Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005902.1 Kokia drynarioides strain JFW-HI SEQ_120253, 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: 14973
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Found at i:2116 original size:17 final size:17
Alignment explanation
Indices: 2091--2130 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2081 TTTTATGCAT
*
2091 AAAACTCACACAAAATC
1 AAAATTCACACAAAATC
2108 AAAATTCACACAAAATC
1 AAAATTCACACAAAATC
*
2125 ATAATT
1 AAAATT
2131 ATGTATGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAATTCACACAAAATC
Found at i:4100 original size:21 final size:20
Alignment explanation
Indices: 4057--4100 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4047 AACCTTAAAT
* *
4057 CTTAAACTCAAACCCTAATC
1 CTTAAACTCAAACCCCAAAC
*
4077 CTTAAACCTTAAACCCCAAAC
1 CTTAAA-CTCAAACCCCAAAC
4098 CTT
1 CTT
4101 GAGGTTCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (20 bp):
CTTAAACTCAAACCCCAAAC
Found at i:4416 original size:6 final size:6
Alignment explanation
Indices: 4407--4466 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
4397 TTAAATTGGT
** * * *
4407 TTTAAA TTTATT TTTAAA TTTAGA TTT-AC TTTAAA TTTAAA TTT-AG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
4453 TTTAAA TTTGAAA T
1 TTTAAA TTT-AAA T
4467 GGTTTTTAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
5 7 0.17
6 30 0.73
7 4 0.10
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:4441 original size:17 final size:17
Alignment explanation
Indices: 4407--4466 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
4397 TTAAATTGGT
*
4407 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-CTTTAAA
*
4425 TTTAGATTTACTTTAAA
1 TTTAAATTTACTTTAAA
*
4442 TTTAAATTTAGTTTAAA
1 TTTAAATTTACTTTAAA
4459 TTTGAAAT
1 TTT-AAAT
4467 GGTTTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
17 24 0.65
18 13 0.35
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:5218 original size:28 final size:28
Alignment explanation
Indices: 5185--5240 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
5175 AAATTAATGG
5185 GTGATAAATGAGGTTATATATTAATAAT
1 GTGATAAATGAGGTTATATATTAATAAT
5213 GTGATAAATGAGGTTATATATTAATAAT
1 GTGATAAATGAGGTTATATATTAATAAT
5241 ATTAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (28 bp):
GTGATAAATGAGGTTATATATTAATAAT
Found at i:5244 original size:9 final size:9
Alignment explanation
Indices: 5230--5336 Score: 61
Period size: 9 Copynumber: 10.8 Consensus size: 9
5220 ATGAGGTTAT
5230 ATATTAATA
1 ATATTAATA
5239 ATATTAATA
1 ATATTAATA
*
5248 ATATTATTA
1 ATATTAATA
*
5257 ATAATAAATA
1 AT-ATTAATA
**
5267 ATGGTAATAA
1 ATATTAAT-A
5277 ATAACGTTAATA
1 AT-A--TTAATA
5289 ATTATTAATAAAA
1 A-TATTAAT---A
*
5302 ATATTATTA
1 ATATTAATA
5311 ATATTAATA
1 ATATTAATA
* *
5320 ATTAATATTA
1 A-TATTAATA
5330 ATATTAA
1 ATATTAA
5337 ATAAAAAAGA
Statistics
Matches: 74, Mismatches: 14, Indels: 20
0.69 0.13 0.19
Matches are distributed among these distances:
9 36 0.49
10 22 0.30
12 9 0.12
13 7 0.09
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (9 bp):
ATATTAATA
Found at i:5255 original size:12 final size:12
Alignment explanation
Indices: 5234--5332 Score: 73
Period size: 12 Copynumber: 8.2 Consensus size: 12
5224 GGTTATATAT
5234 TAATAATATTAA
1 TAATAATATTAA
*
5246 TAATATTATTAA
1 TAATAATATTAA
5258 TAATAAATAATGGTAA
1 TAAT-AAT-AT--TAA
**
5274 TAAATAACGTTAA
1 T-AATAATATTAA
5287 TAAT--TATTAA
1 TAATAATATTAA
*
5297 TAAAAATATT-A
1 TAATAATATTAA
5308 T--TAATATTAA
1 TAATAATATTAA
5318 TAATTAATATTAA
1 TAA-TAATATTAA
5331 TA
1 TA
5333 TTAAATAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 21
0.70 0.08 0.22
Matches are distributed among these distances:
9 6 0.09
10 9 0.13
11 2 0.03
12 22 0.32
13 17 0.25
14 2 0.03
15 1 0.01
16 6 0.09
17 3 0.04
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:5298 original size:57 final size:52
Alignment explanation
Indices: 5202--5326 Score: 128
Period size: 57 Copynumber: 2.3 Consensus size: 52
5192 ATGAGGTTAT
* * * *
5202 ATATTAATAATGTGATAAATGAGGTTATATATTAATAATATTAATAATATTATTA
1 ATATAAATAATGTAATAAATAACGTTATATATTAATAATA--AA-AATATTATTA
*
5257 ATAATAAATAATGGTAATAAATAACGTTA-ATAATTATTAATAAAAATATTATTA
1 AT-ATAAATAAT-GTAATAAATAACGTTATAT-ATTAATAATAAAAATATTATTA
*
5311 ATATTAATAAT-TAATA
1 ATATAAATAATGTAATA
5327 TTAATATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
51 5 0.08
53 8 0.13
54 12 0.20
55 4 0.07
56 10 0.16
57 22 0.36
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (52 bp):
ATATAAATAATGTAATAAATAACGTTATATATTAATAATAAAAATATTATTA
Found at i:5315 original size:6 final size:6
Alignment explanation
Indices: 5306--5336 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
5296 ATAAAAATAT
5306 TATTAA TATTAA TAATTAA TATTAA TATTAA
1 TATTAA TATTAA T-ATTAA TATTAA TATTAA
5337 ATAAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TATTAA
Found at i:5339 original size:13 final size:12
Alignment explanation
Indices: 5306--5336 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
5296 ATAAAAATAT
5306 TATTAATATTAA
1 TATTAATATTAA
5318 TAATTAATATTAA
1 T-ATTAATATTAA
5331 TATTAA
1 TATTAA
5337 ATAAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TATTAATATTAA
Found at i:6466 original size:59 final size:58
Alignment explanation
Indices: 6399--6703 Score: 303
Period size: 59 Copynumber: 5.2 Consensus size: 58
6389 GAAGCTTTTC
* *
6399 AAAATTCCATTTTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTTACCCTCGAA-TTCCA
* *
6458 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCA-TTTAACC-CAAACTTCCA
1 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTTACCCTCGAA-TTCCA
* * *
6515 AAAATTCCATTTTTAACCTCGATTTTTCAAAAAATTACCATTTTACCCTCGGATGCCTA
1 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTTACCCTCGAATTCC-A
** * * ** * * * *
6574 AAAATTCCATTTTAAACCCCAAACTTTCTAAAAACTACCATTTTACCCTCGGATGT-CT
1 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTTACCCTCGAAT-TCCA
* * ** ** * *
6632 AAAATTTCATTTTTGACCTCGAATTTTCCTAAAATTATTATTTTTCCCTCGAGTGTCC-
1 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTTACCCTCGAAT-TCCA
6690 AAAATTACCATTTT
1 AAAATT-CCATTTT
6704 GCCCCCGGGT
Statistics
Matches: 207, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
57 48 0.23
58 63 0.30
59 96 0.46
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTTACCCTCGAATTCCA
Found at i:6534 original size:57 final size:57
Alignment explanation
Indices: 6399--6562 Score: 256
Period size: 57 Copynumber: 2.8 Consensus size: 57
6389 GAAGCTTTTC
* * * *
6399 AAAATTCCATTTTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCA-TTTAACC-CAAACTTCCA
6458 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTAACCCAAACTTCCA
1 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTAACCCAAACTTCCA
* *
6515 AAAATTCCATTTTTAACCTCGATTTTTCAAAAAATTACCATTTTACCC
1 AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTAACCC
6563 TCGGATGCCT
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
57 55 0.56
58 6 0.06
59 38 0.38
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (57 bp):
AAAATTCCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTAACCCAAACTTCCA
Found at i:6607 original size:116 final size:116
Alignment explanation
Indices: 6399--6621 Score: 304
Period size: 116 Copynumber: 1.9 Consensus size: 116
6389 GAAGCTTTTC
* * *
6399 AAAATTCCATTTTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATT
1 AAAATTCCATTTTTAACCCCGATTTTTCAAAAAATTACCATTTTACCCTCGAACTGCCAAAAATT
** * * ** *
6464 CCATTTTTGACCTCGATTTTTCAAAAAATTACCATTTAACCCAAACTTCCA
66 CCATTTTAAACCCCAAACTTTCAAAAAACTACCATTTAACCCAAACTTCCA
* *
6515 AAAATTCCATTTTTAACCTCGATTTTTCAAAAAATTACCATTTTACCCTCGGA-TGCCTAAAAAT
1 AAAATTCCATTTTTAACCCCGATTTTTCAAAAAATTACCATTTTACCCTCGAACTGCC-AAAAAT
* *
6579 TCCATTTTAAACCCCAAACTTTCTAAAAACTACCATTTTACCC
65 TCCATTTTAAACCCCAAACTTTCAAAAAACTACCATTTAACCC
6622 TCGGATGTCT
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
115 3 0.03
116 89 0.97
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (116 bp):
AAAATTCCATTTTTAACCCCGATTTTTCAAAAAATTACCATTTTACCCTCGAACTGCCAAAAATT
CCATTTTAAACCCCAAACTTTCAAAAAACTACCATTTAACCCAAACTTCCA
Found at i:6632 original size:29 final size:28
Alignment explanation
Indices: 6544--6635 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 28
6534 CGATTTTTCA
*
6544 AAAAATTACCATTTTACCCTCGGATGCCT
1 AAAAA-TACCATTTTACCCTCGGATGTCT
* ** *
6573 AAAAATTCCATTTTAAACCC-CAAACTTTCT
1 AAAAATACCATTTT--ACCCTCGGA-TGTCT
6603 AAAAACTACCATTTTACCCTCGGATGTCT
1 AAAAA-TACCATTTTACCCTCGGATGTCT
6632 AAAA
1 AAAA
6636 TTTCATTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
28 8 0.16
29 19 0.39
30 14 0.29
31 8 0.16
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (28 bp):
AAAAATACCATTTTACCCTCGGATGTCT
Found at i:6702 original size:28 final size:28
Alignment explanation
Indices: 6604--6723 Score: 73
Period size: 28 Copynumber: 4.2 Consensus size: 28
6594 AAACTTTCTA
* * *
6604 AAAACTACCATTTTACCCTCG-GATGTCT
1 AAAATTACCATTTTTCCCTCGAG-TGTCC
* * * *
6632 AAAATT-TCATTTTTGACCTCGAATTTTCC
1 AAAATTACCATTTTT-CCCTCG-AGTGTCC
**
6661 TAAAATTATTATTTTTCCCTCGAGTGTCC
1 -AAAATTACCATTTTTCCCTCGAGTGTCC
* * *
6690 AAAATTACCATTTTGCCCCCGGGTGTCC
1 AAAATTACCATTTTTCCCTCGAGTGTCC
6718 ACAAAT
1 A-AAAT
6724 CTCATTTTCA
Statistics
Matches: 70, Mismatches: 16, Indels: 11
0.72 0.16 0.11
Matches are distributed among these distances:
27 6 0.09
28 34 0.49
29 12 0.17
30 11 0.16
31 7 0.10
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.37
Consensus pattern (28 bp):
AAAATTACCATTTTTCCCTCGAGTGTCC
Found at i:14950 original size:2 final size:2
Alignment explanation
Indices: 14943--14973 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14933 TGCTTGGATT
14943 TA TA TA 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 TA TA TA T
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.