Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013648.1 Kokia drynarioides strain JFW-HI SEQ_128676, 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: 5005
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Found at i:2899 original size:41 final size:40
Alignment explanation
Indices: 2828--2960 Score: 133
Period size: 41 Copynumber: 3.2 Consensus size: 40
2818 AAAATCCACT
* *
2828 TTTAGCAGCGCTTTTCCAT-AAGCACTGCTAATGCTCTGATC
1 TTTAGCGGCG-TTTTCCATCAAGCAC-GCTAATGCTCTGACC
* *
2869 TTTAGCGGCGTTTTCCCTCAAGCGACGCTAATGCTCTAACC
1 TTTAGCGGCGTTTTCCATCAAGC-ACGCTAATGCTCTGACC
* * * * *
2910 TTTAGCGACGCTTTCCAACAAGCATTGCCAATGCTCTGACC
1 TTTAGCGGCGTTTTCCATCAAGCA-CGCTAATGCTCTGACC
*
2951 TTTAACGGCG
1 TTTAGCGGCG
2961 CCTTCCCACA
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
40 8 0.11
41 66 0.87
42 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (40 bp):
TTTAGCGGCGTTTTCCATCAAGCACGCTAATGCTCTGACC
Found at i:2967 original size:82 final size:82
Alignment explanation
Indices: 2847--3007 Score: 196
Period size: 82 Copynumber: 2.0 Consensus size: 82
2837 GCTTTTCCAT
* * * ** * *
2847 AAGCACTGCTAATGCTCTGATCTTTAGCGGCGTTTTCCCTCAAGCGACGCTAATGCTCTAACCTT
1 AAGCACTGCCAATGCTCTGACCTTTAACGGCGCCTTCCCACAAACGACGCTAATGCTCTAACCTT
2912 TAGCGACGCTTTCCAAC
66 TAGCGACGCTTTCCAAC
* * ** *
2929 AAGCATTGCCAATGCTCTGACCTTTAACGGCGCCTTCCCACAAACGCCGCTGTTGTTCTAACCTT
1 AAGCACTGCCAATGCTCTGACCTTTAACGGCGCCTTCCCACAAACGACGCTAATGCTCTAACCTT
**
2994 TAGCGGTGCTTTCC
66 TAGCGACGCTTTCC
3008 CATAAACGCC
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.20, C:0.32, G:0.19, T:0.29
Consensus pattern (82 bp):
AAGCACTGCCAATGCTCTGACCTTTAACGGCGCCTTCCCACAAACGACGCTAATGCTCTAACCTT
TAGCGACGCTTTCCAAC
Found at i:3037 original size:41 final size:41
Alignment explanation
Indices: 2859--3048 Score: 152
Period size: 41 Copynumber: 4.6 Consensus size: 41
2849 GCACTGCTAA
* * * * * * *
2859 TGCTCTGATCTTTAGCGGCGTTTTCCCTCAAGCGACGCTAA
1 TGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAT
* * * *
2900 TGCTCTAACCTTTAGCGACGCTTTCCAACAAGCATTGCCA--A-
1 TGCTCTGACCTTTAGCGGCGCTTTCCCACAA--A-CGCCACTAT
* * * *
2941 TGCTCTGACCTTTAACGGCGCCTTCCCACAAACGCCGCTGT
1 TGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAT
* * * *
2982 TGTTCTAACCTTTAGCGGTGCTTTCCCATAAACGCCACTAT
1 TGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAT
*
3023 TGCTCTGACCTTTAGCAGCGCTTTCC
1 TGCTCTGACCTTTAGCGGCGCTTTCC
3049 AAAAAGTGTC
Statistics
Matches: 113, Mismatches: 30, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
38 3 0.03
39 1 0.01
41 106 0.94
42 1 0.01
44 2 0.02
ACGTcount: A:0.19, C:0.33, G:0.18, T:0.30
Consensus pattern (41 bp):
TGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAT
Found at i:4282 original size:22 final size:21
Alignment explanation
Indices: 4198--4282 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 21
4188 AAAACAGCAG
*
4198 CAAAAATAACAGAAAACAACAT
1 CAAAAATAACA-AAAATAACAT
* *
4220 TAAAAATAACAAAAATAGCCAT
1 CAAAAATAACAAAAATA-ACAT
* *
4242 AAAAAAAAAGCAATAAAAATAACAT
1 CAAAAATAA-C---AAAAATAACAT
4267 CAAAAATAACACAAAA
1 CAAAAATAACA-AAAA
4283 ATAGCAATCA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
21 6 0.12
22 24 0.49
23 1 0.02
24 1 0.02
25 10 0.20
26 7 0.14
ACGTcount: A:0.71, C:0.14, G:0.04, T:0.12
Consensus pattern (21 bp):
CAAAAATAACAAAAATAACAT
Found at i:4283 original size:12 final size:12
Alignment explanation
Indices: 4256--4285 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4246 AAAAAGCAAT
4256 AAAAATAACATC
1 AAAAATAACATC
4268 AAAAATAACA-C
1 AAAAATAACATC
4279 AAAAATA
1 AAAAATA
4286 GCAATCAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAATAACATC
Found at i:4341 original size:22 final size:22
Alignment explanation
Indices: 4313--4366 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
4303 TAAAAATTCA
*
4313 AAAACAACAAA-AAAAATCAACC
1 AAAACAACAAATAAAAAGC-ACC
*
4335 AAAACAATAAATAAAAAGCACC
1 AAAACAACAAATAAAAAGCACC
4357 AAAACAACAA
1 AAAACAACAA
4367 TATCATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.72, C:0.20, G:0.02, T:0.06
Consensus pattern (22 bp):
AAAACAACAAATAAAAAGCACC
Found at i:4342 original size:43 final size:44
Alignment explanation
Indices: 4266--4351 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 44
4256 AAAAATAACA
* * * *
4266 TCAAAAATAACACAAAAATAGCAATCAGAACAATAAATAAAAAT
1 TCAAAAACAACACAAAAAAAGCAACCAAAACAATAAATAAAAAT
*
4310 TCAAAAACAACA-AAAAAAATCAACCAAAACAATAAATAAAAA
1 TCAAAAACAACACAAAAAAAGCAACCAAAACAATAAATAAAAA
4352 GCACCAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 26 0.70
44 11 0.30
ACGTcount: A:0.70, C:0.15, G:0.02, T:0.13
Consensus pattern (44 bp):
TCAAAAACAACACAAAAAAAGCAACCAAAACAATAAATAAAAAT
Done.