Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008052.1 Corchorus capsularis cultivar CVL-1 contig08073, 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: 2378
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35


Found at i:1127 original size:33 final size:33

Alignment explanation


    Indices: 1044--1136  Score: 114
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       1034 TTTTAGATGA

                               *   *   *   * 
       1044 TGTTTGCGATGATACTAAACCTAATTTGAGTGT
          1 TGTTTGCGATGATACTAAATCTATTTTAAGTAT

                   *    *                    
       1077 TGTTTGCAATGACACTAAATCTATTTTAAGTAT
          1 TGTTTGCGATGATACTAAATCTATTTTAAGTAT

                  *               *    
       1110 TGTTTGTGATGATACTAAATCTGTTTT
          1 TGTTTGCGATGATACTAAATCTATTTT

       1137 GGATGCTAAT


Statistics
Matches: 50,  Mismatches: 10, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  33   50  1.00

ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44


Consensus pattern (33 bp):   
TGTTTGCGATGATACTAAATCTATTTTAAGTAT

Found at i:1199 original size:33 final size:33

Alignment explanation


    Indices: 1162--1300  Score: 194
    Period size: 33  Copynumber: 4.3  Consensus size: 33

       1152 TGAATACAAA

                                             
       1162 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

                                             
       1195 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

             *               *               
       1228 TTTGTTTTGGTTGATCACAGCATTGCAAATAAT
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

            *         *       *      *      *
       1261 CCTGTTTTGGCTG---ATGGCATTGAAAATAAA
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

                      
       1291 TCTGTTTTGG
          1 TCTGTTTTGG

       1301 GTGACGAGAA


Statistics
Matches: 96,  Mismatches: 10, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  30   22  0.23
  33   74  0.77

ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42


Consensus pattern (33 bp):   
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Done.