Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004636.1 Kokia drynarioides strain JFW-HI SEQ_118160, 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: 31258
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Found at i:7760 original size:18 final size:18
Alignment explanation
Indices: 7737--7781 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
7727 GCAACTATGT
*
7737 TTTTTTAATTTCTATTTA
1 TTTTTTAATTTCTAATTA
*
7755 TTTTTT-ATTTTTAATTA
1 TTTTTTAATTTCTAATTA
*
7772 TTTATTAATT
1 TTTTTTAATT
7782 AAATTGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTAATTTCTAATTA
Found at i:8503 original size:2 final size:2
Alignment explanation
Indices: 8496--8567 Score: 60
Period size: 2 Copynumber: 36.5 Consensus size: 2
8486 GATATTTCCC
* * *
8496 AT AT AT AT AT AT AT AT AT AT AT AC AC AT AC AT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
* *
8539 A- AA AT AT -T CAT AT AC AT AT AT AT A- AT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT A
8568 AACAATCTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
1 3 0.05
2 52 0.90
3 3 0.05
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:8579 original size:28 final size:28
Alignment explanation
Indices: 8498--8569 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
8488 TATTTCCCAT
* * *
8498 ATATAT-ATATATATATATATACACATAC
1 ATATATCATATATA-AAATATTCATATAC
8526 ATATATCATATATAAAATATTCATATAC
1 ATATATCATATATAAAATATTCATATAC
8554 ATATAT-ATAATATAAA
1 ATATATCAT-ATATAAA
8570 CAATCTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 2 0.05
28 30 0.77
29 7 0.18
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATATCATATATAAAATATTCATATAC
Found at i:12087 original size:21 final size:21
Alignment explanation
Indices: 12048--12087 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12038 TAGAGTTGAT
*
12048 TTAATTTATAATAAAAATTTA
1 TTAATTTATAAAAAAAATTTA
12069 TTAATTT-TAAAAAATAATT
1 TTAATTTATAAAAAA-AATT
12088 GAGAGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTTATAAAAAAAATTTA
Found at i:13882 original size:26 final size:25
Alignment explanation
Indices: 13840--13890 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
13830 AAACATTATC
*
13840 AATAAAATAATTATTATCATATTTAA
1 AATAAAATAATTATTAT-AAATTTAA
*
13866 AATAAAATTA-TATTTATAAATTTAA
1 AATAAAATAATTA-TTATAAATTTAA
13891 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
AATAAAATAATTATTATAAATTTAA
Found at i:13958 original size:39 final size:39
Alignment explanation
Indices: 13843--13959 Score: 107
Period size: 39 Copynumber: 3.0 Consensus size: 39
13833 CATTATCAAT
* *
13843 AAAA-TAATTATTATCATATTTAAAATAAAATTATATTT-AT
1 AAAATTAATTATTATCATATTT--AA-AAAATTATTTTTAAC
* * *
13883 AAATTTAATTTTTATTA-ATTATAAAAAATTGA-TTTTAAC
1 AAAATTAATTATTATCATATT-TAAAAAATT-ATTTTTAAC
*
13922 AAAATTAAGTATTATCATATTTAAAAAATTATTTTTAA
1 AAAATTAATTATTATCATATTTAAAAAATTATTTTTAA
13960 TTTATCCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
38 10 0.16
39 32 0.52
40 9 0.15
41 11 0.18
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.46
Consensus pattern (39 bp):
AAAATTAATTATTATCATATTTAAAAAATTATTTTTAAC
Found at i:15728 original size:18 final size:20
Alignment explanation
Indices: 15705--15742 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
15695 ACGTGGTAGT
15705 CCAACTAG-ATTTT-AAGTG
1 CCAACTAGAATTTTCAAGTG
*
15723 CCAACTTGAATTTTCAAGTG
1 CCAACTAGAATTTTCAAGTG
15743 GAATGAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
CCAACTAGAATTTTCAAGTG
Found at i:29232 original size:11 final size:11
Alignment explanation
Indices: 29218--29256 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29208 ATATTAGCTA
29218 TTTATTTATTT
1 TTTATTTATTT
*
29229 TTTAATTATTT
1 TTTATTTATTT
*
29240 TTTATTAATTT
1 TTTATTTATTT
29251 TATTAT
1 T-TTAT
29257 AGATTCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTATTT
Done.