Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007278.1 Kokia drynarioides strain JFW-HI SEQ_121894, 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: 18782
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:2159 original size:14 final size:14
Alignment explanation
Indices: 2140--2168 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2130 AGGAGTTGTA
2140 TGTATGTATGTGTG
1 TGTATGTATGTGTG
2154 TGTATGTATGTGTG
1 TGTATGTATGTGTG
2168 T
1 T
2169 TTTTTCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52
Consensus pattern (14 bp):
TGTATGTATGTGTG
Found at i:2800 original size:50 final size:50
Alignment explanation
Indices: 2724--2864 Score: 153
Period size: 50 Copynumber: 2.8 Consensus size: 50
2714 AACCAAACAG
* * * *
2724 AGCCTTTGTGACAAGTTATCTAAAAGGCTTATGTGGCATATTGTCTAGAA
1 AGCCTTTGTGGCGAGTTATCTAAAAGGCCTATGTGACATATTGTCTAGAA
* *
2774 AGCCTTTGTGGCGAGTTAGT-TGAAAGGCCTATGTGACATATTTTCTAGAA
1 AGCCTTTGTGGCGAGTTA-TCTAAAAGGCCTATGTGACATATTGTCTAGAA
* * * *
2824 AGCC-TTATGGCGAGTTATTTTAAAA-ACCTACGTGACATATT
1 AGCCTTTGTGGCGAGTTA-TCTAAAAGGCCTATGTGACATATT
2865 ATTTGGGAAG
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
49 27 0.35
50 50 0.64
51 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (50 bp):
AGCCTTTGTGGCGAGTTATCTAAAAGGCCTATGTGACATATTGTCTAGAA
Found at i:2859 original size:49 final size:50
Alignment explanation
Indices: 2760--2864 Score: 140
Period size: 49 Copynumber: 2.1 Consensus size: 50
2750 GCTTATGTGG
* ** *
2760 CATATTGTCTAGAAAGCCTTTGTGGCGAGTTAGTTGAAAGGCCTATGTGA
1 CATATTGTCTAGAAAGCCTTTATGGCGAGTTAGTTGAAAAACCTACGTGA
* * *
2810 CATATTTTCTAGAAAGCC-TTATGGCGAGTTATTTTAAAAACCTACGTGA
1 CATATTGTCTAGAAAGCCTTTATGGCGAGTTAGTTGAAAAACCTACGTGA
2859 CATATT
1 CATATT
2865 ATTTGGGAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 31 0.65
50 17 0.35
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (50 bp):
CATATTGTCTAGAAAGCCTTTATGGCGAGTTAGTTGAAAAACCTACGTGA
Found at i:6222 original size:24 final size:23
Alignment explanation
Indices: 6189--6259 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
6179 AATGAGTTAC
* *
6189 AAGGAGATGAAATGTGAAGAGTT
1 AAGGAGATGAAAGGTGAAAAGTT
6212 AAGGAAGATGAAAGGT-AAAATGTT
1 AAGG-AGATGAAAGGTGAAAA-GTT
*
6236 AAGGGTGATGAAAGGTGAAAAGTT
1 AA-GGAGATGAAAGGTGAAAAGTT
6260 GAACATCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 7 0.17
24 28 0.68
25 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (23 bp):
AAGGAGATGAAAGGTGAAAAGTT
Found at i:7139 original size:42 final size:41
Alignment explanation
Indices: 7019--7139 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 41
7009 ACCGCGTTGC
* * * *
7019 GGACAAGCCACTAGTATTTGTAGATAAACTGTCATAGATATGT
1 GGACAAACCACCAGTA--TGTAGATAAACTGTCAAAAATATGT
* * *
7062 -AAGCAAACCACCAGATATGCAGATAAACTGCCAAAAATATGT
1 GGA-CAAACCACCAG-TATGTAGATAAACTGTCAAAAATATGT
* *
7104 GGACAATCCACCAGTAGTGTAGATAAACTATCAAAA
1 GGACAAACCACCAGTA-TGTAGATAAACTGTCAAAA
7140 CTTCCTCCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
41 2 0.03
42 48 0.77
43 10 0.16
44 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.22
Consensus pattern (41 bp):
GGACAAACCACCAGTATGTAGATAAACTGTCAAAAATATGT
Found at i:7408 original size:39 final size:38
Alignment explanation
Indices: 7349--7424 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 38
7339 ATGTTTTTAA
* * *
7349 CATGTGATCAAAATATCAAAAACACTAAACATGACTTAT
1 CATGTAATCAAAATAACAAAAACAATAAACATG-CTTAT
* *
7388 CATGTAATCAGAATAACAAAAACAATAGACATGCTTA
1 CATGTAATCAAAATAACAAAAACAATAAACATGCTTA
7425 CATCATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 4 0.12
39 28 0.88
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (38 bp):
CATGTAATCAAAATAACAAAAACAATAAACATGCTTAT
Found at i:12082 original size:29 final size:29
Alignment explanation
Indices: 12040--12097 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
12030 TACAATAAGA
12040 AAGAACCTATAAGCTTTATTAACTTTGAT
1 AAGAACCTATAAGCTTTATTAACTTTGAT
12069 AAGAACCTATAAGCTTTATTAACTTTGAT
1 AAGAACCTATAAGCTTTATTAACTTTGAT
12098 CCAGCTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (29 bp):
AAGAACCTATAAGCTTTATTAACTTTGAT
Done.