Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012669.1 Kokia drynarioides strain JFW-HI SEQ_127680, 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: 25224
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Warning! 103 characters in sequence are not A, C, G, or T
Found at i:2069 original size:6 final size:6
Alignment explanation
Indices: 2058--2099 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
2048 AGGAAGGTCT
*
2058 GGTGGG GGTGGG GTTGGG GGTGGG GGTGGG GGTGGG GGTGGG
1 GGTGGG GGTGGG GGTGGG GGTGGG GGTGGG GGTGGG GGTGGG
2100 AGTATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (6 bp):
GGTGGG
Found at i:2298 original size:51 final size:51
Alignment explanation
Indices: 2207--2316 Score: 123
Period size: 51 Copynumber: 2.2 Consensus size: 51
2197 CATTTTTTTG
* * * *
2207 AATTTTTTAAAATTAAGATCAAATTGAAATTATTTATAAAATTTTAGGGTT
1 AATTTTATAAAATTAAGATCAAATTGAAATAATTTATAAAAGTTGAGGGTT
* * * *
2258 AATTTTATAAAATTATGATTAAATTGATATAATATT-TAAAAGTTGGGGGTT
1 AATTTTATAAAATTAAGATCAAATTGAAATAAT-TTATAAAAGTTGAGGGTT
*
2309 AAATTTAT
1 AATTTTAT
2317 CACACCTCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 47 0.96
52 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.12, T:0.45
Consensus pattern (51 bp):
AATTTTATAAAATTAAGATCAAATTGAAATAATTTATAAAAGTTGAGGGTT
Found at i:12180 original size:18 final size:19
Alignment explanation
Indices: 12129--12181 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
12119 TTTATTTTTT
*
12129 AAAAA-ATTTGAAAATATA
1 AAAAATATTTAAAAATATA
12147 AAAAATATTTCAAAAATA-A
1 AAAAATATTT-AAAAATATA
12166 AAAAATATTATAAAAA
1 AAAAATATT-TAAAAA
12182 ATTCGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 5 0.16
19 19 0.61
20 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATATTTAAAAATATA
Found at i:12181 original size:20 final size:20
Alignment explanation
Indices: 12139--12183 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
12129 AAAAAATTTG
*
12139 AAAATATAAAAAATATTTCA
1 AAAATATAAAAAATATTTAA
12159 AAAATA-AAAAAATATTATAA
1 AAAATATAAAAAATATT-TAA
12179 AAAAT
1 AAAAT
12184 TCGAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATATAAAAAATATTTAA
Found at i:12498 original size:62 final size:61
Alignment explanation
Indices: 12425--12604 Score: 204
Period size: 62 Copynumber: 2.9 Consensus size: 61
12415 TTATCATAAA
* *
12425 AAAAAGAGGTGTCGGCCATGACATGGTCAACACAAAAAAAAATTCGAA-TTTTTTA-TCCGAC
1 AAAAAGGGGTGTCGGCCATGACATGGTCAACAC--AAAAAAATTCGAATTTTTTTATTCAGAC
* * *
12486 AAAAAGGGGGTGTCGGCCATGACATGGTCAACACTAAAAAATTTGAATTTTTTTTATTCAGAT
1 AAAAA-GGGGTGTCGGCCATGACATGGTCAACACAAAAAAATTCGAA-TTTTTTTATTCAGAC
* * * *
12549 AAAAAGGGGTGTCGGCCAT-ATAATGGACAACATCAAAAAATTTTGAATTTTTTTAT
1 AAAAAGGGGTGTCGGCCATGA-CATGGTCAACA-CAAAAAAATTCGAATTTTTTTAT
12605 CTAAAAAAAG
Statistics
Matches: 104, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
60 11 0.11
61 6 0.06
62 66 0.63
63 21 0.20
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (61 bp):
AAAAAGGGGTGTCGGCCATGACATGGTCAACACAAAAAAATTCGAATTTTTTTATTCAGAC
Found at i:19358 original size:29 final size:29
Alignment explanation
Indices: 19326--19381 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
19316 TAATATCATT
*
19326 TTATATTGA-TAAATTATATAAATAAATAA
1 TTATATTGATTAAA-TATAAAAATAAATAA
*
19355 TTATATTTATTAAATATAAAAATAAAT
1 TTATATTGATTAAATATAAAAATAAAT
19382 TAATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (29 bp):
TTATATTGATTAAATATAAAAATAAATAA
Found at i:19396 original size:29 final size:30
Alignment explanation
Indices: 19335--19396 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
19325 TTTATATTGA
* *
19335 TAAATTATATAAATAAATAATTATATTTAT
1 TAAATTATAAAAATAAATAATAATATTTAT
*
19365 TAAA-TATAAAAATAAATTAATAAT-TTTTT
1 TAAATTATAAAAATAAA-TAATAATATTTAT
19394 TAA
1 TAA
19397 TTCGTATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAAATTATAAAAATAAATAATAATATTTAT
Found at i:22671 original size:30 final size:29
Alignment explanation
Indices: 22613--22676 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
22603 TTTTCAAAAA
* * *
22613 TAAAAAATTTGGTCTCTGTATTTCTATTT
1 TAAAAAATTTAGTCTCTCTATTTATATTT
*
22642 TAAAAAATTTAGTCTCTACTTTTTATATTT
1 TAAAAAATTTAGTCTCT-CTATTTATATTT
*
22672 GAAAA
1 TAAAA
22677 TTTAAATTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.48
Consensus pattern (29 bp):
TAAAAAATTTAGTCTCTCTATTTATATTT
Done.