Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010013.1 Corchorus capsularis cultivar CVL-1 contig10034, 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: 7339
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:76 original size:35 final size:36

Alignment explanation


    Indices: 37--120  Score: 127
    Period size: 35  Copynumber: 2.4  Consensus size: 36

         27 AATATATACT

                                                 
         37 AAACCACGAATAAAGTCAAAAAA-AGAAAAA-CTACA
          1 AAACCACGAATAAAGTCAAAAAAGA-AAAAATCTACA

                   *                          * 
         72 AAACCACAAATAAAGTCAAAAAAGAAAAAATCTATA
          1 AAACCACGAATAAAGTCAAAAAAGAAAAAATCTACA

                         
        108 AAACCACGAATAA
          1 AAACCACGAATAA

        121 TGTGAAATTT


Statistics
Matches: 44,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  35   27  0.61
  36   17  0.39

ACGTcount: A:0.65, C:0.17, G:0.07, T:0.11


Consensus pattern (36 bp):   
AAACCACGAATAAAGTCAAAAAAGAAAAAATCTACA

Found at i:253 original size:19 final size:19

Alignment explanation


    Indices: 225--263  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        215 TATATAAAAT

                 *             
        225 TTTCATTATTAAAATATAA
          1 TTTCAATATTAAAATATAA

                      * *      
        244 TTTCAATATTTATATATAA
          1 TTTCAATATTAAAATATAA

             
        263 T
          1 T

        264 ACCGTCAGTG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51


Consensus pattern (19 bp):   
TTTCAATATTAAAATATAA

Found at i:7249 original size:29 final size:30

Alignment explanation


    Indices: 7217--7281  Score: 78
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       7207 TTTGACCCTC

                  *                       
       7217 GAACTTTAATCTT-GGACATTTTGCCCACT
          1 GAACTTCAATCTTGGGACATTTTGCCCACT

                      *       *        *  
       7246 GAACTTCAATTTTGGGACGTTTTGCCCCCT
          1 GAACTTCAATCTTGGGACATTTTGCCCACT

            *     
       7276 CAACTT
          1 GAACTT

       7282 AACGGCTCCG


Statistics
Matches: 30,  Mismatches: 5, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  29   11  0.37
  30   19  0.63

ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37


Consensus pattern (30 bp):   
GAACTTCAATCTTGGGACATTTTGCCCACT

Done.