Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000852.1 Corchorus capsularis cultivar CVL-1 contig00852, 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, 876
Length: 1460
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:132 original size:17 final size:17
Alignment explanation
Indices: 110--143 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
100 AGTGAAAGGG
* *
110 TTGTTTTTGGAATAAAA
1 TTGTTTTCGAAATAAAA
127 TTGTTTTCGAAATAAAA
1 TTGTTTTCGAAATAAAA
144 GGATGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (17 bp):
TTGTTTTCGAAATAAAA
Found at i:551 original size:17 final size:17
Alignment explanation
Indices: 529--562 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
519 AGTGAAAGGG
* *
529 TTGTTTTTGGAATAAAA
1 TTGTTTTCGAAATAAAA
546 TTGTTTTCGAAATAAAA
1 TTGTTTTCGAAATAAAA
563 GGATGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (17 bp):
TTGTTTTCGAAATAAAA
Found at i:871 original size:420 final size:419
Alignment explanation
Indices: 93--916 Score: 1630
Period size: 420 Copynumber: 2.0 Consensus size: 419
83 AAGACAAAAA
93 ACTCTTTAGTGAAAGGGTTGTTTTTGGAATAAAATTGTTTTCGAAATAAAAGGATGTTTTTTTTG
1 ACTCTTTAGTGAAAGGGTTGTTTTTGGAATAAAATTGTTTTCGAAATAAAAGGATGTTTTTTTTG
158 AAAGTGATAGCAAGACAATTTGCTTTATGTCAACACTGAGCATAAATCCCACATTTCCTTGATCC
66 AAAGTGATAGCAAGACAATTTGCTTTATGTCAACACTGAGCATAAATCCCACATTTCCTTGATCC
223 CAAAATGAGCCCAATTTTTTTTCCTGGAGACCTAATTGAAACAAAAATTCCACATCTTCAGGACA
131 CAAAATGAGCCCAATTTTTTTTCCTGGAGACCTAATTGAAACAAAAATTCCACATCTTCAGGACA
288 TCTTGTTACCTTTCCATATTGCCTTGAGGAAGATTGTTTTTAAAAGTCAAAATTAAAGTCTCCTC
196 TCTTGTTACCTTTCCATATTGCCTTGAGGAAGATTGTTTTTAAAAGTCAAAATTAAAGTCTCCTC
353 CAAACCTTATAAGGGCAAGTTGATGGTAGACAATCCATGTTGTACATTTCCCTACAACCTTGGTC
261 CAAACCTTATAAGGGCAAGTTGATGGTAGACAATCCATGTTGTACATTTCCCTACAACCTTGGTC
418 TTCAAGAGACTTTTCATATCCTTATAATGATTGCAAGCAATAGTCAGCCAAAATGGTGGAATGAA
326 TTCAAGAGACTTTTCATATCCTTATAATGATTGCAAGCAATAGTCAGCCAAAATGGTGGAATGAA
483 ATGCTCAAATTCATGGATTGTCTACCATC
391 ATGCTCAAATTCATGGATTGTCTACCATC
512 ACTCTTTAGTGAAAGGGTTGTTTTTGGAATAAAATTGTTTTCGAAATAAAAGGATGTTTTTTTTG
1 ACTCTTTAGTGAAAGGGTTGTTTTTGGAATAAAATTGTTTTCGAAATAAAAGGATGTTTTTTTTG
577 AAAGTGATAGCAAGACAATTTGCTTTATGTCAACACTGAGCATAAATCCCACATTTCCTTGATCC
66 AAAGTGATAGCAAGACAATTTGCTTTATGTCAACACTGAGCATAAATCCCACATTTCCTTGATCC
642 CAAAATGAGCCCAATTTTTTTTCCTTGGAGACCTAATTGAAACAAAAATTCCACATCTTCAGGAC
131 CAAAATGAGCCCAATTTTTTTTCC-TGGAGACCTAATTGAAACAAAAATTCCACATCTTCAGGAC
*
707 ATCTTGTTACCTTTCCATATTGCCTTGAGGAAGATTGTTTTTAAAAGTCAAAATTCAAGTCTCCT
195 ATCTTGTTACCTTTCCATATTGCCTTGAGGAAGATTGTTTTTAAAAGTCAAAATTAAAGTCTCCT
772 CCAAACCTTATAAGGGCAAGTTGATGGTAGACAATCCATGTTGTACATTTCCCTACAACCTTGGT
260 CCAAACCTTATAAGGGCAAGTTGATGGTAGACAATCCATGTTGTACATTTCCCTACAACCTTGGT
837 CTTCAAGAGACTTTTCATATCCTTATAATGATTGCAAGCAATAGTCAGCCAAAATGGTGGAATGA
325 CTTCAAGAGACTTTTCATATCCTTATAATGATTGCAAGCAATAGTCAGCCAAAATGGTGGAATGA
902 AATGCTCAAATTCAT
390 AATGCTCAAATTCAT
917 CAATACAGAA
Statistics
Matches: 403, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
419 154 0.38
420 249 0.62
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (419 bp):
ACTCTTTAGTGAAAGGGTTGTTTTTGGAATAAAATTGTTTTCGAAATAAAAGGATGTTTTTTTTG
AAAGTGATAGCAAGACAATTTGCTTTATGTCAACACTGAGCATAAATCCCACATTTCCTTGATCC
CAAAATGAGCCCAATTTTTTTTCCTGGAGACCTAATTGAAACAAAAATTCCACATCTTCAGGACA
TCTTGTTACCTTTCCATATTGCCTTGAGGAAGATTGTTTTTAAAAGTCAAAATTAAAGTCTCCTC
CAAACCTTATAAGGGCAAGTTGATGGTAGACAATCCATGTTGTACATTTCCCTACAACCTTGGTC
TTCAAGAGACTTTTCATATCCTTATAATGATTGCAAGCAATAGTCAGCCAAAATGGTGGAATGAA
ATGCTCAAATTCATGGATTGTCTACCATC
Found at i:1119 original size:14 final size:13
Alignment explanation
Indices: 1086--1133 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1076 TTCAAAAGTC
1086 AAAAATGTTTTTCA
1 AAAAATG-TTTTCA
1100 AGAAAATGTTTTCA
1 A-AAAATGTTTTCA
* *
1114 GAAAAAGGTTTTCT
1 -AAAAATGTTTTCA
1128 AAAAAT
1 AAAAAT
1134 TGGTTTTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 5 0.17
14 17 0.59
15 7 0.24
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (13 bp):
AAAAATGTTTTCA
Done.