Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002472.1 Kokia drynarioides strain JFW-HI SEQ_114612, 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: 104644
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:581 original size:25 final size:25
Alignment explanation
Indices: 547--596 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
537 TCTTCTTCTT
547 GACTGAAAACCCTAGAAGCCATTAA
1 GACTGAAAACCCTAGAAGCCATTAA
572 GACTGAAAACCCTAGAAGCCATTAA
1 GACTGAAAACCCTAGAAGCCATTAA
597 AGAAGCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (25 bp):
GACTGAAAACCCTAGAAGCCATTAA
Found at i:3280 original size:41 final size:41
Alignment explanation
Indices: 3191--3282 Score: 175
Period size: 41 Copynumber: 2.2 Consensus size: 41
3181 TCGTTGAGAG
*
3191 TTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACTAGAA
1 TTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACTAGAA
3232 TTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACTAGAA
1 TTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACTAGAA
3273 TTCTTGTTAA
1 TTCTTGTTAA
3283 AATAAAATTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.26, C:0.07, G:0.29, T:0.38
Consensus pattern (41 bp):
TTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACTAGAA
Found at i:8009 original size:2 final size:2
Alignment explanation
Indices: 8002--8026 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7992 ATTTAACTAT
8002 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
8027 TTGTTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12052 original size:13 final size:13
Alignment explanation
Indices: 12034--12073 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
12024 TGCACAAAGT
12034 GATCACTCTTAAG
1 GATCACTCTTAAG
12047 GATCACTCTTAAG
1 GATCACTCTTAAG
12060 GATCACTCTTAAG
1 GATCACTCTTAAG
12073 G
1 G
12074 CTTGAGCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (13 bp):
GATCACTCTTAAG
Found at i:14191 original size:7 final size:7
Alignment explanation
Indices: 14175--14207 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
14165 GTCCGAAGAC
14175 AAAAAA-
1 AAAAAAG
14181 AAAAAAG
1 AAAAAAG
14188 AAAAAAG
1 AAAAAAG
14195 AAAGAAAG
1 AAA-AAAG
14203 AAAAA
1 AAAAA
14208 GCATTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:32713 original size:59 final size:60
Alignment explanation
Indices: 32636--32749 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
32626 AACGCTTTAA
*
32636 GTAAATGGAATAATAGAATCTATTG-AAATTTGACCTTTGGAACTCGTTTTAATGTTGAT
1 GTAAATGAAATAATAGAATCTATTGAAAATTTGACCTTTGGAACTCGTTTTAATGTTGAT
* * *
32695 GTAAATGAAATATTAGAATGTATTGAAAATTTGACTTTTGGAACTCGTTTTAATG
1 GTAAATGAAATAATAGAATCTATTGAAAATTTGACCTTTGGAACTCGTTTTAATG
32750 CTTCAGTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 22 0.44
60 28 0.56
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.39
Consensus pattern (60 bp):
GTAAATGAAATAATAGAATCTATTGAAAATTTGACCTTTGGAACTCGTTTTAATGTTGAT
Found at i:33070 original size:16 final size:16
Alignment explanation
Indices: 33041--33075 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33031 ATGAGTGTCA
*
33041 TATTTGTTATATATTT
1 TATTTGTTAAATATTT
*
33057 TATTTTTTAAATATTT
1 TATTTGTTAAATATTT
33073 TAT
1 TAT
33076 AATATATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTTGTTAAATATTT
Found at i:40308 original size:38 final size:38
Alignment explanation
Indices: 40257--40368 Score: 194
Period size: 38 Copynumber: 3.0 Consensus size: 38
40247 TTGCTAAAAT
40257 ACCTCTTTTAATTTTATAACTATTTTTTCTATATACTA
1 ACCTCTTTTAATTTTATAACTATTTTTTCTATATACTA
40295 ACCTCTTTTAATTTTATAACTATTTTTTCTATA-A-T-
1 ACCTCTTTTAATTTTATAACTATTTTTTCTATATACTA
*
40330 ACCTCTTTTAATTTTATGACTATTTTTTCTATATACTA
1 ACCTCTTTTAATTTTATAACTATTTTTTCTATATACTA
40368 A
1 A
40369 TTAGAATTTC
Statistics
Matches: 70, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
35 32 0.46
36 2 0.03
37 2 0.03
38 34 0.49
ACGTcount: A:0.29, C:0.15, G:0.01, T:0.55
Consensus pattern (38 bp):
ACCTCTTTTAATTTTATAACTATTTTTTCTATATACTA
Found at i:40341 original size:35 final size:35
Alignment explanation
Indices: 40254--40362 Score: 182
Period size: 35 Copynumber: 3.0 Consensus size: 35
40244 TAGTTGCTAA
40254 AATACCTCTTTTAATTTTATAACTATTTTTTCTAT
1 AATACCTCTTTTAATTTTATAACTATTTTTTCTAT
40289 ATACTAACCTCTTTTAATTTTATAACTATTTTTTCTAT
1 A-A-T-ACCTCTTTTAATTTTATAACTATTTTTTCTAT
*
40327 AATACCTCTTTTAATTTTATGACTATTTTTTCTAT
1 AATACCTCTTTTAATTTTATAACTATTTTTTCTAT
40362 A
1 A
40363 TACTAATTAG
Statistics
Matches: 70, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
35 33 0.47
36 2 0.03
37 2 0.03
38 33 0.47
ACGTcount: A:0.28, C:0.15, G:0.01, T:0.56
Consensus pattern (35 bp):
AATACCTCTTTTAATTTTATAACTATTTTTTCTAT
Found at i:56190 original size:24 final size:23
Alignment explanation
Indices: 56163--56207 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
56153 TAAAATTTTT
*
56163 AAATAATTAATATTAATTATTTAG
1 AAATAATTAAAATTAA-TATTTAG
*
56187 AAATATTTAAAATTAATATTT
1 AAATAATTAAAATTAATATTT
56208 TATATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAATAATTAAAATTAATATTTAG
Found at i:56209 original size:24 final size:24
Alignment explanation
Indices: 56150--56209 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
56140 TATATAATCT
* *
56150 AATTAAAATTTT-TAAATAATTAA
1 AATTAATATTTTAGAAATAATTAA
* *
56173 TATTAAT-TATTTAGAAATATTTAA
1 AATTAATAT-TTTAGAAATAATTAA
56197 AATTAATATTTTA
1 AATTAATATTTTA
56210 TATATTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 1 0.03
23 8 0.28
24 19 0.66
25 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AATTAATATTTTAGAAATAATTAA
Found at i:56221 original size:30 final size:31
Alignment explanation
Indices: 56151--56246 Score: 83
Period size: 31 Copynumber: 3.1 Consensus size: 31
56141 ATATAATCTA
* * *
56151 ATTAAAATTTTTAAATAATTAATA-TTAAT-T
1 ATTAAAATATTT-AACAATTAATATTTTATAT
56181 ATTTAGAAATATTTAA-AATTAATATTTTATAT
1 A-TTA-AAATATTTAACAATTAATATTTTATAT
* *
56213 ATTAAAATA-TTAACAATAAATTATTTTTTAT
1 ATTAAAATATTTAACAATTAA-TATTTTATAT
56244 ATT
1 ATT
56247 CTTGCTAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
29 4 0.07
30 19 0.34
31 24 0.43
32 9 0.16
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
ATTAAAATATTTAACAATTAATATTTTATAT
Found at i:60738 original size:18 final size:18
Alignment explanation
Indices: 60715--60749 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60705 TTGTCTTCTT
*
60715 CATTTTCCCTTTTCTCTA
1 CATTTTCCATTTTCTCTA
*
60733 CATTTTTCATTTTCTCT
1 CATTTTCCATTTTCTCT
60750 TCTCTTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
CATTTTCCATTTTCTCTA
Found at i:77180 original size:31 final size:30
Alignment explanation
Indices: 77128--77185 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
77118 TTAACCTCCA
*
77128 TAAAAATAATAAAAATTTAATTTAATTATT
1 TAAAAATAATAAAAATATAATTTAATTATT
* *
77158 TAAAAATTATAAAGATAATAATTTAATT
1 TAAAAATAATAAAAAT-ATAATTTAATT
77186 TCGATTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
TAAAAATAATAAAAATATAATTTAATTATT
Found at i:78253 original size:27 final size:27
Alignment explanation
Indices: 78214--78269 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
78204 TTAAGTACGG
* * *
78214 ATTGGTGCTGCCTATCCCATAGGCACC
1 ATTGGTGCCGCCTACCCCATAGACACC
78241 ATTGGTGCCGCCTACCCCATAGACACC
1 ATTGGTGCCGCCTACCCCATAGACACC
78268 AT
1 AT
78270 CCGAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (27 bp):
ATTGGTGCCGCCTACCCCATAGACACC
Found at i:89094 original size:29 final size:28
Alignment explanation
Indices: 89050--89107 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
89040 CTAAAAAAAT
*
89050 TGAAATACTTATAATTAAATATCTAACA
1 TGAAATACATATAATTAAATATCTAACA
* *
89078 TGAAATAGCATATAATTAGATATGTAACA
1 TGAAATA-CATATAATTAAATATCTAACA
89107 T
1 T
89108 CAACTTCCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (28 bp):
TGAAATACATATAATTAAATATCTAACA
Found at i:96699 original size:52 final size:54
Alignment explanation
Indices: 96589--96704 Score: 164
Period size: 56 Copynumber: 2.1 Consensus size: 54
96579 GACGGTTAAA
* **
96589 GGTTTCTTCCATGTATCAATGAACCAAGAAGAAAGAATACCAAGGGTCACACCTAG
1 GGTTCCTTCCATGTATCAAACAACCAAGAAGAAAGAATACC-A-GGTCACACCTAG
*
96645 GGTTCCTTCCATGTATCAAACAACCAAGAAGAAAGAATA-C-TGTCACACCTAG
1 GGTTCCTTCCATGTATCAAACAACCAAGAAGAAAGAATACCAGGTCACACCTAG
96697 GGTTCCTT
1 GGTTCCTT
96705 AGGAGTCTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
52 19 0.34
55 1 0.02
56 36 0.64
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (54 bp):
GGTTCCTTCCATGTATCAAACAACCAAGAAGAAAGAATACCAGGTCACACCTAG
Found at i:101072 original size:7 final size:7
Alignment explanation
Indices: 101062--101101 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
101052 AAAACACCCA
*
101062 CTTCTCA
1 CTTCTCT
101069 CTTCTCT
1 CTTCTCT
101076 CTTCTCT
1 CTTCTCT
101083 CTTCTCT
1 CTTCTCT
101090 CTTCTCT
1 CTTCTCT
101097 CTTCT
1 CTTCT
101102 TCTGTCGCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (7 bp):
CTTCTCT
Found at i:101114 original size:21 final size:21
Alignment explanation
Indices: 101069--101114 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
101059 CCACTTCTCA
* *
101069 CTTCTCTCTTCTCTCTTCTCT
1 CTTCTCTCTTCTCTCTTCGCC
101090 CTTCTCTCTTCT-TCTGTCGCC
1 CTTCTCTCTTCTCTCT-TCGCC
101111 CTTC
1 CTTC
101115 CCTCCCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.00, C:0.43, G:0.04, T:0.52
Consensus pattern (21 bp):
CTTCTCTCTTCTCTCTTCGCC
Found at i:101371 original size:20 final size:20
Alignment explanation
Indices: 101348--101388 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
101338 ATAATTTTTT
*
101348 TTTTATAAAAAATTCTAAAA
1 TTTTATAAAAAATTCAAAAA
* *
101368 TTTTGTAAAAATTTCAAAAA
1 TTTTATAAAAAATTCAAAAA
101388 T
1 T
101389 CATATTAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TTTTATAAAAAATTCAAAAA
Found at i:104531 original size:16 final size:17
Alignment explanation
Indices: 104507--104539 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
104497 CATTCACTTA
*
104507 AATTATTTATTTGTTTT
1 AATTATTTATTTATTTT
104524 AATT-TTTATTTATTTT
1 AATTATTTATTTATTTT
104540 TCTTTTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
AATTATTTATTTATTTT
Found at i:104620 original size:2 final size:2
Alignment explanation
Indices: 104613--104644 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
104603 ACACTGACAG
104613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.