Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009137.1 Corchorus capsularis cultivar CVL-1 contig09158, 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: 33838
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33


Found at i:20268 original size:32 final size:32

Alignment explanation


    Indices: 20167--20269  Score: 143
    Period size: 32  Copynumber: 3.2  Consensus size: 32

      20157 TTTCACTTCT

                              *    *         
      20167 GACGGCTCTGCCACGGCGGAGCCTCCCCACTAG
          1 GACGGCTCTGCCACGGC-TAGCCGCCCCACTAG

                *           *      *        
      20200 GACGACTCTGCCACGGTTAGCCGTCCCACTAG
          1 GACGGCTCTGCCACGGCTAGCCGCCCCACTAG

                                           *
      20232 GACGGCTCTGCCACGGCTAGCCGCCCCACTAA
          1 GACGGCTCTGCCACGGCTAGCCGCCCCACTAG

                  
      20264 GACGGC
          1 GACGGC

      20270 AAGACTTTTT


Statistics
Matches: 61,  Mismatches: 9, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  32   46  0.75
  33   15  0.25

ACGTcount: A:0.17, C:0.41, G:0.28, T:0.14


Consensus pattern (32 bp):   
GACGGCTCTGCCACGGCTAGCCGCCCCACTAG

Found at i:20350 original size:33 final size:34

Alignment explanation


    Indices: 20308--20392  Score: 104
    Period size: 33  Copynumber: 2.6  Consensus size: 34

      20298 TAGTACCGGT

                               *   *          
      20308 GCCGCCCCAGGGGA-GCGGTCTATCCATGGTAGG
          1 GCCGCCCCAGGGGAGGCGGCCTAGCCATGGTAGG

                                  *          *
      20341 GCCGCCCCA-GGGAGGCGGCCTGGCCATGGTAGT
          1 GCCGCCCCAGGGGAGGCGGCCTAGCCATGGTAGG

                       *        
      20374 GCCGCCCCAGGAG-GGCGGC
          1 GCCGCCCCAGGGGAGGCGGC

      20393 TTGGCAATGG


Statistics
Matches: 45,  Mismatches: 5, Indels: 4
        0.83            0.09        0.07

Matches are distributed among these distances:
  32    4  0.09
  33   39  0.87
  34    2  0.04

ACGTcount: A:0.13, C:0.34, G:0.42, T:0.11


Consensus pattern (34 bp):   
GCCGCCCCAGGGGAGGCGGCCTAGCCATGGTAGG

Found at i:20411 original size:33 final size:31

Alignment explanation


    Indices: 20308--20425  Score: 103
    Period size: 33  Copynumber: 3.6  Consensus size: 31

      20298 TAGTACCGGT

                              *  ** *        
      20308 GCCGCCCCAGGGGAGCGGTCTATCCATGGTAGG
          1 GCCGCCCCAGGGG-GCGGCCTGGCAATGGTA-G

                                    *       
      20341 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAG
          1 GCCGCCCCAGGG-GGCGGCCTGGCAATGGTAG

                                *              
      20373 TGCCGCCCCAGGAGGGCGGCTTGGCAATGGCTCA-
          1 -GCCGCCCCAGG-GGGCGGCCTGGCAATGG-T-AG

                               
      20407 GCCGCCCCAGGGGGACGGC
          1 GCCGCCCCAGGGGG-CGGC

      20426 ACCGGTGGGG


Statistics
Matches: 74,  Mismatches: 5, Indels: 12
        0.81            0.05        0.13

Matches are distributed among these distances:
  32    4  0.05
  33   66  0.89
  34    3  0.04
  35    1  0.01

ACGTcount: A:0.14, C:0.34, G:0.42, T:0.11


Consensus pattern (31 bp):   
GCCGCCCCAGGGGGCGGCCTGGCAATGGTAG

Found at i:30775 original size:18 final size:17

Alignment explanation


    Indices: 30754--30788  Score: 52
    Period size: 18  Copynumber: 2.0  Consensus size: 17

      30744 CTCTAGTGGC

                              
      30754 GGCGGAGGCGGTGGAGAG
          1 GGCGGAGGCGGT-GAGAG

                 *           
      30772 GGCGGTGGCGGTGAGAG
          1 GGCGGAGGCGGTGAGAG

      30789 TGGAGGGATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    5  0.31
  18   11  0.69

ACGTcount: A:0.14, C:0.11, G:0.66, T:0.09


Consensus pattern (17 bp):   
GGCGGAGGCGGTGAGAG
Done.