Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000693.1 Kokia drynarioides strain JFW-HI SEQ_111693, 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: 20318
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:626 original size:23 final size:23
Alignment explanation
Indices: 600--725 Score: 164
Period size: 23 Copynumber: 5.4 Consensus size: 23
590 GAACACTAGC
600 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
623 GCTCTCTGTTATTAGGACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
**
648 GCTCTCTAATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * *
671 GCTCTC-GATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
693 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
716 GCTCTCTGTT
1 GCTCTCTGTT
726 GCCCAGCACT
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.20
23 49 0.56
24 1 0.01
25 20 0.23
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:698 original size:45 final size:47
Alignment explanation
Indices: 609--724 Score: 164
Period size: 45 Copynumber: 2.5 Consensus size: 47
599 CGCTCTCTGT
*
609 TTAGCACTGTGTGTGCTCTCTGTTATTAGGACTGTGTGTGCTCTCTAA
1 TTAGCACTGTGTGTGCTCTCTG-TATTAGGACTGTGTGTACTCTCTAA
* * **
657 TTAGCACTGTGTGTGCTCTC-G-ATTAGTACTTTGTGTACTCTCTGT
1 TTAGCACTGTGTGTGCTCTCTGTATTAGGACTGTGTGTACTCTCTAA
702 TTAGCACTGTGTGTGCTCTCTGT
1 TTAGCACTGTGTGTGCTCTCTGT
725 TGCCCAGCAC
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
45 39 0.64
46 1 0.02
47 1 0.02
48 20 0.33
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (47 bp):
TTAGCACTGTGTGTGCTCTCTGTATTAGGACTGTGTGTACTCTCTAA
Found at i:3053 original size:26 final size:25
Alignment explanation
Indices: 3017--3088 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
3007 CATCACAAAA
3017 AATTTTCATTATTATTTGATAAGTT-T
1 AATTTT-ATTATTATTTGAT-AGTTAT
*
3043 AATTATTATTATTATTTGATATTTGAT
1 AATT-TTATTATTATTTGATAGTT-AT
*
3070 AATTTTATTGTTATTTGAT
1 AATTTTATTATTATTTGAT
3089 TTTAAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 3 0.07
26 31 0.76
27 7 0.17
ACGTcount: A:0.31, C:0.01, G:0.08, T:0.60
Consensus pattern (25 bp):
AATTTTATTATTATTTGATAGTTAT
Found at i:3292 original size:26 final size:25
Alignment explanation
Indices: 3259--3307 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
3249 TTATTTTTCA
**
3259 AAATTATTATATTTTATTATAAATT
1 AAATTATTATATTAAATTATAAATT
*
3284 AAATATATTTTATTAAATTATAAA
1 AAAT-TATTATATTAAATTATAAA
3308 CTAGTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATTATTATATTAAATTATAAATT
Found at i:3307 original size:21 final size:21
Alignment explanation
Indices: 3266--3324 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
3256 TCAAAATTAT
3266 TATATTTTATTATAAATTAAA-
1 TATATTTTATTA-AAATTAAAC
*
3287 TATATTTTATTAAATTATAAAC
1 TATATTTTATTAAAAT-TAAAC
*
3309 TA-GTTTTATTAAAATT
1 TATATTTTATTAAAATT
3325 CCCATGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 4 0.12
21 27 0.82
22 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TATATTTTATTAAAATTAAAC
Found at i:7349 original size:18 final size:18
Alignment explanation
Indices: 7326--7360 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7316 ATTGTGTAGT
*
7326 GCAAATAAATTTTTCTTA
1 GCAAATAAATTATTCTTA
*
7344 GCAAATATATTATTCTT
1 GCAAATAAATTATTCTT
7361 TATTATTAAA
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:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
GCAAATAAATTATTCTTA
Found at i:9535 original size:22 final size:22
Alignment explanation
Indices: 9477--9537 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
9467 TAAAAATGAT
* * **
9477 AAAATTTTAATTTAATCTTTTA
1 AAAATTATAATTTAATATCGTA
* *
9499 AAAATTACATTTTTAATATCGTA
1 AAAATTATA-ATTTAATATCGTA
9522 AAAATTATAATTTAAT
1 AAAATTATAATTTAAT
9538 TTCGATCCCC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAATTATAATTTAATATCGTA
Found at i:11881 original size:20 final size:20
Alignment explanation
Indices: 11853--11895 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11843 TATCTTTATT
* *
11853 AATTTAAAATTTAAAAAAAA
1 AATTAAAAACTTAAAAAAAA
*
11873 AATTAAAAACTTAAATAAAA
1 AATTAAAAACTTAAAAAAAA
11893 AAT
1 AAT
11896 CTTTCATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
AATTAAAAACTTAAAAAAAA
Found at i:15420 original size:93 final size:93
Alignment explanation
Indices: 15261--15443 Score: 321
Period size: 93 Copynumber: 2.0 Consensus size: 93
15251 TTTTTGTTTT
* *
15261 GTAGGTTTTAGCTCAACAAGATATTGCAACATTCACCAACCACTAGGGTTTGACTACCAATCCTC
1 GTAGGTTTCAGCTCAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTACCAATCCTC
* *
15326 CAATTATGCTCAAATCAGCTGTAAATTA
66 CAATTATGCCCAAATCAGCTATAAATTA
*
15354 GTAGGTTTCAGCTCAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTATCAATCCTC
1 GTAGGTTTCAGCTCAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTACCAATCCTC
15419 CAATTATGCCCAAATCAGCTATAAA
66 CAATTATGCCCAAATCAGCTATAAA
15444 ATCTGTTTAC
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (93 bp):
GTAGGTTTCAGCTCAACAAGATATTGCAACATTCACCAAACACTAGGGTTTGACTACCAATCCTC
CAATTATGCCCAAATCAGCTATAAATTA
Found at i:18771 original size:26 final size:25
Alignment explanation
Indices: 18729--18779 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
18719 CTCCAAAATC
* *
18729 AATCTATTTTTTTAAATTAAAAAAAA
1 AATCTATTTATTCAAA-TAAAAAAAA
*
18755 AATCTATTTATTCAAATAATAAAAA
1 AATCTATTTATTCAAATAAAAAAAA
18780 CCCCGAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (25 bp):
AATCTATTTATTCAAATAAAAAAAA
Done.