Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004732.1 Kokia drynarioides strain JFW-HI SEQ_118312, 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: 16929
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Found at i:2366 original size:17 final size:17
Alignment explanation
Indices: 2346--2407 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
2336 ATTTTTTTTC
2346 AAAATTAAAATTATTTA
1 AAAATTAAAATTATTTA
**
2363 AAAAGTATAATAATTATAAA
1 AAAA-T-TAA-AATTATTTA
* *
2383 AAAATTAAATTTTTTTA
1 AAAATTAAAATTATTTA
2400 AAAATTAA
1 AAAATTAA
2408 TTAAATGCTG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 17 0.47
18 4 0.11
19 4 0.11
20 11 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAATTAAAATTATTTA
Found at i:2493 original size:17 final size:17
Alignment explanation
Indices: 2473--2533 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 17
2463 TATTTTTTTC
2473 AAAATTAA-AATTATTTAA
1 AAAATTAATAATTA--TAA
*
2491 AAAGTATAATAATTATAA
1 AAAAT-TAATAATTATAA
* *
2509 AAAATTAAT-TTTTTAA
1 AAAATTAATAATTATAA
2525 AAAATTAAT
1 AAAATTAAT
2534 TAAATACTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
16 14 0.38
17 4 0.11
18 11 0.30
19 3 0.08
20 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAATTAATAATTATAA
Found at i:2502 original size:127 final size:126
Alignment explanation
Indices: 2300--2555 Score: 451
Period size: 127 Copynumber: 2.0 Consensus size: 126
2290 GTGGATGACA
2300 CATCAGTATTTACTTAATTTTTAAAATTAAAAAAATATTTTTTTTCAAAATTAAAATTATTTAAA
1 CATCAGTATTTACTTAATTTTTAAAATTAAAAAAATATTTTTTTTCAAAATTAAAATTATTTAAA
* * **
2365 AAGTATAATAATTATAAAAAAATTAAATTTTTTTAAAAATTAATTAAATGCTGACATGTCATC
66 AAGTATAATAATTAT-AAAAAATT-AATTTTTTAAAAAATTAATTAAATACTGACATACCATC
2428 CATCAGTATTTACTTAATTTTTAAAATTAAAAAAATA-TTTTTTTCAAAATTAAAATTATTTAAA
1 CATCAGTATTTACTTAATTTTTAAAATTAAAAAAATATTTTTTTTCAAAATTAAAATTATTTAAA
2492 AAGTATAATAATTATAAAAAATTAATTTTTTAAAAAATTAATTAAATACTGACATACCATC
66 AAGTATAATAATTATAAAAAATTAATTTTTTAAAAAATTAATTAAATACTGACATACCATC
2553 CAT
1 CAT
2556 GTGACAGTCC
Statistics
Matches: 124, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
125 37 0.30
126 8 0.06
127 42 0.34
128 37 0.30
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (126 bp):
CATCAGTATTTACTTAATTTTTAAAATTAAAAAAATATTTTTTTTCAAAATTAAAATTATTTAAA
AAGTATAATAATTATAAAAAATTAATTTTTTAAAAAATTAATTAAATACTGACATACCATC
Found at i:2979 original size:32 final size:32
Alignment explanation
Indices: 2938--3035 Score: 196
Period size: 32 Copynumber: 3.1 Consensus size: 32
2928 ATTATGACTT
2938 AAAATGATATAATAATTTGGAGTTACACTTCA
1 AAAATGATATAATAATTTGGAGTTACACTTCA
2970 AAAATGATATAATAATTTGGAGTTACACTTCA
1 AAAATGATATAATAATTTGGAGTTACACTTCA
3002 AAAATGATATAATAATTTGGAGTTACACTTCA
1 AAAATGATATAATAATTTGGAGTTACACTTCA
3034 AA
1 AA
3036 TTAATTTTAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (32 bp):
AAAATGATATAATAATTTGGAGTTACACTTCA
Found at i:13580 original size:12 final size:12
Alignment explanation
Indices: 13563--13591 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
13553 TGGTAAACTA
13563 GTAAAATAAAGT
1 GTAAAATAAAGT
13575 GTAAAATAAAGT
1 GTAAAATAAAGT
13587 GTAAA
1 GTAAA
13592 GTAGTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (12 bp):
GTAAAATAAAGT
Done.