Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014223.1 Kokia drynarioides strain JFW-HI SEQ_129256, 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: 73281
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:7766 original size:25 final size:26
Alignment explanation
Indices: 7737--7786 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
7727 TAGCAGACCC
7737 CTAAAATCCAATA-AAATAATGAAAA
1 CTAAAATCCAATATAAATAATGAAAA
* *
7762 CTAAAATCTAATATAAATAGTGAAA
1 CTAAAATCCAATATAAATAATGAAA
7787 CCTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.24
Consensus pattern (26 bp):
CTAAAATCCAATATAAATAATGAAAA
Found at i:7811 original size:28 final size:27
Alignment explanation
Indices: 7749--7856 Score: 110
Period size: 28 Copynumber: 3.9 Consensus size: 27
7739 AAAATCCAAT
* * *
7749 AAAATAATGAAAACT-AAAATCTAATA
1 AAAATAGTGAAACCTAAAAATCTAGTA
*
7775 TAAATAGTGAAACCTTAAAAATCTAGTA
1 AAAATAGTGAAACC-TAAAAATCTAGTA
* * * *
7803 GAAAGAGTGAAATCCTAAATATCTGGTA
1 AAAATAGTGAAA-CCTAAAAATCTAGTA
7831 AAAATAGTGAAAACCTAAAAATCTAG
1 AAAATAGTG-AAACCTAAAAATCTAG
7857 ATTTTTTAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
26 11 0.17
27 1 0.02
28 49 0.74
29 5 0.08
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (27 bp):
AAAATAGTGAAACCTAAAAATCTAGTA
Found at i:9516 original size:30 final size:30
Alignment explanation
Indices: 9473--9564 Score: 141
Period size: 30 Copynumber: 3.1 Consensus size: 30
9463 ACACGAGAAT
* * *
9473 AAGT-TGCTCACACAAGTTGACAATATATC
1 AAGTGTGCTTACACAAGCTGACACTATATC
9502 AAGTGTGCTTACACAAGCTGACACTATATC
1 AAGTGTGCTTACACAAGCTGACACTATATC
*
9532 AAGTGTGCTTACACAAGCTGACACTATTTC
1 AAGTGTGCTTACACAAGCTGACACTATATC
9562 AAG
1 AAG
9565 GTTACCCATT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 4 0.07
30 54 0.93
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (30 bp):
AAGTGTGCTTACACAAGCTGACACTATATC
Found at i:10138 original size:19 final size:20
Alignment explanation
Indices: 10093--10138 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
10083 ACTATGGTTG
*
10093 AAGTACCAATACCTTCCTTT
1 AAGTATCAATACCTTCCTTT
10113 AAGTATCAATA-CTTACCTTT
1 AAGTATCAATACCTT-CCTTT
10133 -AGTATC
1 AAGTATC
10139 GATATCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.37
Consensus pattern (20 bp):
AAGTATCAATACCTTCCTTT
Found at i:11712 original size:14 final size:14
Alignment explanation
Indices: 11693--11733 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
11683 TAAATTATTT
11693 TTTAATTATTTTAA
1 TTTAATTATTTTAA
*
11707 TTTAATTATTTAAAA
1 TTTAATTATTT-TAA
11722 TTTAATTATTTT
1 TTTAATTATTTT
11734 TAAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATTATTTTAA
Found at i:19079 original size:13 final size:13
Alignment explanation
Indices: 19061--19099 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
19051 CCAAAATTTG
19061 AAACTTTGAACTC
1 AAACTTTGAACTC
*
19074 AAACTTTGAACCTT
1 AAACTTTGAA-CTC
*
19088 AAATTTTGAACT
1 AAACTTTGAACT
19100 TTGAATCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (13 bp):
AAACTTTGAACTC
Found at i:19097 original size:14 final size:14
Alignment explanation
Indices: 19061--19098 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
19051 CCAAAATTTG
19061 AAACTTTGAA-CTC
1 AAACTTTGAACCTC
*
19074 AAACTTTGAACCTT
1 AAACTTTGAACCTC
*
19088 AAATTTTGAAC
1 AAACTTTGAAC
19099 TTTGAATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (14 bp):
AAACTTTGAACCTC
Found at i:29258 original size:24 final size:23
Alignment explanation
Indices: 29226--29272 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
29216 AATTAGTTAG
*
29226 TAAATATA-TATTTTATAGAATTA
1 TAAATATATTATTTAAT-GAATTA
29249 TAAATTATATTATTTAATGAATTA
1 TAAA-TATATTATTTAATGAATTA
29273 AAAAATAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TAAATATATTATTTAATGAATTA
Found at i:53258 original size:6 final size:6
Alignment explanation
Indices: 53247--53277 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
53237 ATATTGATGG
*
53247 AGGGAT AGGGAT AGGGAT AGGGAC AGGGAT A
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT A
53278 CGTGGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.03, G:0.48, T:0.13
Consensus pattern (6 bp):
AGGGAT
Found at i:55865 original size:28 final size:29
Alignment explanation
Indices: 55804--55858 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
55794 TTGGGATAAC
*
55804 GATTTAATTATATATATTTTTTGTTGGTA
1 GATTTAATTATATATATTATTTGTTGGTA
*
55833 GATTTAATTATAT-TCTTATTTGTTGG
1 GATTTAATTATATATATTATTTGTTGG
55859 AGTATTTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (29 bp):
GATTTAATTATATATATTATTTGTTGGTA
Found at i:64719 original size:35 final size:35
Alignment explanation
Indices: 64694--64763 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
64684 TATATGCATC
*
64694 GGGCCTGATCTTAAGAACTTAAATATATCTCTACT
1 GGGCCTGATCTTAAGAACTTAAATATATATCTACT
*
64729 GGGCCTGATCTTAAGAACTTAAATATATCTCTACT
1 GGGCCTGATCTTAAGAACTTAAATATATATCTACT
64764 ACTCTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (35 bp):
GGGCCTGATCTTAAGAACTTAAATATATATCTACT
Done.