Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018372.1 Corchorus olitorius cultivar O-4 contig18405, 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: 51575
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:5018 original size:133 final size:133
Alignment explanation
Indices: 4780--5182 Score: 788
Period size: 133 Copynumber: 3.0 Consensus size: 133
4770 ACACAGAAAC
4780 AAAGATCACCACCATAAAAATTGTGAGAGGCAAACTTCATCAAGGTAGCATCAATATTGTCTATT
1 AAAGATCACCACCATAAAAATTGTGAGAGGCAAACTTCATCAAGGTAGCATCAATATTGTCTATT
4845 CCACAATGAAAAGTTAAGGATATACAGGAAGCAGTAAGTTGAAGGCAAACATCGTGTAGGAATAC
66 CCACAATGAAAAGTTAAGGATATACAGGAAGCAGTAAGTTGAAGGCAAACATCGTGTAGGAATAC
4910 TAA
131 TAA
4913 AAAGATCACCACCATAAAAATTGTGAGAGGCAAACTTCATCAAGGTAGCATCAATATTGTCTATT
1 AAAGATCACCACCATAAAAATTGTGAGAGGCAAACTTCATCAAGGTAGCATCAATATTGTCTATT
4978 CCACAATGAAAAGTTAAGGATATACAGGAAGCAGTAAGTTGAAGGCAAACATCGTGTAGGAATAC
66 CCACAATGAAAAGTTAAGGATATACAGGAAGCAGTAAGTTGAAGGCAAACATCGTGTAGGAATAC
5043 TAA
131 TAA
*
5046 AAAGATCACCACCATAAAAATTGTGAGAGGCAAACTTCATCAAGGTAGCATCAATATTTTCTATT
1 AAAGATCACCACCATAAAAATTGTGAGAGGCAAACTTCATCAAGGTAGCATCAATATTGTCTATT
*
5111 CCACAATGAAAAGTTAAGGATATACAGGAAGCAGTAAGTTGAAGGCAAACATCGTGTAAGAATAC
66 CCACAATGAAAAGTTAAGGATATACAGGAAGCAGTAAGTTGAAGGCAAACATCGTGTAGGAATAC
5176 TAA
131 TAA
5179 AAAG
1 AAAG
5183 GTTGAACCTG
Statistics
Matches: 268, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 268 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (133 bp):
AAAGATCACCACCATAAAAATTGTGAGAGGCAAACTTCATCAAGGTAGCATCAATATTGTCTATT
CCACAATGAAAAGTTAAGGATATACAGGAAGCAGTAAGTTGAAGGCAAACATCGTGTAGGAATAC
TAA
Found at i:6924 original size:20 final size:21
Alignment explanation
Indices: 6899--6939 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
6889 CCGTTTAATA
6899 ATTATTATATATA-TAATATT
1 ATTATTATATATATTAATATT
6919 ATTATTATATATATTAATATT
1 ATTATTATATATATTAATATT
6940 CGATCGGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATTATATATATTAATATT
Found at i:6927 original size:18 final size:18
Alignment explanation
Indices: 6894--6936 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6884 TTAGACCGTT
6894 TAATAATTATTATATATA
1 TAATAATTATTATATATA
6912 TAAT-ATTATTATTATATA
1 TAATAATTATTA-TATATA
*
6930 TATTAAT
1 TAATAAT
6937 ATTCGATCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATAATTATTATATATA
Found at i:6939 original size:18 final size:18
Alignment explanation
Indices: 6893--6939 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
6883 TTTAGACCGT
6893 TTAATAATTATTATATATA
1 TTAAT-ATTATTATATATA
*
6912 TAATATTATTATTATATATA
1 T--TAATATTATTATATATA
6932 TTAATATT
1 TTAATATT
6940 CGATCGGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 6 0.25
19 1 0.04
20 14 0.58
21 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATATTATTATATATA
Found at i:7554 original size:91 final size:91
Alignment explanation
Indices: 7406--7583 Score: 234
Period size: 91 Copynumber: 1.9 Consensus size: 91
7396 TTTATTTTTA
*
7406 TTTTTATTTTAAGGTTAAATTCAAAATTAATAATTTATTGTTATAGGATGTTAGAAATAAAATAC
1 TTTTTATTTTAAGGGTAAATTCAAAATTAATAA-TTATTGTTATAGGATGTTAGAAATAAAATAC
* *
7471 AAAACTAATTTCACTAAGTTTAGCCCCC
65 AAAACCAA-TTCACCAAGTTTAGCCCCC
* * * * *
7499 TTTTT-TTTTAAGGGTAAATTCCATAATTAATAA-TATTGTTATAGGGTTTTCGAAATAAAATAT
1 TTTTTATTTTAAGGGTAAATT-CAAAATTAATAATTATTGTTATAGGATGTTAGAAATAAAATAC
*
7562 ATAACCAATTCACCAAGTTTAG
65 AAAACCAATTCACCAAGTTTAG
7584 GCTAAATTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
90 13 0.17
91 32 0.43
92 14 0.19
93 16 0.21
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (91 bp):
TTTTTATTTTAAGGGTAAATTCAAAATTAATAATTATTGTTATAGGATGTTAGAAATAAAATACA
AAACCAATTCACCAAGTTTAGCCCCC
Found at i:21056 original size:2 final size:2
Alignment explanation
Indices: 21049--21083 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21039 CACCTGCTCT
21049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21084 TGGTAATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27246 original size:18 final size:19
Alignment explanation
Indices: 27205--27252 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
27195 TTAAAATGCC
27205 GTTAATGTTTATTCTGAAT
1 GTTAATGTTTATTCTGAAT
* *
27224 G-TAATTTTTATTCT-CAT
1 GTTAATGTTTATTCTGAAT
27241 GTTAATGTTTAT
1 GTTAATGTTTAT
27253 ATCCAATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.84
19 1 0.04
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (19 bp):
GTTAATGTTTATTCTGAAT
Found at i:35854 original size:2 final size:2
Alignment explanation
Indices: 35847--35888 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
35837 AGATTAACTT
35847 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
35889 CTTAAAACCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.