Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007963.1 Kokia drynarioides strain JFW-HI SEQ_122611, 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: 6768
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:888 original size:20 final size:22
Alignment explanation
Indices: 863--913 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 22
853 TTGATATTAT
863 TTAG-AAATTTTA-ATAATACA
1 TTAGAAAATTTTATATAATACA
883 TTAGAAAATTTTATATAAT--A
1 TTAGAAAATTTTATATAATACA
903 TTA-AAAATTTT
1 TTAGAAAATTTT
914 GGTATCGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.28
20 8 0.28
21 8 0.28
22 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
TTAGAAAATTTTATATAATACA
Found at i:1521 original size:29 final size:29
Alignment explanation
Indices: 1468--1533 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1458 CAAAAAATTT
**
1468 AACTTTTAAGGGTTTTAAATTTTTTTTACC
1 AACTTTTAAGGGACTTAAATTTTTTTT-CC
1498 AACTTTTAA-GGACTTAAATTTTTTTTCC
1 AACTTTTAAGGGACTTAAATTTTTTTTCC
1526 AA-TTTTAA
1 AACTTTTAA
1534 AAAAATCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 6 0.18
28 4 0.12
29 15 0.44
30 9 0.26
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.52
Consensus pattern (29 bp):
AACTTTTAAGGGACTTAAATTTTTTTTCC
Found at i:2880 original size:16 final size:16
Alignment explanation
Indices: 2852--2890 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2842 TTGAACCGAG
2852 ATTTTTGAGATTTTTA
1 ATTTTTGAGATTTTTA
2868 ATTTGTTGA-ATTTTTA
1 ATTT-TTGAGATTTTTA
2884 ATATTTT
1 AT-TTTT
2891 TAATCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (16 bp):
ATTTTTGAGATTTTTA
Found at i:5277 original size:16 final size:15
Alignment explanation
Indices: 5234--5282 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
5224 TAAAATAAAG
5234 AAAA-ATTA-AAAA-
1 AAAACATTAGAAAAT
5246 AAAACATTAGAAAAT
1 AAAACATTAGAAAAT
*
5261 AAAACATTAGATCAAT
1 AAAACATTAGA-AAAT
5277 AAAACA
1 AAAACA
5283 CGTTCAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 4 0.12
13 4 0.12
14 4 0.12
15 11 0.34
16 9 0.28
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.18
Consensus pattern (15 bp):
AAAACATTAGAAAAT
Found at i:5609 original size:23 final size:23
Alignment explanation
Indices: 5583--5641 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
5573 CATAAGGCAG
*
5583 AAGCATGTCACAAGATAGAGAAA
1 AAGCATGTCACAAGACAGAGAAA
* * *
5606 AAGCGTG-CTATAAGACAGAGGAA
1 AAGCATGTC-ACAAGACAGAGAAA
5629 AAGCATGTCACAA
1 AAGCATGTCACAA
5642 AAGCAGATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 1 0.04
23 26 0.93
24 1 0.04
ACGTcount: A:0.47, C:0.15, G:0.24, T:0.14
Consensus pattern (23 bp):
AAGCATGTCACAAGACAGAGAAA
Found at i:6327 original size:12 final size:12
Alignment explanation
Indices: 6310--6339 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6300 AATATTTAAA
*
6310 TATTTTCTTTTC
1 TATTTTCTTATC
6322 TATTTTCTTATC
1 TATTTTCTTATC
6334 TATTTT
1 TATTTT
6340 AATAATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTTTCTTATC
Done.