Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014337.1 Kokia drynarioides strain JFW-HI SEQ_129374, 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: 23669
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:1270 original size:45 final size:45
Alignment explanation
Indices: 1219--1322 Score: 208
Period size: 45 Copynumber: 2.3 Consensus size: 45
1209 AATCATGTGA
1219 CTTCAGTTTTCCAATGGCAGGAATCTCAGTAAAATCCAAATGTTG
1 CTTCAGTTTTCCAATGGCAGGAATCTCAGTAAAATCCAAATGTTG
1264 CTTCAGTTTTCCAATGGCAGGAATCTCAGTAAAATCCAAATGTTG
1 CTTCAGTTTTCCAATGGCAGGAATCTCAGTAAAATCCAAATGTTG
1309 CTTCAGTTTTCCAA
1 CTTCAGTTTTCCAA
1323 CGGATATATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (45 bp):
CTTCAGTTTTCCAATGGCAGGAATCTCAGTAAAATCCAAATGTTG
Found at i:8755 original size:65 final size:65
Alignment explanation
Indices: 8679--8810 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
8669 CTAAGTGAAG
8679 AAATTTTTTAATTCAAATTGATAATGACAGATGAAATCTAGGTAGTGTTTCACTTTTTGGTTGTT
1 AAATTTTTTAATTCAAATTGATAATGACAGATGAAATCTAGGTAGTGTTTCACTTTTTGGTTGTT
8744 AAATTTTTTAATTCAAATTGATAATGACAGATGAAATCTAGGTAGTGTTTCACTTTTTGGTTGTT
1 AAATTTTTTAATTCAAATTGATAATGACAGATGAAATCTAGGTAGTGTTTCACTTTTTGGTTGTT
8809 AA
1 AA
8811 TCGTTTGTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.44
Consensus pattern (65 bp):
AAATTTTTTAATTCAAATTGATAATGACAGATGAAATCTAGGTAGTGTTTCACTTTTTGGTTGTT
Found at i:10694 original size:23 final size:22
Alignment explanation
Indices: 10664--10836 Score: 163
Period size: 23 Copynumber: 7.5 Consensus size: 22
10654 ACGCTAGCAC
*
10664 GCTTACTGTTTAGCACTGTGTGT
1 GCTTACTGTTTCGCACT-TGTGT
10687 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
10710 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
*
10733 GCTTACTGTTTCGCACCTTATGT
1 GCTTACTGTTTCGCA-CTTGTGT
*
10756 G-TCTACTGATT-GCACTGTGTGT
1 GCT-TACTGTTTCGCACT-TGTGT
* * *
10778 GCCTATTGGATT-GCACTGTGTGT
1 GCTTACT-GTTTCGCACT-TGTGT
10801 GCTTACTGTTTCCCCAGCACTTGTGT
1 GCTTACTGTTT---C-GCACTTGTGT
10827 GCTTACTGTT
1 GCTTACTGTT
10837 AAGTACTTCG
Statistics
Matches: 130, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.02
22 16 0.12
23 89 0.68
24 3 0.02
26 15 0.12
27 5 0.04
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (22 bp):
GCTTACTGTTTCGCACTTGTGT
Found at i:17715 original size:36 final size:35
Alignment explanation
Indices: 17643--17740 Score: 153
Period size: 35 Copynumber: 2.8 Consensus size: 35
17633 TGGTAACAAG
*
17643 CATGACCTTTGGGTCAACAGGAGTAAAATGATCAT
1 CATGACCTTTGGGTCAACAGGAGTAAAATGAGCAT
*
17678 CATGACCTTTGGGTCAACATCGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACA-GGAGTAAAATGAGCAT
17714 CATGACCTTTGGG-CAACAAGGAGTAAA
1 CATGACCTTTGGGTCAAC-AGGAGTAAA
17741 TCTGATATTG
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
35 30 0.52
36 28 0.48
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (35 bp):
CATGACCTTTGGGTCAACAGGAGTAAAATGAGCAT
Found at i:20778 original size:23 final size:23
Alignment explanation
Indices: 20733--20779 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
20723 TAAAAAAATA
*
20733 TCATATTTATATAATTAAGATAT
1 TCATATTTATATAATTAACATAT
*
20756 TCATA-TTATATACTATAACATAT
1 TCATATTTATATAAT-TAACATAT
20779 T
1 T
20780 TATTAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (23 bp):
TCATATTTATATAATTAACATAT
Found at i:21477 original size:13 final size:13
Alignment explanation
Indices: 21449--21500 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
21439 CATATATATT
21449 TAATAATTTT-AA
1 TAATAATTTTAAA
21461 TAATAATTTTAAA
1 TAATAATTTTAAA
*
21474 TAATATTCTTTAAA
1 TAATAAT-TTTAAA
* *
21488 AAATTATTTTAAA
1 TAATAATTTTAAA
21501 AAATTTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.29
13 14 0.41
14 10 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATAATTTTAAA
Done.