Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005411.1 Corchorus capsularis cultivar CVL-1 contig05429, 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: 3795
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:3712 original size:198 final size:195

Alignment explanation


    Indices: 3263--3795  Score: 610
    Period size: 198  Copynumber: 2.7  Consensus size: 195

       3253 ACTTTATATT

                               *           * *                               
       3263 ATTTTTCTTATAGGATTATCATACAATACACTTTTCAGTGTAAATTTTACACTCCATAA---GTT
          1 ATTTTTCTTATAGGATTATTATACAATACA-ATATCAGTGTAAATTTTA-ACTCCATAAGCGGTT

              *       * *   *             *                  * *            *
       3325 AAGAAGTTGAAACATAGCACATTTCATAATCAATTAAATATTTAATATCAACACATATTCCTTAC
         64 AATAAGTTGACATATACCACATTTCATAATTAA-TAAATATTTAATATCTATACATATTCC-TAA

              **                   *  *   **  *              *   *           
       3390 GGAAACACATGTCAACCCTTAAATCCTGCATTTGTAGTCTGCTAAATTCGACTGACGGTGCATAG
        127 GGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAATTCCACTAACGGTGCATAG

                
       3455 TATA
        192 TATA

                                          * *        *                       
       3459 ATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTACATTTTAGACTCCATAAGCGGTTT
          1 ATTTTTCTTATAGGATTATTATACAATACAATATCAGTGTAAATTTTA-ACTCCATAAGCGG-TT

                 *            * *  *                                         
       3524 AATAATTTGACATATACCCCGTTACATAATTAATAAAATATTTAATATCTATACATATTCTCTAA
         64 AATAAGTTGACATATACCACATTTCATAATTAAT-AAATATTTAATATCTATACATATTC-CTAA

                                                                    *   *    
       3589 GGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAA-TCCACTAACTGTGTATAG
        127 GGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAATTCCACTAACGGTGCATAG

                
       3653 TATA
        192 TATA

                                                                             
       3657 ATTTTTCTTATAGGATTATTATACAATACAATATCAGTGTAAGATTTGT-ACTCCATAAGCGGGT
          1 ATTTTTCTTATAGGATTATTATACAATACAATATCAGTGTAA-ATTT-TAACTCCATAAGC-GGT

                             * *               *                     *       
       3721 TAATAAGTTGACATATATCTCATTTCATAATTAATTAATATTTAATAT-TAATACATCTTCCCTA
         63 TAATAAGTTGACATATACCACATTTCATAATTAATAAATATTTAATATCT-ATACATATT-CCTA

                       
       3785 AGGGGACACAT
        126 AGGGGACACAT


Statistics
Matches: 288,  Mismatches: 38, Indels: 21
        0.83            0.11        0.06

Matches are distributed among these distances:
 195   24  0.08
 196   30  0.10
 197   34  0.12
 198  102  0.35
 199   96  0.33
 200    2  0.01

ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36


Consensus pattern (195 bp):   
ATTTTTCTTATAGGATTATTATACAATACAATATCAGTGTAAATTTTAACTCCATAAGCGGTTAA
TAAGTTGACATATACCACATTTCATAATTAATAAATATTTAATATCTATACATATTCCTAAGGGG
ACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAATTCCACTAACGGTGCATAGTATA
Done.