Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004357.1 Kokia drynarioides strain JFW-HI SEQ_117708, 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: 13921
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1070 original size:3 final size:3
Alignment explanation
Indices: 1049--1082 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1039 AAAGCCTACT
* *
1049 TTA TTA TCA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1083 AGTTGAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1668 original size:27 final size:28
Alignment explanation
Indices: 1638--1694 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
1628 TAATAATATG
*
1638 TAAAAT-ATTTTTTAAAATCAAATATAA
1 TAAAATAATATTTTAAAATCAAATATAA
**
1665 T-AAATAATATTTTAAAATTTAATATAA
1 TAAAATAATATTTTAAAATCAAATATAA
1692 TAA
1 TAA
1695 TATTTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 4 0.16
27 20 0.80
28 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAATAATATTTTAAAATCAAATATAA
Found at i:1707 original size:24 final size:23
Alignment explanation
Indices: 1657--1727 Score: 90
Period size: 24 Copynumber: 3.1 Consensus size: 23
1647 TTTTAAAATC
* *
1657 AAATATAATA-AATAATATTTTA
1 AAATTTAATATAATAATATTTAA
1679 AAATTTAATATAATAATATTTAA
1 AAATTTAATATAATAATATTTAA
* *
1702 ATAATTTAATATAATGATATATAA
1 A-AATTTAATATAATAATATTTAA
1726 AA
1 AA
1728 TACAAATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 9 0.21
23 13 0.30
24 21 0.49
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (23 bp):
AAATTTAATATAATAATATTTAA
Found at i:2011 original size:54 final size:55
Alignment explanation
Indices: 1939--2043 Score: 176
Period size: 54 Copynumber: 1.9 Consensus size: 55
1929 AGTCGATACC
*
1939 AAAAAATTAATTTCAAAATATATTTTAAATTTAATTATTTATTATTTATTTGTAG
1 AAAAAATTAATTTCAAAATATATTTTAAATTTAAATATTTATTATTTATTTGTAG
* *
1994 AAAAAA-TAATTTTAAAATATATTTTGAATTTAAATATTTATTATTTATTT
1 AAAAAATTAATTTCAAAATATATTTTAAATTTAAATATTTATTATTTATTT
2044 TGAATCTATT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 41 0.87
55 6 0.13
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (55 bp):
AAAAAATTAATTTCAAAATATATTTTAAATTTAAATATTTATTATTTATTTGTAG
Found at i:2042 original size:26 final size:26
Alignment explanation
Indices: 1959--2048 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 26
1949 TTTCAAAATA
* *
1959 TATTTTAAATTTAATTATTTATTATT
1 TATTTTGAATTTAAATATTTATTATT
* ** *
1985 TATTTGTAGAA--AAAATAATTTTAAAATA
1 TATTT-T-GAATTTAAAT-A-TTTATTATT
2013 TATTTTGAATTTAAATATTTATTATT
1 TATTTTGAATTTAAATATTTATTATT
2039 TATTTTGAAT
1 TATTTTGAAT
2049 CTATTGAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
26 27 0.56
27 4 0.08
28 17 0.35
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TATTTTGAATTTAAATATTTATTATT
Found at i:3299 original size:21 final size:21
Alignment explanation
Indices: 3275--3317 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3265 TATAAATTAT
*
3275 AAAA-AATTACTATATTTTTAA
1 AAAACAATTAATAT-TTTTTAA
*
3296 AAAACATTTAATATTTTTTAA
1 AAAACAATTAATATTTTTTAA
3317 A
1 A
3318 TCACACTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAACAATTAATATTTTTTAA
Found at i:10041 original size:29 final size:30
Alignment explanation
Indices: 9980--10041 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
9970 TTGAATGCAT
*
9980 TTTAATTCTTTAAAAATAATAAAATTTTGA
1 TTTAATTCTTTAAAAATAATAAAATTATGA
* *
10010 TTTAATAT-TTTAAAATTTATAAAATTAT-A
1 TTTAAT-TCTTTAAAAATAATAAAATTATGA
10039 TTT
1 TTT
10042 TTATTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.14
30 23 0.82
31 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTAATTCTTTAAAAATAATAAAATTATGA
Found at i:12786 original size:177 final size:176
Alignment explanation
Indices: 12501--13035 Score: 935
Period size: 177 Copynumber: 3.0 Consensus size: 176
12491 TGGTGGGAAG
*
12501 GAAGTACCTGAAATCAATGGTACTGGAGAAACAGAAGTTCCAAGGGACGAGGAAAATAGAAGTCT
1 GAAGTACCTGAAATCAATGGTACTGGAGAAACAGAAGTTCCAAGGGACGAGGAAAAAAGAAGTCT
12566 CAAGTCTGATACAGTAATTGAGATGCCTGTAAAAGGAGATACTGATCAGGGACAAGAGAGTACAG
66 CAAGTCTGATACAGTAATTGAGATGCCTGTAAAAGGAGATACTGATCAGGGACAAGAGAGTACAG
12631 AAGTAAAAGGCGCCGCAGCTGGTCTCGATTCAGTAGATGGTGGAGAT
131 AAGTAAAAGG-GCCGCAGCTGGTCTCGATTCAGTAGATGGTGGAGAT
* *
12678 GAAGTACCTGACATCAATGGTACTGGAGAAACAGAAGTTCCAAGGGACAAGGAAAAAAGAAGTCT
1 GAAGTACCTGAAATCAATGGTACTGGAGAAACAGAAGTTCCAAGGGACGAGGAAAAAAGAAGTCT
*
12743 CAAGTCTGATGCAGTAATTGAGATGCCTGTAAAAGGAGATACTGATCAGGGACAAGAGAGTACAG
66 CAAGTCTGATACAGTAATTGAGATGCCTGTAAAAGGAGATACTGATCAGGGACAAGAGAGTACAG
* *
12808 AAGTAAAAGAGGCCGCAGCTGTTCTCAATTCAGTAGATGGTGGAGAT
131 AAGTAAAAG-GGCCGCAGCTGGTCTCGATTCAGTAGATGGTGGAGAT
* *
12855 GAAGTACCTGAAACCAATGGTACTGGAGAAACAGAAGTTCCAAGGGATGAGGAAAAAAGAAGTCT
1 GAAGTACCTGAAATCAATGGTACTGGAGAAACAGAAGTTCCAAGGGACGAGGAAAAAAGAAGTCT
*
12920 CAAGTCTGATACAGTAATTAAGATGCCTGTAAAAGGAGATACTGATCAGGGACAAGAGAGTACAG
66 CAAGTCTGATACAGTAATTGAGATGCCTGTAAAAGGAGATACTGATCAGGGACAAGAGAGTACAG
* * *
12985 AAGTAAAAGGGGCTGCAGCTGGTCTCGATTCAGAAGATGTTGGAGAT
131 AAGTAAAA-GGGCCGCAGCTGGTCTCGATTCAGTAGATGGTGGAGAT
13032 GAAG
1 GAAG
13036 ATGAAAAAGC
Statistics
Matches: 339, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
177 337 0.99
178 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.19
Consensus pattern (176 bp):
GAAGTACCTGAAATCAATGGTACTGGAGAAACAGAAGTTCCAAGGGACGAGGAAAAAAGAAGTCT
CAAGTCTGATACAGTAATTGAGATGCCTGTAAAAGGAGATACTGATCAGGGACAAGAGAGTACAG
AAGTAAAAGGGCCGCAGCTGGTCTCGATTCAGTAGATGGTGGAGAT
Done.