Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017298.1 Corchorus olitorius cultivar O-4 contig17331, 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: 27665
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:6146 original size:19 final size:18
Alignment explanation
Indices: 6101--6152 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
6091 CATAAGTCTT
*
6101 TTAATAATAATTATTCAA
1 TTAATAATTATTATTCAA
* *
6119 TAAAATAATTATTATTTAA
1 T-TAATAATTATTATTCAA
6138 TTAATTAATTTATTA
1 TTAA-TAA-TTATTA
6153 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 3 0.11
19 18 0.67
20 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATAATTATTATTCAA
Found at i:6769 original size:13 final size:15
Alignment explanation
Indices: 6738--6770 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6728 TGTTTTCTAG
6738 TTTAATTGTTTACTT
1 TTTAATTGTTTACTT
6753 TTTAATTG-TTA-TT
1 TTTAATTGTTTACTT
6766 TTTAA
1 TTTAA
6771 ACCCCTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 3 0.17
15 8 0.44
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTAATTGTTTACTT
Found at i:9015 original size:154 final size:154
Alignment explanation
Indices: 8735--9044 Score: 602
Period size: 154 Copynumber: 2.0 Consensus size: 154
8725 TAATCAATGC
8735 CAAAGGCATCCACTGCATTAACCTCTCACGGCAACAAAGATGGCATTGTCATTCCTAGCTATTCA
1 CAAAGGCATCCACTGCATTAACCTCTCACGGCAACAAAGATGGCATTGTCATTCCTAGCTATTCA
8800 TGGAGTCGCCCTCAGCAAAATTGGTTATTTATTTCCTTATTTCTTCTTTTTACCTTCATATTTTT
66 TGGAGTCGCCCTCAGCAAAATTGGTTATTTATTTCCTTATTTCTTCTTTTTACCTTCATATTTTT
*
8865 GTGTTCATATTCTTCTAATCTTAT
131 GTGCTCATATTCTTCTAATCTTAT
*
8889 CAAAGGCATCGACTGCATTAACCTCTCACGGCAACAAAGATGGCATTGTCATTCCTAGCTATTCA
1 CAAAGGCATCCACTGCATTAACCTCTCACGGCAACAAAGATGGCATTGTCATTCCTAGCTATTCA
8954 TGGAGTCGCCCTCAGCAAAATTGGTTATTTATTTCCTTATTTCTTCTTTTTACCTTCATATTTTT
66 TGGAGTCGCCCTCAGCAAAATTGGTTATTTATTTCCTTATTTCTTCTTTTTACCTTCATATTTTT
9019 GTGCTCATATTCTTCTAATCTTAT
131 GTGCTCATATTCTTCTAATCTTAT
9043 CA
1 CA
9045 TATTTGCTTT
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 154 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.40
Consensus pattern (154 bp):
CAAAGGCATCCACTGCATTAACCTCTCACGGCAACAAAGATGGCATTGTCATTCCTAGCTATTCA
TGGAGTCGCCCTCAGCAAAATTGGTTATTTATTTCCTTATTTCTTCTTTTTACCTTCATATTTTT
GTGCTCATATTCTTCTAATCTTAT
Found at i:21106 original size:51 final size:51
Alignment explanation
Indices: 21051--21152 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
21041 AAAAACACAC
21051 AAGCTCTCTCCATTTTTTTTCGCTGCCACTGAAGCACAAGAAAGCTCTCAT
1 AAGCTCTCTCCATTTTTTTTCGCTGCCACTGAAGCACAAGAAAGCTCTCAT
21102 AAGCTCTCTCCATTTTTTTTCGCTGCCACTGAAGCACAAGAAAGCTCTCAT
1 AAGCTCTCTCCATTTTTTTTCGCTGCCACTGAAGCACAAGAAAGCTCTCAT
21153 TCTCTCTACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.31
Consensus pattern (51 bp):
AAGCTCTCTCCATTTTTTTTCGCTGCCACTGAAGCACAAGAAAGCTCTCAT
Found at i:27163 original size:162 final size:164
Alignment explanation
Indices: 26850--27192 Score: 491
Period size: 162 Copynumber: 2.1 Consensus size: 164
26840 GTCTGAAACG
* * *
26850 CAGACGCCGC-CATTCAGTGGCGTTTTGATAGAAAGACGCCGCCATATTAATATATGGAGGGAGA
1 CAGACGCCGCTAATT-AGTGGCGTCTTGAAAGAAAGACGCCGCCATATTAATATATGGAGGGAGA
*
26914 GATTTTTTTTCTCCTTTTTTTGGGGGGAAAAATTCCCTCCCCACTAAAACAAAGAAAGTTTCCAA
65 GATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAAAACAAAGAAAGTTTCCAA
*
26979 CTCTACACCTATAATATATAGCGGCGTTTT-GACAT
130 CTCTACACCTATAATATATAGCGGCGTTTTCGA-AC
* *
27014 CAGACGCCGCTAATTAGTGGCGTCTTGAAAAGAAA-ACGCCGCTATTTTAATATATGGAGGGAGA
1 CAGACGCCGCTAATTAGTGGCGTCTTG-AAAGAAAGACGCCGCCATATTAATATATGGAGGGAGA
* * *
27078 GA-TTTTTTTC-CCTTTTTTTGGAGGGAAAAATTCCCTCCTC-CTAAAACAAAGAAATTTTAGCA
65 GATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAAAACAAAGAAAGTTT-CCA
* *
27140 ACTCTACGCCTATAATATATAGCGGCGTTTTCTAAC
129 ACTCTACACCTATAATATATAGCGGCGTTTTCGAAC
*
27176 CAGACGCCGCTACTTAG
1 CAGACGCCGCTAATTAG
27193 AAAGGAGAAA
Statistics
Matches: 162, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
161 17 0.10
162 77 0.48
163 9 0.06
164 50 0.31
165 9 0.06
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (164 bp):
CAGACGCCGCTAATTAGTGGCGTCTTGAAAGAAAGACGCCGCCATATTAATATATGGAGGGAGAG
ATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAAAACAAAGAAAGTTTCCAAC
TCTACACCTATAATATATAGCGGCGTTTTCGAAC
Done.