Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016176.1 Corchorus capsularis cultivar CVL-1 contig16197, 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: 10805
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:1983 original size:20 final size:20
Alignment explanation
Indices: 1960--1998 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1950 GGAGATATAT
1960 ATATAATAATAATAATATTA
1 ATATAATAATAATAATATTA
* *
1980 ATATAATAGTAGTAATATT
1 ATATAATAATAATAATATT
1999 TTTTTTTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
ATATAATAATAATAATATTA
Found at i:2281 original size:23 final size:21
Alignment explanation
Indices: 2255--2302 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2245 TGGTAATAGT
*
2255 AATTACTGCTGCATCAAATAAAA
1 AATTACTG--GCATCAAAAAAAA
* *
2278 AATTCCTGGTATCAAAAAAAA
1 AATTACTGGCATCAAAAAAAA
2299 AATT
1 AATT
2303 CAAACTGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 15 0.68
23 7 0.32
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (21 bp):
AATTACTGGCATCAAAAAAAA
Found at i:2893 original size:38 final size:38
Alignment explanation
Indices: 2842--2917 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2832 GTCCCTGAAC
2842 TCTTGAAAATGACCAAATTAACCCTTCCATCTAAACTT
1 TCTTGAAAATGACCAAATTAACCCTTCCATCTAAACTT
2880 TCTTGAAAATGACCAAATTAACCCTTCCATCTAAACTT
1 TCTTGAAAATGACCAAATTAACCCTTCCATCTAAACTT
2918 CCGTCTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (38 bp):
TCTTGAAAATGACCAAATTAACCCTTCCATCTAAACTT
Found at i:2952 original size:13 final size:13
Alignment explanation
Indices: 2936--2960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2926 TTCGGCCGCG
2936 TCATCAGGCCACA
1 TCATCAGGCCACA
2949 TCATCAGGCCAC
1 TCATCAGGCCAC
2961 GTCACCATTT
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:0.28, C:0.40, G:0.16, T:0.16
Consensus pattern (13 bp):
TCATCAGGCCACA
Found at i:6007 original size:161 final size:162
Alignment explanation
Indices: 5736--6061 Score: 627
Period size: 161 Copynumber: 2.0 Consensus size: 162
5726 CAAATAGTAA
5736 CTTTTTCACAAAGTTCCCAAAATACCCTCAATCATCAACCCAAATAACGAAAAAATCCGAGTATG
1 CTTTTTCACAAAGTTCCCAAAATACCCTCAATCATCAACCCAAATAACGAAAAAATCCGAGTATG
* *
5801 AAAGTTCCAAAATACCCCTCCTCATTTATTCTTCAATTCATGAGATGATTTGGTTTGATTGGTTT
66 AAAGTTCCAAAATACCCCTCCTCATTTATTCTTCAATTCATGAGATGATTTGATTTGATTGATTT
5866 TTTGGTATTTTCATTTCCTCCTTTTATTGTTT
131 TTTGGTATTTTCATTTCCTCCTTTTATTGTTT
5898 CTTTTTCACAAAGTTCCCAAAATACCCTCAATCATCAACCCAAATAACGAAAAAA-CCGAGTATG
1 CTTTTTCACAAAGTTCCCAAAATACCCTCAATCATCAACCCAAATAACGAAAAAATCCGAGTATG
5962 AAAGTTCCAAAATACCCCTCCTCATTTATTCTTCAATTCATGAGATGATTTGATTTGATTGATTT
66 AAAGTTCCAAAATACCCCTCCTCATTTATTCTTCAATTCATGAGATGATTTGATTTGATTGATTT
6027 TTTGGTATTTTCATTTCCTCCTTTTATTGTTT
131 TTTGGTATTTTCATTTCCTCCTTTTATTGTTT
6059 CTT
1 CTT
6062 ATAATATATA
Statistics
Matches: 162, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
161 107 0.66
162 55 0.34
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (162 bp):
CTTTTTCACAAAGTTCCCAAAATACCCTCAATCATCAACCCAAATAACGAAAAAATCCGAGTATG
AAAGTTCCAAAATACCCCTCCTCATTTATTCTTCAATTCATGAGATGATTTGATTTGATTGATTT
TTTGGTATTTTCATTTCCTCCTTTTATTGTTT
Found at i:7965 original size:30 final size:30
Alignment explanation
Indices: 7918--7977 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
7908 TGATAAAATC
7918 AGTCAAACGTGTATTTACAGCAGGATTCAA
1 AGTCAAACGTGTATTTACAGCAGGATTCAA
* *
7948 AGTC-AACAGTGTGTTTACAGCGGGATTCAA
1 AGTCAAAC-GTGTATTTACAGCAGGATTCAA
7978 GATTGAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (30 bp):
AGTCAAACGTGTATTTACAGCAGGATTCAA
Found at i:9308 original size:39 final size:39
Alignment explanation
Indices: 9263--9355 Score: 150
Period size: 39 Copynumber: 2.4 Consensus size: 39
9253 AATCATGACG
*
9263 AGATCTGACAGTGAGAGCAGCAAATCTGCATCCTTTGGA
1 AGATCTGACAGTGAGAGCAGCAAATCTGCATCCTCTGGA
* *
9302 AGATCTGATAGTGAGAGCAGCAAATCTGCATCCTCTGGT
1 AGATCTGACAGTGAGAGCAGCAAATCTGCATCCTCTGGA
*
9341 AGATCAGACAGTGAG
1 AGATCTGACAGTGAG
9356 TGCAACGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (39 bp):
AGATCTGACAGTGAGAGCAGCAAATCTGCATCCTCTGGA
Found at i:9700 original size:83 final size:83
Alignment explanation
Indices: 9550--9707 Score: 208
Period size: 83 Copynumber: 1.9 Consensus size: 83
9540 CCGAGAAGTA
* * * * *
9550 GCCACTGCTAGAAGATGGGGCCTACCAAGGACCGATAATATGAAATCCTTGGATATCCTACGAGG
1 GCCACTGCCAGAAGATGGGGCATACCAAGGACCGATAATATAAAATCCTTGGATACCCAACGAGG
9615 TGGCGTAAAATCGATGTG
66 TGGCGTAAAATCGATGTG
** ** * *
9633 GCCACTGCCAGAAGATGGGGCATACCAAGGATTGATGTTATAAAATCTTTGGATACCCAACGGGG
1 GCCACTGCCAGAAGATGGGGCATACCAAGGACCGATAATATAAAATCCTTGGATACCCAACGAGG
*
9698 TGGTGTAAAA
66 TGGCGTAAAA
9708 ACCTTCGGAA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
83 63 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (83 bp):
GCCACTGCCAGAAGATGGGGCATACCAAGGACCGATAATATAAAATCCTTGGATACCCAACGAGG
TGGCGTAAAATCGATGTG
Found at i:10138 original size:79 final size:79
Alignment explanation
Indices: 10005--10161 Score: 269
Period size: 79 Copynumber: 2.0 Consensus size: 79
9995 TTGGACAAGG
* * **
10005 ATCGATTTGAATCATTAGTGTTTAAGTTGGGCGTTGCTAATCTTCACGTGCCAACTTGAGGAGGG
1 ATCGATTTGAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACGCACCAACTTGAGGAGGG
10070 AGTGATGAAATCAA
66 AGTGATGAAATCAA
*
10084 ATCGATTTGAATCATTAGTGTTCAAGTTGGGCGTTGCAAATTTTCACGCACCAACTTGAGGAGGG
1 ATCGATTTGAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACGCACCAACTTGAGGAGGG
10149 AGTGATGAAATCA
66 AGTGATGAAATCA
10162 GTCAAACCTG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (79 bp):
ATCGATTTGAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACGCACCAACTTGAGGAGGG
AGTGATGAAATCAA
Done.