Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013216.1 Corchorus olitorius cultivar O-4 contig13249, 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: 26678
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:3425 original size:9 final size:9

Alignment explanation


    Indices: 3411--3437  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

       3401 CAACCAACAT

                     
       3411 CAAAACAAA
          1 CAAAACAAA

                     
       3420 CAAAACAAA
          1 CAAAACAAA

                     
       3429 CAAAACAAA
          1 CAAAACAAA

       3438 GCAACCATTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00


Consensus pattern (9 bp):   
CAAAACAAA

Found at i:8259 original size:30 final size:29

Alignment explanation


    Indices: 8222--8443  Score: 245
    Period size: 29  Copynumber: 7.7  Consensus size: 29

       8212 ACTCAGAGTA

                                       * 
       8222 TGCAAAAATGACCAAAATGCCCCTGGACG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                                *         
       8251 TGCAAAAAATGACCAAAATGTCCCTGGATG
          1 TGC-AAAAATGACCAAAATGCCCCTGGATG

              *   * *       *    **      
       8281 TGTAAATACGACCAAAGTGCCTTTGGATG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

               *    *  *             *   *
       8310 TGCCAAAACGATCAAAATGCCCCTGAATTA
          1 TGCAAAAATGACCAAAATGCCCCTGGA-TG

                                  *      
       8340 TGCAAAAATGACCAAAATGCCCTTGGATG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                                           
       8369 TGGC--AAATGACCAAAATGCCCCTAGG-TG
          1 T-GCAAAAATGACCAAAATGCCCCT-GGATG

                                  *      
       8397 TGCAAAAATGACCAAAATGCCCTTGGATG
          1 TGCAAAAATGACCAAAATGCCCCTGGATG

                               
       8426 TGC-AAAATGACCAAAATG
          1 TGCAAAAATGACCAAAATG

       8444 ACCAAAATAA


Statistics
Matches: 160,  Mismatches: 26, Indels: 15
        0.80            0.13        0.07

Matches are distributed among these distances:
  27    2  0.01
  28   38  0.24
  29   69  0.43
  30   51  0.32

ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20


Consensus pattern (29 bp):   
TGCAAAAATGACCAAAATGCCCCTGGATG

Found at i:8412 original size:57 final size:57

Alignment explanation


    Indices: 8222--8443  Score: 259
    Period size: 59  Copynumber: 3.8  Consensus size: 57

       8212 ACTCAGAGTA

                                  *    *                     *          
       8222 TGCAAAAATGACCAAAATGCCCCTGGACGTGCAAAAAATGACCAAAATGTCCCT-GGATG
          1 TGCAAAAATGACCAAAATGCCCTTGGATGTGC--AAAATGACCAAAATGCCCCTAGG-TG

              *   * *       *    *               *  *              ** *
       8281 TGTAAATACGACCAAAGTGCCTTTGGATGTGCCAAAACGATCAAAATGCCCCTGAATTA
          1 TGCAAAAATGACCAAAATGCCCTTGGATGTG-CAAAATGACCAAAATGCCCCT-AGGTG

                                                                      
       8340 TGCAAAAATGACCAAAATGCCCTTGGATGTGGC-AAATGACCAAAATGCCCCTAGGTG
          1 TGCAAAAATGACCAAAATGCCCTTGGATGT-GCAAAATGACCAAAATGCCCCTAGGTG

                                                           
       8397 TGCAAAAATGACCAAAATGCCCTTGGATGTGCAAAATGACCAAAATG
          1 TGCAAAAATGACCAAAATGCCCTTGGATGTGCAAAATGACCAAAATG

       8444 ACCAAAATAA


Statistics
Matches: 135,  Mismatches: 23, Indels: 12
        0.79            0.14        0.07

Matches are distributed among these distances:
  56    2  0.01
  57   46  0.34
  58   34  0.25
  59   51  0.38
  60    2  0.01

ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20


Consensus pattern (57 bp):   
TGCAAAAATGACCAAAATGCCCTTGGATGTGCAAAATGACCAAAATGCCCCTAGGTG
Done.