Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014345.1 Kokia drynarioides strain JFW-HI SEQ_129382, 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: 9267
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Found at i:938 original size:24 final size:26
Alignment explanation
Indices: 911--958 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
901 AGAGAAATCT
911 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
935 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
959 CCCTTGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:1059 original size:25 final size:25
Alignment explanation
Indices: 1031--1134 Score: 126
Period size: 25 Copynumber: 4.3 Consensus size: 25
1021 GCTTACTATT
*
1031 CAGCACTCTGTGTGCTTCTGTTACC
1 CAGCACTGTGTGTGCTTCTGTTACC
1056 CAGCACTGTGTGTGCTTCTGTT---
1 CAGCACTGTGTGTGCTTCTGTTACC
*
1078 CAACAC-GTGTGTGCTTCTGTTACC
1 CAGCACTGTGTGTGCTTCTGTTACC
* * *
1102 CAGCATTGTGTGTGCTTTTGTTTCC
1 CAGCACTGTGTGTGCTTCTGTTACC
1127 CTAGCACT
1 C-AGCACT
1135 TATGCACTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
21 15 0.22
22 5 0.07
24 4 0.06
25 38 0.57
26 5 0.07
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.38
Consensus pattern (25 bp):
CAGCACTGTGTGTGCTTCTGTTACC
Found at i:4794 original size:36 final size:35
Alignment explanation
Indices: 4715--4794 Score: 83
Period size: 36 Copynumber: 2.2 Consensus size: 35
4705 AAAATTAAAC
*
4715 ATTAAAATCCCAAAATAATTTAATAACATATTAAT
1 ATTAAAATCCCAAAATAATTTAATAACATAATAAT
* *
4750 ATGAAAAATCCCCAAAAT-ATTTCATAACGAGTAATAA-
1 AT-TAAAAT-CCCAAAATAATTTAATAAC-A-TAATAAT
4787 ATTAAAAT
1 ATTAAAAT
4795 GATTAAAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
35 2 0.05
36 19 0.51
37 11 0.30
38 5 0.14
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (35 bp):
ATTAAAATCCCAAAATAATTTAATAACATAATAAT
Found at i:4951 original size:15 final size:15
Alignment explanation
Indices: 4931--4971 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
4921 ATTTTATATG
4931 GAATTTTGAATTGAA
1 GAATTTTGAATTGAA
4946 GAATTTTGAATTGAA
1 GAATTTTGAATTGAA
4961 GAATTTT-AATT
1 GAATTTTGAATT
4972 ATGGAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (15 bp):
GAATTTTGAATTGAA
Found at i:6756 original size:13 final size:12
Alignment explanation
Indices: 6738--6796 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
6728 TGGTCAAAGA
6738 AAAGTCAACGATC
1 AAAGTCAACG-TC
**
6751 AAAGTCAAAATC
1 AAAGTCAACGTC
*
6763 AAAGGTCAAAGTC
1 AAA-GTCAACGTC
*
6776 AAAGTCGACTGTC
1 AAAGTCAAC-GTC
6789 AAAGTCAA
1 AAAGTCAA
6797 TGAGTCTGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
12 9 0.24
13 29 0.76
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.17
Consensus pattern (12 bp):
AAAGTCAACGTC
Found at i:6776 original size:6 final size:6
Alignment explanation
Indices: 6738--6796 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
6728 TGGTCAAAGA
* * **
6738 AAAGTC AACGATC AAAGTC AAAATC AAAGGTC AAAGTC AAAGTC GACTGTC
1 AAAGTC AAAG-TC AAAGTC AAAGTC AAA-GTC AAAGTC AAAGTC -AAAGTC
6789 AAAGTC AA
1 AAAGTC AA
6797 TGAGTCTGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 28 0.67
7 14 0.33
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAGTC
Done.