Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014252.1 Kokia drynarioides strain JFW-HI SEQ_129285, 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: 9583
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1201 original size:18 final size:18
Alignment explanation
Indices: 1160--1235 Score: 93
Period size: 18 Copynumber: 4.3 Consensus size: 18
1150 CCAAATTCAT
*
1160 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAAA
* *
1178 -TTAAATTTGTTGTAAAA
1 TTTAAATTTATTTTAAAA
*
1195 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAAA
*
1213 TTTAAAATTATTTT-AAA
1 TTTAAATTTATTTTAAAA
1230 TTTAAA
1 TTTAAA
1236 ATAAATAAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
17 23 0.46
18 27 0.54
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:1231 original size:35 final size:35
Alignment explanation
Indices: 1160--1235 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
1150 CCAAATTCAT
* *
1160 TTTAAATTTATTTTAAGATTAAATTTGTTGTAAAA
1 TTTAAATTTATTTTAAGATTAAAATTATTGTAAAA
*
1195 TTTAAATTTATTTTTAA-ATTTAAAATTATT-TTAAA
1 TTTAAATTTA-TTTTAAGA-TTAAAATTATTGTAAAA
1230 TTTAAA
1 TTTAAA
1236 ATAAATAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 21 0.58
36 15 0.42
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAAATTATTGTAAAA
Found at i:1237 original size:17 final size:17
Alignment explanation
Indices: 1160--1235 Score: 91
Period size: 17 Copynumber: 4.4 Consensus size: 17
1150 CCAAATTCAT
1160 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
1178 -TTAAATTTGTTGTAAAA
1 TTTAAATTTATT-TTAAA
1195 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
1213 TTTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
1230 TTTAAA
1 TTTAAA
1236 ATAAATAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
17 24 0.48
18 24 0.48
19 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:1938 original size:16 final size:16
Alignment explanation
Indices: 1895--1930 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1885 TACTAAATGC
*
1895 AATAAATGA-ATTAAT
1 AATAAATAATATTAAT
1910 AATAAATAATATTAAT
1 AATAAATAATATTAAT
1926 AATAA
1 AATAA
1931 CAACTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AATAAATAATATTAAT
Found at i:3067 original size:30 final size:29
Alignment explanation
Indices: 2996--3313 Score: 229
Period size: 30 Copynumber: 10.8 Consensus size: 29
2986 GAAGGTCCCT
*
2996 AAACTATCCAAAAATTTCATTTTTACCTCC-
1 AAACT-TCCAAAAATTCCATTTTTACC-CCA
* * *
3026 GAACTTTCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* * *
3056 AAACTTCCAAAAATTCAAATTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
*
3085 GAACTTCCAAAAA-TCTCATTTTTGACCCCA
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCA
*
3115 AAACTTCCAAAAATTTCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTACCC-CA
* * * *
3144 GAACTTTCAAAAATCCCATTTTTTACCCTA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCA
* * *
3174 AAACTTCCAAAAA-TCTCTTTTTTAACCACG
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCA
* *
3204 AAACTTCAAAAAATTCCA--TTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * * *
3231 GAACTTCCAAAAATGCCATTTTTTATCTCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCA
* * *
3261 AGATTTCCAAAAATTCCATTTTT-GCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
3289 CGAA-TGTCTAAAAATTCCATTTTTA
1 -AAACT-TCCAAAAATTCCATTTTTA
3314 AACAACGAAT
Statistics
Matches: 224, Mismatches: 47, Indels: 34
0.73 0.15 0.11
Matches are distributed among these distances:
27 19 0.08
28 9 0.04
29 86 0.38
30 107 0.48
31 3 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:3089 original size:59 final size:59
Alignment explanation
Indices: 2996--3253 Score: 292
Period size: 59 Copynumber: 4.4 Consensus size: 59
2986 GAAGGTCCCT
*
2996 AAACTATCCAAAAATTTCATTTTTACCTCCGAACTTTCAAAAATCCCATTTTTAACCCCA
1 AAACT-TCCAAAAATTTCATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTAACCCCA
* * * *
3056 AAACTTCCAAAAA-TTCAAATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCA
1 AAACTTCCAAAAATTTC-ATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTAACCCCA
* * *
3115 AAACTTCCAAAAATTTCATTTTTACCCTCGAACTTTCAAAAATCCCATTTTTTACCCTA
1 AAACTTCCAAAAATTTCATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTAACCCCA
* * * * * *
3174 AAACTTCCAAAAATCTCTTTTTTAACCACGAAAC-TTCAAAAAATTCCA--TTT-ACCCCC
1 AAACTTCCAAAAATTTCATTTTTACCCCCG-AACTTTC-AAAAATCCCATTTTTAACCCCA
* **
3231 GAACTTCCAAAAATGCCATTTTT
1 AAACTTCCAAAAATTTCATTTTT
3254 TATCTCAAGA
Statistics
Matches: 172, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
57 23 0.13
58 6 0.03
59 123 0.72
60 20 0.12
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTTCATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTAACCCCA
Found at i:5040 original size:40 final size:39
Alignment explanation
Indices: 4985--5084 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 39
4975 ATAGAAAACT
* *
4985 TCAAGCTACGGCTTAACAGGCTATGAGCCTGTAATAAGAA
1 TCAAGCTACGGCTTAACAGACTATGAGCCAGTAATAAG-A
* **
5025 TCAAGCTTCGGCTTAACAGACTATGAGCCAGTGTTAAGA
1 TCAAGCTACGGCTTAACAGACTATGAGCCAGTAATAAGA
5064 TCCAAGCTACGGCTTAACAGA
1 T-CAAGCTACGGCTTAACAGA
5085 TTATAAACCG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 2 0.04
40 51 0.96
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (39 bp):
TCAAGCTACGGCTTAACAGACTATGAGCCAGTAATAAGA
Found at i:7195 original size:53 final size:54
Alignment explanation
Indices: 7061--7198 Score: 140
Period size: 53 Copynumber: 2.5 Consensus size: 54
7051 TCCTCTCAAA
* * * *
7061 CTTTTACTTCGTCCTAAAAAAATTTACTTCACTGAAACCCCCCCAAAACTTTTTTC
1 CTTTTACTT--TCCTCAAAAACTTTACTTCCCCGAAACCCCCCCAAAACTTTTTTC
*
7117 CTTTTACTTTCCTTCAAAAAC-TTACTTCCCCGAAA-CTCCCCAAAA-TTTGTTTC
1 CTTTTACTTTCC-TCAAAAACTTTACTTCCCCGAAACCCCCCCAAAACTTT-TTTC
* *
7170 CTTTTGCTTTCC-CTAAAACTTTTACTTCC
1 CTTTTACTTTCCTCAAAAAC-TTTACTTCC
7199 TTCTAAACCC
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
51 6 0.08
52 3 0.04
53 32 0.45
54 15 0.21
55 6 0.08
56 9 0.13
ACGTcount: A:0.26, C:0.31, G:0.04, T:0.39
Consensus pattern (54 bp):
CTTTTACTTTCCTCAAAAACTTTACTTCCCCGAAACCCCCCCAAAACTTTTTTC
Found at i:7985 original size:25 final size:25
Alignment explanation
Indices: 7957--8010 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
7947 TCTTTTGTAC
7957 ATTT-AAG-ATTTAATTTTTTATTTTT
1 ATTTCAAGAATTTAA-TTTTT-TTTTT
7982 ATTTCAAGAATTTAATTTTTTTTTT
1 ATTTCAAGAATTTAATTTTTTTTTT
8007 ATTT
1 ATTT
8011 TTCATATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 13 0.48
26 8 0.30
27 6 0.22
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (25 bp):
ATTTCAAGAATTTAATTTTTTTTTT
Done.