Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008046.1 Kokia drynarioides strain JFW-HI SEQ_122702, 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: 3240
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:755 original size:57 final size:57
Alignment explanation
Indices: 667--781 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
657 TTTATTAAGA
*
667 TATTGTTAATGTTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC
1 TATTGTTAATGCTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC
724 TATTGTTAATGCTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC
1 TATTGTTAATGCTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC
781 T
1 T
782 GTTTATGGGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (57 bp):
TATTGTTAATGCTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC
Found at i:928 original size:16 final size:18
Alignment explanation
Indices: 907--942 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
897 GTTTGTAATG
907 TTTTATAT-TT-TGTTAT
1 TTTTATATATTATGTTAT
923 TTTTATATATTATGTTAT
1 TTTTATATATTATGTTAT
941 TT
1 TT
943 ATAACACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (18 bp):
TTTTATATATTATGTTAT
Found at i:1087 original size:33 final size:34
Alignment explanation
Indices: 1016--1088 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 34
1006 TCTTCAGTTG
1016 AATATATATAAAATATTAATAAATAAAAAAATAT
1 AATATATATAAAATATTAATAAATAAAAAAATAT
* ** *
1050 AATAT-TATTAAATATTAA-ATTTAAAATAATAT
1 AATATATATAAAATATTAATAAATAAAAAAATAT
1082 AA-ATATA
1 AATATATA
1089 CATTTTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 2 0.06
32 15 0.44
33 12 0.35
34 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (34 bp):
AATATATATAAAATATTAATAAATAAAAAAATAT
Found at i:2689 original size:17 final size:17
Alignment explanation
Indices: 2667--2724 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
2657 TTAAGTTTAT
2667 TTTAAAAATTAAATTTG
1 TTTAAAAATTAAATTTG
*
2684 TTTAAAAATTTAAATTTA
1 TTTAAAAA-TTAAATTTG
** *
2702 TTTTGAATTTAAATTTG
1 TTTAAAAATTAAATTTG
2719 ATTTAA
1 -TTTAA
2725 GTTTAAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 16 0.50
18 16 0.50
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
TTTAAAAATTAAATTTG
Found at i:2729 original size:17 final size:16
Alignment explanation
Indices: 2690--2766 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 16
2680 TTTGTTTAAA
2690 AATTTAAATTTATTTTG
1 AATTTAAATTTA-TTTG
2707 AATTTAAATTTGATTT-
1 AATTTAAATTT-ATTTG
*
2723 AAGTTTAAATTTATTTTCA
1 AA-TTTAAATTTA-TTT-G
* *
2742 AATTTAAAATTATTATA
1 AATTTAAATTTATT-TG
2759 AATTTAAA
1 AATTTAAA
2767 ATAAGTAAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
16 3 0.06
17 37 0.70
18 11 0.21
19 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (16 bp):
AATTTAAATTTATTTG
Found at i:2768 original size:17 final size:17
Alignment explanation
Indices: 2656--2766 Score: 107
Period size: 18 Copynumber: 6.4 Consensus size: 17
2646 CCAAACTCTC
*
2656 TTTAAGTTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
2674 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
*
2692 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
*
2709 TTTAAATTTGA-TTTAAG
1 TTTAAATTT-ATTTTAAA
2726 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
2744 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
2761 TTTAAA
1 TTTAAA
2767 ATAAGTAAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
16 1 0.01
17 36 0.47
18 39 0.51
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Done.