Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012550.1 Kokia drynarioides strain JFW-HI SEQ_127559, 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: 5027
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Found at i:2724 original size:29 final size:27
Alignment explanation
Indices: 2663--3103 Score: 292
Period size: 29 Copynumber: 15.0 Consensus size: 27
2653 AATTTCAAAC
* * **
2663 GTTCGGGAGTAAAATGGTAATTTTAAAA
1 GTTCGGG-GTAAAATGGGATTTTTGGAA
*
2691 GGTTCAGGGTCAAGAATGGGATTTTTGGAA
1 -GTTCGGGGT-AA-AATGGGATTTTTGGAA
*
2721 GTTCGGGGGTAAAATGGTAATTTTTGGAA
1 GTTC-GGGGTAAAATGG-GATTTTTGGAA
* * *
2750 GGTTTGTGGTAAAAAATGGGACTTTTGGAA
1 -GTTCGGGGT--AAAATGGGATTTTTGGAA
**
2780 GTTCGAGGGTAAAATAGTAATTTTTGGAA
1 GTTCG-GGGTAAAAT-GGGATTTTTGGAA
2809 GGTTCGGGGTTAAAATGGGA-TTTTGGAA
1 -GTTCGGGG-TAAAATGGGATTTTTGGAA
* * * *
2837 GTTTGGGGGTAAAATAGTAATTTTGGAA
1 G-TTCGGGGTAAAATGGGATTTTTGGAA
*
2865 GGTTCAGGGTTAAAAATGGGACTTTTTGGAA
1 -GTTC-GGGGT-AAAATGGGA-TTTTTGGAA
* *
2896 GTTTGGGGGTAAAATGGTAATTTTTGGAA
1 G-TTCGGGGTAAAATGG-GATTTTTGGAA
* *
2925 GGTTTAGGGTTAAAAATGGGATTTTTGGAA
1 -G-TTCGGGGT-AAAATGGGATTTTTGGAA
*
2955 GTTCGGGGGTAAAATGGTAATTTCTT-GAA
1 GTTC-GGGGTAAAATGG-GATTT-TTGGAA
* *
2984 GGTTCGGGGTTAAAAATGGGATTTGTGGAG
1 -GTTCGGGG-T-AAAATGGGATTTTTGGAA
**
3014 GTTCGGGGGTAAAATTGCAATTTTTGGAA
1 GTTC-GGGGTAAAA-TGGGATTTTTGGAA
*
3043 GGTTCGAGGTCAAAAATGGGATTTTTTGGAA
1 -GTTCGGGGT--AAAATGGGA-TTTTTGGAA
*
3074 GTTCGAGGGTAAAATGGTAATTTTTGGAA
1 GTTCG-GGGTAAAATGG-GATTTTTGGAA
3103 G
1 G
3104 GTTTAGGACC
Statistics
Matches: 329, Mismatches: 47, Indels: 72
0.73 0.10 0.16
Matches are distributed among these distances:
27 9 0.03
28 49 0.15
29 121 0.37
30 103 0.31
31 47 0.14
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (27 bp):
GTTCGGGGTAAAATGGGATTTTTGGAA
Found at i:2781 original size:59 final size:58
Alignment explanation
Indices: 2663--3106 Score: 583
Period size: 59 Copynumber: 7.6 Consensus size: 58
2653 AATTTCAAAC
* ** * *
2663 GTTCGGGAGTAAAATGGTAA-TTTTAAAAGGTTCAGGGTCAAGAATGGGATTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTC-GGGTTAAAAATGGGATTTTTGGAA
* * *
2721 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTTGTGGTAAAAAATGGGACTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCG-GGTTAAAAATGGGATTTTTGGAA
* *
2780 GTTCGAGGGTAAAATAGTAATTTTTGGAAGGTTCGGGGTT-AAAATGGGA-TTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTC-GGGTTAAAAATGGGATTTTTGGAA
* *
2837 GTTTGGGGGTAAAATAGTAA-TTTTGGAAGGTTCAGGGTTAAAAATGGGACTTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTC-GGGTTAAAAATGGGA-TTTTTGGAA
* *
2896 GTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTTAAAAATGGGATTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGG-TTCGGGTTAAAAATGGGATTTTTGGAA
* *
2955 GTTCGGGGGTAAAATGGTAATTTCTT-GAAGGTTCGGGGTTAAAAATGGGATTTGTGGAG
1 GTTCGGGGGTAAAATGGTAATTT-TTGGAAGGTTC-GGGTTAAAAATGGGATTTTTGGAA
* * *
3014 GTTCGGGGGTAAAATTGCAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCG-GGTTAAAAATGGGA-TTTTTGGAA
*
3074 GTTCGAGGGTAAAATGGTAATTTTTGGAAGGTT
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTT
3107 TAGGACCTCC
Statistics
Matches: 345, Mismatches: 28, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
56 18 0.05
57 35 0.10
58 34 0.10
59 191 0.55
60 65 0.19
61 2 0.01
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (58 bp):
GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGTTAAAAATGGGATTTTTGGAA
Found at i:4324 original size:7 final size:7
Alignment explanation
Indices: 4312--4350 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
4302 TCGTGTTTTT
4312 TTATTAA
1 TTATTAA
4319 TTATTAA
1 TTATTAA
*
4326 TTAATAA
1 TTATTAA
4333 TTATTAA
1 TTATTAA
4340 -TATT-A
1 TTATTAA
4345 TTATTA
1 TTATTA
4351 TTAATATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 1 0.04
6 8 0.29
7 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATTAA
Found at i:4352 original size:15 final size:15
Alignment explanation
Indices: 4312--4357 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4302 TCGTGTTTTT
4312 TTATTAATTATTAAT-
1 TTATT-ATTATTAATA
* *
4327 TAATAATTATTAATA
1 TTATTATTATTAATA
4342 TTATTATTATTAATA
1 TTATTATTATTAATA
4357 T
1 T
4358 CAAAACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:4465 original size:19 final size:18
Alignment explanation
Indices: 4427--4468 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
4417 ATTAGTATTA
*
4427 TTATTAATATTAAAACAG
1 TTATTAATATTAAAAAAG
4445 TTATTAATATTAAAAAAAG
1 TTATTAATATT-AAAAAAG
4464 TTATT
1 TTATT
4469 GAAACGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
TTATTAATATTAAAAAAG
Found at i:4999 original size:15 final size:15
Alignment explanation
Indices: 4976--5027 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
4966 TTTGGTCATC
4976 TGTAATTGGGCCATT
1 TGTAATTGGGCCATT
* *
4991 TGTATTTGGGCCATC
1 TGTAATTGGGCCATT
5006 TGTAATTGGGCCATT
1 TGTAATTGGGCCATT
5021 TGTAATT
1 TGTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.42
Consensus pattern (15 bp):
TGTAATTGGGCCATT
Done.