Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010643.1 Kokia drynarioides strain JFW-HI SEQ_125586, 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: 11554
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Found at i:3836 original size:14 final size:14
Alignment explanation
Indices: 3817--3844 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3807 TGGTTGATGA
3817 TATTGTTGGCACAG
1 TATTGTTGGCACAG
3831 TATTGTTGGCACAG
1 TATTGTTGGCACAG
3845 GTATCTTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (14 bp):
TATTGTTGGCACAG
Found at i:10404 original size:21 final size:20
Alignment explanation
Indices: 10374--10415 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
10364 GCACATTCGG
10374 GGGTAAAAATGGAATTTTTA
1 GGGTAAAAATGGAATTTTTA
*
10394 GGGTCAAAAATGGATTTTTTA
1 GGGT-AAAAATGGAATTTTTA
10415 G
1 G
10416 ACATCCAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (20 bp):
GGGTAAAAATGGAATTTTTA
Found at i:10550 original size:30 final size:30
Alignment explanation
Indices: 10438--10895 Score: 496
Period size: 30 Copynumber: 15.4 Consensus size: 30
10428 AAAATGATAT
*
10438 TTTTTGTAAGTTTCGAGGTCAAAAATGGAA
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAA
* *
10468 -ATTTGGAAGTTTTGAGGTC-AAAATGGAA
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAA
*
10496 TTTTTGCAAG-TTCGAGGATC-AAAATGGAA
1 TTTTTGGAAGTTTCGAGG-TCAAAAATGGAA
10525 TTTTTGGAAGTTTCGAGGTCAAAAATGGAA
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAA
10555 TTTTTGGAAG-TTCG-GCTGTC-AAAATGGAA
1 TTTTTGGAAGTTTCGAG--GTCAAAAATGGAA
* * *
10584 TTTTTGGAAATTTTGAGGTTAAAAATGGAA
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAA
* * *
10614 TTTTTGGAAGTTTTGGGGTAAAAAATGGAA
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAA
* *
10644 TTTTTGGAAGCTTTAG-GGTAAAAAATGGAA
1 TTTTTGGAAG-TTTCGAGGTCAAAAATGGAA
* *
10674 TTTTTGGAAGTTTAGAGGGT-AAATATGGAA
1 TTTTTGGAAGTTTCGA-GGTCAAAAATGGAA
**
10704 TTTTTGGAAGTTTTAAGGTCAAAAATGGAA
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAA
*
10734 TTTTTGGAAGTTTCG-GAGTAAAAAATGGAA
1 TTTTTGGAAGTTTCGAG-GTCAAAAATGGAA
* * *
10764 TTTTTTGAAG-TTCGGGGGT-AAAAATGGAT
1 TTTTTGGAAGTTTC-GAGGTCAAAAATGGAA
*
10793 TTTTTGGAAGTTTCAAGGGT-AAAAATGGAA
1 TTTTTGGAAGTTTCGA-GGTCAAAAATGGAA
*
10823 TTTTTGGAAGGTTCGAGGTCAAAAATGGAA
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAA
* *
10853 TTTTTTGAAG-TCCGAGGGT-AAAAATGGAA
1 TTTTTGGAAGTTTCGA-GGTCAAAAATGGAA
*
10882 ATTTTGGACAGTTT
1 TTTTTGGA-AGTTT
10896 AGGAACCTCT
Statistics
Matches: 372, Mismatches: 34, Indels: 43
0.83 0.08 0.10
Matches are distributed among these distances:
28 16 0.04
29 122 0.33
30 224 0.60
31 10 0.03
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.35
Consensus pattern (30 bp):
TTTTTGGAAGTTTCGAGGTCAAAAATGGAA
Found at i:10644 original size:89 final size:86
Alignment explanation
Indices: 10438--10895 Score: 515
Period size: 89 Copynumber: 5.2 Consensus size: 86
10428 AAAATGATAT
* * *
10438 TTTTTGTAAGTTTCGAGGTCAAAAATGGAA-ATTTGGAAGTTTTGAGGTCAAAATGGAATTTTTG
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG-TTCG-GGTCAAAATGGAATTTTTG
* * *
10502 CAAGTTCGAGGATCAAAATGGAA
64 GAAGTTCGAGGGTAAAAATGGAA
10525 TTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGCTGTCAAAATGGAATTTTTG
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGG--GTCAAAATGGAATTTTTG
* * *
10590 GAAATTTTGAGGTTAAAAATGGAA
64 G-AAGTTCGAGGGTAAAAATGGAA
* * * * *
10614 TTTTTGGAAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGCTTTAGGGTAAAAAATGGAATTTTT
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG--TTCGGGT-CAAAATGGAATTTTT
* *
10679 GGAAGTTTAGAGGGTAAATATGGAA
63 GGAAG-TTCGAGGGTAAAAATGGAA
** *
10704 TTTTTGGAAGTTTTAAGGTCAAAAATGGAATTTTTGGAAGTTTCGGAGTAAAAAATGGAATTTTT
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG-TTCGG-GT-CAAAATGGAATTTTT
* * *
10769 TGAAGTTCGGGGGTAAAAATGGAT
63 GGAAGTTCGAGGGTAAAAATGGAA
*
10793 TTTTTGGAAGTTTCAAGGGT-AAAAATGGAATTTTTGGAAGGTTCGAGGTCAAAAATGGAATTTT
1 TTTTTGGAAGTTTCGA-GGTCAAAAATGGAATTTTTGGAA-GTTCG-GGTC-AAAATGGAATTTT
* *
10857 TTGAAGTCCGAGGGTAAAAATGGAA
62 TGGAAGTTCGAGGGTAAAAATGGAA
*
10882 ATTTTGGACAGTTT
1 TTTTTGGA-AGTTT
10896 AGGAACCTCT
Statistics
Matches: 325, Mismatches: 32, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
86 1 0.00
87 32 0.10
88 26 0.08
89 161 0.50
90 101 0.31
91 4 0.01
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.35
Consensus pattern (86 bp):
TTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGTCAAAATGGAATTTTTGGA
AGTTCGAGGGTAAAAATGGAA
Done.