Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013388.1 Kokia drynarioides strain JFW-HI SEQ_128411, 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: 3964
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Found at i:1496 original size:18 final size:18
Alignment explanation
Indices: 1473--1509 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1463 TTTGTGATCA
1473 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
1491 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
1509 A
1 A
1510 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:2815 original size:8 final size:8
Alignment explanation
Indices: 2796--2953 Score: 54
Period size: 8 Copynumber: 18.2 Consensus size: 8
2786 TTTAAATATG
2796 TTTTATTAA
1 TTTTA-TAA
2805 TTTTATAA
1 TTTTATAA
2813 -TTTATTAGA
1 TTTTA-TA-A
*
2822 TTTTTTTAA
1 -TTTTATAA
2831 TATTTATAAA
1 T-TTTAT-AA
*
2841 TTTT-TAT
1 TTTTATAA
*
2848 TTTTATTA
1 TTTTATAA
2856 TTTTATAA
1 TTTTATAA
*
2864 GTATGTATCAA
1 -T-TTTAT-AA
2875 TTTTA-ATA
1 TTTTATA-A
*
2883 TTTTAAAA
1 TTTTATAA
2891 TTTTAATAA
1 TTTT-ATAA
* *
2900 TTTTTCTGAT
1 -TTTTAT-AA
*
2910 TTTTATATTT
1 TTTTATA--A
*
2920 TTTTATAT
1 TTTTATAA
2928 TTTTATAA
1 TTTTATAA
*
2936 TCTTTATGA
1 T-TTTATAA
2945 TTTT-TAA
1 TTTTATAA
2952 TT
1 TT
2954 ATTTTTATGA
Statistics
Matches: 116, Mismatches: 15, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
7 14 0.12
8 39 0.34
9 35 0.30
10 23 0.20
11 5 0.04
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (8 bp):
TTTTATAA
Found at i:2844 original size:16 final size:16
Alignment explanation
Indices: 2825--2898 Score: 60
Period size: 16 Copynumber: 4.5 Consensus size: 16
2815 TATTAGATTT
2825 TTTTAATATTTATAAA
1 TTTTAATATTTATAAA
* * * *
2841 TTTTTATTTTTATTAT
1 TTTTAATATTTATAAA
* *
2857 TTTATAAGTATGTATCAA
1 TTT-TAA-TATTTATAAA
2875 TTTTAATATTT-TAAAA
1 TTTTAATATTTAT-AAA
2891 TTTTAATA
1 TTTTAATA
2899 ATTTTTCTGA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
15 1 0.02
16 29 0.66
17 5 0.11
18 9 0.20
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTAATATTTATAAA
Found at i:2911 original size:18 final size:18
Alignment explanation
Indices: 2890--2963 Score: 69
Period size: 19 Copynumber: 4.1 Consensus size: 18
2880 ATATTTTAAA
*
2890 ATTTTAATAATTTTTCTG
1 ATTTTAATAATTTTTATG
* *
2908 ATTTTTATATTTTTTTAT-
1 ATTTTAATA-ATTTTTATG
* *
2926 ATTTTTATAATCTTTATG
1 ATTTTAATAATTTTTATG
*
2944 ATTTTTAATTATTTTTATG
1 A-TTTTAATAATTTTTATG
2963 A
1 A
2964 GAAATATTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
17 6 0.13
18 18 0.40
19 21 0.47
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (18 bp):
ATTTTAATAATTTTTATG
Found at i:2946 original size:36 final size:36
Alignment explanation
Indices: 2844--2961 Score: 107
Period size: 36 Copynumber: 3.3 Consensus size: 36
2834 TTATAAATTT
* * * *
2844 TTATTTTTATTATTTT-ATAAGTATGTATCAATTTTAA
1 TTATTTTTA-TATTTTAATAA-TCTTTATGATTTTTAA
* * * *
2881 -TATTTTAAAATTTTAATAATTTTTCTGATTTTTATA
1 TTATTTTTATATTTTAATAATCTTTATGATTTTTA-A
*
2917 TT-TTTTTATATTTTTATAATCTTTATGATTTTTAA
1 TTATTTTTATATTTTAATAATCTTTATGATTTTTAA
2952 TTATTTTTAT
1 TTATTTTTAT
2962 GAGAAATATT
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
35 18 0.28
36 46 0.71
37 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (36 bp):
TTATTTTTATATTTTAATAATCTTTATGATTTTTAA
Done.