Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000939.1 Kokia drynarioides strain JFW-HI SEQ_112097, 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: 18727
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5552 original size:32 final size:32
Alignment explanation
Indices: 5511--5579 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
5501 TCTCTGACCC
* *
5511 TTATAATGGTGAATTTAGAAATGAGAAATGAA
1 TTATAATGGTAAATTTAGAAATGAAAAATGAA
*
5543 TTATAATGGTAAATTTAGAAATGAAAAATGGA
1 TTATAATGGTAAATTTAGAAATGAAAAATGAA
5575 TTATA
1 TTATA
5580 TTTGTTCGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (32 bp):
TTATAATGGTAAATTTAGAAATGAAAAATGAA
Found at i:6745 original size:56 final size:54
Alignment explanation
Indices: 6618--6745 Score: 127
Period size: 55 Copynumber: 2.4 Consensus size: 54
6608 AGCTTTTNTT
* * *
6618 TGAGGTTAAGGAGAAA-TAAAAGTTTTGGGGAAAGCAAAAGGAAAAAAAAGTTA
1 TGAGGTTTAGGGGAAAGTAAAAGTTTTGGGGAAAGCAAAAGGAAAAAAAAATTA
* * * * *
6671 TAAGGGTTT-GGGGGAAGTAAAAGTTTTGGGAGGAAAG-TAAATGAAAAAAAAATTT
1 TGA-GGTTTAGGGGAAAGTAAAAGTTTT-GG-GGAAAGCAAAAGGAAAAAAAAATTA
6726 TGGAGGTTTAGGGGAAAGTA
1 T-GAGGTTTAGGGGAAAGTA
6746 TCAATTTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
53 7 0.12
54 14 0.24
55 22 0.37
56 16 0.27
ACGTcount: A:0.45, C:0.01, G:0.32, T:0.23
Consensus pattern (54 bp):
TGAGGTTTAGGGGAAAGTAAAAGTTTTGGGGAAAGCAAAAGGAAAAAAAAATTA
Found at i:7360 original size:24 final size:24
Alignment explanation
Indices: 7301--7361 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
7291 TAGACTAATA
* *
7301 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
* *
7325 --AGTTTAATTGAAACAATTAAAT
1 AGAGTTTAACTGAAACAAATAAAT
7347 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
7362 GATTATTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 18 0.60
24 12 0.40
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:9311 original size:24 final size:24
Alignment explanation
Indices: 9283--9339 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
9273 TAGACTAATA
* *
9283 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
9307 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
9331 AGAGTTTAA
1 AGAGTTTAA
9340 ATGAAAGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:9863 original size:6 final size:7
Alignment explanation
Indices: 9845--9880 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
9835 AATAAAATGA
*
9845 TAAAAAG
1 TAAAAAT
9852 TAAAAAT
1 TAAAAAT
9859 TAAAAAT
1 TAAAAAT
9866 TAAAAAT
1 TAAAAAT
9873 TAAAAAT
1 TAAAAAT
9880 T
1 T
9881 CTATATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (7 bp):
TAAAAAT
Found at i:11273 original size:115 final size:115
Alignment explanation
Indices: 11066--11287 Score: 426
Period size: 115 Copynumber: 1.9 Consensus size: 115
11056 TCTCTCATAG
11066 GTGATAGCCCCACTGATAACTTAGCAAGATTCACATCGGTTTGTTGACCCTCTAACATTTCCAAG
1 GTGATAGCCCCACTGATAACTTAGCAAGATTCACATCGGTTTGTTGACCCTCTAACATTTCCAAG
*
11131 GGGGTCTTCGTAACACTCCTCCGATCTACTGAGATAATGTTCATTATTGA
66 GGGGTCTTCGTAACACTCCTCCAATCTACTGAGATAATGTTCATTATTGA
*
11181 GTGATAGCCCCACTGATAACTTAGCAAGATTCACTTCGGTTTGTTGACCCTCTAACATTTCCAAG
1 GTGATAGCCCCACTGATAACTTAGCAAGATTCACATCGGTTTGTTGACCCTCTAACATTTCCAAG
11246 GGGGTCTTCGTAACACTCCTCCAATCTACTGAGATAATGTTC
66 GGGGTCTTCGTAACACTCCTCCAATCTACTGAGATAATGTTC
11288 TTCCAATAAT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 105 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (115 bp):
GTGATAGCCCCACTGATAACTTAGCAAGATTCACATCGGTTTGTTGACCCTCTAACATTTCCAAG
GGGGTCTTCGTAACACTCCTCCAATCTACTGAGATAATGTTCATTATTGA
Found at i:14707 original size:22 final size:22
Alignment explanation
Indices: 14682--14726 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
14672 AAGTCTAAGG
14682 CACATTCTCAACACTCAACATA
1 CACATTCTCAACACTCAACATA
14704 CACATTCTCAACACTCAACATA
1 CACATTCTCAACACTCAACATA
14726 C
1 C
14727 TATGGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (22 bp):
CACATTCTCAACACTCAACATA
Done.