Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015133.1 Kokia drynarioides strain JFW-HI SEQ_130177, 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: 46691
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:3621 original size:23 final size:23
Alignment explanation
Indices: 3578--3621 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3568 GAAATTAAGT
**
3578 TGTAATTTTTACGATAATAAAAA
1 TGTAATTTTTAAAATAATAAAAA
*
3601 TGTAATTTTTAAAATATTAAA
1 TGTAATTTTTAAAATAATAAA
3622 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (23 bp):
TGTAATTTTTAAAATAATAAAAA
Found at i:4085 original size:13 final size:13
Alignment explanation
Indices: 4069--4097 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4059 ATTATTTAAA
4069 TTTGTATTTATCT
1 TTTGTATTTATCT
4082 TTTGTATTTATCT
1 TTTGTATTTATCT
4095 TTT
1 TTT
4098 AGAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (13 bp):
TTTGTATTTATCT
Found at i:4881 original size:15 final size:16
Alignment explanation
Indices: 4861--4890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4851 CTTCCCTATT
4861 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
4876 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
4891 TTTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:4883 original size:22 final size:22
Alignment explanation
Indices: 4856--4916 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
4846 TTCGACTTCC
4856 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
4878 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
*
4900 -T-TGTTTCTTTTATTTTT
1 CTAT-TTTCTTTTACTTTT
4917 CCTTAGATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 1 0.03
21 18 0.50
22 17 0.47
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.74
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:5821 original size:29 final size:30
Alignment explanation
Indices: 5779--5858 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
5769 TAATTTGATC
*
5779 AAATCAAAATTTCATGTATAAAATTGCACA-
1 AAATC-AAAGTTCATGTATAAAATTGCACAT
* *
5809 AAATCAAAGTTCATGTATACAGTTGCACATT
1 AAATCAAAGTTCATGTATAAAATTGCACA-T
*
5840 AAATCATAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
5859 GTTTTGGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 21 0.48
30 5 0.11
31 18 0.41
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.33
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGCACAT
Found at i:23679 original size:2 final size:2
Alignment explanation
Indices: 23636--23660 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23626 CCTCTCACAA
23636 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
23661 AATAAAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23707 original size:16 final size:16
Alignment explanation
Indices: 23679--23717 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
23669 CCTTAATATA
*
23679 TTTATATTTTTTTATTAG
1 TTTA-ATTTTTTT-TAAG
23697 TTTAATTTTTTTTAAG
1 TTTAATTTTTTTTAAG
23713 TTTAA
1 TTTAA
23718 AAAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 8 0.40
18 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTAATTTTTTTTAAG
Found at i:24566 original size:18 final size:16
Alignment explanation
Indices: 24531--24585 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
24521 ATATTATTTA
*
24531 TATATTTATATTAT-AT
1 TATAATTATATT-TGAT
24547 TATAAATTATCATTTGAT
1 TAT-AATTAT-ATTTGAT
24565 TATAATTATATTT-A-
1 TATAATTATATTTGAT
24579 TATAATT
1 TATAATT
24586 TTAAAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 7 0.20
15 1 0.03
16 7 0.20
17 12 0.34
18 8 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TATAATTATATTTGAT
Found at i:43308 original size:29 final size:29
Alignment explanation
Indices: 43254--43309 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
43244 TTAATTATTC
*
43254 GACTTTTTCTTTTAAATTTTGCATAATTT
1 GACTTTTTCTTTTAAATTTGGCATAATTT
*
43283 GACTTTTTCTTTTAAATTTGGGATAAT
1 GACTTTTTCTTTTAAATTTGGCATAAT
43310 ATCAACTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (29 bp):
GACTTTTTCTTTTAAATTTGGCATAATTT
Done.