Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006416.1 Corchorus capsularis cultivar CVL-1 contig06437, 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, 957

Length: 1595
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36


Found at i:626 original size:332 final size:330

Alignment explanation


    Indices: 1--818  Score: 984
    Period size: 332  Copynumber: 2.5  Consensus size: 330

                                                   *         *               
          1 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTAAG-AAAAATATGAAA
          1 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAA

                          *            *                         *           
         65 AACGATATT-AAAAGGTCGAAAAGTCCCCCAATCTTTTTGGCGTTAAATTATAAATATTTTATGA
         66 AACGATATTAAAAACGT-GAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGA

                                        *    *        * *                    
        129 GTATTTTATCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTTCAAAATTTTAGCCAAAATCG
        130 GTATTTTATCCAAAAATTGAGGAAAAATCTTTCCGGTCATTTGTACAAAATTTTAGCCAAAATCG

             *  *                          *     *  *                        
        194 TGTAGTAACCATCACAGTTTTTGGCTAAAAACGCATTTCGGGGCCCTGACTCAGCATTGCATGAT
        195 TATAATAACCATCACAGTTTTTGGCTAAAAAAGCATTACGAGGCCC-GACTCAGCATTGCATGAT

            *   *     *                 *        *           *          *    
        259 TTTTGGCGCCGACACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTT
        259 CTTTCGCGCCAACACTCCTTGAAATATCCATATTCATATAATAAAATCTCAGCCACATTGAATTT

                   
        324 AAGAATT
        324 AAGAATT

                     *                          *                            
        331 TGTTTTTACCAGCATCTGAATCTTGTTTCGATTTAAATAAAAATTAATTCAGAAAAAATATGAAA
          1 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAA

               *                       * *              *           *        
        396 AACAATATTAAAAACGTGAAAAGTCCTTCTATCTTTTTGGCGTTGAATTATATATTCTTTTATGA
         66 AACGATATTAAAAACGTGAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATA-TATTTTATGA

                    *                *                                 *     
        461 GTATTTTAGCCAAAAATTGAGGAAATATCTTTCCGGTCAATTTGTACAAAATTTTAGCCGAAATC
        130 GTATTTTATCCAAAAATTGAGGAAAAATCTTTCCGGTC-ATTTGTACAAAATTTTAGCCAAAATC

                     *      *                           *       **           
        526 GTATAATAATCATC-CCGATTTTTGGCTAAAAAAGCATTAC-AGTCCC-AC-GGGCAATTTTGCA
        194 GTATAATAACCATCACAG-TTTTTGGCTAAAAAAGCATTACGAGGCCCGACTCAGC-A--TTGCA

             *           *  *                           * **                 
        587 TTATCTTTCGCGCTAAGACTCCTTGAAATATCCATATTCATATAGTCCAATCTCAGCCACATTGA
        255 TGATCTTTCGCGCCAACACTCCTTGAAATATCCATATTCATATAATAAAATCTCAGCCACATTGA

                   *   
        652 ATTTAAGGATT
        320 ATTTAAGAATT

                           *        *    *             *       *          *  
        663 TGTTTTTACGAGCATTTGAATCTTATTTCAATTTAATTAAAAAGTAATTCAAAAAAGAATATTAA
          1 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAA-AATATGAA

                     *    *  *               *        **                *    
        728 AAACGATATGAAAAGCGGGAAAAGTCCTCCAATTTTTTTGGCAATAAATTATATATATTTCATGA
         65 AAACGATATTAAAAACGTGAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGA

            *                          
        793 CTATTTTATCCAAAAATT-ATGGAAAA
        130 GTATTTTATCCAAAAATTGA-GGAAAA

        819 TTTTTTCTAG


Statistics
Matches: 412,  Mismatches: 66, Indels: 18
        0.83            0.13        0.04

Matches are distributed among these distances:
 329    2  0.00
 330   51  0.12
 331   53  0.13
 332  200  0.49
 333  106  0.26

ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36


Consensus pattern (330 bp):   
TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAA
AACGATATTAAAAACGTGAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAG
TATTTTATCCAAAAATTGAGGAAAAATCTTTCCGGTCATTTGTACAAAATTTTAGCCAAAATCGT
ATAATAACCATCACAGTTTTTGGCTAAAAAAGCATTACGAGGCCCGACTCAGCATTGCATGATCT
TTCGCGCCAACACTCCTTGAAATATCCATATTCATATAATAAAATCTCAGCCACATTGAATTTAA
GAATT
Done.