Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002713.1 Kokia drynarioides strain JFW-HI SEQ_115007, 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: 20683
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1461 original size:13 final size:13
Alignment explanation
Indices: 1422--1462 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1412 TGACCAACCG
1422 TTGATCGTTGACT
1 TTGATCGTTGACT
* * *
1435 TTGACCATTAACT
1 TTGATCGTTGACT
1448 TTGATCGTTGACT
1 TTGATCGTTGACT
1461 TT
1 TT
1463 TTTCGAAAAC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (13 bp):
TTGATCGTTGACT
Found at i:10167 original size:22 final size:22
Alignment explanation
Indices: 10142--10186 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
10132 ACTCGATACC
10142 CTCTATTTCATCCAAGGATGCT
1 CTCTATTTCATCCAAGGATGCT
*
10164 CTCTATTTCATCCAAGGTTGCT
1 CTCTATTTCATCCAAGGATGCT
10186 C
1 C
10187 CACCTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.38
Consensus pattern (22 bp):
CTCTATTTCATCCAAGGATGCT
Found at i:14494 original size:20 final size:19
Alignment explanation
Indices: 14446--14496 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
14436 TTTAAAAATT
14446 TAATTT-ATTTGTTTAAGAA
1 TAATTTAATTT-TTTAAGAA
*
14465 TAATTTAATTTTTTAATAA
1 TAATTTAATTTTTTAAGAA
14484 TAATTTAAATTTT
1 TAATTT-AATTTT
14497 AGTTTTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
TAATTTAATTTTTTAAGAA
Found at i:16649 original size:41 final size:35
Alignment explanation
Indices: 16574--16643 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
16564 AGATAGGATT
16574 TTGGTTTTCTTTGAAGAAGAGAATGAGGAAAATGA
1 TTGGTTTTCTTTGAAGAAGAGAATGAGGAAAATGA
16609 TTGGTTTTCTTTGAAGAAGAGAATGAGGAAAATGA
1 TTGGTTTTCTTTGAAGAAGAGAATGAGGAAAATGA
16644 AAATGAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (35 bp):
TTGGTTTTCTTTGAAGAAGAGAATGAGGAAAATGA
Found at i:16976 original size:30 final size:30
Alignment explanation
Indices: 16863--17155 Score: 278
Period size: 30 Copynumber: 9.9 Consensus size: 30
16853 GTTTTCTTTG
*
16863 AAAATTATATTTTGACCCCT-AACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* *
16892 AAAATTACATTTTGACCCC-AAACTTCTCT
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * * *
16921 AAAATTTCATTTTAAACCCTTAAACTTTTAC
1 AAAATTACATTTT-GACCCCTAAACTTTTCC
* **
16952 AAAATTATATTTTGACCTTTAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
**
16982 AAAATTACATTTTGACCAATAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * *
17012 AAAATTACATTTTAACTCCTAAACTTCTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * * *
17042 AAAATCACATTTT-AACCCTTAACTATTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* *
17071 AAAAATCACATTTTGA-CCC-AAACTTCTCC
1 -AAAATTACATTTTGACCCCTAAACTTTTCC
* * *
17100 GAAATCACATTTT-AACCC-AAAC-TTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
*
17127 TAAAATTACATTTTTACCCCTAAACTTTT
1 -AAAATTACATTTTGACCCCTAAACTTTT
17156 TTTGAAATTA
Statistics
Matches: 218, Mismatches: 36, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
27 5 0.02
28 30 0.14
29 59 0.27
30 102 0.47
31 22 0.10
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAACTTTTCC
Found at i:16994 original size:15 final size:15
Alignment explanation
Indices: 16976--17024 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
16966 ACCTTTAAAC
16976 TTTTCCAAAATTACA
1 TTTTCCAAAATTACA
16991 TTTTGACCAATAA--AC-
1 TTTT--CCAA-AATTACA
17006 TTTTCCAAAATTACA
1 TTTTCCAAAATTACA
17021 TTTT
1 TTTT
17025 AACTCCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 2 0.07
13 4 0.14
14 2 0.07
15 12 0.43
16 2 0.07
17 4 0.14
18 2 0.07
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (15 bp):
TTTTCCAAAATTACA
Found at i:16994 original size:90 final size:88
Alignment explanation
Indices: 16863--17155 Score: 308
Period size: 90 Copynumber: 3.3 Consensus size: 88
16853 GTTTTCTTTG
* * *
16863 AAAATTATATTTTGACCCCTAACTTTTCCAAAATTACATTTTGACCCCAAACTTCTCTAAAATTT
1 AAAATTATATTTTGACCCTTAACTTTTCCAAAATTACATTTTGACCCCAAACTTCTCCAAAATTA
*
16928 CATTTTAAAC-CCTTAAACTTTTAC
66 CATTTT-AACTCC-TAAACTTCTAC
* ** *
16952 AAAATTATATTTTGACCTTTAAACTTTTCCAAAATTACATTTTGACCAATAAACTTTTCCAAAAT
1 AAAATTATATTTTGACCCTT-AACTTTTCCAAAATTACATTTTGACC-CCAAACTTCTCCAAAAT
*
17017 TACATTTTAACTCCTAAACTTCTCC
64 TACATTTTAACTCCTAAACTTCTAC
* * * * * * *
17042 AAAATCACATTTTAACCCTTAACTATTCCAAAAATCACATTTTGA-CCCAAACTTCTCCGAAATC
1 AAAATTATATTTTGACCCTTAACTTTTCC-AAAATTACATTTTGACCCCAAACTTCTCCAAAATT
*
17106 ACATTTTAAC-CC-AAACTT-TCC
65 ACATTTTAACTCCTAAACTTCTAC
* * *
17127 TAAAATTACATTTTTACCCCTAAACTTTT
1 -AAAATTATATTTTGA-CCCTTAACTTTT
17156 TTTGAAATTA
Statistics
Matches: 174, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
85 3 0.02
86 19 0.11
87 12 0.07
88 23 0.13
89 27 0.16
90 68 0.39
91 22 0.13
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (88 bp):
AAAATTATATTTTGACCCTTAACTTTTCCAAAATTACATTTTGACCCCAAACTTCTCCAAAATTA
CATTTTAACTCCTAAACTTCTAC
Done.