Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006708.1 Kokia drynarioides strain JFW-HI SEQ_121304, 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: 33680
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:150 original size:24 final size:23
Alignment explanation
Indices: 112--157 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
102 TTTCATTTTA
* *
112 AAAAAAATATTTTTAAATACTAG
1 AAAAAAATATATTTAAAAACTAG
135 AAAAAAATATAATTTAAAAACTA
1 AAAAAAATAT-ATTTAAAAACTA
158 AATATAAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAAATATATTTAAAAACTAG
Found at i:1858 original size:27 final size:27
Alignment explanation
Indices: 1826--1883 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
1816 ACCTGTGAAA
1826 TCAACTTAAGTTAGCTTTATAGTGATT
1 TCAACTTAAGTTAGCTTTATAGTGATT
1853 TCAACTTAAGTTAGCTTTATAGTGATT
1 TCAACTTAAGTTAGCTTTATAGTGATT
1880 TCAA
1 TCAA
1884 ACTCTACAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (27 bp):
TCAACTTAAGTTAGCTTTATAGTGATT
Found at i:13010 original size:21 final size:21
Alignment explanation
Indices: 12985--13036 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12975 TAAAACCATG
12985 AAAACCCAAT-ACCCAAACCCT
1 AAAACCCAATCACCCAAA-CCT
*
13006 AAAACCAAATCACCCAAACCT
1 AAAACCCAATCACCCAAACCT
*
13027 TAAACCCAAT
1 AAAACCCAAT
13037 TCGATTTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAACCCAATCACCCAAACCT
Found at i:13020 original size:22 final size:21
Alignment explanation
Indices: 12985--13035 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
12975 TAAAACCATG
*
12985 AAAACCCAATACCCAAACCCT
1 AAAACCAAATACCCAAACCCT
*
13006 AAAACCAAATCACCCAAACCTT
1 AAAACCAAAT-ACCCAAACCCT
*
13028 AAACCCAA
1 AAAACCAA
13036 TTCGATTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.51, C:0.39, G:0.00, T:0.10
Consensus pattern (21 bp):
AAAACCAAATACCCAAACCCT
Found at i:13118 original size:7 final size:7
Alignment explanation
Indices: 13094--13155 Score: 52
Period size: 7 Copynumber: 8.9 Consensus size: 7
13084 AAATCCGATT
13094 GTTGACC
1 GTTGACC
*
13101 ATTGACC
1 GTTGACC
*
13108 GTTGACT
1 GTTGACC
**
13115 GTTGATA
1 GTTGACC
*
13122 GTTGATC
1 GTTGACC
13129 GTTGACC
1 GTTGACC
* *
13136 ATTGGCC
1 GTTGACC
*
13143 GTTGATC
1 GTTGACC
13150 GTTGAC
1 GTTGAC
13156 TTTTTGGGTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (7 bp):
GTTGACC
Found at i:14974 original size:5 final size:5
Alignment explanation
Indices: 14964--15036 Score: 76
Period size: 5 Copynumber: 14.6 Consensus size: 5
14954 GAACATATAT
* * * * *
14964 TATCA TATCA TAACA TAACA TATCA GATCA TAACA TGTCA TATCGA -ATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATC-A TATCA
*
15014 TATCA TATCA TATTA TATCA TAT
1 TATCA TATCA TATCA TATCA TAT
15037 AATGTCCTAC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
4 1 0.02
5 54 0.96
6 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (5 bp):
TATCA
Found at i:15769 original size:36 final size:35
Alignment explanation
Indices: 15719--15813 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 35
15709 ACACGGCCTA
* *
15719 CCCACACAGTCTACAAAATCACACAT-G-AATGTATGC
1 CCCACACGGGCTACAAAATCACACATAGCAA-G--TGC
15755 CCCACACGGGCTACAAAATCACACATAGCCAAGTGC
1 CCCACACGGGCTACAAAATCACACATAG-CAAGTGC
*
15791 CTCACACGGGCTACAAAATCACA
1 CCCACACGGGCTACAAAATCACA
15814 AACGGCCAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
36 49 0.92
37 1 0.02
38 1 0.02
39 2 0.04
ACGTcount: A:0.38, C:0.34, G:0.14, T:0.15
Consensus pattern (35 bp):
CCCACACGGGCTACAAAATCACACATAGCAAGTGC
Found at i:15822 original size:36 final size:36
Alignment explanation
Indices: 15752--15834 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
15742 CATGAATGTA
* * *
15752 TGCCCCACACGGGCTACAAAATCACACATAGCCAAG
1 TGCCTCACACGGGCTACAAAATCACAAACAGCCAAG
*
15788 TGCCTCACACGGGCTACAAAATCACAAACGGCCAAG
1 TGCCTCACACGGGCTACAAAATCACAAACAGCCAAG
15824 TGCCTCACACG
1 TGCCTCACACG
15835 ACCTACCCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.34, C:0.36, G:0.18, T:0.12
Consensus pattern (36 bp):
TGCCTCACACGGGCTACAAAATCACAAACAGCCAAG
Found at i:15855 original size:49 final size:49
Alignment explanation
Indices: 15793--15895 Score: 134
Period size: 49 Copynumber: 2.1 Consensus size: 49
15783 CCAAGTGCCT
* * *
15793 CACACGGGCTACAAAATCACAAACGGCCAAGTGCCTCACACGACCTACC
1 CACATGGGCTACAAAATCACAAACGACCAAGTGCCCCACACGACCTACC
* * * * *
15842 CACATGGGCTACAAAATCACACACGATCATGTGCCCCACACGGCCTACT
1 CACATGGGCTACAAAATCACAAACGACCAAGTGCCCCACACGACCTACC
15891 CACAT
1 CACAT
15896 AGTCATGTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.33, C:0.38, G:0.16, T:0.14
Consensus pattern (49 bp):
CACATGGGCTACAAAATCACAAACGACCAAGTGCCCCACACGACCTACC
Found at i:26447 original size:36 final size:36
Alignment explanation
Indices: 26392--26492 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
26382 TAGTAATAGG
*
26392 CATGACCTTCAGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTCAGGTCAACAGGGAGTAAAATGAGCAC
** *
26428 CATGACCTTTGGGTTAACAGGGAGTAAAATGAGCAC
1 CATGACCTTCAGGTCAACAGGGAGTAAAATGAGCAC
*
26464 CATGACC-TCAGTGTCAACAGGGAATAAAA
1 CATGACCTTCAG-GTCAACAGGGAGTAAAA
26493 CGTATAATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 2 0.04
36 54 0.96
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.20
Consensus pattern (36 bp):
CATGACCTTCAGGTCAACAGGGAGTAAAATGAGCAC
Found at i:32884 original size:22 final size:23
Alignment explanation
Indices: 32837--32884 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
32827 CGGTCTAAGG
* *
32837 AAAAATAAAAGAAACA-A-AATT
1 AAAAATAAAAAAAAAATAGAATT
32858 AAAAATAAAAAAAAAATAGAATT
1 AAAAATAAAAAAAAAATAGAATT
32881 AAAA
1 AAAA
32885 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 1 0.04
23 8 0.35
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (23 bp):
AAAAATAAAAAAAAAATAGAATT
Done.