Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008259.1 Kokia drynarioides strain JFW-HI SEQ_122924, 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: 40427
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:8825 original size:20 final size:20
Alignment explanation
Indices: 8800--8838 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
8790 CTGTTTCTCA
8800 GAAATACAA-ATTTGAGGAGG
1 GAAATA-AACATTTGAGGAGG
8820 GAAATAAAGCATTTGAGGA
1 GAAATAAA-CATTTGAGGA
8839 TCTTAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 6 0.35
21 9 0.53
ACGTcount: A:0.46, C:0.05, G:0.28, T:0.21
Consensus pattern (20 bp):
GAAATAAACATTTGAGGAGG
Found at i:10589 original size:5 final size:6
Alignment explanation
Indices: 10574--10598 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
10564 ACATTATATC
10574 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
10599 TTCCATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:14985 original size:27 final size:25
Alignment explanation
Indices: 14948--15003 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
14938 TTTTACTTAA
*
14948 AAAAAACTAAAATTAATTCTAAAAAAT
1 AAAAAACT-AAATTAAAT-TAAAAAAT
* *
14975 AAAAAATTAAATTAAATTAAAAGAT
1 AAAAAACTAAATTAAATTAAAAAAT
15000 AAAA
1 AAAA
15004 TGATGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.42
26 8 0.31
27 7 0.27
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAAAACTAAATTAAATTAAAAAAT
Found at i:16180 original size:6 final size:6
Alignment explanation
Indices: 16171--16197 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16161 GGCGATACCG
16171 ATCCCT ATCCCT ATCCCT ATCCCT ATC
1 ATCCCT ATCCCT ATCCCT ATCCCT ATC
16198 TCTGTCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (6 bp):
ATCCCT
Found at i:25708 original size:8 final size:8
Alignment explanation
Indices: 25697--25728 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
25687 GTTTATTAGT
25697 TTTATATA
1 TTTATATA
25705 TTTATATA
1 TTTATATA
25713 TTTATATA
1 TTTATATA
*
25721 TTTTTATA
1 TTTATATA
25729 ATTTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTATATA
Found at i:25739 original size:16 final size:17
Alignment explanation
Indices: 25697--25806 Score: 64
Period size: 16 Copynumber: 6.4 Consensus size: 17
25687 GTTTATTAGT
*
25697 TTTATATATTTATAT-A
1 TTTATATATTTTTATAA
25713 TTTATATATTTTTATAA
1 TTTATATATTTTTATAA
* *
25730 TTTTTA-ATTTTCATAAA
1 TTTATATATTTTTAT-AA
* * * *
25747 CTTATAAATTTTAATTA
1 TTTATATATTTTTATAA
* * *
25764 TTTA-AAAATATTATAA
1 TTTATATATTTTTATAA
*
25780 GCATTATATATTTTTATAAA
1 --TTTATATATTTTTAT-AA
25800 TTTATAT
1 TTTATAT
25807 TTCATATATT
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
16 29 0.41
17 16 0.23
18 16 0.23
19 7 0.10
20 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (17 bp):
TTTATATATTTTTATAA
Found at i:27978 original size:14 final size:14
Alignment explanation
Indices: 27934--27984 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
27924 CAGTCAAATG
27934 GAAAAGAAAATTAA
1 GAAAAGAAAATTAA
*
27948 -AAAA-AAAA-GAA
1 GAAAAGAAAATTAA
27959 TCGAAAAGAAAATTAA
1 --GAAAAGAAAATTAA
27975 GAAAAGAAAA
1 GAAAAGAAAA
27985 AAGATGAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
11 2 0.07
12 4 0.13
13 4 0.13
14 14 0.47
15 4 0.13
16 2 0.07
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.10
Consensus pattern (14 bp):
GAAAAGAAAATTAA
Found at i:28785 original size:18 final size:19
Alignment explanation
Indices: 28762--28805 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
28752 CCAAAATTTA
28762 ATTTTAATATTT-TTAT-AC
1 ATTTTAAT-TTTATTATCAC
28780 ATTTTAATTTTATTATGCAC
1 ATTTTAATTTTATTAT-CAC
28800 ATTTTA
1 ATTTTA
28806 TTACTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
20 8 0.35
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTAATTTTATTATCAC
Found at i:36319 original size:19 final size:19
Alignment explanation
Indices: 36292--36344 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
36282 ATCATTAAGG
* * *
36292 TTAAGTTAATTAGGTTTAA
1 TTAAATTAATTAAGATTAA
36311 TTAAATTAATTAAGATTAA
1 TTAAATTAATTAAGATTAA
*
36330 TTAGATTTAATTAAG
1 TTA-AATTAATTAAG
36345 GTATAAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (19 bp):
TTAAATTAATTAAGATTAA
Found at i:37073 original size:2 final size:2
Alignment explanation
Indices: 37066--37091 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37056 TTTTAATGTG
37066 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
37092 CACGAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40091 original size:15 final size:16
Alignment explanation
Indices: 40066--40096 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
40056 TACCCATAGA
40066 AAAGAGAAGAGAAGAG
1 AAAGAGAAGAGAAGAG
40082 AAAG-GAAGAGAAGAG
1 AAAGAGAAGAGAAGAG
40097 GAATGGGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (16 bp):
AAAGAGAAGAGAAGAG
Done.