Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007982.1 Kokia drynarioides strain JFW-HI SEQ_122633, 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: 12682
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:6232 original size:22 final size:22
Alignment explanation
Indices: 6204--6246 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6194 ATAGGTCACT
*
6204 ACAATAAATTAGGTCTACCACG
1 ACAATAAAATAGGTCTACCACG
6226 ACAATAAAATAGGTCTACCAC
1 ACAATAAAATAGGTCTACCAC
6247 TACACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (22 bp):
ACAATAAAATAGGTCTACCACG
Found at i:6522 original size:38 final size:38
Alignment explanation
Indices: 6421--6725 Score: 347
Period size: 38 Copynumber: 8.1 Consensus size: 38
6411 GGGCTGGAAA
* *
6421 AGACCTAGTC-AAGGACGACCTTTAAAAAAGGTTGGGAT
1 AGACCTTGTCTAA-GACAACCTTTAAAAAAGGTTGGGAT
** * *
6459 AGGTCTTGTCTAAGGCAACCTTTTAAAAAAGGTTGAGAT
1 AGACCTTGTCTAAGACAACC-TTTAAAAAAGGTTGGGAT
* *
6498 AGACCTTATCTAAGACAACCTTTAAAAAAGGTTGAGAT
1 AGACCTTGTCTAAGACAACCTTTAAAAAAGGTTGGGAT
* *
6536 AAACCTTGTTTAAGACAACCTTT--AAAAGGTTGGGAT
1 AGACCTTGTCTAAGACAACCTTTAAAAAAGGTTGGGAT
* * *
6572 AGATCTTGTCTAAGACAACCTTTTAAAAAGATTGGGAT
1 AGACCTTGTCTAAGACAACCTTTAAAAAAGGTTGGGAT
*
6610 AAACCTTGTCTAAGACAACCTTTTAAAAAA-GTTGGGAT
1 AGACCTTGTCTAAGACAACC-TTTAAAAAAGGTTGGGAT
* * *
6648 AGACCTTGTCTAAGGCAACCTTTAAAAAAAGTTGAGAT
1 AGACCTTGTCTAAGACAACCTTTAAAAAAGGTTGGGAT
*
6686 AGACAC--GTCTAA-AGCAACC-TTGAAAAAGGTTGGGAT
1 AGAC-CTTGTCTAAGA-CAACCTTTAAAAAAGGTTGGGAT
6722 AGAC
1 AGAC
6726 ACATGTAAAG
Statistics
Matches: 230, Mismatches: 29, Indels: 18
0.83 0.10 0.06
Matches are distributed among these distances:
36 50 0.22
37 20 0.09
38 116 0.50
39 44 0.19
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (38 bp):
AGACCTTGTCTAAGACAACCTTTAAAAAAGGTTGGGAT
Found at i:6594 original size:74 final size:76
Alignment explanation
Indices: 6421--6725 Score: 354
Period size: 74 Copynumber: 4.1 Consensus size: 76
6411 GGGCTGGAAA
* * * *** *
6421 AGACCTAGTC-AAGGACGACCTTTAAAAAAGGTTGGGATAGGTCTTGTCTAAGGCAACCTTTTAA
1 AGACCTTGTCTAA-GACAACCTTTAAAAAAGGTTGAGATAAACCTTGTCTAAGACAACCTTTT-A
*
6485 AAAAGGTTGAGAT
64 AAAAGGTTGGGAT
* *
6498 AGACCTTATCTAAGACAACCTTTAAAAAAGGTTGAGATAAACCTTGTTTAAGACAACC-TTT-AA
1 AGACCTTGTCTAAGACAACCTTTAAAAAAGGTTGAGATAAACCTTGTCTAAGACAACCTTTTAAA
6561 AAGGTTGGGAT
66 AAGGTTGGGAT
* * * *
6572 AGATCTTGTCTAAGACAACCTTTTAAAAAGATTGGGATAAACCTTGTCTAAGACAACCTTTTAAA
1 AGACCTTGTCTAAGACAACCTTTAAAAAAGGTTGAGATAAACCTTGTCTAAGACAACCTTTTAAA
*
6637 AAAGTTGGGAT
66 AAGGTTGGGAT
* * * *
6648 AGACCTTGTCTAAGGCAACCTTTAAAAAAAGTTGAGATAGACAC--GTCTAA-AGCAACC-TTGA
1 AGACCTTGTCTAAGACAACCTTTAAAAAAGGTTGAGATAAAC-CTTGTCTAAGA-CAACCTTTTA
6709 AAAAGGTTGGGAT
64 AAAAGGTTGGGAT
6722 AGAC
1 AGAC
6726 ACATGTAAAG
Statistics
Matches: 197, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
74 84 0.43
75 14 0.07
76 50 0.25
77 47 0.24
78 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (76 bp):
AGACCTTGTCTAAGACAACCTTTAAAAAAGGTTGAGATAAACCTTGTCTAAGACAACCTTTTAAA
AAGGTTGGGAT
Found at i:6712 original size:112 final size:113
Alignment explanation
Indices: 6421--6722 Score: 346
Period size: 112 Copynumber: 2.7 Consensus size: 113
6411 GGGCTGGAAA
* * * *
6421 AGACCTAGTC-AAGGACGACCTTTAAAAAAGGTTGGGATAGGTCTTGTCTAAGGCAACCTTTTAA
1 AGACCTTGTCTAAGG-CAACCTTTAAAAAAGGTTGGGATA-GACTTGTCTAAAGCAACC-TTTAA
* *
6485 AAAAGGTTGAGATAGACCTTATCTAAGACAACCTTTAAAAAAGGTTGAGAT
63 AAAAGGTTGGGATAAACCTTATCTAAGACAACCTTTAAAAAAGGTTGAGAT
* * * *
6536 AAACCTTGTTTAAGACAACCTTT--AAAAGGTTGGGATAGATCTTGTCT-AAGACAACCTTTTAA
1 AGACCTTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGA-CTTGTCTAAAG-CAACCTTTAAA
* * *
6598 AAAGATTGGGATAAACCTTGTCTAAGACAACCTTTTAAAAAA-GTTGGGAT
64 AAAGGTTGGGATAAACCTTATCTAAGACAACC-TTTAAAAAAGGTTGAGAT
* * ** *
6648 AGACCTTGTCTAAGGCAACCTTTAAAAAAAGTTGAGATAGACACGTCTAAAGCAACC-TTGAAAA
1 AGACCTTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACTTGTCTAAAGCAACCTTTAAAAA
6712 AGGTTGGGATA
66 AGGTTGGGATA
6723 GACACATGTA
Statistics
Matches: 158, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
112 79 0.50
113 45 0.28
114 17 0.11
115 14 0.09
116 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
AGACCTTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACTTGTCTAAAGCAACCTTTAAAAA
AGGTTGGGATAAACCTTATCTAAGACAACCTTTAAAAAAGGTTGAGAT
Found at i:11816 original size:2 final size:2
Alignment explanation
Indices: 11811--11842 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11801 TATATATATA
11811 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
11843 AAGTGATAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.