Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002712.1 Kokia drynarioides strain JFW-HI SEQ_115004, 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: 42391
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:3807 original size:20 final size:20
Alignment explanation
Indices: 3782--3820 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3772 TTAACAAACT
3782 TTTAATTATAATATAATATA
1 TTTAATTATAATATAATATA
* *
3802 TTTAATTTTTATATAATAT
1 TTTAATTATAATATAATAT
3821 TATGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATTATAATATAATATA
Found at i:4859 original size:3 final size:3
Alignment explanation
Indices: 4851--4875 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4841 TAACAGATCC
4851 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
4876 CCATGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:17038 original size:23 final size:22
Alignment explanation
Indices: 17002--17053 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
16992 ATATGGCATA
* *
17002 AAAATATTTA-TTTTATATTATT
1 AAAATATTCATTTTTATACTA-T
17024 AAAATATTCATTTTTTATACTAT
1 AAAATATTCA-TTTTTATACTAT
17047 AAAATAT
1 AAAATAT
17054 GAATATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 8 0.31
24 9 0.35
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
AAAATATTCATTTTTATACTAT
Found at i:25273 original size:26 final size:26
Alignment explanation
Indices: 25244--25302 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
25234 AAGAGTATCT
*
25244 TGTAATAATATAATTTATTTTAAATA
1 TGTAATAATATAATTTATTTAAAATA
25270 TGTAATAATATAATTTATTTAAAATA
1 TGTAATAATATAATTTATTTAAAATA
25296 TGTAATA
1 TGTAATA
25303 CTATTTTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
TGTAATAATATAATTTATTTAAAATA
Found at i:27738 original size:12 final size:11
Alignment explanation
Indices: 27721--27753 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
27711 TGAAAAAGAG
27721 TTTTTTTATTT
1 TTTTTTTATTT
27732 TTTTTTTATTT
1 TTTTTTTATTT
27743 TTTTTTT-TTT
1 TTTTTTTATTT
27753 T
1 T
27754 AATTTATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:27748 original size:16 final size:17
Alignment explanation
Indices: 27723--27758 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
27713 AAAAAGAGTT
*
27723 TTTTTATTTTTTTTTTA
1 TTTTTATTTTTTTTTAA
27740 TTTTT-TTTTTTTTTAA
1 TTTTTATTTTTTTTTAA
27756 TTT
1 TTT
27759 ATCTGCCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTTATTTTTTTTTAA
Found at i:27749 original size:15 final size:16
Alignment explanation
Indices: 27724--27760 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
27714 AAAAGAGTTT
27724 TTTTATTTTTTTTTTA
1 TTTTATTTTTTTTTTA
27740 TTTT-TTTTTTTTTTA
1 TTTTATTTTTTTTTTA
*
27755 ATTTAT
1 TTTTAT
27761 CTGCCTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTATTTTTTTTTTA
Found at i:28254 original size:70 final size:70
Alignment explanation
Indices: 28141--28281 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
28131 CTGATAGGGA
28141 GAAAATTTTATTTCATGTTCATGGTATTTGTTTTAAAAGGTAAAGAAATAAAATGGTGAAATATA
1 GAAAATTTTATTTCATGTTCATGGTATTTGTTTTAAAAGGTAAAGAAATAAAATGGTGAAATATA
28206 GATTT
66 GATTT
28211 GAAAATTTTATTTCATGTTCATGGTATTTGTTTTAAAAGGTAAAGAAATAAAATGGTGAAATATA
1 GAAAATTTTATTTCATGTTCATGGTATTTGTTTTAAAAGGTAAAGAAATAAAATGGTGAAATATA
28276 GATTT
66 GATTT
28281 G
1 G
28282 TTCTTCACTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.40
Consensus pattern (70 bp):
GAAAATTTTATTTCATGTTCATGGTATTTGTTTTAAAAGGTAAAGAAATAAAATGGTGAAATATA
GATTT
Found at i:31266 original size:24 final size:25
Alignment explanation
Indices: 31233--31285 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
31223 ATTGATTCGA
*
31233 TATATATTTGTACTTATTTTATACT
1 TATATATTTGTACATATTTTATACT
* *
31258 TATA-ATTTGTACATGTTTTGTACT
1 TATATATTTGTACATATTTTATACT
31282 TATA
1 TATA
31286 GTTGTAGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.57
Consensus pattern (25 bp):
TATATATTTGTACATATTTTATACT
Found at i:39244 original size:54 final size:54
Alignment explanation
Indices: 39179--39281 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
39169 TTTGATAGTG
39179 TTGAGCTTCCTGCTGGAGAAGAGACATCCATCCCATGGTTTGAAAATATGACCA
1 TTGAGCTTCCTGCTGGAGAAGAGACATCCATCCCATGGTTTGAAAATATGACCA
* * * *
39233 TTGAGGTTCCTGCTGGAGTAGAGGCGTCCATCCCATGGTTTGAAAATAT
1 TTGAGCTTCCTGCTGGAGAAGAGACATCCATCCCATGGTTTGAAAATAT
39282 TTCAGAGACT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (54 bp):
TTGAGCTTCCTGCTGGAGAAGAGACATCCATCCCATGGTTTGAAAATATGACCA
Done.