Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006848.1 Kokia drynarioides strain JFW-HI SEQ_121447, 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: 20808
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1690 original size:31 final size:32
Alignment explanation
Indices: 1654--1758 Score: 185
Period size: 32 Copynumber: 3.3 Consensus size: 32
1644 TTTCATTTCA
1654 CAACAAGTCAC-AGAAAAACCATATTTCGTCG
1 CAACAAGTCACAAGAAAAACCATATTTCGTCG
1685 CAACAAGTCACAAGAAAAACCATATTTCGTCG
1 CAACAAGTCACAAGAAAAACCATATTTCGTCG
* *
1717 CAACAAGTCACGAGAAAAACCGTATTTCGTCG
1 CAACAAGTCACAAGAAAAACCATATTTCGTCG
1749 CAACAAGTCA
1 CAACAAGTCA
1759 AAAGCCAACA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 11 0.15
32 60 0.85
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (32 bp):
CAACAAGTCACAAGAAAAACCATATTTCGTCG
Found at i:3217 original size:30 final size:30
Alignment explanation
Indices: 3181--3239 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
3171 TGACAAAATC
3181 ATTTAGTCACTATATAAATTCATTGGAACG
1 ATTTAGTCACTATATAAATTCATTGGAACG
3211 ATTTAGTCACTATATAAATTCATTGGAAC
1 ATTTAGTCACTATATAAATTCATTGGAAC
3240 TACGTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (30 bp):
ATTTAGTCACTATATAAATTCATTGGAACG
Found at i:7612 original size:11 final size:10
Alignment explanation
Indices: 7596--7660 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 10
7586 TCGTTAGTTT
7596 TATTTTGTATG
1 TATTTT-TATG
7607 TATTTTTATG
1 TATTTTTATG
7617 ATATTATTATTAT-
1 -TA-T-TT-TTATG
7630 TATTTTGTATG
1 TATTTT-TATG
7641 TATTTTTATG
1 TATTTTTATG
*
7651 ATATTATTAT
1 -TATTTTTAT
7661 CATTTGTCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
9 1 0.02
10 13 0.28
11 23 0.50
12 3 0.07
13 2 0.04
14 4 0.09
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (10 bp):
TATTTTTATG
Found at i:7615 original size:17 final size:17
Alignment explanation
Indices: 7593--7649 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
7583 TACTCGTTAG
7593 TTTTATTTTGTATGTAT
1 TTTTATTTTGTATGTAT
*
7610 TTTTATGATAT-TAT-TAT
1 TTTTAT--TTTGTATGTAT
*
7627 TATTATTTTGTATGTAT
1 TTTTATTTTGTATGTAT
7644 TTTTAT
1 TTTTAT
7650 GATATTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 2 0.06
16 3 0.09
17 22 0.69
18 3 0.09
19 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (17 bp):
TTTTATTTTGTATGTAT
Found at i:7635 original size:34 final size:34
Alignment explanation
Indices: 7595--7660 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
7585 CTCGTTAGTT
7595 TTATTTTGTATGTATTTTTATGATATTATTATTA
1 TTATTTTGTATGTATTTTTATGATATTATTATTA
7629 TTATTTTGTATGTATTTTTATGATATTATTAT
1 TTATTTTGTATGTATTTTTATGATATTATTAT
7661 CATTTGTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (34 bp):
TTATTTTGTATGTATTTTTATGATATTATTATTA
Found at i:10406 original size:16 final size:17
Alignment explanation
Indices: 10374--10406 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10364 CAAAAATGAC
*
10374 TTCAAACTTTGAAATAA
1 TTCAAACTTTAAAATAA
10391 TTCAAAC-TTAAAATAA
1 TTCAAACTTTAAAATAA
10407 ATGTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (17 bp):
TTCAAACTTTAAAATAA
Found at i:11688 original size:61 final size:58
Alignment explanation
Indices: 11583--11715 Score: 185
Period size: 61 Copynumber: 2.2 Consensus size: 58
11573 TACACTAGTA
* *
11583 GTCACCCAACTATTAGTGAATTCTTTTTTGGTCACCCAATTATGAAAAGTTAAAAAATG
1 GTCA-CCAACTATTAGTAAATTCTTTTTTGGTCACCCAACTATGAAAAGTTAAAAAATG
* * *
11642 GTCACCTAACTATTAGTAAATTTATTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATT
1 GTCACC-AACTATTAGTAAA-TT-CTTTTTTGGTCACCCAACTATGAAAAGTTAAAAAATG
11703 GTCACCAACTATT
1 GTCACCAACTATT
11716 CAATTTTGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
58 2 0.03
59 16 0.24
60 9 0.14
61 39 0.59
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (58 bp):
GTCACCAACTATTAGTAAATTCTTTTTTGGTCACCCAACTATGAAAAGTTAAAAAATG
Found at i:19118 original size:17 final size:17
Alignment explanation
Indices: 19096--19134 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
19086 CTCCACCTTG
* *
19096 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCGACGA
19113 ACAAGAACTCTCGACGA
1 ACAAGAACTCTCGACGA
19130 ACAAG
1 ACAAG
19135 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCGACGA
Done.