Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008220.1 Corchorus olitorius cultivar O-4 contig08247, 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:0.23, C:0.22, G:0.20, T:0.36


Found at i:679 original size:18 final size:18

Alignment explanation


    Indices: 656--692  Score: 65
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        646 TTTCTTGCTT

                              
        656 AATGGAAAGAAATGAAGC
          1 AATGGAAAGAAATGAAGC

                       *      
        674 AATGGAAAGAATTGAAGC
          1 AATGGAAAGAAATGAAGC

             
        692 A
          1 A

        693 TTTTTTGGTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.54, C:0.05, G:0.27, T:0.14


Consensus pattern (18 bp):   
AATGGAAAGAAATGAAGC

Found at i:1438 original size:14 final size:13

Alignment explanation


    Indices: 1409--1458  Score: 57
    Period size: 14  Copynumber: 3.6  Consensus size: 13

       1399 CCCTCATTTC

                           
       1409 TTTCTTTTTCTCTTT
          1 TTTC-TTTTCT-TTT

                          
       1424 TTTCTTTTCCTTTT
          1 TTTCTTTT-CTTTT

                         
       1438 TTTCTTTT-TTTT
          1 TTTCTTTTCTTTT

                     
       1450 TCTTCTTTT
          1 T-TTCTTTT

       1459 TT


Statistics
Matches: 33,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
  12    5  0.15
  13    7  0.21
  14   15  0.45
  15    6  0.18

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (13 bp):   
TTTCTTTTCTTTT

Found at i:1457 original size:21 final size:22

Alignment explanation


    Indices: 1405--1460  Score: 71
    Period size: 21  Copynumber: 2.6  Consensus size: 22

       1395 AGGACCCTCA

                         *         
       1405 TTTCTTTCTTTTTCTCTTTTTTC
          1 TTTC-TTCTTTTTTTCTTTTTTC

                 *                
       1428 TTT-TCCTTTTTTTCTTTTTT-
          1 TTTCTTCTTTTTTTCTTTTTTC

                         
       1448 TTTCTTCTTTTTT
          1 TTTCTTCTTTTTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  20    3  0.10
  21   23  0.79
  23    3  0.10

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (22 bp):   
TTTCTTCTTTTTTTCTTTTTTC
Done.