Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001806.1 Corchorus capsularis cultivar CVL-1 contig01807, 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: 2798
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:631 original size:31 final size:30

Alignment explanation


    Indices: 529--632  Score: 93
    Period size: 31  Copynumber: 3.4  Consensus size: 30

        519 GCTAAATAAC

                                ****       
        529 CAATTCAGGATATAACGTTTGTGGAAACGAT
          1 CAATTCAGGATATAACG-TTACAAAAACGAT

                 **            *      *  *
        560 CAATTTGGGATATAACGTTTCAAAAATG-C
          1 CAATTCAGGATATAACGTTACAAAAACGAT

                                           
        589 CAATTCAGGATATAACGTTACATAAAACGAT
          1 CAATTCAGGATATAACGTTACA-AAAACGAT

               *         
        620 CAAATCAGGATAT
          1 CAATTCAGGATAT

        633 GGTCTGACGG


Statistics
Matches: 57,  Mismatches: 14, Indels: 4
        0.76            0.19        0.05

Matches are distributed among these distances:
  29   19  0.33
  30   11  0.19
  31   27  0.47

ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28


Consensus pattern (30 bp):   
CAATTCAGGATATAACGTTACAAAAACGAT

Found at i:736 original size:14 final size:14

Alignment explanation


    Indices: 717--769  Score: 54
    Period size: 14  Copynumber: 3.8  Consensus size: 14

        707 GATTTTTTTA

                          
        717 AAAATAAAAAAATT
          1 AAAATAAAAAAATT

                      *    
        731 AAAATAAATATAA-T
          1 AAAATAAA-AAAATT

                    *    *
        745 AAAATAAATAAATG
          1 AAAATAAAAAAATT

               *       
        759 AAATTAAAAAA
          1 AAAATAAAAAA

        770 TAAATTATTA


Statistics
Matches: 31,  Mismatches: 6, Indels: 4
        0.76            0.15        0.10

Matches are distributed among these distances:
  13    2  0.06
  14   26  0.84
  15    3  0.10

ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23


Consensus pattern (14 bp):   
AAAATAAAAAAATT

Found at i:753 original size:18 final size:17

Alignment explanation


    Indices: 731--774  Score: 54
    Period size: 18  Copynumber: 2.5  Consensus size: 17

        721 TAAAAAAATT

                              
        731 AAAATAAAT-ATAATAAA
          1 AAAATAAATGA-AATAAA

                           *  
        748 ATAAATAAATGAAATTAA
          1 A-AAATAAATGAAATAAA

                     
        766 AAAATAAAT
          1 AAAATAAAT

        775 TATTAAATAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  17    9  0.38
  18   14  0.58
  19    1  0.04

ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25


Consensus pattern (17 bp):   
AAAATAAATGAAATAAA
Done.