Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000079.1 Kokia drynarioides strain JFW-HI SEQ_110702, 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: 9004
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:1826 original size:5 final size:6
Alignment explanation
Indices: 1808--1854 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
1798 GGCAACCCGA
** *
1808 TTATTT TTATTT TTA-TT TTATTT TTATTT TTATAA TTATAT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
1855 CCTTTTTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:1828 original size:11 final size:11
Alignment explanation
Indices: 1812--1837 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1802 ACCCGATTAT
1812 TTTTATTTTTA
1 TTTTATTTTTA
1823 TTTTATTTTTA
1 TTTTATTTTTA
1834 TTTT
1 TTTT
1838 TATAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:1830 original size:17 final size:18
Alignment explanation
Indices: 1807--1854 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
1797 AGGCAACCCG
1807 ATTATTTTTATTTTTAT-
1 ATTATTTTTATTTTTATA
*
1824 TTTATTTTTATTTTTATA
1 ATTATTTTTATTTTTATA
*
1842 ATTATATTTATTT
1 ATTATTTTTATTT
1855 CCTTTTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTATTTTTATTTTTATA
Found at i:3425 original size:19 final size:20
Alignment explanation
Indices: 3403--3447 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
3393 TTTTATTAGG
3403 ATTTAAT-ATTTAAGATAT-T
1 ATTTAATCATTTAA-ATATGT
*
3422 ATTT-ATCATTTAAATTTGT
1 ATTTAATCATTTAAATATGT
3441 ATTTAAT
1 ATTTAAT
3448 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 5 0.23
19 15 0.68
20 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTAATCATTTAAATATGT
Found at i:4283 original size:20 final size:21
Alignment explanation
Indices: 4258--4302 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
4248 TTTCTATTTC
*
4258 TTTTAATTCTATTT-TTTTAT
1 TTTTAATTATATTTCTTTTAT
*
4278 TTTTAATTATGTTTCTTTTAT
1 TTTTAATTATATTTCTTTTAT
4299 TTTT
1 TTTT
4303 CCTCAGATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTAATTATATTTCTTTTAT
Found at i:5164 original size:29 final size:29
Alignment explanation
Indices: 5131--5223 Score: 168
Period size: 29 Copynumber: 3.2 Consensus size: 29
5121 CACATGGCCA
5131 TGTGACCCACACGGTCTAGCACACGATCG
1 TGTGACCCACACGGTCTAGCACACGATCG
*
5160 TGTGACCCACACGGTCTAGCACACGATCA
1 TGTGACCCACACGGTCTAGCACACGATCG
*
5189 TGTGACCCACACGGTCTACCACACGATCG
1 TGTGACCCACACGGTCTAGCACACGATCG
5218 TGTGAC
1 TGTGAC
5224 GCAGAGCAGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.18
Consensus pattern (29 bp):
TGTGACCCACACGGTCTAGCACACGATCG
Found at i:7839 original size:28 final size:28
Alignment explanation
Indices: 7768--7832 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
7758 GAGAATTGAG
7768 AAATATAGGAATTAAAAATGACCAAAAA
1 AAATATAGGAATTAAAAATGACCAAAAA
**
7796 AAATATAGGAATTAAAAATGACCAAATT
1 AAATATAGGAATTAAAAATGACCAAAAA
7824 AAATATAGG
1 AAATATAGG
7833 GAGTAAATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (28 bp):
AAATATAGGAATTAAAAATGACCAAAAA
Done.