Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005191.1 Kokia drynarioides strain JFW-HI SEQ_119050, 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: 18402
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Found at i:1227 original size:25 final size:26
Alignment explanation
Indices: 1178--1227 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1168 TTTGAAAAAA
*
1178 AAAAGTTTTGAAGGTTTGGGGGAAGT
1 AAAAGTTTTGAAGGTTTGGAGGAAGT
*
1204 AAAAGTTTTGGAGG-TTGGAGGAAG
1 AAAAGTTTTGAAGGTTTGGAGGAAG
1228 GGAGGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.32, C:0.00, G:0.40, T:0.28
Consensus pattern (26 bp):
AAAAGTTTTGAAGGTTTGGAGGAAGT
Found at i:3407 original size:16 final size:16
Alignment explanation
Indices: 3386--3417 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3376 TTAAAACGAA
3386 TTTAAAAAAAATTGAG
1 TTTAAAAAAAATTGAG
*
3402 TTTAAAAATAATTGAG
1 TTTAAAAAAAATTGAG
3418 GAAAATGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.34
Consensus pattern (16 bp):
TTTAAAAAAAATTGAG
Found at i:4534 original size:8 final size:8
Alignment explanation
Indices: 4521--4553 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
4511 TTATACATAA
4521 TATATAGG
1 TATATAGG
4529 TATATAGG
1 TATATAGG
4537 TATATAGG
1 TATATAGG
*
4545 TATAGAGG
1 TATATAGG
4553 T
1 T
4554 TTAGTATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (8 bp):
TATATAGG
Found at i:5058 original size:118 final size:119
Alignment explanation
Indices: 4841--5059 Score: 334
Period size: 118 Copynumber: 1.8 Consensus size: 119
4831 GATATTAGTG
* *
4841 AATTTTCTTCTCCTCTACCCGTGGTTTTTCCCCAAAAGGGTTTCCACGTAAAATTTGTGTGTTCT
1 AATTTTCTTCTCCTCTACCCGTGGTTTTTCCCCAAAAGGATTTCCACGTAAAA-TTCTGTGTTCT
4906 TTCTATATTTTATTTTCTTTGCAATATTTCTTCATTGTCCACACTCGTTGCACCA
65 TTCTATATTTTATTTTCTTTGCAATATTTCTTCATTGTCCACACTCGTTGCACCA
* * * *
4961 AATTTTCTTCTCTTCTGCTCGTGGTTTTCTCCCGAAAA-GATTTCCACGTAAAA-TCTGTGTTCT
1 AATTTTCTTCTCCTCTACCCGTGGTTTT-TCCCCAAAAGGATTTCCACGTAAAATTCTGTGTTCT
* *
5024 TTCTCTTTTTTATTTTCTTTGCAATATTTCTTCATT
65 TTCTATATTTTATTTTCTTTGCAATATTTCTTCATT
5060 ATCGACATTC
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
118 43 0.48
120 39 0.43
121 8 0.09
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (119 bp):
AATTTTCTTCTCCTCTACCCGTGGTTTTTCCCCAAAAGGATTTCCACGTAAAATTCTGTGTTCTT
TCTATATTTTATTTTCTTTGCAATATTTCTTCATTGTCCACACTCGTTGCACCA
Found at i:7685 original size:13 final size:13
Alignment explanation
Indices: 7667--7694 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7657 AACTCTATTT
7667 TTTAGGATTAATA
1 TTTAGGATTAATA
7680 TTTAGGATTAATA
1 TTTAGGATTAATA
7693 TT
1 TT
7695 ATTTTATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTAGGATTAATA
Found at i:7812 original size:25 final size:23
Alignment explanation
Indices: 7771--7816 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
7761 CCAATTAGGG
7771 AATTATTGTTTAGATTTAATTAT
1 AATTATTGTTTAGATTTAATTAT
*
7794 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
7817 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTAT
Found at i:14418 original size:18 final size:18
Alignment explanation
Indices: 14395--14439 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
14385 ATATGTTTTT
14395 AAAAAAAATGAAAAAATC
1 AAAAAAAATGAAAAAATC
* *
14413 AAAAAAATTGAAAAATTC
1 AAAAAAAATGAAAAAATC
14431 AAAAAAAAT
1 AAAAAAAAT
14440 TAGTATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (18 bp):
AAAAAAAATGAAAAAATC
Found at i:15443 original size:16 final size:17
Alignment explanation
Indices: 15422--15465 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
15412 AAAAAAAGTC
15422 AAAAAGAAAATT-GAAA
1 AAAAAGAAAATTAGAAA
*
15438 AGAAAGAAAATTGAGAAA
1 AAAAAGAAAATT-AGAAA
15456 AAAAAGAAAA
1 AAAAAGAAAA
15466 AGAAAAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
18 13 0.54
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (17 bp):
AAAAAGAAAATTAGAAA
Found at i:15479 original size:7 final size:6
Alignment explanation
Indices: 15393--15480 Score: 51
Period size: 6 Copynumber: 14.3 Consensus size: 6
15383 TTTATTGTTT
*
15393 AGAAAA AGAAAA A-AAAA AGAAAAAA AGTCAAAA AGAAAA TTG-AAA AG--AA
1 AGAAAA AGAAAA AGAAAA AG--AAAA AG--AAAA AGAAAA -AGAAAA AGAAAA
* *
15442 AGAAAA TTGAGAA A-AAAA AGAAAA AGAAAA AGACAAA AG
1 AGAAAA -AGAAAA AGAAAA AGAAAA AGAAAA AGA-AAA AG
15481 TGTATTTGAG
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.06
5 10 0.15
6 29 0.45
7 10 0.15
8 12 0.18
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (6 bp):
AGAAAA
Done.