Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004403.1 Kokia drynarioides strain JFW-HI SEQ_117783, 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: 11762
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Found at i:1688 original size:12 final size:12
Alignment explanation
Indices: 1672--1714 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1662 AAATAAATAT
*
1672 TAATTTTAATTT
1 TAATTTTAATTA
**
1684 TAATTTTAGCTA
1 TAATTTTAATTA
1696 TAATTTTTAATTA
1 TAA-TTTTAATTA
1709 TAATTT
1 TAATTT
1715 GAAATAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (12 bp):
TAATTTTAATTA
Found at i:1712 original size:54 final size:54
Alignment explanation
Indices: 1654--1791 Score: 178
Period size: 50 Copynumber: 2.6 Consensus size: 54
1644 AAACATAAAA
*
1654 ATAATTTGAAATAAATATTAATTTTAATTTTAATTTTAGCTATAA-TTTTTAATT
1 ATAATTTGAAATAAATATT-ATTTTAATTTTAATTTAAGCTATAATTTTTTAATT
* *
1708 ATAATTTGAAATAAATATTA-TTTAA--TT-ATTTAAGTTATAATTTTTTATTT
1 ATAATTTGAAATAAATATTATTTTAATTTTAATTTAAGCTATAATTTTTTAATT
* * *
1758 TTTATTTGAAATAAATATTATTTTAATTATAATT
1 ATAATTTGAAATAAATATTATTTTAATTTTAATT
1792 GTTTCAATTT
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
49 11 0.15
50 28 0.38
51 5 0.07
52 5 0.07
53 2 0.03
54 22 0.30
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.55
Consensus pattern (54 bp):
ATAATTTGAAATAAATATTATTTTAATTTTAATTTAAGCTATAATTTTTTAATT
Found at i:2037 original size:19 final size:19
Alignment explanation
Indices: 2008--2074 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1998 TTTAATTTTC
2008 ATTTC-AACTATAATTTAA
1 ATTTCAAACTATAATTTAA
*
2026 ATTTCAAACTATAAGTTAA
1 ATTTCAAACTATAATTTAA
*
2045 ATTTTAAACTAGT-ATTTAA
1 ATTTCAAACTA-TAATTTAA
*
2064 ATTTTAAACTA
1 ATTTCAAACTA
2075 GTATTTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 5 0.11
19 38 0.86
20 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTTCAAACTATAATTTAA
Found at i:2075 original size:19 final size:19
Alignment explanation
Indices: 2020--2080 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
2010 TTCAACTATA
*
2020 ATTTAAATTTCAAACTA-T
1 ATTTAAATTTTAAACTAGT
*
2038 AAGTTAAATTTTAAACTAGT
1 -ATTTAAATTTTAAACTAGT
2058 ATTTAAATTTTAAACTAGT
1 ATTTAAATTTTAAACTAGT
2077 ATTT
1 ATTT
2081 TATTTTGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 37 0.97
20 1 0.03
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (19 bp):
ATTTAAATTTTAAACTAGT
Found at i:10447 original size:19 final size:19
Alignment explanation
Indices: 10423--10484 Score: 124
Period size: 19 Copynumber: 3.3 Consensus size: 19
10413 AGCACTACAA
10423 AAGTAATGAATGATCATTT
1 AAGTAATGAATGATCATTT
10442 AAGTAATGAATGATCATTT
1 AAGTAATGAATGATCATTT
10461 AAGTAATGAATGATCATTT
1 AAGTAATGAATGATCATTT
10480 AAGTA
1 AAGTA
10485 CTCATGCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (19 bp):
AAGTAATGAATGATCATTT
Found at i:10676 original size:25 final size:23
Alignment explanation
Indices: 10619--10771 Score: 132
Period size: 23 Copynumber: 6.5 Consensus size: 23
10609 TATACGAAAC
*
10619 AAACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
10641 GGGCAACAGAGAACACACACAGTGCT
1 ---AAACAGAGAGCACACACAGTGCT
* * *
10667 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
10690 AATA-AGAGAGCACACAAAGTGCT
1 AA-ACAGAGAGCACACACAGTGCT
* *
10713 AATCAGAGAGCACACACAGTGTT
1 AAACAGAGAGCACACACAGTGCT
*
10736 AATAACAGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
10761 AAACAGAGAGC
1 AAACAGAGAGC
10772 GCGCTAGTGT
Statistics
Matches: 106, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
23 66 0.62
24 3 0.03
25 28 0.26
26 9 0.08
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:10704 original size:46 final size:48
Alignment explanation
Indices: 10645--10771 Score: 152
Period size: 46 Copynumber: 2.7 Consensus size: 48
10635 AGTGCTGGGC
* *
10645 AACAGAGAACACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * * **
10693 -A-AGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGTTAAT
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
*
10739 AACAGAGAGCACGAGAC-GTGCTAAACAGAGAGC
1 AACAGAGAGCAC-ACACAGTGCTAAACAGAGAGC
10772 GCGCTAGTGT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
46 38 0.58
47 2 0.03
48 24 0.36
49 2 0.03
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (48 bp):
AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Done.