Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007819.1 Kokia drynarioides strain JFW-HI SEQ_122455, 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: 69107
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:11 original size:6 final size:6
Alignment explanation
Indices: 1--26 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1 GTGCTG GTGCTG GTGCTG GTGCTG GT
1 GTGCTG GTGCTG GTGCTG GTGCTG GT
27 TTTACTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
GTGCTG
Found at i:4010 original size:6 final size:7
Alignment explanation
Indices: 3992--4016 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3982 GAAAGGGGAA
3992 ATTTTTT
1 ATTTTTT
3999 ATTTTTT
1 ATTTTTT
4006 ATTTTTT
1 ATTTTTT
4013 ATTT
1 ATTT
4017 AAAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
ATTTTTT
Found at i:4182 original size:27 final size:27
Alignment explanation
Indices: 4144--4198 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
4134 GTAAATCTGC
4144 TTGTCAGCTCTGAATCTCCCACTTTGG
1 TTGTCAGCTCTGAATCTCCCACTTTGG
4171 TTGTCAGCTCTGAATCTCCCACTTTGG
1 TTGTCAGCTCTGAATCTCCCACTTTGG
4198 T
1 T
4199 CGTTGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (27 bp):
TTGTCAGCTCTGAATCTCCCACTTTGG
Found at i:12734 original size:32 final size:32
Alignment explanation
Indices: 12698--12761 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
12688 TCATAAACTT
* *
12698 ATAAATTGATTACTTGAATTTAATAAATCATG
1 ATAAATTAATTAATTGAATTTAATAAATCATG
* * *
12730 ATAAATTAATTAATTTAATTTGATAACTCATG
1 ATAAATTAATTAATTGAATTTAATAAATCATG
12762 TTGATTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAAATCATG
Found at i:14607 original size:24 final size:24
Alignment explanation
Indices: 14558--14610 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
14548 AATAATATTT
* *
14558 ACTCTGTTTATTTGTTTTAATTAA
1 ACTCTGTTTATTTGTTTGAATCAA
*
14582 ACTCTGTTTATTTGTTTGAGTCAA
1 ACTCTGTTTATTTGTTTGAATCAA
14606 ACTCT
1 ACTCT
14611 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53
Consensus pattern (24 bp):
ACTCTGTTTATTTGTTTGAATCAA
Found at i:16769 original size:8 final size:8
Alignment explanation
Indices: 16756--16790 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
16746 TGTGCTATTT
16756 TTAAATCA
1 TTAAATCA
16764 TTAAATCA
1 TTAAATCA
16772 TTAAATCA
1 TTAAATCA
16780 TTAAATCA
1 TTAAATCA
16788 TTA
1 TTA
16791 CATGAGATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (8 bp):
TTAAATCA
Found at i:45537 original size:18 final size:18
Alignment explanation
Indices: 45514--45549 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
45504 TTTTCACCTG
45514 TGTATCTTAATTTTTCAA
1 TGTATCTTAATTTTTCAA
45532 TGTATCTTAATTTTTCAA
1 TGTATCTTAATTTTTCAA
45550 CATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (18 bp):
TGTATCTTAATTTTTCAA
Found at i:49692 original size:29 final size:30
Alignment explanation
Indices: 49643--49721 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
49633 GATTCATAGT
* *
49643 TAAAATTTCAAGTGTATAATTATACA-AAA
1 TAAAAATTCAAGTATATAATTATACATAAA
*
49672 TAAAAATTCAAGTATCA-AATTGTACATTAAA
1 TAAAAATTCAAGTAT-ATAATTATACA-TAAA
*
49703 TAAAAGTTC-A-TATATAATT
1 TAAAAATTCAAGTATATAATT
49722 TTATTATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 2 0.05
31 11 0.26
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (30 bp):
TAAAAATTCAAGTATATAATTATACATAAA
Found at i:50058 original size:23 final size:24
Alignment explanation
Indices: 50012--50064 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
50002 ATTATCGTAT
* * *
50012 ATATTTTTTTTAAAATTGATAATA
1 ATATTATTTTTAAAATTAAGAATA
50036 ATATTATTTTTAAAA-TAAGAATA
1 ATATTATTTTTAAAATTAAGAATA
*
50059 AAATTA
1 ATATTA
50065 ATAAACACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
ATATTATTTTTAAAATTAAGAATA
Found at i:66029 original size:22 final size:22
Alignment explanation
Indices: 66001--66044 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
65991 ACAAGAAAAC
66001 AGGAATATCCTCTAGCCGATAT
1 AGGAATATCCTCTAGCCGATAT
66023 AGGAATATCCTCTAGCCGATAT
1 AGGAATATCCTCTAGCCGATAT
66045 GATATGAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (22 bp):
AGGAATATCCTCTAGCCGATAT
Found at i:68315 original size:18 final size:18
Alignment explanation
Indices: 68292--68334 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
68282 GATTTTCTTT
* *
68292 TATTTTTGCA-ATATTTA
1 TATTTTTTCAGATATATA
*
68309 TATTTTTTTAGATATATA
1 TATTTTTTCAGATATATA
68327 TATTTTTT
1 TATTTTTT
68335 TAACTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (18 bp):
TATTTTTTCAGATATATA
Found at i:68343 original size:19 final size:18
Alignment explanation
Indices: 68302--68336 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
68292 TATTTTTGCA
*
68302 ATATTTATATTTTTTTAG
1 ATATATATATTTTTTTAG
68320 ATATATATATTTTTTTA
1 ATATATATATTTTTTTA
68337 ACTTATAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATATATATTTTTTTAG
Done.