Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005748.1 Kokia drynarioides strain JFW-HI SEQ_119995, 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: 43005
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:287 original size:40 final size:38
Alignment explanation
Indices: 148--324 Score: 178
Period size: 37 Copynumber: 4.6 Consensus size: 38
138 TTACATAGTA
* * *
148 TTCAGGCTGTGTGCCTAGTAGGCTTCGTGTCGGTGTA-
1 TTCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* ** *
185 TTCAGGCTGTGTGCCTAGCAGGCTTCAAGCTGGTGTAT
1 TTCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGGTGTAT
* *
223 TT-GGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTATT
1 TTCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGGTGTA-T
* * *
261 TATCGGGCTTAGTGCCTAGCAAGCTTCGTGCCGGTGTATAT
1 T-TCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGGTG--TAT
*
302 TATCAGGCTTTGAGCCTAGCAGG
1 T-TCAGGCTTTGTGCCTAGCAGG
325 TTTCATGTCG
Statistics
Matches: 116, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
37 60 0.52
38 4 0.03
39 1 0.01
40 29 0.25
41 20 0.17
42 2 0.02
ACGTcount: A:0.14, C:0.20, G:0.32, T:0.33
Consensus pattern (38 bp):
TTCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGGTGTAT
Found at i:398 original size:13 final size:13
Alignment explanation
Indices: 388--416 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
378 AAGGTATGTG
388 ATGTTTATATGAT
1 ATGTTTATATGAT
401 ATGTTTATATGAT
1 ATGTTTATATGAT
414 ATG
1 ATG
417 GAAAGATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (13 bp):
ATGTTTATATGAT
Found at i:2769 original size:29 final size:30
Alignment explanation
Indices: 2700--2779 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
2690 ATTCCAAAAC
* *
2700 TATACATGAACTTTGATTTAATGTGTAATTG
1 TATACATGAACTTTGATTT-ATATGCAATTG
* *
2731 TGTACATGAACTTTGATTT-TATGCAATTT
1 TATACATGAACTTTGATTTATATGCAATTG
* *
2760 TATATATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
2780 GATCAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 13 0.32
30 10 0.24
31 18 0.44
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATATGCAATTG
Found at i:4009 original size:20 final size:19
Alignment explanation
Indices: 3986--4041 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
3976 TTTTTTTTGT
3986 AATTTTTTACGATTTTT-ATA
1 AATTTTTTA--ATTTTTAATA
4006 AATTTTTTTAATTTTTAATA
1 AA-TTTTTTAATTTTTAATA
*
4026 AATTTTCTAATTTTTA
1 AATTTTTTAATTTTTA
4042 TTATAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 19 0.58
20 7 0.21
21 7 0.21
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTTTAATTTTTAATA
Found at i:4011 original size:19 final size:19
Alignment explanation
Indices: 3979--4031 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
3969 TTACAACTTT
* * *
3979 TTTTTGTAATTTTTTACGA
1 TTTTTATAAATTTTTACAA
**
3998 TTTTTATAAATTTTTTTAA
1 TTTTTATAAATTTTTACAA
4017 TTTTTAATAAATTTT
1 TTTTT-ATAAATTTT
4032 CTAATTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (19 bp):
TTTTTATAAATTTTTACAA
Found at i:9942 original size:113 final size:113
Alignment explanation
Indices: 9739--9944 Score: 270
Period size: 113 Copynumber: 1.8 Consensus size: 113
9729 TTCACTGTTG
* * * * * *
9739 ATAGCTTTGTGCGTTAGCTTAGCTATCTATATCTGAAATGCATTTGACCTTAAAGTTGAAAGAGT
1 ATAGCTTTGTGCATTAACTTAGCTATCTATATCTGAAATACATTTGACCTTAAAGGTAAAAAAGT
9804 AAAAAGCTATACTGTGAGATCTAAAAGGGTTTTTGAGTGCTGACACTT
66 AAAAAGCTATACTGTGAGATCTAAAAGGGTTTTTGAGTGCTGACACTT
* * * * * * *
9852 ATAGTTTTGTGCATTAACTTAGCTTTCTATATTTGAATTACGTTTGTCCTTATAGGTAAAAAAGT
1 ATAGCTTTGTGCATTAACTTAGCTATCTATATCTGAAATACATTTGACCTTAAAGGTAAAAAAGT
*
9917 AGAAAA-CTATATTGTGAGATCTAAAAGG
66 A-AAAAGCTATACTGTGAGATCTAAAAGG
9945 ATAGCTGAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
113 74 0.95
114 4 0.05
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (113 bp):
ATAGCTTTGTGCATTAACTTAGCTATCTATATCTGAAATACATTTGACCTTAAAGGTAAAAAAGT
AAAAAGCTATACTGTGAGATCTAAAAGGGTTTTTGAGTGCTGACACTT
Found at i:17889 original size:3 final size:3
Alignment explanation
Indices: 17881--17906 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17871 CTGTGGTGCA
17881 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
17907 CAATCCAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:22229 original size:21 final size:21
Alignment explanation
Indices: 22204--22243 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22194 AGGGTTTCTA
*
22204 AAAAAAGTTAACGATCAACGG
1 AAAAAAGTCAACGATCAACGG
*
22225 AAAAAAGTCAACGGTCAAC
1 AAAAAAGTCAACGATCAAC
22244 AATCAATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (21 bp):
AAAAAAGTCAACGATCAACGG
Found at i:27245 original size:18 final size:18
Alignment explanation
Indices: 27224--27293 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 18
27214 ATAATTATTT
27224 TTTAAAAAATAAAAAATA
1 TTTAAAAAATAAAAAATA
27242 TTT-AAAAAT--AAAATA
1 TTTAAAAAATAAAAAATA
27257 TTTAAAAAATTTAAAAAATA
1 TTTAAAAAA--TAAAAAATA
** *
27277 TTTTGAAAATATAAAAT
1 TTTAAAAAATAAAAAAT
27294 TCAATATTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
15 9 0.20
16 5 0.11
17 6 0.14
18 11 0.25
20 13 0.30
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (18 bp):
TTTAAAAAATAAAAAATA
Found at i:27250 original size:35 final size:34
Alignment explanation
Indices: 27224--27293 Score: 97
Period size: 33 Copynumber: 2.0 Consensus size: 34
27214 ATAATTATTT
27224 TTTAAAAAA-TAAAAAATATTTAAAAATAAAATA
1 TTTAAAAAATTAAAAAATATTTAAAAATAAAATA
27257 TTTAAAAAATTTAAAAAATATTTTGAAAATATAAAAT
1 TTTAAAAAA-TTAAAAAATA-TTT-AAAA-ATAAAAT
27294 TCAATATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 9 0.28
35 9 0.28
36 3 0.09
37 4 0.12
38 7 0.22
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (34 bp):
TTTAAAAAATTAAAAAATATTTAAAAATAAAATA
Found at i:27253 original size:24 final size:24
Alignment explanation
Indices: 27226--27273 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
27216 AATTATTTTT
27226 TAAAA-AATAAAAAATATTTAAAAA
1 TAAAATAATAAAAAA-ATTTAAAAA
* *
27250 TAAAATATTTAAAAAATTTAAAAA
1 TAAAATAATAAAAAAATTTAAAAA
27274 ATATTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (24 bp):
TAAAATAATAAAAAAATTTAAAAA
Found at i:27256 original size:15 final size:15
Alignment explanation
Indices: 27236--27264 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27226 TAAAAAATAA
27236 AAAATATTTAAAAAT
1 AAAATATTTAAAAAT
27251 AAAATATTTAAAAA
1 AAAATATTTAAAAA
27265 ATTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATTTAAAAAT
Found at i:27705 original size:18 final size:19
Alignment explanation
Indices: 27678--27720 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
27668 ATAACATTGA
*
27678 ATTTTGAAAAT-TATTTAT
1 ATTTTAAAAATCTATTTAT
*
27696 ATTTTAAAAATCTTTTTAT
1 ATTTTAAAAATCTATTTAT
*
27715 TTTTTA
1 ATTTTA
27721 TTTTTTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTAAAAATCTATTTAT
Done.