Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001603.1 Kokia drynarioides strain JFW-HI SEQ_113229, 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: 5478
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Found at i:1835 original size:13 final size:13
Alignment explanation
Indices: 1819--1861 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1809 ATTTTCATAT
1819 TTTTTTAATTTAA
1 TTTTTTAATTTAA
1832 -TTTTTACATTTAA
1 TTTTTTA-ATTTAA
* *
1845 TTTTTTTATTTTA
1 TTTTTTAATTTAA
1858 TTTT
1 TTTT
1862 ATAGGTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 6 0.23
13 15 0.58
14 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTAATTTAA
Found at i:1837 original size:12 final size:13
Alignment explanation
Indices: 1820--1849 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1810 TTTTCATATT
1820 TTTTTA-ATTTAA
1 TTTTTACATTTAA
1832 TTTTTACATTTAA
1 TTTTTACATTTAA
1845 TTTTT
1 TTTTT
1850 TTATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTACATTTAA
Found at i:3469 original size:136 final size:136
Alignment explanation
Indices: 3296--3567 Score: 481
Period size: 136 Copynumber: 2.0 Consensus size: 136
3286 AACTTGTGCT
* * *
3296 TCGTGTAAGTGATAAAAAGATTACTCTTAAAGCACGTGATTTTGTTAGAGTCCTAAATGAGTATA
1 TCGTGTAAGTGATAAAAAAAATACTCTTAAAGCACGTGATTTTGTTAGAGTCATAAATGAGTATA
3361 ATGATGATAATTGTTTTGTTAATGTTAGTAACCATATGACTCAACACTTTTTCCAGGAAATCACT
66 ATGATGATAATTGTTTTGTTAATGTTAGTAACCATATGACTCAACACTTTTTCCAGGAAATCACT
3426 AATGAA
131 AATGAA
* *
3432 TCGTGTAGGTGATAAAAAAAATACTCTTAAAGCACGTGATTTTGTTAGAGTCATGAATGAGTATA
1 TCGTGTAAGTGATAAAAAAAATACTCTTAAAGCACGTGATTTTGTTAGAGTCATAAATGAGTATA
* *
3497 ATGATGATAATTGTTTTGTTAATGTTAGTAACCATGTGACTCAACACTTTTTGCAGGAAATCACT
66 ATGATGATAATTGTTTTGTTAATGTTAGTAACCATATGACTCAACACTTTTTCCAGGAAATCACT
3562 AATGAA
131 AATGAA
3568 AGCATGATGG
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 129 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (136 bp):
TCGTGTAAGTGATAAAAAAAATACTCTTAAAGCACGTGATTTTGTTAGAGTCATAAATGAGTATA
ATGATGATAATTGTTTTGTTAATGTTAGTAACCATATGACTCAACACTTTTTCCAGGAAATCACT
AATGAA
Found at i:5123 original size:32 final size:32
Alignment explanation
Indices: 5087--5167 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
5077 TGTTTAGAAA
* *
5087 AAAAAGAAAAAAAAAGTCGA-AAAGAAAAATTG
1 AAAAAGAAAAAAAAAATCGAGAAA-AAAAATAG
* *
5119 AAAAA-AAAAAAGAAAATTGAGGAAAAAAATAG
1 AAAAAGAAAAAA-AAAATCGAGAAAAAAAATAG
5151 AAAAAGAAAAAGAAAAA
1 AAAAAGAAAAA-AAAAA
5168 GACAAAAGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 6 0.15
32 23 0.56
33 11 0.27
34 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (32 bp):
AAAAAGAAAAAAAAAATCGAGAAAAAAAATAG
Found at i:5128 original size:13 final size:12
Alignment explanation
Indices: 5084--5134 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
5074 TATTGTTTAG
5084 AAAAAAAA-GAA
1 AAAAAAAATGAA
*
5095 AAAAAAAGTCGAA
1 AAAAAAAAT-GAA
*
5108 AAGAAAAATTGAA
1 AA-AAAAAATGAA
*
5121 AAAAAAAAAGAA
1 AAAAAAAATGAA
5133 AA
1 AA
5135 TTGAGGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 7 0.21
12 10 0.30
13 10 0.30
14 6 0.18
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:5131 original size:20 final size:20
Alignment explanation
Indices: 5106--5174 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
5096 AAAAAAGTCG
5106 AAAAGAAAAATTGAAAAAAA
1 AAAAGAAAAATTGAAAAAAA
*
5126 AAAAG-AAAATTGAGGAAAAA
1 AAAAGAAAAATTGA-AAAAAA
* *
5146 AATAGAAAAA--GAAAAAGA
1 AAAAGAAAAATTGAAAAAAA
5164 AAAAGACAAAA
1 AAAAGA-AAAA
5175 GTGTGTTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
18 9 0.22
19 14 0.34
20 14 0.34
21 4 0.10
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAATTGAAAAAAA
Found at i:5174 original size:7 final size:6
Alignment explanation
Indices: 5106--5175 Score: 52
Period size: 6 Copynumber: 10.8 Consensus size: 6
5096 AAAAAAGTCG
* * *
5106 AAAAGA AAAATTGA AAAAAA AAAAGA AAATTGAGG AAAA-A AATAGA AAAAGA
1 AAAAGA AAAA--GA AAAAGA AAAAGA AAA---AGA AAAAGA AAAAGA AAAAGA
5158 AAAAGA AAAAGA CAAAAG
1 AAAAGA AAAAGA -AAAAG
5176 TGTGTTTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
5 3 0.06
6 32 0.63
7 5 0.10
8 6 0.12
9 5 0.10
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (6 bp):
AAAAGA
Done.