Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017817.1 Corchorus olitorius cultivar O-4 contig17850, 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: 13856
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2847 original size:22 final size:22
Alignment explanation
Indices: 2821--2876 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
2811 TTCCGGTGGC
2821 GGTGGCGGTGGCAGTCATGGTG
1 GGTGGCGGTGGCAGTCATGGTG
*
2843 GGTGGCGGTGGCAGTTATGGTG
1 GGTGGCGGTGGCAGTCATGGTG
*
2865 GGTGGCTGTGGC
1 GGTGGCGGTGGC
2877 GTTGACAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.07, C:0.12, G:0.55, T:0.25
Consensus pattern (22 bp):
GGTGGCGGTGGCAGTCATGGTG
Found at i:2887 original size:22 final size:22
Alignment explanation
Indices: 2821--2887 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
2811 TTCCGGTGGC
* **
2821 GGTGGCGGTGGCAGTCATGGTG
1 GGTGGCGGTGGCAGTTACAGTG
**
2843 GGTGGCGGTGGCAGTTATGGTG
1 GGTGGCGGTGGCAGTTACAGTG
*
2865 GGTGGCTGTGGC-GTTGACAGTG
1 GGTGGCGGTGGCAGTT-ACAGTG
2887 G
1 G
2888 TTCCATGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 3 0.08
22 37 0.93
ACGTcount: A:0.09, C:0.12, G:0.54, T:0.25
Consensus pattern (22 bp):
GGTGGCGGTGGCAGTTACAGTG
Found at i:4985 original size:20 final size:20
Alignment explanation
Indices: 4960--4999 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4950 CAAAACTCGT
4960 ACTTTTATATATAGTATAGA
1 ACTTTTATATATAGTATAGA
4980 ACTTTTATATATAGTATAGA
1 ACTTTTATATATAGTATAGA
5000 TAAGTTCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (20 bp):
ACTTTTATATATAGTATAGA
Found at i:6365 original size:18 final size:18
Alignment explanation
Indices: 6333--6367 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6323 TTCATGTTAA
*
6333 TAAACCAATTACAAATGT
1 TAAACCAACTACAAATGT
*
6351 TAAACCAACTGCAAATG
1 TAAACCAACTACAAATG
6368 ATGTTTCCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.23
Consensus pattern (18 bp):
TAAACCAACTACAAATGT
Found at i:6928 original size:27 final size:26
Alignment explanation
Indices: 6874--6934 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
6864 CTAAATTTTC
6874 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
6902 ATTATTTAATAATGGCAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
6929 A-TATTT
1 ATTATTT
6935 GAAAAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:7306 original size:15 final size:16
Alignment explanation
Indices: 7271--7310 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
7261 TAAAATTTAA
7271 TCATATAATTATTGAT
1 TCATATAATTATTGAT
7287 TCATATAATTATTG-T
1 TCATATAATTATTGAT
7302 TCATATAAT
1 TCATATAAT
7311 GAAGTTTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (16 bp):
TCATATAATTATTGAT
Found at i:7609 original size:16 final size:16
Alignment explanation
Indices: 7585--7632 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
7575 ACAACTCTAC
*
7585 TTATAATTAATTTAAA
1 TTATTATTAATTTAAA
7601 TTATTATTAATTT-AA
1 TTATTATTAATTTAAA
7616 TT-TTCATTTAATTTAAA
1 TTATT-A-TTAATTTAAA
7633 CGCGATAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.07
15 5 0.18
16 19 0.68
17 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTATTAATTTAAA
Found at i:10226 original size:16 final size:16
Alignment explanation
Indices: 10207--10238 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
10197 TTACCTTTTG
10207 TATTTGACAAGAATAA
1 TATTTGACAAGAATAA
10223 TATTTGACAAGAATAA
1 TATTTGACAAGAATAA
10239 GTGATTACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (16 bp):
TATTTGACAAGAATAA
Found at i:10412 original size:22 final size:22
Alignment explanation
Indices: 10386--10428 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
10376 ATATGGAAAA
10386 TTTTTATTGGTTTTATAAGTGT
1 TTTTTATTGGTTTTATAAGTGT
* *
10408 TTTTTTTTGGTTTTGTAAGTG
1 TTTTTATTGGTTTTATAAGTG
10429 ATTCACTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.65
Consensus pattern (22 bp):
TTTTTATTGGTTTTATAAGTGT
Found at i:13822 original size:209 final size:209
Alignment explanation
Indices: 13462--13856 Score: 781
Period size: 209 Copynumber: 1.9 Consensus size: 209
13452 AACTTTCAAT
13462 CCGGAGATCCATTCGAGTCAATTCAAGTGTCCGTGGAAAGAGGATTCAAGGCTCTACAACTTTCA
1 CCGGAGATCCATTCGAGTCAATTCAAGTGTCCGTGGAAAGAGGATTCAAGGCTCTACAACTTTCA
*
13527 TTAAGGACTTGGAGGCTAATTTTGACTTGAAGAGAGTGAAAATGTTGAAGAAAGTTGAAGATCGG
66 TTAAGGACTTGGAGGCTAATTTTGACTTGAAGAGAGTGAAAACGTTGAAGAAAGTTGAAGATCGG
13592 TGAAATCCTGACGAACTCCAAGTTGGGGCCAACTTACCCCTCAAGTTGGGGCCAGGTTGAAACCC
131 TGAAATCCTGACGAACTCCAAGTTGGGGCCAACTTACCCCTCAAGTTGGGGCCAGGTTGAAACCC
13657 TGAAGTTTGCGCAA
196 TGAAGTTTGCGCAA
13671 CCGGAGATCCATTCGAGTCAATTCAAGTGTCCGTGGAAAGAGGATTCAAGGCTCTACAACTTTCA
1 CCGGAGATCCATTCGAGTCAATTCAAGTGTCCGTGGAAAGAGGATTCAAGGCTCTACAACTTTCA
13736 TTAAGGACTTGGAGGCTAATTTTGACTTGAAGAGAGTGAAAACGTTGAAGAAAGTTGAAGATCGG
66 TTAAGGACTTGGAGGCTAATTTTGACTTGAAGAGAGTGAAAACGTTGAAGAAAGTTGAAGATCGG
13801 TGAAATCCTGACGAACTCCAAGTTGGGGCCAACTTACCCCTCAAGTTGGGGCCAGG
131 TGAAATCCTGACGAACTCCAAGTTGGGGCCAACTTACCCCTCAAGTTGGGGCCAGG
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
209 185 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (209 bp):
CCGGAGATCCATTCGAGTCAATTCAAGTGTCCGTGGAAAGAGGATTCAAGGCTCTACAACTTTCA
TTAAGGACTTGGAGGCTAATTTTGACTTGAAGAGAGTGAAAACGTTGAAGAAAGTTGAAGATCGG
TGAAATCCTGACGAACTCCAAGTTGGGGCCAACTTACCCCTCAAGTTGGGGCCAGGTTGAAACCC
TGAAGTTTGCGCAA
Done.