Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000668.1 Kokia drynarioides strain JFW-HI SEQ_111656, 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: 3425
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Found at i:886 original size:14 final size:15
Alignment explanation
Indices: 859--888 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
849 ATTTTATTAT
859 TTATAAATAATAAAA
1 TTATAAATAATAAAA
874 TTATAAA-AATAAAA
1 TTATAAATAATAAAA
888 T
1 T
889 AAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTATAAATAATAAAA
Found at i:922 original size:42 final size:42
Alignment explanation
Indices: 876--1006 Score: 157
Period size: 42 Copynumber: 3.3 Consensus size: 42
866 TAATAAAATT
876 ATAAAAATAAAATAAAATAAATATTTTTATGATTATATTTTA
1 ATAAAAATAAAATAAAATAAATATTTTTATGATTATATTTTA
* * * * * **
918 ATAAAAAT-AAAT---TTTATTATTTTTA-AATAATAAATT-
1 ATAAAAATAAAATAAAATAAATATTTTTATGATTATATTTTA
954 ATAAAAATAAAATAAAATAAATATTTTTATGATTATATTTTA
1 ATAAAAATAAAATAAAATAAATATTTTTATGATTATATTTTA
996 ATAAAAATAAA
1 ATAAAAATAAA
1007 TTTTATTATT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
36 8 0.12
37 11 0.16
38 10 0.14
40 10 0.14
41 11 0.16
42 19 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (42 bp):
ATAAAAATAAAATAAAATAAATATTTTTATGATTATATTTTA
Found at i:927 original size:37 final size:37
Alignment explanation
Indices: 884--1006 Score: 131
Period size: 37 Copynumber: 3.2 Consensus size: 37
874 TTATAAAAAT
884 AAAATAAAATAAATATTTTTATGATTATATTTTAATA
1 AAAATAAAATAAATATTTTTATGATTATATTTTAATA
* * * * * * *
921 AAAATAAATTTTATTATTTTTAAAT-AATAAATTATAAAAA
1 AAAATAAA-ATAAATATTTTT--ATGATTATATT-TTAATA
961 TAAAATAAAATAAATATTTTTATGATTATATTTTAATA
1 -AAAATAAAATAAATATTTTTATGATTATATTTTAATA
999 AAAATAAA
1 AAAATAAA
1007 TTTTATTATT
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
37 16 0.24
38 15 0.23
39 12 0.18
40 15 0.23
41 8 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (37 bp):
AAAATAAAATAAATATTTTTATGATTATATTTTAATA
Found at i:936 original size:26 final size:25
Alignment explanation
Indices: 907--1022 Score: 76
Period size: 28 Copynumber: 4.5 Consensus size: 25
897 TATTTTTATG
907 ATTATATTTTAATAAAAATAAATTTT
1 ATTATATTTTAA-AAAAATAAATTTT
* *
933 ATTAT-TTTT-AAATAATAAATTATA
1 ATTATATTTTAAAAAAATAAATT-TT
** *** **
957 AAAATAAAATAAAATAAATATTTTTAT
1 ATTATATTTTAAAA-AAATAAATTT-T
984 GATTATATTTTAATAAAAATAAATTTT
1 -ATTATATTTTAA-AAAAATAAATTTT
1011 ATTAT-TTTTAAA
1 ATTATATTTTAAA
1023 TAATAAAATG
Statistics
Matches: 65, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
23 10 0.15
24 6 0.09
25 11 0.17
26 14 0.22
27 7 0.11
28 15 0.23
29 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (25 bp):
ATTATATTTTAAAAAAATAAATTTT
Found at i:971 original size:78 final size:78
Alignment explanation
Indices: 849--1029 Score: 344
Period size: 78 Copynumber: 2.3 Consensus size: 78
839 CTCTAAGACC
*
849 ATTTTATTATTTATAAATAATAAAATTATAAAAATAAAATAAAATAAATATTTTTATGATTATAT
1 ATTTTATTATTTTTAAATAAT-AAATTATAAAAATAAAATAAAATAAATATTTTTATGATTATAT
914 TTTAATAAAAATAA
65 TTTAATAAAAATAA
928 ATTTTATTATTTTTAAATAATAAATTATAAAAATAAAATAAAATAAATATTTTTATGATTATATT
1 ATTTTATTATTTTTAAATAATAAATTATAAAAATAAAATAAAATAAATATTTTTATGATTATATT
993 TTAATAAAAATAA
66 TTAATAAAAATAA
1006 ATTTTATTATTTTTAAATAATAAA
1 ATTTTATTATTTTTAAATAATAAA
1030 ATGGGTTTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
78 81 0.80
79 20 0.20
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (78 bp):
ATTTTATTATTTTTAAATAATAAATTATAAAAATAAAATAAAATAAATATTTTTATGATTATATT
TTAATAAAAATAA
Found at i:2430 original size:19 final size:17
Alignment explanation
Indices: 2375--2424 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 17
2365 TTTTACTACA
2375 AAATATTTATTATTAAT
1 AAATATTTATTATTAAT
*
2392 --ATATTTATAATTGTAAT
1 AAATATTTATTA-T-TAAT
2409 AAATATTTATTATTAA
1 AAATATTTATTATTAA
2425 AATAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 9 0.33
16 1 0.04
17 7 0.26
18 1 0.04
19 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
AAATATTTATTATTAAT
Found at i:2475 original size:22 final size:22
Alignment explanation
Indices: 2435--2490 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
2425 AATAAAATTG
*
2435 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
2455 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
2477 TATTAATAATTTAT
1 AAATAATAAATTAT
2491 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Done.