Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013104.1 Kokia drynarioides strain JFW-HI SEQ_128122, 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: 12116
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7568 original size:27 final size:26
Alignment explanation
Indices: 7522--7608 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 26
7512 AAAAATATGT
*
7522 TTTTATA-ATTTTTATACTTTTATATATAA
1 TTTTATATATTTTTCT--TTTTA-ATA-AA
7551 TTTTA-ATAATTTTTCTTTTTAATAAA
1 TTTTATAT-ATTTTTCTTTTTAATAAA
*
7577 TTTTATATATTTTTGAATTTTTAA-AAA
1 TTTTATATATTTTT--CTTTTTAATAAA
7604 TTTTA
1 TTTTA
7609 AAAATTTAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
26 13 0.25
27 13 0.25
28 13 0.25
29 5 0.10
30 7 0.14
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (26 bp):
TTTTATATATTTTTCTTTTTAATAAA
Found at i:7615 original size:27 final size:26
Alignment explanation
Indices: 7528--7615 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 26
7518 ATGTTTTTAT
*
7528 AATTTTTATACTTTTATATATAATTTTAAT
1 AATTTTTAT--TTTTA-ATA-AATTTTAAA
* *
7558 AATTTTTCTTTTTAATAAATTTTATA
1 AATTTTTATTTTTAATAAATTTTAAA
*
7584 TATTTTTGAATTTTTAA-AAATTTTAAA
1 AATTTTT--ATTTTTAATAAATTTTAAA
7611 AATTT
1 AATTT
7616 AATTAATTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
26 13 0.27
27 16 0.33
28 12 0.24
30 8 0.16
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (26 bp):
AATTTTTATTTTTAATAAATTTTAAA
Found at i:8172 original size:18 final size:19
Alignment explanation
Indices: 8135--8172 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
8125 TTTTAAATTT
8135 TTTAAAAATTCAAAAAAAA
1 TTTAAAAATTCAAAAAAAA
* *
8154 TTTACAAATT-AAAATAAA
1 TTTAAAAATTCAAAAAAAA
8172 T
1 T
8173 AAATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
TTTAAAAATTCAAAAAAAA
Found at i:9318 original size:15 final size:14
Alignment explanation
Indices: 9272--9319 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
9262 GTATGACCAC
9272 ATTTGA-TTAATTA
1 ATTTGATTTAATTA
9285 ATTTG-TTT-A-TA
1 ATTTGATTTAATTA
*
9296 ATTAGATTTAATTA
1 ATTTGATTTAATTA
9310 ATGTTGATTT
1 AT-TTGATTT
9320 GCCCAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 6 0.21
12 4 0.14
13 8 0.29
14 4 0.14
15 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (14 bp):
ATTTGATTTAATTA
Found at i:9834 original size:14 final size:14
Alignment explanation
Indices: 9815--9841 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9805 GATCCATAAT
9815 TGAATTTAACCAAA
1 TGAATTTAACCAAA
9829 TGAATTTAACCAA
1 TGAATTTAACCAA
9842 TACTATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (14 bp):
TGAATTTAACCAAA
Found at i:12037 original size:21 final size:20
Alignment explanation
Indices: 11999--12037 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
11989 GTGCAAAAGA
*
11999 CTTACAAGAAGGGAGATTGG
1 CTTACAAGAAGCGAGATTGG
12019 CTTACAAGAAAGCGAGATT
1 CTTACAAG-AAGCGAGATT
12038 CATTGATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (20 bp):
CTTACAAGAAGCGAGATTGG
Done.