Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013960.1 Corchorus olitorius cultivar O-4 contig13993, 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: 14178
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:7127 original size:19 final size:19
Alignment explanation
Indices: 7105--7146 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
7095 TTATATGGAA
*
7105 ATAAACATGGATGCAAATG
1 ATAAACATGGATCCAAATG
7124 ATAAACATGGATCCAAATG
1 ATAAACATGGATCCAAATG
7143 ATAA
1 ATAA
7147 TTTCTTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (19 bp):
ATAAACATGGATCCAAATG
Found at i:8353 original size:13 final size:13
Alignment explanation
Indices: 8337--8361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8327 GAAAAAAAAA
8337 AGAAAACAAAATG
1 AGAAAACAAAATG
8350 AGAAAACAAAAT
1 AGAAAACAAAAT
8362 TTTGGTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.12, T:0.08
Consensus pattern (13 bp):
AGAAAACAAAATG
Found at i:8679 original size:12 final size:12
Alignment explanation
Indices: 8647--8681 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
8637 TTGTTTTGTT
*
8647 TTGTTGCTATGG
1 TTGTTGCTGTGG
8659 TTGTTGCTGTGG
1 TTGTTGCTGTGG
8671 TTGTTGCTGTG
1 TTGTTGCTGTG
8682 ACAGTGTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.09, G:0.37, T:0.51
Consensus pattern (12 bp):
TTGTTGCTGTGG
Found at i:10504 original size:20 final size:20
Alignment explanation
Indices: 10461--10505 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10451 CCCACGAATT
** *
10461 AATGTAACGGGATATTCAAG
1 AATGTAACGGGATACGCAAA
*
10481 AATGTAGCGGGATACGCAAA
1 AATGTAACGGGATACGCAAA
10501 AATGT
1 AATGT
10506 GACTTGGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.22
Consensus pattern (20 bp):
AATGTAACGGGATACGCAAA
Found at i:12041 original size:202 final size:202
Alignment explanation
Indices: 11597--12207 Score: 1084
Period size: 202 Copynumber: 3.0 Consensus size: 202
11587 GCTTAATAAC
* **
11597 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGAAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTTTAGTGAATAA
* *
11662 GATACAACACATTATTATTATATATAAAACTATACAAAAAAAAAAGTAGTTGAACATTAGTAGTT
66 GATACAACACATTATTATTATATATAAAACTATAC-CAAAAAAAAGTAGTTGAACATTAGTGGTT
*
11727 GATGTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
130 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
*
11792 CCGAATTA
195 CCGATTTA
11800 TTTATCAATGGTGAATGTTATTAATTTTTTAAG-CTAAGATTACTAACAAAGTTTTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTTTAGTGAATAA
11864 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
11929 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
11994 CGATTTA
196 CGATTTA
12001 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTTTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTTTAGTGAATAA
* *
12066 GATACAACACATTACTATTATATATATAGAACTATACC-AAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTATTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGT
*
12130 TGATTTATTAAATTAAATTAGAACAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGA
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
12194 TCCGATTTA
194 TCCGATTTA
12203 TTTAT
1 TTTAT
12208 TATTAAGGAA
Statistics
Matches: 395, Mismatches: 10, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
201 131 0.33
202 138 0.35
203 117 0.30
204 9 0.02
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTTTAGTGAATAA
GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
CGATTTA
Found at i:12344 original size:21 final size:21
Alignment explanation
Indices: 12318--12383 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 21
12308 CCTAAGAATT
12318 TTATTAATGTAAGTATTTCAG
1 TTATTAATGTAAGTATTTCAG
* *
12339 TTATT-A--T-AGTATTACAT
1 TTATTAATGTAAGTATTTCAG
*
12356 TTAATTAATGTAAGTATTTTAG
1 TT-ATTAATGTAAGTATTTCAG
12378 TTATTA
1 TTATTA
12384 TATATATTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 10 0.29
18 4 0.11
19 1 0.03
20 1 0.03
21 10 0.29
22 9 0.26
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.52
Consensus pattern (21 bp):
TTATTAATGTAAGTATTTCAG
Found at i:12371 original size:39 final size:40
Alignment explanation
Indices: 12315--12395 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
12305 ATACCTAAGA
* *
12315 ATTTTATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
12354 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
12394 AT
1 AT
12396 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Done.