Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008221.1 Kokia drynarioides strain JFW-HI SEQ_122885, 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: 19652
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:2602 original size:19 final size:18
Alignment explanation
Indices: 2570--2605 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
2560 TATTTTATAT
2570 TATTTAATTATATTATTG
1 TATTTAATTATATTATTG
2588 TATTTAATATATATTATT
1 TATTTAAT-TATATTATT
2606 AACCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTTAATTATATTATTG
Found at i:3507 original size:14 final size:16
Alignment explanation
Indices: 3474--3512 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
3464 TTAAATCTTA
*
3474 AAATTAAAAAATATAG
1 AAATTAAAAAATATAC
3490 AAA-TAAAAAATAT-C
1 AAATTAAAAAATATAC
3504 AAATTAAAA
1 AAATTAAAA
3513 TATAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 15 0.71
16 3 0.14
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATTAAAAAATATAC
Found at i:6807 original size:31 final size:30
Alignment explanation
Indices: 6757--6814 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
6747 AAAATTATAC
*
6757 AATAATAATTTTAATAATTCGATAATTTAA
1 AATAATAATTTTAATAATTCAATAATTTAA
6787 AATAA-AATTTTTAAATAATTCAATAATT
1 AATAATAA-TTTT-AATAATTCAATAATT
6815 ATTTTGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 2 0.08
30 9 0.36
31 14 0.56
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (30 bp):
AATAATAATTTTAATAATTCAATAATTTAA
Found at i:15487 original size:22 final size:23
Alignment explanation
Indices: 15456--15501 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
15446 TTTATAAGTG
15456 AAATATTTTATGT-ATTTATTTTT
1 AAATATTTTAT-TAATTTATTTTT
15479 AAAT-TTTTATTACATTTATTTTT
1 AAATATTTTATTA-ATTTATTTTT
15502 GTGTGTACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.05
22 6 0.29
23 14 0.67
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
AAATATTTTATTAATTTATTTTT
Found at i:17841 original size:19 final size:19
Alignment explanation
Indices: 17819--17872 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
17809 TAAAATCATT
17819 AAAAATAGTAAAAAAAATA
1 AAAAATAGTAAAAAAAATA
* **
17838 AAAAATATTAAAAATTATA
1 AAAAATAGTAAAAAAAATA
17857 AAAGAATATGTAAAAA
1 AAA-AATA-GTAAAAA
17873 TATATACAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 19 0.66
20 4 0.14
21 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAAATAGTAAAAAAAATA
Found at i:17877 original size:12 final size:10
Alignment explanation
Indices: 17810--17877 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
17800 TTTTATACTT
17810 AAAATCATT-A
1 AAAAT-ATTAA
*
17820 AAAATAGTAA
1 AAAATATTAA
*
17830 AAAA-AATAA
1 AAAATATTAA
17839 AAAATATTAA
1 AAAATATTAA
*
17849 AAATTA-TAA
1 AAAATATTAA
17858 AAGAATATGTAA
1 AA-AATAT-TAA
17870 AAATATAT
1 AAA-ATAT
17878 ACAAGTTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 15 0.32
10 22 0.47
11 1 0.02
12 9 0.19
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (10 bp):
AAAATATTAA
Found at i:18003 original size:20 final size:21
Alignment explanation
Indices: 17956--18003 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
17946 AAATTCTAAC
17956 ATAT-AAAAATATAGAAAAGT
1 ATATAAAAAATATAGAAAAGT
* * *
17976 ACAAAAAAAAT-TAGAAAATT
1 ATATAAAAAATATAGAAAAGT
17996 ATATAAAA
1 ATATAAAA
18004 TTACAAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (21 bp):
ATATAAAAAATATAGAAAAGT
Found at i:18289 original size:29 final size:28
Alignment explanation
Indices: 18257--18322 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
18247 ATATTTTTTG
18257 TAATTTT-TAACATTTATATATATAGTCTT
1 TAATTTTATAACATTT-TATA-ATAGTCTT
* **
18286 TAATATTTATAATATTTTATAATTTTCTT
1 TAAT-TTTATAACATTTTATAATAGTCTT
18315 TAATTTTA
1 TAATTTTA
18323 ATAATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 4 0.12
29 14 0.44
30 7 0.22
31 7 0.22
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (28 bp):
TAATTTTATAACATTTTATAATAGTCTT
Done.