Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011832.1 Kokia drynarioides strain JFW-HI SEQ_126828, 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: 30757
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1523 original size:12 final size:12
Alignment explanation
Indices: 1506--1535 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1496 AAATCAACCA
*
1506 AATAATAATAGT
1 AATAATAATACT
1518 AATAATAATACT
1 AATAATAATACT
1530 AATAAT
1 AATAAT
1536 GGCAATGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (12 bp):
AATAATAATACT
Found at i:5693 original size:29 final size:32
Alignment explanation
Indices: 5661--5728 Score: 72
Period size: 34 Copynumber: 2.2 Consensus size: 32
5651 AAATCTATAC
* *
5661 TAAATATATACA-A-TTATT-AAATATTAAAA
1 TAAATATATAAATATTTATTAAAAAATTAAAA
5690 TAAAATAATATAAATATTTATTAAAAAATTAAAA
1 T-AAAT-ATATAAATATTTATTAAAAAATTAAAA
5724 -AAATA
1 TAAATA
5729 ATATGGGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
29 1 0.03
30 4 0.12
31 7 0.22
32 5 0.16
33 5 0.16
34 10 0.31
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (32 bp):
TAAATATATAAATATTTATTAAAAAATTAAAA
Found at i:10106 original size:31 final size:32
Alignment explanation
Indices: 10046--10111 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
10036 AAGTCTAATC
*
10046 GTAACTTCTAGTTCAGTAATATTTTATTGTAT
1 GTAACTTCTAATTCAGTAATATTTTATTGTAT
10078 GTAACTTCTAATTCAGTAATA-TTTATTGTAT
1 GTAACTTCTAATTCAGTAATATTTTATTGTAT
10109 GTA
1 GTA
10112 TATCGTCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
GTAACTTCTAATTCAGTAATATTTTATTGTAT
Found at i:11382 original size:31 final size:28
Alignment explanation
Indices: 11299--11383 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 28
11289 GAATGCTTCC
11299 TTTAACAGACTTAGCCACAAAGGCTTCCCT
1 TTTAACAGA-TT-GCCACAAAGGCTTCCCT
* * *
11329 TTTAGTATAGATAGCCATAAAGGCTTCCCTT
1 TTTA--ACAGATTGCCACAAAGGCTTCCC-T
11360 TTTAACAGAGTCTGCCACAAAGGC
1 TTTAACAGA-T-TGCCACAAAGGC
11384 CTTCTTACGA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
29 4 0.09
30 20 0.45
31 16 0.36
32 4 0.09
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (28 bp):
TTTAACAGATTGCCACAAAGGCTTCCCT
Found at i:19994 original size:42 final size:42
Alignment explanation
Indices: 19947--20033 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
19937 ACCACTTTGT
19947 AATGCTTCGACAACTTTGAAATGACCTGAGCACCTTGATCGA
1 AATGCTTCGACAACTTTGAAATGACCTGAGCACCTTGATCGA
19989 AATGCTTCGACAACTTTGAAATGACCTGAGCACCTTGATCGA
1 AATGCTTCGACAACTTTGAAATGACCTGAGCACCTTGATCGA
20031 AAT
1 AAT
20034 TTCCCTGGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (42 bp):
AATGCTTCGACAACTTTGAAATGACCTGAGCACCTTGATCGA
Found at i:20011 original size:19 final size:19
Alignment explanation
Indices: 19940--20011 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
19930 TCACCGCACC
*
19940 ACTTTGTAATGCTTCGACA
1 ACTTTGAAATGCTTCGACA
*
19959 ACTTTGAAATGACCT-GAGCA
1 ACTTTGAAATG-CTTCGA-CA
*
19979 CCTTGATCGAAATGCTTCGACA
1 ACTT--T-GAAATGCTTCGACA
20001 ACTTTGAAATG
1 ACTTTGAAATG
20012 ACCTGAGCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
19 18 0.43
20 8 0.19
22 8 0.19
23 8 0.19
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (19 bp):
ACTTTGAAATGCTTCGACA
Found at i:25244 original size:43 final size:43
Alignment explanation
Indices: 25192--25279 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
25182 TTTTGTGAAG
25192 TTTACCCATTTTGGGTGGTATTTAAACTTCTTTTTCTCCTTGT
1 TTTACCCATTTTGGGTGGTATTTAAACTTCTTTTTCTCCTTGT
25235 TTTACCCATTTTGGGTGGTATTTAAACTTCTTTTTCTCCTTGT
1 TTTACCCATTTTGGGTGGTATTTAAACTTCTTTTTCTCCTTGT
25278 TT
1 TT
25280 GACTTTTAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.55
Consensus pattern (43 bp):
TTTACCCATTTTGGGTGGTATTTAAACTTCTTTTTCTCCTTGT
Found at i:29933 original size:15 final size:14
Alignment explanation
Indices: 29908--29938 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
29898 TAAGTAGATG
29908 AAAAAATATAATAA
1 AAAAAATATAATAA
29922 AAAAAATAATAATAA
1 AAAAAAT-ATAATAA
29937 AA
1 AA
29939 CTTGTGGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAAATATAATAA
Found at i:30238 original size:10 final size:10
Alignment explanation
Indices: 30223--30248 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
30213 TGTGAAAAAA
30223 TATATATATT
1 TATATATATT
30233 TATATATATT
1 TATATATATT
30243 TATATA
1 TATATA
30249 GAAAAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATATATATT
Done.