Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001278.1 Corchorus capsularis cultivar CVL-1 contig01278, 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, 927

Length: 1545
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30


Found at i:522 original size:61 final size:62

Alignment explanation


    Indices: 393--653  Score: 337
    Period size: 61  Copynumber: 4.2  Consensus size: 62

        383 AAAAATATAT

                                                     **                    
        393 ATAGCGGTCGTCTAGACGCCGCTATATTTAAGGGTTTTTTATTAAAAAAATCTCAAATTAAAA
          1 ATAGCGG-CGTCTAGACGCCGCTATATTTAAGGGTTTTTTAAAAAAAAAATCTCAAATTAAAA

            *       *           *                            *            
        456 TTAGCGGCATCTAGACGCCGTTATATTTAA-GGTTTTTTAAAAAAAAAAACTCAAATTAAAA
          1 ATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTAAAAAAAAAATCTCAAATTAAAA

                                                    **                   *
        517 ATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTT-TTAAAAAAATCTCAAATTAAAT
          1 ATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTAAAAAAAAAATCTCAAATTAAAA

               *           *        *                                        
        578 ATAACGGCGTCTAGATGCCGCTATTTTTAAGGGTTTTTTTTTTAAAAAAAAAATCTCAAATTAAA
          1 ATAGCGGCGTCTAGACGCCGCTATATTTAAGGG----TTTTTTAAAAAAAAAATCTCAAATTAAA

            *
        643 T
         62 A

               *      
        644 ATAACGGCGT
          1 ATAGCGGCGT

        654 TTCCTTACTA


Statistics
Matches: 174,  Mismatches: 18, Indels: 9
        0.87            0.09        0.04

Matches are distributed among these distances:
  61  103  0.59
  62   29  0.17
  63    6  0.03
  65    6  0.03
  66   30  0.17

ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34


Consensus pattern (62 bp):   
ATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTAAAAAAAAAATCTCAAATTAAAA

Found at i:608 original size:122 final size:125

Alignment explanation


    Indices: 393--653  Score: 377
    Period size: 122  Copynumber: 2.1  Consensus size: 125

        383 AAAAATATAT

                                                                             
        393 ATAGCGGTCGTCTAGACGCCGCTATATTTAAGGGTTTTTTATTAAAAAAATCTCAAATTAAAATT
          1 ATAGCGG-CGTCTAGACGCCGCTATATTTAAGGGTTTTTTATTAAAAAAATCTCAAATTAAAATT

             *                *                                          
        458 AGCGGCATCTAGACGCCGTTATATTTAA-GG-TTTTTTAAAAAAAAAAACTCAAATTAAAA
         65 AACGGCATCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAAAAACTCAAATTAAAA

                                                                             
        517 ATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTT-TTAAAAAAATCTCAAATT-AAATAT
          1 ATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTATTAAAAAAATCTCAAATTAAAAT-T

                  *      *        *                            *           *
        580 AACGGCGTCTAGATGCCGCTATTTTTAAGGGTTTTTTTTTTAAAAAAAAAATCTCAAATTAAAT
         65 AACGGCATCTAGACGCCGCTATATTTAAGGG---TTTTTTTAAAAAAAAAAACTCAAATTAAAA

               *      
        644 ATAACGGCGT
          1 ATAGCGGCGT

        654 TTCCTTACTA


Statistics
Matches: 123,  Mismatches: 8, Indels: 9
        0.88            0.06        0.06

Matches are distributed among these distances:
 121    4  0.03
 122   42  0.34
 123   34  0.28
 124    7  0.06
 127   36  0.29

ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34


Consensus pattern (125 bp):   
ATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTATTAAAAAAATCTCAAATTAAAATTA
ACGGCATCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAAAAACTCAAATTAAAA
Done.