Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007794.1 Kokia drynarioides strain JFW-HI SEQ_122428, 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: 26601
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:855 original size:16 final size:16
Alignment explanation
Indices: 834--867 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
824 ATAATTTTTT
*
834 AAAATATAATTCTAAA
1 AAAATAAAATTCTAAA
850 AAAATAAAATTCTAAA
1 AAAATAAAATTCTAAA
866 AA
1 AA
868 TATGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAAATTCTAAA
Found at i:2729 original size:23 final size:23
Alignment explanation
Indices: 2699--2744 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2689 AATGTCTTTC
2699 TTGTTGTGTTTGCTTCATAGTTT
1 TTGTTGTGTTTGCTTCATAGTTT
2722 TTGTTGTGTTTGCTTCATAGTTT
1 TTGTTGTGTTTGCTTCATAGTTT
2745 GACAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.61
Consensus pattern (23 bp):
TTGTTGTGTTTGCTTCATAGTTT
Found at i:6256 original size:2 final size:2
Alignment explanation
Indices: 6249--6279 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6239 AAATTATAAG
6249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6280 TAAAAGCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10296 original size:22 final size:22
Alignment explanation
Indices: 10228--10301 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 22
10218 TATTAAAAAA
10228 ATAAAGATATATTAAATATGTT-AT
1 ATAAA-AT-TATTAAATAT-TTAAT
* **
10252 A-AAAATTTCAGTAAATAAATAAT
1 ATAAAA-TT-ATTAAATATTTAAT
10275 ATAAAATTATTAAATATTTAAT
1 ATAAAATTATTAAATATTTAAT
10297 -TAAAA
1 ATAAAA
10302 CAATATAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
21 5 0.12
22 14 0.35
23 16 0.40
24 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAAAATTATTAAATATTTAAT
Found at i:13264 original size:15 final size:16
Alignment explanation
Indices: 13235--13268 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
13225 GAGTATTATA
13235 TATTTTTAAAAAAAAT
1 TATTTTTAAAAAAAAT
*
13251 TATTTTTAATAAAAAT
1 TATTTTTAAAAAAAAT
13267 TA
1 TA
13269 ATCTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTTTAAAAAAAAT
Found at i:19249 original size:6 final size:6
Alignment explanation
Indices: 19212--19258 Score: 51
Period size: 6 Copynumber: 7.3 Consensus size: 6
19202 ATCCGCTATA
19212 TTTTTC TTTCTTC ATTTTCTC TTTTT- TATTTTC TTTTTC TTTTTC TT
1 TTTTTC TTT-TTC -TTTT-TC TTTTTC T-TTTTC TTTTTC TTTTTC TT
19259 CTAAACAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 1 0.03
6 21 0.58
7 9 0.25
8 5 0.14
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:19417 original size:27 final size:26
Alignment explanation
Indices: 19384--19439 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
19374 TTATTTATAA
*
19384 ATTTTTAAAAAATAAATTAAAAATTTT
1 ATTTTTAAAAAATAAAAT-AAAATTTT
* *
19411 ATTTTTAGAAAATAAAATATAATTTT
1 ATTTTTAAAAAATAAAATAAAATTTT
19437 ATT
1 ATT
19440 ATTACTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTTTTAAAAAATAAAATAAAATTTT
Found at i:26566 original size:23 final size:23
Alignment explanation
Indices: 26540--26585 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
26530 GTTAATATTA
26540 TAATAAAT-TTTAAAATAAAAATT
1 TAATAAATATTT-AAATAAAAATT
* *
26563 TAATATATATTTATATAAAAATT
1 TAATAAATATTTAAATAAAAATT
26586 ATTGGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAAATATTTAAATAAAAATT
Done.