Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012162.1 Kokia drynarioides strain JFW-HI SEQ_127163, 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: 11754
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Found at i:10328 original size:29 final size:28
Alignment explanation
Indices: 10296--10358 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
10286 AAAATGAGAC
10296 TTTTCGGATACTTAGGGGTAAAATGGTAA
1 TTTT-GGATACTTAGGGGTAAAATGGTAA
** *
10325 TTTTGGATTTTTAGGGGTAAAATTGTAA
1 TTTTGGATACTTAGGGGTAAAATGGTAA
10353 TTTTGG
1 TTTTGG
10359 GAAAGTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (28 bp):
TTTTGGATACTTAGGGGTAAAATGGTAA
Found at i:10385 original size:30 final size:30
Alignment explanation
Indices: 10315--10594 Score: 297
Period size: 30 Copynumber: 9.4 Consensus size: 30
10305 ACTTAGGGGT
*
10315 AAAATGGTAA-TTTTGG-ATTTTTAGGGGT-A
1 AAAATGG-AATTTTTGGAAGTTTT-GGGGTCA
* * * *
10344 AAATTGTAATTTTGGGAAAGTTTTGGGGT-T
1 AAAATGGAATTTTTGG-AAGTTTTGGGGTCA
** *
10374 AAAATGGAATTTTTGGAAGTTTTAAGGTCT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
*
10404 AAAATGGAATTTTTGGAAG-TTTGGGCG-AA
1 AAAATGGAATTTTTGGAAGTTTTGGG-GTCA
* *
10433 AAAATGGAATTTTTGAAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
** *
10463 AAAATGGAATTTTTTAAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* *
10493 AAAAAGGAATTTTTGGAAG-TTCGAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTCA
10522 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* *
10552 AAAATGGAATTTTTGGAAGTTTCGGGCTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
10582 AAAATGGAATTTT
1 AAAATGGAATTTT
10595 CGGATAGTCT
Statistics
Matches: 214, Mismatches: 27, Indels: 19
0.82 0.10 0.07
Matches are distributed among these distances:
28 2 0.01
29 68 0.32
30 139 0.65
31 5 0.02
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTCA
Found at i:10388 original size:59 final size:58
Alignment explanation
Indices: 10310--10594 Score: 240
Period size: 59 Copynumber: 4.8 Consensus size: 58
10300 CGGATACTTA
* * *
10310 GGGGT-AAAATGGTAA-TTTTGGATTTTTAGGGGTAAAATTGTAATTTTGGGAAAGTTTT
1 GGGGTAAAAATGG-AATTTTTGGATTTTTAGGGGTAAAAATGGAATTTTTGG-AAGTTTT
* * * *
10368 GGGGTTAAAATGGAATTTTTGGAAGTTTTA-AGGTCTAAAATGGAATTTTTGGAAG-TTT
1 GGGGTAAAAATGGAATTTTTGG-ATTTTTAGGGGT-AAAAATGGAATTTTTGGAAGTTTT
* * * **
10426 GGGCGAAAAAATGGAATTTTTGAAAGTTTTA-GGGTCAAAAATGGAATTTTTTAAAGTTTT
1 GGG-GTAAAAATGGAATTTTTG-GATTTTTAGGGGT-AAAAATGGAATTTTTGGAAGTTTT
* * ** *
10486 AGGGTCAAAAAAGGAATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGT-AAAAATGGAATTTTTGGATTTTTAG-GGGTAAAAATGGAATTTTTGGAAGTTTT
** * *
10545 GGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGCTCAAAAATGGAATTTT
1 GGGGT-AAAAATGGAATTTTTGGATTTTTAGGGGT-AAAAATGGAATTTT
10595 CGGATAGTCT
Statistics
Matches: 188, Mismatches: 27, Indels: 22
0.79 0.11 0.09
Matches are distributed among these distances:
58 15 0.08
59 112 0.60
60 61 0.32
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.36
Consensus pattern (58 bp):
GGGGTAAAAATGGAATTTTTGGATTTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTT
Found at i:10583 original size:89 final size:88
Alignment explanation
Indices: 10338--10594 Score: 338
Period size: 89 Copynumber: 2.9 Consensus size: 88
10328 TGGATTTTTA
* * * * *
10338 GGGGTAAAATTGTAATTTTGGGAAAGTTTTGGGGT-TAAAATGGAATTTTTGGAAGTTTTAAGGT
1 GGGGTAAAAATGGAATTTTTGG-AAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTAGGGT
* *
10402 CTAAAATGGAATTTTTGGAAGTTT
65 CAAAAATGGAATTTTTGGAAGTTC
* * * **
10426 GGGCGAAAAAATGGAATTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTTAAAGTTTTAGGGT
1 GGG-GTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTAGGGT
*
10491 CAAAAAAGGAATTTTTGGAAGTTC
65 CAAAAATGGAATTTTTGGAAGTTC
*
10515 GAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAG-TTTCGGGC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTAGGG-
10579 TCAAAAATGGAATTTT
64 TCAAAAATGGAATTTT
10595 CGGATAGTCT
Statistics
Matches: 145, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
88 20 0.14
89 123 0.85
90 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (88 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTAGGGTC
AAAAATGGAATTTTTGGAAGTTC
Found at i:11659 original size:3 final size:3
Alignment explanation
Indices: 11651--11703 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
11641 GACCTTTCGG
* * *
11651 TTA TTA TTA TTA TTA ATA TCTA TTA TTA TTA -TA TTA TTA ATA ATA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
11696 TTAA TTA T
1 TT-A TTA T
11704 AGTTGCCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:11676 original size:16 final size:14
Alignment explanation
Indices: 11652--11689 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 14
11642 ACCTTTCGGT
11652 TATTATTATTATTAA
1 TATTATTATTATT-A
11667 TATCTATTATTATTA
1 TAT-TATTATTATTA
11682 TATTATTA
1 TATTATTA
11690 ATAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.23
15 7 0.32
16 10 0.45
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATTATTATTA
Done.