Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000561.1 Kokia drynarioides strain JFW-HI SEQ_111475, 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: 4113
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Found at i:1053 original size:21 final size:20
Alignment explanation
Indices: 1027--1076 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
1017 TCTCTATCCA
1027 ATTTTTTTTTA-TCTATTTTTT
1 ATTTTTTTTTATTC-A-TTTTT
*
1048 ATTTTTTAATTATTCATTTTT
1 ATTTTTT-TTTATTCATTTTT
1069 ATTTTTTT
1 ATTTTTTT
1077 GAAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 19 0.76
22 4 0.16
23 2 0.08
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (20 bp):
ATTTTTTTTTATTCATTTTT
Found at i:1351 original size:17 final size:17
Alignment explanation
Indices: 1326--1358 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1316 AAAATAATTC
*
1326 TTATTATAGTATATTAT
1 TTATGATAGTATATTAT
1343 TTATGATAGTATATTA
1 TTATGATAGTATATTA
1359 GTTCATGCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TTATGATAGTATATTAT
Found at i:2431 original size:22 final size:21
Alignment explanation
Indices: 2398--2452 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2388 TTAATATCAA
*
2398 TTTTAATATTTTT-AATAAGTT
1 TTTTTATATTTTTCAA-AAGTT
2419 TTTTTATATTTTTCAAAAGTT
1 TTTTTATATTTTTCAAAAGTT
*
2440 TTTAATATATTTT
1 TTT-TTATATTTT
2453 ATGCGTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTATATTTTTCAAAAGTT
Found at i:2493 original size:9 final size:9
Alignment explanation
Indices: 2481--2578 Score: 51
Period size: 9 Copynumber: 10.6 Consensus size: 9
2471 TTAAATATTT
2481 TTTTATTAA
1 TTTTATTAA
*
2490 TTTTATAAAA
1 TTTTAT-TAA
*
2500 ATTTA-TAA
1 TTTTATTAA
2508 -TTTATTAAA
1 TTTTATT-AA
*
2517 ATTTATTAGA
1 TTTTATTA-A
2527 -TTTATTATA
1 TTTTATTA-A
2536 TTTT-TATAA
1 TTTTAT-TAA
**
2545 TATTTAAAAA
1 T-TTTATTAA
2555 TTTATATTAA
1 TTT-TATTAA
*
2565 TTTTATTAT
1 TTTTATTAA
2574 TTTTA
1 TTTTA
2579 AATATTTAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
7 4 0.06
8 3 0.04
9 32 0.46
10 31 0.44
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTATTAA
Found at i:2498 original size:23 final size:22
Alignment explanation
Indices: 2458--2503 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2448 ATTTTATGCG
*
2458 TTTTTATAAAATTTTAAATATT
1 TTTTTATAAAATTTTAAAAATT
* *
2480 TTTTTATTAATTTTATAAAAATT
1 TTTTTATAAAATTT-TAAAAATT
2503 T
1 T
2504 ATAATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTATAAAATTTTAAAAATT
Found at i:2517 original size:17 final size:17
Alignment explanation
Indices: 2491--2560 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
2481 TTTTATTAAT
2491 TTTATAAAAATTTATAA
1 TTTATAAAAATTTATAA
*
2508 TTTATTAAAATTTATTAGA
1 TTTATAAAAATTTA-TA-A
* **
2527 TTTATTATATTTTTATAA
1 TTTA-TAAAAATTTATAA
2545 TATT-TAAAAATTTATA
1 T-TTATAAAAATTTATA
2561 TTAATTTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
17 22 0.54
18 4 0.10
19 9 0.22
20 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTATAAAAATTTATAA
Found at i:2531 original size:19 final size:18
Alignment explanation
Indices: 2482--2533 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 18
2472 TAAATATTTT
*
2482 TTTATTAATTTTATAAAAA
1 TTTATTAA-TTTATTAAAA
2501 TTTA-TAATTTATTAAAA
1 TTTATTAATTTATTAAAA
2518 TTTATTAGATTTATTA
1 TTTATTA-ATTTATTA
2534 TATTTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 13 0.43
18 5 0.17
19 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTATTAATTTATTAAAA
Found at i:2558 original size:28 final size:27
Alignment explanation
Indices: 2475--2586 Score: 77
Period size: 28 Copynumber: 4.0 Consensus size: 27
2465 AAAATTTTAA
* *
2475 ATATTTTTTTATTAATTTTATAAAAATTT
1 ATATATTTTTA-TAATATT-TAAAAATTT
* *
2504 ATA-ATTTATTA-AA-ATTTATTAGATTT
1 ATATATTT-TTATAATATTTA-AAAATTT
2530 ATTATATTTTTATAATATTTAAAAATTT
1 A-TATATTTTTATAATATTTAAAAATTT
* * * *
2558 ATATTAATTTTATTATTTTTAAATATTT
1 ATA-TATTTTTATAATATTTAAAAATTT
2586 A
1 A
2587 GATTAAATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
25 2 0.03
26 8 0.12
27 9 0.14
28 36 0.55
29 11 0.17
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (27 bp):
ATATATTTTTATAATATTTAAAAATTT
Found at i:2591 original size:28 final size:28
Alignment explanation
Indices: 2537--2592 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2527 TTTATTATAT
*
2537 TTTTATAATATTTAAAAATTTATATTAA
1 TTTTATAATATTTAAAAATTTAGATTAA
* * *
2565 TTTTATTATTTTTAAATATTTAGATTAA
1 TTTTATAATATTTAAAAATTTAGATTAA
2593 ATTAAAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTATAATATTTAAAAATTTAGATTAA
Found at i:2812 original size:16 final size:14
Alignment explanation
Indices: 2793--2826 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
2783 TATAAGCCTT
2793 TTATAAATGTTATATA
1 TTATAAAT-TT-TATA
2809 TTATAAATTTTATA
1 TTATAAATTTTATA
2823 TTAT
1 TTAT
2827 TGTTGACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATAAATTTTATA
Done.