Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024492.1 Corchorus olitorius cultivar O-4 contig24525, 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: 3690
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Found at i:1084 original size:237 final size:235
Alignment explanation
Indices: 664--1135 Score: 899
Period size: 237 Copynumber: 2.0 Consensus size: 235
654 AACTTAGGGT
664 TCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGTGATACTTGATTGTTTGTGAATCTTGT
1 TCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGTGATACTTGATTGTTTGTGAATCTTGT
729 GTTCTAAAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGATTCACC
66 GTTCTAAAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGATTCACC
794 TTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAGATATT
131 TTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAGATATT
859 CAAGGCTAGATTTTGAATCTAACACAACTAGATTCGTATCA
196 CAAGGCTAGA-TTTGAATCTAACACAACTAGATTCGTATCA
* *
900 TCTTCAAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGTGTTGCTTGATTGTTTGTGAATCTTG
1 TCTTC-AATCTTGTAGAGTCCTAGCAAACAATTAAGTTGTGATACTTGATTGTTTGTGAATCTTG
*
965 TGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGATTCAC
65 TGTTCTAAAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGATTCAC
1030 CTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAGATAT
130 CTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAGATAT
1095 TCAAGGCTAGATTTGAATCTAACACAACTAGATTCGTATCA
195 TCAAGGCTAGATTTGAATCTAACACAACTAGATTCGTATCA
1136 ATTGGTAATC
Statistics
Matches: 232, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
236 35 0.15
237 197 0.85
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (235 bp):
TCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGTGATACTTGATTGTTTGTGAATCTTGT
GTTCTAAAGTTAACAATTGCAGGTCTAATTGGAGACTTTGGGCCGACGAAAGAAGAGGATTCACC
TTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGAAGTTCAAGTCGACTTTGATAGATATT
CAAGGCTAGATTTGAATCTAACACAACTAGATTCGTATCA
Done.