Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020579.1 Corchorus olitorius cultivar O-4 contig20612, 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: 13737
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Found at i:324 original size:13 final size:12
Alignment explanation
Indices: 306--350 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
296 ATTTTATTAC
306 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
319 TGTTTTATAAAT
1 TGTTTTATAAAT
*
331 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
345 TGTTTT
1 TGTTTT
351 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:7129 original size:219 final size:219
Alignment explanation
Indices: 6748--7188 Score: 828
Period size: 219 Copynumber: 2.0 Consensus size: 219
6738 TGGGAGGTTG
*
6748 AACGCGACCATGTGGATAGGAGCTGGGAAAGGATTTTTGTCAACTCCCATGTCCTTCTTTGGCGC
1 AACGCGACCATGTGGATAGGAGCTGGGAAAGGATTTTTGTCAACTCCCATGTCCTTCTTCGGCGC
*
6813 CTCGGGGAACTTCAATATTCCCTTTTCTATCTTTTCTTGTACTATGTTTTTGAACACAATACAGT
66 CTCAGGGAACTTCAATATTCCCTTTTCTATCTTTTCTTGTACTATGTTTTTGAACACAATACAGT
*
6878 TGTTGGTTGGGTGCCTCCAGGAGTCGTGGTACTTGCAATATTTTCTTCCTTTGATGTCCTCAGGT
131 TGTTGGTTGGGTGCCTCCAGGAGTCGTGGTACTTGCAATATTCTCTTCCTTTGATGTCCTCAGGT
6943 GAAGGAAGGACATGTCCAGGTGGC
196 GAAGGAAGGACATGTCCAGGTGGC
*
6967 AACGCGACCATGTGGATAGGAGCTGGGAAAGGATTTTTGTCAACTTCCATGTCCTTCTTCGGCGC
1 AACGCGACCATGTGGATAGGAGCTGGGAAAGGATTTTTGTCAACTCCCATGTCCTTCTTCGGCGC
*
7032 CTCAGGGAACTTCAATATTCCCTTTTCTATCTTTTCTTGTACTATGTTTTTGAACACAGTACAGT
66 CTCAGGGAACTTCAATATTCCCTTTTCTATCTTTTCTTGTACTATGTTTTTGAACACAATACAGT
*
7097 TGTTGGTTGGGTGCCTCCAGGAGTCTTGGTACTTGCAATATTCTCTTCCTTTGATGTCCTCAGGT
131 TGTTGGTTGGGTGCCTCCAGGAGTCGTGGTACTTGCAATATTCTCTTCCTTTGATGTCCTCAGGT
7162 GAAGGAAGGACATGTCCAGGTGGC
196 GAAGGAAGGACATGTCCAGGTGGC
7186 AAC
1 AAC
7189 TTAATCATAC
Statistics
Matches: 216, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
219 216 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (219 bp):
AACGCGACCATGTGGATAGGAGCTGGGAAAGGATTTTTGTCAACTCCCATGTCCTTCTTCGGCGC
CTCAGGGAACTTCAATATTCCCTTTTCTATCTTTTCTTGTACTATGTTTTTGAACACAATACAGT
TGTTGGTTGGGTGCCTCCAGGAGTCGTGGTACTTGCAATATTCTCTTCCTTTGATGTCCTCAGGT
GAAGGAAGGACATGTCCAGGTGGC
Found at i:9121 original size:374 final size:374
Alignment explanation
Indices: 8432--9178 Score: 1422
Period size: 374 Copynumber: 2.0 Consensus size: 374
8422 TTGTCTCGGA
*
8432 TCTTGGGCTATCTGTTGGATTTGCCCCCGAGTCTATCTTCTACTTGACCAATCTGAGCCAGGATG
1 TCTTGGGCTATCTGTTGGATTTGCCCCCGAGTCTATCTTCTACTTGACCAATCTGAGCCAAGATG
8497 TTCTCACGGTCTTGAATCATCTGCTCCTTAAAAGAGTCATTAACCTCCTTAAGTTGGTCATGAGA
66 TTCTCACGGTCTTGAATCATCTGCTCCTTAAAAGAGTCATTAACCTCCTTAAGTTGGTCATGAGA
*
8562 TTTGTTCATCTGATCTATAGATCTCATAAGTTGCTGCATCCTCTGTTCCTATGCCAAAGAAATTT
131 TTTGTTCATCTGATCTATAGATCTCATAAATTGCTGCATCCTCTGTTCCTATGCCAAAGAAATTT
*
8627 CATTCATGGCTTCAGTGAGGTATTGCAACAAGACCTTTGAATCAGATTCCAAAGGTAATTGTGAA
196 CATTCATGGCTTCAATGAGGTATTGCAACAAGACCTTTGAATCAGATTCCAAAGGTAATTGTGAA
*
8692 GGATTTGCCACGTTTTTGCTTCTGGTTTGCATAACATGGCTAGATCTACCTTCATCAACCTTAGG
261 GGATCTGCCACGTTTTTGCTTCTGGTTTGCATAACATGGCTAGATCTACCTTCATCAACCTTAGG
8757 TGGCATGTTTACCACTTGGTAGGACTTAGAAAGAAGGAGAGGAAAAAGG
326 TGGCATGTTTACCACTTGGTAGGACTTAGAAAGAAGGAGAGGAAAAAGG
8806 TCTTGGGCTATCTGTTGGATTTGCCCCCGAGTCTATCTTCTACTTGACCAATCTGAGCCAAGATG
1 TCTTGGGCTATCTGTTGGATTTGCCCCCGAGTCTATCTTCTACTTGACCAATCTGAGCCAAGATG
8871 TTCTCACGGTCTTGAATCATCTGCTCCTTAAAAGAGTCATTAACCTCCTTAAGTTGGTCATGAGA
66 TTCTCACGGTCTTGAATCATCTGCTCCTTAAAAGAGTCATTAACCTCCTTAAGTTGGTCATGAGA
*
8936 TTTGTTCATCTGATCTATAGATCTCATAAATTGCTGCATCCTCTGTTCCTGTGCCAAAGAAATTT
131 TTTGTTCATCTGATCTATAGATCTCATAAATTGCTGCATCCTCTGTTCCTATGCCAAAGAAATTT
*
9001 CATTCATGGCTTCAATGAGGTATTGCAACAAGACCTTTTAATCAGATTCCAAAGGTAATTGTGAA
196 CATTCATGGCTTCAATGAGGTATTGCAACAAGACCTTTGAATCAGATTCCAAAGGTAATTGTGAA
9066 GGATCTGCCACGTTTTTGCTTCTGGTTTGCATAACATGGCTAGATCTACCTTCATCAACCTTAGG
261 GGATCTGCCACGTTTTTGCTTCTGGTTTGCATAACATGGCTAGATCTACCTTCATCAACCTTAGG
* *
9131 TGGCATGTTTACCTCTTGGTAGGACTTAGAAAGAAGGAGAGGGAAAAG
326 TGGCATGTTTACCACTTGGTAGGACTTAGAAAGAAGGAGAGGAAAAAG
9179 AAAAAGTAAA
Statistics
Matches: 365, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
374 365 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (374 bp):
TCTTGGGCTATCTGTTGGATTTGCCCCCGAGTCTATCTTCTACTTGACCAATCTGAGCCAAGATG
TTCTCACGGTCTTGAATCATCTGCTCCTTAAAAGAGTCATTAACCTCCTTAAGTTGGTCATGAGA
TTTGTTCATCTGATCTATAGATCTCATAAATTGCTGCATCCTCTGTTCCTATGCCAAAGAAATTT
CATTCATGGCTTCAATGAGGTATTGCAACAAGACCTTTGAATCAGATTCCAAAGGTAATTGTGAA
GGATCTGCCACGTTTTTGCTTCTGGTTTGCATAACATGGCTAGATCTACCTTCATCAACCTTAGG
TGGCATGTTTACCACTTGGTAGGACTTAGAAAGAAGGAGAGGAAAAAGG
Done.