Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021483.1 Corchorus olitorius cultivar O-4 contig21516, 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: 3914
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:1023 original size:18 final size:18

Alignment explanation


    Indices: 985--1026  Score: 57
    Period size: 18  Copynumber: 2.3  Consensus size: 18

        975 TATTCTAAGA

                          *** 
        985 TTTTTCTTTTTTTTTTTG
          1 TTTTTCTTTTTTTTGGAG

                              
       1003 TTTTTCTTTTTTTTGGAG
          1 TTTTTCTTTTTTTTGGAG

                  
       1021 TTTTTC
          1 TTTTTC

       1027 AAAATGCAAT


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.02, C:0.07, G:0.10, T:0.81


Consensus pattern (18 bp):   
TTTTTCTTTTTTTTGGAG

Found at i:2404 original size:22 final size:22

Alignment explanation


    Indices: 2373--2416  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2363 TTCTTTCCGC

                       *          
       2373 AACAACTTCTGTCCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

                 *      *         
       2395 AACAAGTTCTGGGCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

       2417 TCCTGCGCAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25


Consensus pattern (22 bp):   
AACAACTTCTGGCCCGAAGTTG

Found at i:3263 original size:16 final size:17

Alignment explanation


    Indices: 3242--3273  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       3232 GAAATTGCGT

                             
       3242 TTTATTTTTCT-TTTTC
          1 TTTATTTTTCTATTTTC

                            
       3258 TTTATTTTTCTATTTT
          1 TTTATTTTTCTATTTT

       3274 AATTTGCACT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81


Consensus pattern (17 bp):   
TTTATTTTTCTATTTTC
Done.