Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003417.1 Corchorus capsularis cultivar CVL-1 contig03425, 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, 663

Length: 1106
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31


Found at i:775 original size:166 final size:167

Alignment explanation


    Indices: 499--824  Score: 426
    Period size: 166  Copynumber: 2.0  Consensus size: 167

        489 TCATTTGCCA

                        *           *            *                           
        499 ATTGAGAAATGATCAAAAAGTTTAGTTATTTAATCCCGTCAAGAATAAAAAATTAGGACATTTAA
          1 ATTGAGAAATGACCAAAAAGTTTACTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA

            *                *            ** *    *          ** *            
        564 GTAATCTGCCAAATAGGTAAAGACGAAAAATGTTAGTTCTCTAACT-CATCATCAA-TCCTTGAT
         66 ATAATCTGCCAAATAGGAAAAGACGAAAAAAATAAGTTATCTAACTCCAAAAGCAAGT-CTTGAT

                         *                         
        627 -GGAGATCATTTATTAATTCCACTACTCTATTTAATTCC
        130 AGG-GATCATTTAATAATTCCACTACTCTATTTAATTCC

                                                           *    *   *        
        665 ATTGAGAAATGACCAAAAA-TATTACTTATTTAATCCCCTCAAGAATCAAAAGTTATGACATTTA
          1 ATTGAGAAATGACCAAAAAGT-TTACTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTA

                         *                                                 * 
        729 AATAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTATCTAACTCCAAAAGCAAGTCTTGGT
         65 AATAATCTGCCAAATAGGAAAAGACGAAAAAAATAAGTTATCTAACTCCAAAAGCAAGTCTTGAT

                   *                       
        794 AGGGATCTTTTAATAATTCCACTACTCTATT
        130 AGGGATCATTTAATAATTCCACTACTCTATT

        825 AAAGTTTAGG


Statistics
Matches: 137,  Mismatches: 19, Indels: 7
        0.84            0.12        0.04

Matches are distributed among these distances:
 165    1  0.01
 166   96  0.70
 167   37  0.27
 168    3  0.02

ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31


Consensus pattern (167 bp):   
ATTGAGAAATGACCAAAAAGTTTACTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
ATAATCTGCCAAATAGGAAAAGACGAAAAAAATAAGTTATCTAACTCCAAAAGCAAGTCTTGATA
GGGATCATTTAATAATTCCACTACTCTATTTAATTCC

Found at i:933 original size:45 final size:45

Alignment explanation


    Indices: 883--972  Score: 153
    Period size: 45  Copynumber: 2.0  Consensus size: 45

        873 GATTACTTCT

                                                         
        883 CCAGCTCATCAGTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
          1 CCAGCTCATCAGTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC

                  *    *    *                            
        928 CCAGCTTATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
          1 CCAGCTCATCAGTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC

        973 TACTCTATTA


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32


Consensus pattern (45 bp):   
CCAGCTCATCAGTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
Done.