTTGCCCCC
131 CCATTTTACCCCC
2011 CCGTGCATCC
Statistics
Matches: 428, Mismatches: 55, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
174 6 0.01
175 40 0.09
176 154 0.36
177 218 0.51
178 10 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (177 bp):
TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACATTTCAA
AAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCTAAAAATTA
CCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCAAACT
Found at i:1984 original size:29 final size:29
Alignment explanation
Indices: 1481--2004 Score: 128
Period size: 30 Copynumber: 17.9 Consensus size: 29
1471 CATTTTACCC
* *
1481 CCGAA-CTTCCAAAAATCCCATTTTTGAC
1 CCGAACCTTCCAAAAATACCATTTTTGAT
* ****
1509 CTCGAACTTTCCAAAAATTACCATTTTACCC
1 C-CGAACCTTCCAAAAA-TACCATTTTTGAT
* *
1540 CCGAA-CTTCCAAAAATCCCATTTTTTA-
1 CCGAACCTTCCAAAAATACCATTTTTGAT
* ** ****
1567 CCTTAAAATTTCCAAAAATTACCATTTTACCC
1 CC--GAACCTTCCAAAAA-TACCATTTTTGAT
* * *
1599 CCGAA-C-TCCAAAAAATCCCATTTTTAAC
1 CCGAACCTTCC-AAAAATACCATTTTTGAT
* *
1627 CTCGAACCTTCTAAAAATTACCA-TTTT-ACC
1 C-CGAACCTTCCAAAAA-TACCATTTTTGA-T
*
1657 CTCGAA-CTTCCAAAAATCCCATTTTTGA-
1 C-CGAACCTTCCAAAAATACCATTTTTGAT
* * ****
1685 CCATAAACTTTCCAAAAATTACCATTTTACCC
1 CC--GAACCTTCCAAAAA-TACCATTTTTGAT
* * * *
1717 CCGAA-CTCCCAAAAATCCCATTTTTAACC
1 CCGAACCTTCCAAAAATACCATTTTTGA-T
* * *
1746 CCGAACCTTCTAAAAATTACCA-TTTTAAC
1 CCGAACCTTCCAAAAA-TACCATTTTTGAT
* * * * * * *
1775 CCTAAACAT-CTAAAATCCCATTTTTAAC
1 CCGAACCTTCCAAAAATACCATTTTTGAT
* * * ****
1803 CCTAAACTTTCAAAAAATTACCATTTTACCC
1 CC-GAACCTTCCAAAAA-TACCATTTTTGAT
* * * *
1834 CCGAA-CTTCCATAAATTCTATTTTTGAC
1 CCGAACCTTCCAAAAATACCATTTTTGAT
* * * **
1862 CTCAAACCTTCTAAAAATTACCATTTTAGCC
1 C-CGAACCTTCCAAAAA-TACCATTTTTGAT
* *
1893 CCGAA-CTTCTAAAAATCCCATTTTTGAT
1 CCGAACCTTCCAAAAATACCATTTTTGAT
** * *
1921 CCGAACCTTTTGAAAATTACCA-TTTT-ACC
1 CCGAACC-TTCCAAAAATACCATTTTTGA-T
*
1950 CTCGAA-CTTCCAAAAATCCCATTTTTGATT
1 C-CGAACCTTCCAAAAATACCATTTTTGA-T
*
1980 CCGAACCTTCCAAAACTACCATTTT
1 CCGAACCTTCCAAAAATACCATTTT
2005 GCCCCCCCGT
Statistics
Matches: 366, Mismatches: 92, Indels: 74
0.69 0.17 0.14
Matches are distributed among these distances:
27 7 0.02
28 82 0.22
29 99 0.27
30 117 0.32
31 57 0.16
32 4 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
CCGAACCTTCCAAAAATACCATTTTTGAT
Done.