Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005073.1 Kokia drynarioides strain JFW-HI SEQ_118880, 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: 14012
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2513 original size:3 final size:3
Alignment explanation
Indices: 2498--2527 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2488 AATTTAACAA
*
2498 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2528 GTTAATTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:8975 original size:16 final size:17
Alignment explanation
Indices: 8954--8987 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
8944 CTAAGAGCCT
8954 GGCTTG-TGTAGCTTAG
1 GGCTTGATGTAGCTTAG
8970 GGCTTGACTGTAGCTTAG
1 GGCTTGA-TGTAGCTTAG
8988 ATACGTGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (17 bp):
GGCTTGATGTAGCTTAG
Found at i:13461 original size:11 final size:11
Alignment explanation
Indices: 13445--13528 Score: 69
Period size: 11 Copynumber: 7.1 Consensus size: 11
13435 GGGGACCAAC
* *
13445 GAAAAATGAAG
1 GAAAAAAGAAA
13456 GAAAAAAGAAA
1 GAAAAAAGAAA
13467 GAAAAAAGAGAA
1 GAAAAAAGA-AA
13479 TGAAAGAAAGAAA
1 -GAAA-AAAGAAA
* *
13492 GAAAGAAGAAG
1 GAAAAAAGAAA
*
13503 GAAGAAAGAGAA
1 GAAAAAAGA-AA
13515 GAAAGAGAAGAAA
1 GAAA-A-AAGAAA
13528 G
1 G
13529 GGAAGAAGGA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
11 30 0.51
12 10 0.17
13 10 0.17
14 9 0.15
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:13469 original size:4 final size:4
Alignment explanation
Indices: 13456--13528 Score: 73
Period size: 4 Copynumber: 18.2 Consensus size: 4
13446 AAAAATGAAG
13456 GAAA -AAA GAAA GAAA -AAA GAGAA TGAAA GAAA GAAA GAAA G-AA G-AA
1 GAAA GAAA GAAA GAAA GAAA GA-AA -GAAA GAAA GAAA GAAA GAAA GAAA
*
13502 GGAA GAAA GAGAA GAAA GAGAA GAAA G
1 GAAA GAAA GA-AA GAAA GA-AA GAAA G
13529 GGAAGAAGGA
Statistics
Matches: 61, Mismatches: 1, Indels: 14
0.80 0.01 0.18
Matches are distributed among these distances:
3 12 0.20
4 35 0.57
5 12 0.20
6 2 0.03
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:13507 original size:22 final size:21
Alignment explanation
Indices: 13460--13528 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 21
13450 ATGAAGGAAA
13460 AAAGAAAGAAA-AAAGAGAATG
1 AAAGAAAGAAAGAAAGAGAA-G
13481 AAAGAAAGAAAGAAAGAAGAAG
1 AAAGAAAGAAAGAAAG-AGAAG
*
13503 GAAGAAAGAGAAGAAAGAGAAG
1 AAAGAAAGA-AAGAAAGAGAAG
13525 AAAG
1 AAAG
13529 GGAAGAAGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 11 0.26
22 21 0.49
23 11 0.26
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (21 bp):
AAAGAAAGAAAGAAAGAGAAG
Found at i:13511 original size:36 final size:36
Alignment explanation
Indices: 13456--13528 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
13446 AAAAATGAAG
13456 GAAAAAAGAAAGAAAAAAGAGAATGAAAGA-AAGAAA
1 GAAAAAAGAAAGAAAAAAGAGAA-GAAAGAGAAGAAA
* * *
13492 GAAAGAAGAAGGAAGAAAGAGAAGAAAGAGAAGAAA
1 GAAAAAAGAAAGAAAAAAGAGAAGAAAGAGAAGAAA
13528 G
1 G
13529 GGAAGAAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (36 bp):
GAAAAAAGAAAGAAAAAAGAGAAGAAAGAGAAGAAA
Found at i:13543 original size:36 final size:35
Alignment explanation
Indices: 13456--13562 Score: 101
Period size: 36 Copynumber: 3.0 Consensus size: 35
13446 AAAAATGAAG
* *
13456 GAAAAAAGAAAGAAAAAAGAGAATGAAAGA-AAGAAA
1 GAAAGAAG-AAGAAGAAAGAGAA-GAAAGAGAAGAAA
13492 GAAAGAAGAAGGAAGAAAGAGAAGAAAGAGAAGAAA
1 GAAAGAAGAA-GAAGAAAGAGAAGAAAGAGAAGAAA
* * * * *
13528 GGGAAGAAGGAGAAGAAGGGGAAGAAGGAG-AGAAA
1 -GAAAGAAGAAGAAGAAAGAGAAGAAAGAGAAGAAA
13563 AAAAAAGGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
35 13 0.21
36 40 0.66
37 8 0.13
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (35 bp):
GAAAGAAGAAGAAGAAAGAGAAGAAAGAGAAGAAA
Found at i:13554 original size:9 final size:9
Alignment explanation
Indices: 13461--13562 Score: 90
Period size: 9 Copynumber: 11.7 Consensus size: 9
13451 TGAAGGAAAA
13461 AAGAAAGA-
1 AAGAAAGAG
13469 AA-AAAGAG
1 AAGAAAGAG
13477 AATGAAAGA-
1 AA-GAAAGAG
13486 AAGAAAGA-
1 AAGAAAGAG
13494 AAG-AAGAAGG
1 AAGAAAG-A-G
13504 AAGAAAGAG
1 AAGAAAGAG
13513 AAGAAAGAG
1 AAGAAAGAG
*
13522 AAGAAAGGG
1 AAGAAAGAG
*
13531 AAGAAGGAG
1 AAGAAAGAG
* *
13540 AAGAAGGGG
1 AAGAAAGAG
*
13549 AAGAAGGAG
1 AAGAAAGAG
13558 -AGAAA
1 AAGAAA
13563 AAAAAAGGTA
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
7 8 0.10
8 18 0.22
9 43 0.53
10 9 0.11
11 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (9 bp):
AAGAAAGAG
Found at i:13947 original size:20 final size:21
Alignment explanation
Indices: 13908--13947 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13898 ATTTACTTTA
13908 ATTTAATTTTGCTAGTTAGTG
1 ATTTAATTTTGCTAGTTAGTG
* *
13929 ATTTTATTTTG-TTGTTAGT
1 ATTTAATTTTGCTAGTTAGT
13948 AGTAGTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (21 bp):
ATTTAATTTTGCTAGTTAGTG
Done.