Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005657.1 Kokia drynarioides strain JFW-HI SEQ_119827, 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: 9313
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:99 original size:3 final size:3
Alignment explanation
Indices: 93--125 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
83 TACTTTTATT
93 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
126 TACTTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5251 original size:18 final size:18
Alignment explanation
Indices: 5228--5265 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5218 CAAGCTTGAG
5228 GAAGAAGAAGCA-GAGAAA
1 GAAGAAGAA-CATGAGAAA
*
5246 GAAGAAGGACATGAGAAA
1 GAAGAAGAACATGAGAAA
5264 GA
1 GA
5266 GAATTAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.58, C:0.05, G:0.34, T:0.03
Consensus pattern (18 bp):
GAAGAAGAACATGAGAAA
Found at i:5759 original size:18 final size:18
Alignment explanation
Indices: 5733--5769 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5723 ATGCATCTTA
5733 TTTAGTTGTCATTACATT
1 TTTAGTTGTCATTACATT
* *
5751 TTTATTTGTCATTGCATT
1 TTTAGTTGTCATTACATT
5769 T
1 T
5770 CATTTATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (18 bp):
TTTAGTTGTCATTACATT
Found at i:5808 original size:17 final size:17
Alignment explanation
Indices: 5762--5804 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
5752 TTATTTGTCA
5762 TTGCATTTCATTTATTAG
1 TTGCATTTCA-TTATTAG
5780 -TGCATTTTCATTA-TAG
1 TTGCA-TTTCATTATTAG
5796 TTGCATTTC
1 TTGCATTTC
5805 CATTCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (17 bp):
TTGCATTTCATTATTAG
Found at i:8755 original size:41 final size:41
Alignment explanation
Indices: 8689--9014 Score: 299
Period size: 41 Copynumber: 8.0 Consensus size: 41
8679 CATTAAACAT
* *
8689 AAGCACTGTTAAAGGTCAGAGCAATAGCGACGCTTATGAGA
1 AAGCGCTGCTAAAGGTCAGAGCAATAGCGACGCTTATGAGA
* * * *
8730 AAGCGCTGCTAAAGGTCATATCAATACCGACGCTTAT-AGGC
1 AAGCGCTGCTAAAGGTCAGAGCAATAGCGACGCTTATGA-GA
* ** * ** **
8771 AAGCACCACTAAAGGTCAGATCAATAGCGGTGCTTATGATC
1 AAGCGCTGCTAAAGGTCAGAGCAATAGCGACGCTTATGAGA
* * ** *
8812 AAGCGCCGCTAAAGGTCAGAGCAATAACGGTGCTTATGAGG
1 AAGCGCTGCTAAAGGTCAGAGCAATAGCGACGCTTATGAGA
* *
8853 AAGCG-TCGCTAAAGGTCAGATCAATAGCG-GGCTTATGAGA
1 AAGCGCT-GCTAAAGGTCAGAGCAATAGCGACGCTTATGAGA
* * *
8893 AAGCG-TCGCTAAAGGTCATATCAATAGCGACGCTTATGGGA
1 AAGCGCT-GCTAAAGGTCAGAGCAATAGCGACGCTTATGAGA
* *
8934 AAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGTA-A
1 AAGCGCTGCTAAAGGTCAGAGCAATAGCGACGCTTATG-AGA
* * *
8975 AAGCGC--C-AAAGGTCAGTGCATTAGCGACGCTTATGTGA
1 AAGCGCTGCTAAAGGTCAGAGCAATAGCGACGCTTATGAGA
9013 AA
1 AA
9015 AACGCCGTTA
Statistics
Matches: 241, Mismatches: 37, Indels: 17
0.82 0.13 0.06
Matches are distributed among these distances:
38 28 0.12
39 1 0.00
40 38 0.16
41 173 0.72
42 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (41 bp):
AAGCGCTGCTAAAGGTCAGAGCAATAGCGACGCTTATGAGA
Found at i:8826 original size:82 final size:81
Alignment explanation
Indices: 8698--8981 Score: 356
Period size: 82 Copynumber: 3.5 Consensus size: 81
8688 TAAGCACTGT
* * *
8698 TAAAGGTCAGAGCAATAGCGACGCTTATGAGAAAGCGCTGCTAAAGGTCATATCAATACCGACGC
1 TAAAGGTCAGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCATATCAATAACGACGC
* *
8763 TTATAGGCAAGCACCAC
66 TTATAGG-AAGCGCCGC
* * ** * * **
8780 TAAAGGTCAGATCAATAGCGGTGCTTATGATCAAGCGCCGCTAAAGGTCAGAGCAATAACGGTGC
1 TAAAGGTCAGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCATATCAATAACGACGC
*
8845 TTATGAGGAAGCGTCGC
66 TTAT-AGGAAGCGCCGC
* * *
8862 TAAAGGTCAGATCAATAGCGG-GCTTATGAGAAAGCGTCGCTAAAGGTCATATCAATAGCGACGC
1 TAAAGGTCAGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCATATCAATAACGACGC
*
8926 TTATGGGAAAGCGCCGC
66 TTATAGG-AAGCGCCGC
8943 TAAAGGTCAGAGCAATAGCGGCGCTTATGTA-AAAGCGCC
1 TAAAGGTCAGAGCAATAGCGGCGCTTATG-AGAAAGCGCC
8982 AAAGGTCAGT
Statistics
Matches: 172, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 2 0.01
81 67 0.39
82 99 0.58
83 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (81 bp):
TAAAGGTCAGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCATATCAATAACGACGC
TTATAGGAAGCGCCGC
Done.