Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001199.1 Kokia drynarioides strain JFW-HI SEQ_112544, 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: 39665
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:66 original size:25 final size:24
Alignment explanation
Indices: 35--83 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
25 AATTTAAAAT
35 TTATATTAATATTAAATAAATATAA
1 TTATATTAATATTAAA-AAATATAA
*
60 TTATATTAATATTAAAATATATAA
1 TTATATTAATATTAAAAAATATAA
84 ACCCTCATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATATTAATATTAAAAAATATAA
Found at i:1405 original size:24 final size:24
Alignment explanation
Indices: 1377--1427 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1367 AGAAATAATC
* *
1377 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
1401 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
1425 TTT
1 TTT
1428 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:1977 original size:41 final size:41
Alignment explanation
Indices: 1932--2102 Score: 209
Period size: 41 Copynumber: 4.2 Consensus size: 41
1922 AGTTTTTGCC
* * *
1932 ATAAACGCCACTAATGCTCTTACCTTTTGCGGGGTTTTCTT
1 ATAAACGCCGCTAATACTCTTACCTTTTGCGGCGTTTTCTT
* * * *
1973 ATAAACGCCGCTAATACTCTCACATTTTGTGGCGTTTTCTC
1 ATAAACGCCGCTAATACTCTTACCTTTTGCGGCGTTTTCTT
* * *
2014 ATAAACGCCGCTAATACTCTTACTTTTTGCGACATTTTCTT
1 ATAAACGCCGCTAATACTCTTACCTTTTGCGGCGTTTTCTT
* * *
2055 ATAAACGCCGCTAATGCT-TTACCTTTTGCGGCATTTTTCTC
1 ATAAACGCCGCTAATACTCTTACCTTTTGCGGC-GTTTTCTT
2096 ATAAACG
1 ATAAACG
2103 TTGCTATTGC
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
40 12 0.11
41 99 0.89
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (41 bp):
ATAAACGCCGCTAATACTCTTACCTTTTGCGGCGTTTTCTT
Found at i:5987 original size:63 final size:63
Alignment explanation
Indices: 5888--6015 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 63
5878 ACCTAGTAAA
* * * * *
5888 ATTTAAACTCTAATATTTTGGTTTACACTTAATCTTTTTGCATGAAATGAATTTCATTCATCT
1 ATTTAAACTCTAATATCTTGGTCTACACTTAATCTTTTCGCATGAAATAAATTTCACTCATCT
5951 ATTTAAACTCTAATATCTTGGTCTACACTTAATCTTTTCGCATGAAATAAATTTCACTCATCT
1 ATTTAAACTCTAATATCTTGGTCTACACTTAATCTTTTCGCATGAAATAAATTTCACTCATCT
6014 AT
1 AT
6016 ATATTTGTCT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (63 bp):
ATTTAAACTCTAATATCTTGGTCTACACTTAATCTTTTCGCATGAAATAAATTTCACTCATCT
Found at i:13730 original size:2 final size:2
Alignment explanation
Indices: 13723--13747 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13713 TATTTAAAAG
13723 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
13748 TATTTTTTAA
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:15278 original size:21 final size:21
Alignment explanation
Indices: 15254--15294 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15244 ATTCACCAAA
*
15254 AAAAATATTTAATAATCAATG
1 AAAAATATTTAAGAATCAATG
*
15275 AAAAATATTTACGAATCAAT
1 AAAAATATTTAAGAATCAAT
15295 ATTGTATCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (21 bp):
AAAAATATTTAAGAATCAATG
Found at i:16628 original size:21 final size:22
Alignment explanation
Indices: 16582--16628 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
16572 AGTTAAGATG
* *
16582 TATTTTATATTGAGTTAATTTT
1 TATTTTATATTGAGTTAATGTA
16604 TATTTTA-ATTGA-TTGAATGTA
1 TATTTTATATTGAGTT-AATGTA
16625 TATT
1 TATT
16629 ATTTGTGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 13 0.59
22 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (22 bp):
TATTTTATATTGAGTTAATGTA
Found at i:28351 original size:6 final size:6
Alignment explanation
Indices: 28336--28366 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28326 TTATTGAATT
*
28336 AATAAC AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA A
28367 TATATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:31355 original size:19 final size:21
Alignment explanation
Indices: 31329--31372 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
31319 ATAAGAATGT
*
31329 AAAA-ATT-AAATGAAAA-AA
1 AAAATATTAAAATAAAAATAA
31347 AAAATATTAAAATAAAAATAA
1 AAAATATTAAAATAAAAATAA
31368 AAAAT
1 AAAAT
31373 GACTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 3 0.14
20 8 0.36
21 7 0.32
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAATATTAAAATAAAAATAA
Found at i:32474 original size:20 final size:20
Alignment explanation
Indices: 32436--32474 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
32426 ATTAAAGGGC
**
32436 TTAACATTTTTTATGATTTT
1 TTAACATTTTTTAAAATTTT
*
32456 TTAATATTTTTTAAAATTT
1 TTAACATTTTTTAAAATTT
32475 AAAAGTACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TTAACATTTTTTAAAATTTT
Found at i:33087 original size:29 final size:30
Alignment explanation
Indices: 33054--33118 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
33044 AAATTTTACG
33054 TATAAAATCGCACA-AAATCAAAATTCATA
1 TATAAAATCGCACATAAATCAAAATTCATA
*** *
33083 TATAAAATTTTATATTAAATCAAAATTCATA
1 TATAAAATCGCACA-TAAATCAAAATTCATA
33114 TATAA
1 TATAA
33119 TATTTTACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 10 0.33
31 20 0.67
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.34
Consensus pattern (30 bp):
TATAAAATCGCACATAAATCAAAATTCATA
Done.