Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001669.1 Corchorus capsularis cultivar CVL-1 contig01669, 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: 1736
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35


Found at i:1505 original size:323 final size:323

Alignment explanation


    Indices: 471--1658  Score: 1437
    Period size: 323  Copynumber: 3.7  Consensus size: 323

        461 TGTTCTTGCC

                  *                                        *         *       
        471 TAAAAATGCGTTCCGGAGCCCCGGCTCAATGTT-GCATGATTTTTGGTACAAAGACTTCTTGAAA
          1 TAAAAACGCGTTCCGGAGCCCCGGCTCAAT-TTCGCATGATTTTTGGCACAAAGACTCCTTGAAA

               *         *    *                *                   *     *  *
        535 TATTTATATTTATGGAACCAATTGTCAGCCACATTTGATATAAGGATTTGTTTTTAT-GAGAATT
         65 TATCTATATTTATCGAACAAATTGTCAGCCACATTGGATATAAGGATTTGTTTTTTTCGAGCATC

             *                                         *                     
        599 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAACTGAAAAAACGATATTAGAAGC
        130 TCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATTGAAAAAACGATATTAGAAGC

              *                     *     *                  *    *    *     
        663 GTAAAAAGCCCGTCAATCTTTTTGACGTTGTATTATATATTTTTTCTGATTATTATGGCGAAAAA
        195 GTGAAAAG-CCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA

                      *                     *                              **
        728 TTGAGAAAAATCTTTTCGGG-CAAGTTTTTAGTCGAAATCGTGTAATAACCATCACGGATTTTGG
        259 TTGAGAAAAAACTTTTCGGGTCAA-TTTTTAGCCGAAATCGTGTAATAACCATCACGG-TTTTTT

              
        792 GA
        322 GA

                    *   *             *                     *      *         
        794 TAAAAACGTGTTTCGGAGCCCCGGCTTAATTTCGCATGATTTTTGGCAGAAAGACACCTTGAAAT
          1 TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTCGCATGATTTTTGGCACAAAGACTCCTTGAAAT

                                          ***          *                     
        859 ATCTATATTTATCGAACAAAGTT-TCAGCCTTTTTGGATATAAAGATTTGTTTTTTTCGAGCATC
         66 ATCTATATTTATCGAACAAA-TTGTCAGCCACATTGGATATAAGGATTTGTTTTTTTCGAGCATC

                        **                    *                              
        923 TCAATCTTGTTTATATTTAATTAGAAATTAATTCTGAAAAAAATAATGAAAAAACGATATTAGAA
        130 TCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAT--TGAAAAAACGATATTAGAA

              *       *                                                 *    
        988 GCTTGGAAAACCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGTAAAA
        193 GCGT-GAAAAGCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAA

                                     *      *                        *       
       1053 AATTGAG-AAAAACTTTTCGGGTCAGTTTTTAACCGAAATCGTGTAATAACCATCACAG-TTTTT
        257 AATTGAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTT

              *
       1116 GCC
        322 G-A

                  *                *        *             *     *   *        
       1119 TAAAAATGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGTACAAAAACTTCTTGAAAT
          1 TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTCGCATGATTTTTGGCACAAAGACTCCTTGAAAT

              *              *           *     *                  *        * 
       1184 ATTTATATTTATCGAACCAATTGTCAGCCCCATTGAATATAAGGATTTGTTTTTGT-GAGCATTT
         66 ATCTATATTTATCGAACAAATTGTCAGCCACATTGGATATAAGGATTTGTTTTTTTCGAGCATCT

            *    *            *                               *    *         
       1248 GAATCGTGTTTCGATTTATTTAGAAATTAATTCAG-AAAAAATTGAAAAAGCGATTTTAGAAGCG
        131 CAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATTGAAAAAACGATATTAGAAGCG

                         *                       *                           
       1312 TGAAAAGCCGATCGATCTTTTTGGCGTTGAATTATATGTTTCTTT-T-AGTATTGTGGCAAAAAA
        196 TGAAAAGCCG-TCAATCTTTTTGGCGTTGAATTATATATTT-TTTCTGAGTATTGTGGCAAAAAA

                              *                *     *    *                  
       1375 TTGAGAAAAAAAACTTTTTGGGTCAATTTTTAGCCAAAATCATGTATTAACC-TCACGGTTTTTT
        259 TTGAG--AAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTT

             *
       1439 GT
        322 GA

                                 *                           *               
       1441 TAAAAACGCGTTCCGGGAGCCACGGCTCAATTTCGCATGATTTTTGGCAGAAAGACTCCTTGAAA
          1 TAAAAACGCGTTCC-GGAGCCCCGGCTCAATTTCGCATGATTTTTGGCACAAAGACTCCTTGAAA

                      *   *      * *       **        *                       
       1506 TATCTATATTCATCAAACAAAGTCTCAGCCATTTTGGATATTAGGATTTGTTTTTTTTCGAGCAT
         65 TATCTATATTTATCGAACAAATTGTCAGCCACATTGGATATAAGGATTTG-TTTTTTTCGAGCAT

                                                        *               **   
       1571 CTCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAATGAAAAAACGATATTCCAAG
        129 CTCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATTGAAAAAACGATATTAGAAG

             *  *                  
       1636 CTTGGAAAGCCCGTCAATCTTTT
        194 CGTGAAAAG-CCGTCAATCTTTT

       1659 AGCCAAAGAA


Statistics
Matches: 730,  Mismatches: 114, Indels: 39
        0.83            0.13        0.04

Matches are distributed among these distances:
 320   29  0.04
 321   49  0.07
 322   23  0.03
 323  231  0.32
 324   87  0.12
 325  144  0.20
 326   81  0.11
 327   82  0.11
 328    4  0.01

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


Consensus pattern (323 bp):   
TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTCGCATGATTTTTGGCACAAAGACTCCTTGAAAT
ATCTATATTTATCGAACAAATTGTCAGCCACATTGGATATAAGGATTTGTTTTTTTCGAGCATCT
CAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATTGAAAAAACGATATTAGAAGCG
TGAAAAGCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
GAGAAAAAACTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTTGA
Done.