Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007720.1 Kokia drynarioides strain JFW-HI SEQ_122353, 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: 24583
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--30 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31 GAAGGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351 original size:19 final size:20
Alignment explanation
Indices: 329--376 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
319 TTTATTGCTT
*
329 ATATATTTTA-ATATTTAAA
1 ATATATTTTACATATTCAAA
*
348 ATATAGTTTACATATTCAAA
1 ATATATTTTACATATTCAAA
*
368 TTATATTTT
1 ATATATTTT
377 TAAATAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATATTTTACATATTCAAA
Found at i:6096 original size:19 final size:19
Alignment explanation
Indices: 6053--6098 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
6043 TGGAAAAATA
*
6053 ATTTTTAAAAAATAAATTG
1 ATTTATAAAAAATAAATTG
* *
6072 ATTTTATAAAAAATAATTTT
1 A-TTTATAAAAAATAAATTG
6092 ATTTATA
1 ATTTATA
6099 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTTATAAAAAATAAATTG
Found at i:6618 original size:34 final size:38
Alignment explanation
Indices: 6579--6656 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 38
6569 GTACTATAGA
*
6579 ATATTTATTATT-AAATGTT-TATAAA-TTGTAAT-AT
1 ATATTTATTATTCAAATATTATATAAATTTGTAATAAT
*
6613 ATATTTATTATTCAAATATTAATATAAATTTTTAATAAT
1 ATATTTATTATTCAAATATT-ATATAAATTTGTAATAAT
6652 ATATT
1 ATATT
6657 AATAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 12 0.32
35 6 0.16
37 6 0.16
38 6 0.16
39 7 0.19
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (38 bp):
ATATTTATTATTCAAATATTATATAAATTTGTAATAAT
Found at i:8464 original size:46 final size:47
Alignment explanation
Indices: 8381--8469 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 47
8371 ACTTCATATC
* * * *
8381 TTTCTATATTATTCTTGTCATCTCGGGTGACCTGACAACGATGACTT
1 TTTCTATATTATACTTATCATCCCGGGTGACCCGACAACGATGACTT
* * *
8428 TTTCTAT-TTATACTTATCTTCCCGGGTGGCCCGACAATGATG
1 TTTCTATATTATACTTATCATCCCGGGTGACCCGACAACGATG
8470 GTTACTCTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
46 28 0.80
47 7 0.20
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.39
Consensus pattern (47 bp):
TTTCTATATTATACTTATCATCCCGGGTGACCCGACAACGATGACTT
Found at i:14731 original size:19 final size:18
Alignment explanation
Indices: 14692--14747 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
14682 AAATTAATAA
*
14692 TCAAAATAATTTTCAAAAAT
1 TCAAAA-AATTTT-TAAAAT
*
14712 TGAAAACAATTTTTAAAAT
1 TCAAAA-AATTTTTAAAAT
*
14731 TCAAAATATTTTTAAAA
1 TCAAAAAATTTTTAAAA
14748 ATTCTAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 10 0.32
19 10 0.32
20 11 0.35
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (18 bp):
TCAAAAAATTTTTAAAAT
Found at i:14748 original size:19 final size:19
Alignment explanation
Indices: 14692--14756 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
14682 AAATTAATAA
*
14692 TCAAAATAATTTTCAAAAAT
1 TCAAAAT-ATTTTTAAAAAT
* *
14712 TGAAAACAATTTTT-AAAAT
1 TCAAAA-TATTTTTAAAAAT
14731 TCAAAATATTTTTAAAAAT
1 TCAAAATATTTTTAAAAAT
*
14750 TCTAAAT
1 TCAAAAT
14757 TTTGTATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
18 6 0.16
19 21 0.57
20 10 0.27
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (19 bp):
TCAAAATATTTTTAAAAAT
Found at i:16421 original size:44 final size:44
Alignment explanation
Indices: 16358--16446 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
16348 GAATATTTAC
16358 TCAAATACTTGGTGTGCTTAGTTTTCTTGTGGCTTTCAGGTTCT
1 TCAAATACTTGGTGTGCTTAGTTTTCTTGTGGCTTTCAGGTTCT
16402 TCAAATACTTGGTGTGCTTAGTTTTCTTGTGGCTTTCAGGTTCT
1 TCAAATACTTGGTGTGCTTAGTTTTCTTGTGGCTTTCAGGTTCT
16446 T
1 T
16447 TCATTGCTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.48
Consensus pattern (44 bp):
TCAAATACTTGGTGTGCTTAGTTTTCTTGTGGCTTTCAGGTTCT
Found at i:17968 original size:22 final size:22
Alignment explanation
Indices: 17943--17992 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
17933 ATTATAATAC
17943 TTAAAAAAACAAACAT-AAAATT
1 TTAAAAAAACAAA-ATCAAAATT
**
17965 TTAAAAAAATTAAATCAAAATT
1 TTAAAAAAACAAAATCAAAATT
17987 TTAAAA
1 TTAAAA
17993 TAAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (22 bp):
TTAAAAAAACAAAATCAAAATT
Found at i:17990 original size:13 final size:12
Alignment explanation
Indices: 17957--18011 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
17947 AAAAACAAAC
17957 ATAAAATTTTAA
1 ATAAAATTTTAA
17969 A-AAAA--TTAA
1 ATAAAATTTTAA
17978 ATCAAAATTTTAAA
1 AT-AAAATTTT-AA
*
17992 ATAAAATATTAA
1 ATAAAATTTTAA
18004 ATAAAATT
1 ATAAAATT
18012 ATTATTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
9 5 0.14
11 8 0.22
12 10 0.28
13 9 0.25
14 4 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAAAATTTTAA
Found at i:18014 original size:13 final size:13
Alignment explanation
Indices: 17973--18015 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
17963 TTTTAAAAAA
17973 ATTAAATCAAAATT
1 ATTAAAT-AAAATT
17987 -TTAAAATAAAA-T
1 ATT-AAATAAAATT
17999 ATTAAATAAAATT
1 ATTAAATAAAATT
18012 ATTA
1 ATTA
18016 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 9 0.35
13 13 0.50
14 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTAAATAAAATT
Found at i:24389 original size:8 final size:8
Alignment explanation
Indices: 24361--24401 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
24351 CGATTCAGGG
24361 TATA-TTA
1 TATACTTA
*
24368 TATACATA
1 TATACTTA
24376 TATACTTA
1 TATACTTA
24384 TATACTTA
1 TATACTTA
*
24392 CAT-CTTA
1 TATACTTA
24399 TAT
1 TAT
24402 TATTCTGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 10 0.34
8 19 0.66
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (8 bp):
TATACTTA
Done.