Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012608.1 Kokia drynarioides strain JFW-HI SEQ_127617, 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: 8462
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Found at i:6589 original size:96 final size:96
Alignment explanation
Indices: 6400--6591 Score: 219
Period size: 96 Copynumber: 2.0 Consensus size: 96
6390 TTTTTACGAA
** *
6400 AAGGATATTTGATTATCTCGACTCGAAGAAAGGTTGCACATAGTAAGTTAAGGCGCAATATTTTA
1 AAGGATATTTGATTATCTCGACTCGAAGAAAAATTGCACATAGTAAGTTAAGGCACAATATTTTA
* *
6465 GAACCGAAGATAAGGAAACATTGTCTCGATT
66 GAACCGAAGATAAAGAAACATTGCCTCGATT
* * * * * * *
6496 AAGGGTATTTGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTTC
1 AAGGATATTTGATTATCTCGACTCGAAGAAAAATTGCACATAGTAAGTTAAGGCACAATATTTTA
*
6560 GAAGCTCGAA-ATATAAG-AATATTGCCTCGATT
66 GAA-C-CGAAGATA-AAGAAACATTGCCTCGATT
6592 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
95 8 0.10
96 66 0.82
97 6 0.08
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (96 bp):
AAGGATATTTGATTATCTCGACTCGAAGAAAAATTGCACATAGTAAGTTAAGGCACAATATTTTA
GAACCGAAGATAAAGAAACATTGCCTCGATT
Found at i:6859 original size:28 final size:28
Alignment explanation
Indices: 6809--6871 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
6799 AAAATGAGAC
6809 TTTTCGGATACTCAGGGGCAAAATGGTAA
1 TTTT-GGATACTCAGGGGCAAAATGGTAA
* * * *
6838 TTTTGGATTCTCGGGGGTAAAATGGTAG
1 TTTTGGATACTCAGGGGCAAAATGGTAA
6866 TTTTGG
1 TTTTGG
6872 GAAAATTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.35
Consensus pattern (28 bp):
TTTTGGATACTCAGGGGCAAAATGGTAA
Found at i:7062 original size:59 final size:59
Alignment explanation
Indices: 6991--7409 Score: 476
Period size: 59 Copynumber: 7.1 Consensus size: 59
6981 AATTTTAAGG
* * * *
6991 AGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTAGAGAGTAAGAATGAAATTTTTGGA
1 AGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA
* * *
7050 AGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT-TAGGGGTAAAAATGGAATTTTTTGGA
1 AGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAAT-GAAATTTTTGGA
* ** * *
7110 AGTTTT-ATGGTTAAAAATGATATTTTTGGAAGTTC-AGGGGTAAAAATGGAATTTTTTGA
1 AGTTTTGA-GGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGAAATTTTTGGA
* * *
7169 AG-TTTCATGGACAAAAATCGGATTTTTGGAAGTTCGAGGGTAAAAAT-AGAATTTTTGGA
1 AGTTTTGA-GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGA-AATTTTTGGA
*
7228 AGTTTTGAGGAT-AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTGGA
1 AGTTTTGAGG-TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA
* * * *
7287 AGTTTTG-GGTAAAAAATGGGATTTTTGGAAGTTCGATGGTAAAAAAGGAATTTTTGGA
1 AGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA
** * * *
7345 AGTTTTG-GTGTCAAAAATTAGATTTTTGGAAGTTCGATGGTAAAAAAGGAATTTTTGGA
1 AGTTTTGAG-GTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA
7404 TAGTTT
1 -AGTTT
7410 AGGGACCCTC
Statistics
Matches: 316, Mismatches: 31, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
57 1 0.00
58 57 0.18
59 196 0.62
60 62 0.20
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.36
Consensus pattern (59 bp):
AGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTGGA
Found at i:7077 original size:30 final size:29
Alignment explanation
Indices: 7003--7409 Score: 345
Period size: 29 Copynumber: 13.8 Consensus size: 29
6993 TTTTGGGGTC
* *
7003 AAAAATGGGATTTTTGGAAG-TTAGAGAGT
1 AAAAATGGAATTTTTGGAAGTTTCGAG-GT
* *
7032 AAGAATGAAATTTTTGGAAGTTTCGAGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
* * *
7061 CAAAAATGGGATTTTTGGAAGTTTAGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGAGGT
*
7091 AAAAATGGAATTTTTTGGAAGTTT-TATGGTT
1 AAAAATGGAA-TTTTTGGAAGTTTCGA-GG-T
*
7122 AAAAAT-GATATTTTTGGAAG-TTCAGGGGT
1 AAAAATGGA-ATTTTTGGAAGTTTC-GAGGT
* *
7151 AAAAATGGAATTTTTTGAAGTTTC-ATGGAC
1 AAAAATGGAATTTTTGGAAGTTTCGA-GG-T
7181 AAAAATCGG-ATTTTTGGAAG-TTCGAGGGT
1 AAAAAT-GGAATTTTTGGAAGTTTCGA-GGT
* *
7210 AAAAATAGAATTTTTGGAAGTTTTGAGGAT
1 AAAAATGGAATTTTTGGAAGTTTCGAGG-T
* *
7240 AAAAATGGGATTTTTGGAAG-TTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTC-GAGGT
* *
7269 AAAAATGAAATTTTTGGAAGTTTTG-GGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
*
7297 AAAAAATGGGATTTTTGGAAG-TTCGATGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGA-GGT
* *
7327 AAAAAAGGAATTTTTGGAAGTTTTG-GTGT
1 AAAAATGGAATTTTTGGAAGTTTCGAG-GT
*
7356 CAAAAAT-TAGATTTTTGGAAG-TTCGATGGT
1 -AAAAATGGA-ATTTTTGGAAGTTTCGA-GGT
*
7386 AAAAAAGGAATTTTTGGATAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
7410 AGGGACCCTC
Statistics
Matches: 307, Mismatches: 40, Indels: 60
0.75 0.10 0.15
Matches are distributed among these distances:
28 8 0.03
29 149 0.49
30 137 0.45
31 13 0.04
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGT
Found at i:8384 original size:23 final size:24
Alignment explanation
Indices: 8340--8390 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 24
8330 TTTCCCTTTT
8340 TTATTATTAAAACATAATTTATTA
1 TTATTATTAAAACATAATTTATTA
8364 TTATT-TTAAAA-AT-A-TTATTA
1 TTATTATTAAAACATAATTTATTA
8384 TTATTAT
1 TTATTAT
8391 CAATATATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.42
21 2 0.08
22 2 0.08
23 6 0.23
24 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATTATTAAAACATAATTTATTA
Found at i:8398 original size:20 final size:20
Alignment explanation
Indices: 8340--8410 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
8330 TTTCCCTTTT
*
8340 TTATTATTA-AAACATAATTTA
1 TTATTATTATAAAAAT-A-TTA
*
8361 TTATTATTTTAAAAATATTA
1 TTATTATTATAAAAATATTA
* *
8381 TTATTATTATCAATATATTCA
1 TTATTATTATAAAAATATT-A
*
8402 TTGTTATTA
1 TTATTATTA
8411 AATAATCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 19 0.45
21 18 0.43
22 5 0.12
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (20 bp):
TTATTATTATAAAAATATTA
Found at i:8408 original size:18 final size:18
Alignment explanation
Indices: 8359--8396 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
8349 AAACATAATT
**
8359 TATTATTATT-TTAAAAA
1 TATTATTATTATTATCAA
8376 TATTATTATTATTATCAA
1 TATTATTATTATTATCAA
8394 TAT
1 TAT
8397 ATTCATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTATTATTATCAA
Done.