Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009234.1 Kokia drynarioides strain JFW-HI SEQ_123939, 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: 13089
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:4240 original size:21 final size:21
Alignment explanation
Indices: 4207--4246 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4197 CGTGTTCTTG
* *
4207 GTTTTAGGGTTTGAGGTTTGA
1 GTTTTAAGATTTGAGGTTTGA
*
4228 GTTTTAAGATTTGGGGTTT
1 GTTTTAAGATTTGAGGTTT
4247 AGGATTATAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (21 bp):
GTTTTAAGATTTGAGGTTTGA
Found at i:4573 original size:41 final size:41
Alignment explanation
Indices: 4522--4687 Score: 246
Period size: 41 Copynumber: 4.0 Consensus size: 41
4512 ACCCTTAAGG
* *
4522 ATTTTGTAGGTAAAATTTCTAATTCTTTCTTATTTTAAATAT
1 ATTTT-TAGGTAAAATTTCTTATTCTTTCCTATTTTAAATAT
4564 ATTTTTAGGTAAAATTTCTTATTCTTTCCTATTTTAAATAT
1 ATTTTTAGGTAAAATTTCTTATTCTTTCCTATTTTAAATAT
*
4605 A-TTTTAGGTAAATTTTCTTATTCTTTCCTATTTTAAATAT
1 ATTTTTAGGTAAAATTTCTTATTCTTTCCTATTTTAAATAT
* * *
4645 ATTATTT-GGTAAATTTTATTATTCTTTCCTATTTTAAGTAT
1 ATT-TTTAGGTAAAATTTCTTATTCTTTCCTATTTTAAATAT
4686 AT
1 AT
4688 ACCAATGTGT
Statistics
Matches: 117, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
40 39 0.33
41 70 0.60
42 8 0.07
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (41 bp):
ATTTTTAGGTAAAATTTCTTATTCTTTCCTATTTTAAATAT
Found at i:4622 original size:81 final size:81
Alignment explanation
Indices: 4528--4687 Score: 250
Period size: 81 Copynumber: 2.0 Consensus size: 81
4518 AAGGATTTTG
* *
4528 TAGGTAAAATTTCTAATTCTTTCTTATTTTAAATATATT-TTTAGGTAAAATTTCTTATTCTTTC
1 TAGGTAAAATTTCTAATTCTTTCCTATTTTAAATATATTATTT-GGTAAAATTTATTATTCTTTC
4592 CTATTTTAAATATATTT
65 CTATTTTAAATATATTT
* * *
4609 TAGGTAAATTTTCTTATTCTTTCCTATTTTAAATATATTATTTGGTAAATTTTATTATTCTTTCC
1 TAGGTAAAATTTCTAATTCTTTCCTATTTTAAATATATTATTTGGTAAAATTTATTATTCTTTCC
*
4674 TATTTTAAGTATAT
66 TATTTTAAATATAT
4688 ACCAATGTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
81 69 0.96
82 3 0.04
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (81 bp):
TAGGTAAAATTTCTAATTCTTTCCTATTTTAAATATATTATTTGGTAAAATTTATTATTCTTTCC
TATTTTAAATATATTT
Found at i:4707 original size:47 final size:41
Alignment explanation
Indices: 4543--4714 Score: 152
Period size: 41 Copynumber: 4.0 Consensus size: 41
4533 AAAATTTCTA
* ** * *
4543 ATTCTTTCTTATTTTAAATATA-TTTTTAGGTAAAATTTCTT
1 ATTCTTTCCTATTTTAAATATACAATTTA-GTAAATTTTATT
* *
4584 ATTCTTTCCTATTTTAAATAT--ATTTTAGGTAAATTTTCTT
1 ATTCTTTCCTATTTTAAATATACAATTTA-GTAAATTTTATT
** *
4624 ATTCTTTCCTATTTTAAATATATTATTTGGTAAATTTTATT
1 ATTCTTTCCTATTTTAAATATACAATTTAGTAAATTTTATT
4665 ATTCTTTCCTATTTTAAGTATATACCAATGTGTAGTACAATTTTACTT
1 ATTCTTTCCTATTTTAA--ATATA-CAAT-T-TAGTA-AATTTTA-TT
4713 AT
1 AT
4715 AGTATATAAT
Statistics
Matches: 112, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
40 38 0.34
41 48 0.43
42 3 0.03
43 5 0.04
44 2 0.02
45 1 0.01
46 4 0.04
47 7 0.06
48 4 0.04
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (41 bp):
ATTCTTTCCTATTTTAAATATACAATTTAGTAAATTTTATT
Found at i:5564 original size:17 final size:17
Alignment explanation
Indices: 5542--5576 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5532 TAGTAACGTG
5542 TATCCCCAAAGAACAAT
1 TATCCCCAAAGAACAAT
5559 TATCCCCAAAGAACAAT
1 TATCCCCAAAGAACAAT
5576 T
1 T
5577 TCAAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.29, G:0.06, T:0.20
Consensus pattern (17 bp):
TATCCCCAAAGAACAAT
Found at i:8637 original size:33 final size:33
Alignment explanation
Indices: 8595--8657 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
8585 CGAACAAAAT
8595 GATGAAGTTGCACC-GATAAATGTTCCAATCAAA
1 GATGAAGTTGC-CCAGATAAATGTTCCAATCAAA
*
8628 GATGAAGTTGCCCAGATAAATGTTTCAATC
1 GATGAAGTTGCCCAGATAAATGTTCCAATC
8658 CTTGATGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (33 bp):
GATGAAGTTGCCCAGATAAATGTTCCAATCAAA
Found at i:8665 original size:33 final size:33
Alignment explanation
Indices: 8592--8667 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
8582 AGTCGAACAA
8592 AATGATGAAGTTGCACCGATAAATGTTCCAATC
1 AATGATGAAGTTGCACCGATAAATGTTCCAATC
* *
8625 AAAGATGAAGTTGC-CCAGATAAATGTTTCAATC
1 AATGATGAAGTTGCACC-GATAAATGTTCCAATC
**
8658 CTTGATGAAG
1 AATGATGAAG
8668 CTTCTTGACA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28
Consensus pattern (33 bp):
AATGATGAAGTTGCACCGATAAATGTTCCAATC
Done.