Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000562.1 Kokia drynarioides strain JFW-HI SEQ_111476, 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: 27333
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:382 original size:3 final size:3
Alignment explanation
Indices: 374--398 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
364 ACATGTAACT
374 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
399 CATTTTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:813 original size:16 final size:16
Alignment explanation
Indices: 788--818 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
778 TATAAAACAA
788 TATCTAAAAGTCCCAT
1 TATCTAAAAGTCCCAT
*
804 TATCTTAAAGTCCCA
1 TATCTAAAAGTCCCA
819 ATATTGTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TATCTAAAAGTCCCAT
Found at i:9895 original size:32 final size:33
Alignment explanation
Indices: 9854--9934 Score: 146
Period size: 34 Copynumber: 2.5 Consensus size: 33
9844 ACATCGAATT
9854 AGCTTTCTTGAGTTTCTTCAAAT-AAAAAAAAA
1 AGCTTTCTTGAGTTTCTTCAAATAAAAAAAAAA
9886 AGCTTTCTTGAGTTTCTTCAAATAAAAAAAAAAA
1 AGCTTTCTTGAGTTTCTTCAAAT-AAAAAAAAAA
9920 AGCTTTCTTGAGTTT
1 AGCTTTCTTGAGTTT
9935 GATTGAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 23 0.49
34 24 0.51
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (33 bp):
AGCTTTCTTGAGTTTCTTCAAATAAAAAAAAAA
Found at i:11642 original size:21 final size:21
Alignment explanation
Indices: 11618--11671 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11608 AAATTTGAAA
11618 TTTACTTTTTATATTTTTATT
1 TTTACTTTTTATATTTTTATT
***
11639 TTTAAGAATTTA-ATTTTTATT
1 TTT-ACTTTTTATATTTTTATT
11660 TTTACTTTTTAT
1 TTTACTTTTTAT
11672 TTTGAAATTC
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
20 5 0.20
21 15 0.60
22 5 0.20
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTACTTTTTATATTTTTATT
Found at i:11842 original size:32 final size:29
Alignment explanation
Indices: 11801--11869 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
11791 ACAGTTAAAT
*
11801 TTAAA-TTTTAAAATCTAAAATATAAAAAAAA
1 TTAAATTTTTAAAA-ATAAAA-AT-AAAAAAA
* *
11832 TTAAATTTTTAAAAATAAAAATATAACAA
1 TTAAATTTTTAAAAATAAAAATAAAAAAA
11861 TTAAATTTT
1 TTAAATTTT
11870 AAATTTACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.41
30 2 0.06
31 10 0.29
32 8 0.24
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAATTTTTAAAAATAAAAATAAAAAAA
Found at i:17637 original size:2 final size:2
Alignment explanation
Indices: 17630--17654 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17620 ATGTTCTTTT
17630 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 T
17655 TATTATCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22566 original size:26 final size:26
Alignment explanation
Indices: 22532--22584 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
22522 CAACTAAGTT
* *
22532 TTAACAGAACCAATTGATCAAATCAA
1 TTAACAGAACCAATCGATCAAACCAA
* *
22558 TTAATAGAATCAATCGATCAAACCAA
1 TTAACAGAACCAATCGATCAAACCAA
22584 T
1 T
22585 CACTACAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.25
Consensus pattern (26 bp):
TTAACAGAACCAATCGATCAAACCAA
Done.