Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014500.1 Kokia drynarioides strain JFW-HI SEQ_129539, 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: 36868
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:20289 original size:16 final size:15
Alignment explanation
Indices: 20250--20279 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20240 TAAATTATTG
*
20250 CATTTTTTTGTCTTT
1 CATTGTTTTGTCTTT
20265 CATTGTTTTGTCTTT
1 CATTGTTTTGTCTTT
20280 ATTTTGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.13, G:0.10, T:0.70
Consensus pattern (15 bp):
CATTGTTTTGTCTTT
Found at i:30551 original size:13 final size:13
Alignment explanation
Indices: 30530--30563 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
30520 ACAGTATAAT
30530 AATAATAATCCTA
1 AATAATAATCCTA
*
30543 AATATTAATCCTA
1 AATAATAATCCTA
*
30556 AAAAATAA
1 AATAATAA
30564 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:31546 original size:18 final size:17
Alignment explanation
Indices: 31521--31559 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
31511 TTTTTCTGAA
31521 TTTTA-TTTTTTCGATTT
1 TTTTATTTTTTTC-ATTT
31538 TTTTCATTTTTTTCATTT
1 TTTT-ATTTTTTTCATTT
31556 TTTT
1 TTTT
31560 TGACTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTTTCATTT
Found at i:31570 original size:10 final size:9
Alignment explanation
Indices: 31526--31559 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
31516 CTGAATTTTA
31526 TTTTTTCGAT
1 TTTTTTC-AT
31536 TTTTTTCAT
1 TTTTTTCAT
31545 TTTTTTCAT
1 TTTTTTCAT
31554 TTTTTT
1 TTTTTT
31560 TGACTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:31578 original size:9 final size:10
Alignment explanation
Indices: 31526--31571 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
31516 CTGAATTTTA
31526 TTTTTTCGA-T
1 TTTTTTC-ATT
31536 TTTTTTCA-T
1 TTTTTTCATT
31545 TTTTTTCATT
1 TTTTTTCATT
*
31555 TTTTTTGACTT
1 TTTTTTCA-TT
31566 TTTTTT
1 TTTTTT
31572 TCTTTTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 10 0.30
10 15 0.45
11 8 0.24
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:32514 original size:6 final size:6
Alignment explanation
Indices: 32503--32562 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
32493 TTGCATATTT
* * *
32503 AAAATA AAAATA AAAATA AAAAT- AAAAT- AAAATA AAACTA AATATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
32549 AAAATG AAAATA AA
1 AAAATA AAAATA AA
32563 TATACTAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 10 0.21
6 37 0.79
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:32533 original size:28 final size:29
Alignment explanation
Indices: 32502--32562 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
32492 ATTGCATATT
32502 TAAAATAAAAATAAAAATAAAAAT-AAAA
1 TAAAATAAAAATAAAAATAAAAATGAAAA
* * *
32530 TAAAATAAAACTAAATATGAAAATGAAAA
1 TAAAATAAAAATAAAAATAAAAATGAAAA
32559 TAAA
1 TAAA
32563 TATACTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (29 bp):
TAAAATAAAAATAAAAATAAAAATGAAAA
Found at i:34840 original size:13 final size:13
Alignment explanation
Indices: 34819--34852 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
34809 ACAATATAAT
34819 AATAATAATCCTA
1 AATAATAATCCTA
*
34832 AATATTAATCCTA
1 AATAATAATCCTA
*
34845 AAAAATAA
1 AATAATAA
34853 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Done.