Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013590.1 Corchorus capsularis cultivar CVL-1 contig13611, 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: 5892
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29


Found at i:340 original size:20 final size:20

Alignment explanation


    Indices: 315--360  Score: 56
    Period size: 20  Copynumber: 2.3  Consensus size: 20

        305 TCATATAAGA

                        *       
        315 TAATGCCAAACTGCTAATGC
          1 TAATGCCAAACTACTAATGC

                   *     *      
        335 TAATGCCTAACTATTAATGC
          1 TAATGCCAAACTACTAATGC

            *     
        355 GAATGC
          1 TAATGC

        361 TGATGCCTAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28


Consensus pattern (20 bp):   
TAATGCCAAACTACTAATGC

Found at i:366 original size:26 final size:26

Alignment explanation


    Indices: 330--419  Score: 87
    Period size: 26  Copynumber: 3.6  Consensus size: 26

        320 CCAAACTGCT

                                      
        330 AATGCTAATGCCTAACTATTAATGCG
          1 AATGCTAATGCCTAACTATTAATGCG

                  *        * ***      
        356 AATGCTGATGCCTAAATGCGAATGC-
          1 AATGCTAATGCCTAACTATTAATGCG

                      *               
        381 --TGCTAATGTCTAACTATTAATGCG
          1 AATGCTAATGCCTAACTATTAATGCG

                * *        
        405 AATGTTGATGCCTAA
          1 AATGCTAATGCCTAA

        420 TGCAGAGTGC


Statistics
Matches: 47,  Mismatches: 14, Indels: 6
        0.70            0.21        0.09

Matches are distributed among these distances:
  23   17  0.36
  26   30  0.64

ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Consensus pattern (26 bp):   
AATGCTAATGCCTAACTATTAATGCG

Found at i:2304 original size:33 final size:33

Alignment explanation


    Indices: 2267--2374  Score: 94
    Period size: 33  Copynumber: 3.3  Consensus size: 33

       2257 GCCGAGTCAT

                                   *          
       2267 GTGGCCGAGTG-TGGCCGGGCATGGACATGTCGC
          1 GTGGCCG-GTGATGGCCGGGCATCGACATGTCGC

                                   **        
       2300 GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
          1 GTGGCCGGTGATGGCCGGGCATCGACATGTCGC

            *      *    *           **  *     
       2333 ATGGCCGTTG-TTGCGCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTGATGGC-CGGGCATCGACATGTCGC

            *        
       2366 ATGGCCGGT
          1 GTGGCCGGT

       2375 CACTTGTGCT


Statistics
Matches: 65,  Mismatches: 8, Indels: 4
        0.84            0.10        0.05

Matches are distributed among these distances:
  32    6  0.09
  33   59  0.91

ACGTcount: A:0.11, C:0.28, G:0.40, T:0.21


Consensus pattern (33 bp):   
GTGGCCGGTGATGGCCGGGCATCGACATGTCGC
Done.