Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012948.1 Kokia drynarioides strain JFW-HI SEQ_127966, 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: 40707
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:2528 original size:6 final size:6
Alignment explanation
Indices: 2517--2553 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
2507 CGTATAAAAA
2517 ACACCC ACACCC ACACCC ACACCC ACACCC ACACCC A
1 ACACCC ACACCC ACACCC ACACCC ACACCC ACACCC A
2554 TGCTTTGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (6 bp):
ACACCC
Found at i:8935 original size:19 final size:18
Alignment explanation
Indices: 8913--8950 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
8903 AAAATTACAA
8913 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAA-ATTTAT
8932 AAAAATTCAAAAATTTAT
1 AAAAATTCAAAAATTTAT
8950 A
1 A
8951 TTTTAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Found at i:9023 original size:17 final size:18
Alignment explanation
Indices: 9003--9037 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8993 TTTCTAAAAT
*
9003 AATAATT-TTGAAATTTA
1 AATAATTATTCAAATTTA
9020 AATAATTATTCAAATTTA
1 AATAATTATTCAAATTTA
9038 CCATACTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
AATAATTATTCAAATTTA
Found at i:22710 original size:20 final size:20
Alignment explanation
Indices: 22682--22739 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
22672 TGTCATCTGT
* *
22682 ATATCTTTTTCAATAATTTA
1 ATATTTTTTTCAATAATGTA
22702 ATATTTTTTT-AATTAATGTA
1 ATATTTTTTTCAA-TAATGTA
* *
22722 ATATTATTTTCATTAATG
1 ATATTTTTTTCAATAATG
22740 ACAAAAGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.91
21 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (20 bp):
ATATTTTTTTCAATAATGTA
Found at i:38490 original size:16 final size:18
Alignment explanation
Indices: 38451--38484 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38441 TAAATTTATA
38451 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
38468 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
38485 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:38607 original size:16 final size:16
Alignment explanation
Indices: 38588--38634 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
38578 ATTTTTTAAT
38588 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
38604 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
38620 AAATAAAATAATATA
1 AAATAAAA-AATATA
38635 AATATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:40014 original size:4 final size:4
Alignment explanation
Indices: 39994--40060 Score: 64
Period size: 4 Copynumber: 16.5 Consensus size: 4
39984 AAATAAACGG
* * * *
39994 GAAA TAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
40044 G-AA GAAG GAAA GAAA GA
1 GAAA GAAA GAAA GAAA GA
40061 TAATGTGTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.79
5 8 0.15
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:40019 original size:17 final size:17
Alignment explanation
Indices: 39994--40060 Score: 67
Period size: 15 Copynumber: 4.4 Consensus size: 17
39984 AAATAAACGG
*
39994 GAAATAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
40011 GAAAGAAAGAAAGG-AA
1 GAAAGAAAGAAAGGAAA
*
40027 G-AAG---GAGAGGAAA
1 GAAAGAAAGAAAGGAAA
40040 GAAAG-AAG-AAGGAAA
1 GAAAGAAAGAAAGGAAA
40055 GAAAGA
1 GAAAGA
40061 TAATGTGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 5 0.12
13 3 0.07
14 3 0.07
15 14 0.33
16 4 0.10
17 13 0.31
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Done.