Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015848.1 Corchorus capsularis cultivar CVL-1 contig15869, 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: 23284
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:11284 original size:17 final size:17

Alignment explanation


    Indices: 11258--11291  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      11248 TTAGATGCTA

                 *           
      11258 TATGTTTTGCATTTTAT
          1 TATGTATTGCATTTTAT

                             
      11275 TATGTATTGCATTTTAT
          1 TATGTATTGCATTTTAT

      11292 CATGACATTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.21, C:0.06, G:0.12, T:0.62


Consensus pattern (17 bp):   
TATGTATTGCATTTTAT

Found at i:11303 original size:18 final size:17

Alignment explanation


    Indices: 11264--11304  Score: 55
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      11254 GCTATATGTT

                       *   * 
      11264 TTGCATTTTATTATGTA
          1 TTGCATTTTATCATGCA

                              
      11281 TTGCATTTTATCATGACA
          1 TTGCATTTTATCATG-CA

                  
      11299 TTGCAT
          1 TTGCAT

      11305 GCATTTTACT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  17   14  0.67
  18    7  0.33

ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51


Consensus pattern (17 bp):   
TTGCATTTTATCATGCA

Found at i:11454 original size:15 final size:15

Alignment explanation


    Indices: 11434--11467  Score: 68
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      11424 GCTTCTACTT

                           
      11434 TCTTTGTGAATTAAA
          1 TCTTTGTGAATTAAA

                           
      11449 TCTTTGTGAATTAAA
          1 TCTTTGTGAATTAAA

                
      11464 TCTT
          1 TCTT

      11468 ACATGTGCTC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50


Consensus pattern (15 bp):   
TCTTTGTGAATTAAA

Found at i:16610 original size:15 final size:15

Alignment explanation


    Indices: 16590--16628  Score: 51
    Period size: 15  Copynumber: 2.6  Consensus size: 15

      16580 TTCAACTTCA

                      * *  
      16590 GCTGAGAAGGTTTCT
          1 GCTGAGAAGGCTGCT

                    *      
      16605 GCTGAGAAAGCTGCT
          1 GCTGAGAAGGCTGCT

                     
      16620 GCTGAGAAG
          1 GCTGAGAAG

      16629 CCCCTTGGTA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23


Consensus pattern (15 bp):   
GCTGAGAAGGCTGCT
Done.