Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013329.1 Kokia drynarioides strain JFW-HI SEQ_128351, 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: 32398
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Warning! 110 characters in sequence are not A, C, G, or T
Found at i:200 original size:14 final size:14
Alignment explanation
Indices: 181--211 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
171 TCATAAAAAA
*
181 TATTATAATTTTTT
1 TATTATAATTTATT
195 TATTATAATTTATT
1 TATTATAATTTATT
209 TAT
1 TAT
212 AAAAGTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATAATTTATT
Found at i:3092 original size:72 final size:72
Alignment explanation
Indices: 3010--3152 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 72
3000 GTGGTGCAGG
*
3010 CTGTTGTTTCTTGGTTTGATGGGATCGGTTTTCTGGTTTGAGCATGCAGTCTATTGCTGCTCTGC
1 CTGTTGTTTCTTGGTTAGATGGGATCGGTTTTCTGGTTTGAGCATGCAGTCTATTGCTGCTCTGC
3075 TTTGCTA
66 TTTGCTA
* ** * *
3082 CTGTTGTTTCTTGGTTAGCTGGGATTTGTTTTCTGGTTTGAGCATGCAGTCTGTTGCTGCTTTGC
1 CTGTTGTTTCTTGGTTAGATGGGATCGGTTTTCTGGTTTGAGCATGCAGTCTATTGCTGCTCTGC
3147 TTTGCT
66 TTTGCT
3153 GTTTTGGCAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (72 bp):
CTGTTGTTTCTTGGTTAGATGGGATCGGTTTTCTGGTTTGAGCATGCAGTCTATTGCTGCTCTGC
TTTGCTA
Found at i:11406 original size:13 final size:12
Alignment explanation
Indices: 11388--11421 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
11378 AAATAGAAAA
11388 CATTTTCTATTTT
1 CATTTT-TATTTT
11401 CATTTTTATTTT
1 CATTTTTATTTT
11413 CTATTTTTA
1 C-ATTTTTA
11422 AAAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (12 bp):
CATTTTTATTTT
Found at i:11602 original size:136 final size:136
Alignment explanation
Indices: 11434--11705 Score: 508
Period size: 136 Copynumber: 2.0 Consensus size: 136
11424 AAAAAAAAAG
*
11434 AGAAACACTAAAGTAGTCGAAACTTAACTAAAAATATGACTAAGGCAAGTGCACCTATCAATTAA
1 AGAAACACTAAAGTAGTCGAAACTTAACTAAAAATATGACTAAGACAAGTGCACCTATCAATTAA
*
11499 TAGTATAGTTATGGTAAACATAGATATCGTTCCCACGAGAACCAAAAGTACTAGTAATAACTGTC
66 TAGTATAGTTACGGTAAACATAGATATCGTTCCCACGAGAACCAAAAGTACTAGTAATAACTGTC
11564 TTCCTA
131 TTCCTA
*
11570 AGAAACACTAAAGTAGTCGAAACTTAACTAAAAATATGACTAAGATAAGTGCACCTATCAATTAA
1 AGAAACACTAAAGTAGTCGAAACTTAACTAAAAATATGACTAAGACAAGTGCACCTATCAATTAA
*
11635 TAGTATAGTTACGGTAAGCATAGATATCGTTCCCACGAGAACCAAAAGTACTAGTAATAACTGTC
66 TAGTATAGTTACGGTAAACATAGATATCGTTCCCACGAGAACCAAAAGTACTAGTAATAACTGTC
11700 TTCCTA
131 TTCCTA
11706 TTATTTAACC
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 132 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (136 bp):
AGAAACACTAAAGTAGTCGAAACTTAACTAAAAATATGACTAAGACAAGTGCACCTATCAATTAA
TAGTATAGTTACGGTAAACATAGATATCGTTCCCACGAGAACCAAAAGTACTAGTAATAACTGTC
TTCCTA
Found at i:13688 original size:19 final size:20
Alignment explanation
Indices: 13664--13708 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
13654 CACATTTGTC
13664 TTTTTTTTTCT-TTTTCTTT
1 TTTTTTTTTCTATTTTCTTT
13683 TTTTTTTTTCTCAATTTTCTTT
1 TTTTTTTTTCT--ATTTTCTTT
13705 TTTT
1 TTTT
13709 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
22 12 0.52
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTTTTCTATTTTCTTT
Found at i:13796 original size:20 final size:21
Alignment explanation
Indices: 13771--13815 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
13761 NNNNNNNNTT
13771 TTTTTTTTTTCTCAA-TTTTC
1 TTTTTTTTTTCTCAATTTTTC
*
13791 TTTTTTTTTTTTCAATTTTTC
1 TTTTTTTTTTCTCAATTTTTC
13812 TTTT
1 TTTT
13816 CAACTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTTTTCTCAATTTTTC
Found at i:13796 original size:21 final size:21
Alignment explanation
Indices: 13770--13815 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
13760 NNNNNNNNNT
13770 TTTTTTTTTTTCTCAA-TTTTC
1 TTTTTTTTTTT-TCAATTTTTC
13791 TTTTTTTTTTTTCAATTTTTC
1 TTTTTTTTTTTTCAATTTTTC
13812 TTTT
1 TTTT
13816 CAACTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTTTTTTCAATTTTTC
Found at i:14659 original size:5 final size:5
Alignment explanation
Indices: 14649--14720 Score: 72
Period size: 5 Copynumber: 12.8 Consensus size: 5
14639 ATTGCATAAT
14649 TAAAA TAAAA TTAAAAA TAAAA TAAAA TAAAA TAAAA CTAAAAA TAAAAA
1 TAAAA TAAAA -T-AAAA TAAAA TAAAA TAAAA TAAAA -T-AAAA T-AAAA
14699 TAAAAA TAAATA TGAAAA TAAA
1 T-AAAA TAAA-A T-AAAA TAAA
14721 TATACTAATT
Statistics
Matches: 61, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
5 30 0.49
6 20 0.33
7 11 0.18
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:14669 original size:6 final size:6
Alignment explanation
Indices: 14650--14720 Score: 85
Period size: 6 Copynumber: 12.3 Consensus size: 6
14640 TTGCATAATT
* *
14650 AAAATA AAATTA AAAAT- AAAAT- AAAAT- AAAATA AAACTA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
14695 AAAATA AAAATA AATATG AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
14721 TATACTAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
5 15 0.27
6 41 0.73
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:17647 original size:18 final size:19
Alignment explanation
Indices: 17612--17654 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
17602 TTAGAAAAAT
*
17612 TAAATTAAAAATGCAAATAA
1 TAAAATAAAAAT-CAAATAA
17632 TAAAATAAAAAT-AAATAA
1 TAAAATAAAAATCAAATAA
17650 TAAAA
1 TAAAA
17655 AAATGGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
20 11 0.50
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAATAAAAATCAAATAA
Found at i:18297 original size:25 final size:23
Alignment explanation
Indices: 18268--18313 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
18258 GTTGGATCCA
18268 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
18293 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
18314 CCCTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:30280 original size:31 final size:31
Alignment explanation
Indices: 30223--30281 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
30213 TTTTGTTATT
* *
30223 TATTAAAAATAATAATAATTTAATTTTTGTA
1 TATTAAAAAAAATAATAAATTAATTTTTGTA
*
30254 TATTAGAAAAAAAT-ATAAATTGATTTTT
1 TATTA-AAAAAAATAATAAATTAATTTTT
30282 TTCATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 17 0.71
32 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (31 bp):
TATTAAAAAAAATAATAAATTAATTTTTGTA
Found at i:30678 original size:17 final size:18
Alignment explanation
Indices: 30656--30704 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
30646 GTTTTCAAAA
30656 AATTATAAAAA-ATATAG
1 AATTATAAAAATATATAG
*
30673 AATTATTTAAAAATTATTTAG
1 AATTA--TAAAAA-TATATAG
30694 AATTATAAAAA
1 AATTATAAAAA
30705 GTTTTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
19 12 0.44
21 10 0.37
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (18 bp):
AATTATAAAAATATATAG
Done.