Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007829.1 Kokia drynarioides strain JFW-HI SEQ_122465, 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: 13817
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Found at i:1281 original size:16 final size:19
Alignment explanation
Indices: 1237--1279 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1227 ACATAATACA
1237 AATATAAAATAAGATAAAT
1 AATATAAAATAAGATAAAT
1256 AAT-TAAAATAA-A-AAAT
1 AATATAAAATAAGATAAAT
1272 AATATAAA
1 AATATAAA
1280 TACAAGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.30
17 5 0.22
18 8 0.35
19 3 0.13
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATATAAAATAAGATAAAT
Found at i:3273 original size:25 final size:26
Alignment explanation
Indices: 3218--3274 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
3208 TGTTACAATC
*
3218 TATTTAAAATTTTTATATTTTTTTGTA
1 TATTTAAAA-TTTTATATTTTTTTCTA
*
3245 TATTTAAAA-TTTA-ATTTTTTATCTT
1 TATTTAAAATTTTATATTTTTT-TCTA
3270 TATTT
1 TATTT
3275 TTAAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.26
25 11 0.41
27 9 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (26 bp):
TATTTAAAATTTTATATTTTTTTCTA
Found at i:4354 original size:22 final size:22
Alignment explanation
Indices: 4329--4371 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4319 GTTCATTTCT
* *
4329 AGGCTTATATGTCTCGAGAAAA
1 AGGCTTAAATGTCTCAAGAAAA
4351 AGGCTTAAATGTCTCAAGAAA
1 AGGCTTAAATGTCTCAAGAAA
4372 GTGTCATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (22 bp):
AGGCTTAAATGTCTCAAGAAAA
Found at i:4438 original size:22 final size:22
Alignment explanation
Indices: 4413--4468 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4403 AGTTATCCTA
* *
4413 TCTCGAGACAAATGAGTGAATG
1 TCTCGAGACAAAAGAATGAATG
* **
4435 TCTCAAGACAAAAGAATTTATG
1 TCTCGAGACAAAAGAATGAATG
4457 TCTCGAGACAAA
1 TCTCGAGACAAA
4469 GTCTAATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (22 bp):
TCTCGAGACAAAAGAATGAATG
Found at i:6761 original size:15 final size:17
Alignment explanation
Indices: 6738--6775 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
6728 AATTTAATCA
*
6738 TTTATACTTTT-A-TCT
1 TTTACACTTTTCACTCT
6753 TTTACACTTTTCACTCT
1 TTTACACTTTTCACTCT
6770 TTTACA
1 TTTACA
6776 ATTTAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTACACTTTTCACTCT
Found at i:8474 original size:15 final size:16
Alignment explanation
Indices: 8442--8477 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
8432 TTATTTTTTA
8442 TGAATTATAAATATTT
1 TGAATTATAAATATTT
*
8458 TGAATTTTAAA-ATTT
1 TGAATTATAAATATTT
8473 TGAAT
1 TGAAT
8478 ATTTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (16 bp):
TGAATTATAAATATTT
Done.