Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005518.1 Corchorus capsularis cultivar CVL-1 contig05536, 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, 929

Length: 1549
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37


Found at i:962 original size:325 final size:317

Alignment explanation


    Indices: 1--1170  Score: 1490
    Period size: 325  Copynumber: 3.6  Consensus size: 317

                                 *                                           
          1 TCATGATTTTTGGCAGAAAGCGTCCTTGAAATATCTAAATTCATCGAACCAAATCTCAGCCACAA
          1 TCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTAAATTCATCGAACCAAATCTCAGCCACAA

                   *               *         *   *             *             
         66 TGGATTTCAGGATTTGTTTTTACAAGCATCTGATTTTTTTTCGGTTTAATTTAAAATAAATTAGG
         66 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTGTTTCGGTTTAATTAAAAATAAATTAGG

                                                *                    *       
        131 -AAAAATGGAAAAACTAT-TTCGGAAACGTGAAAAACCCTTCAATTTTTTTTGCTTTGAATTAAA
        131 AAAAAATGGAAAAACTATATT-GGAAACGTGAAAAATCCTTCAATTTTTTTTGCTTTAAATTAAA

                        *       **                  *                   *    
        194 TATTTTTTCTGATTATTGTGACGAAAATTTCAGAAAAAAACTTTCGGGTCACTTTTTAGCCGAAA
        195 TATTTTTTCTGAGTATT-TGGTGAAAATTTCAGAAAAAAAATTTCGGGTCACTTTTTAGCAGAAA

                  *                 *                          *          
        259 T-TGT-GT-ACTATCACGG-TTTTGGGGATAAAAAACGCGTTTTGGGGCCTATCTCAGTTTT
        259 TCTGTACTAACTATCACGGTTTTTTGGG-T-AAAAACGCGTTTTGGGGCC-GTCTCAGTTTT

                       *  *                                       *          
        317 TCATGATTTTTTGCTGAAAGCCTCCTTGAAATATCTAAATTCATCGAACCAAATTTCAGCCACAA
          1 TCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTAAATTCATCGAACCAAATCTCAGCCACAA

                       *   **     *                  *                       
        382 TGGATTT-AGGGTTTAATTTTATGAGCATCTGAATTTGTTTTGGTTTAATTAAAAATAAATTAGG
         66 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTGTTTCGGTTTAATTAAAAATAAATTAGG

            *            * *           *        *                            
        446 GAAAAATGGAAAACCGATATTGGAAACATGAAAAATTCTTCAATATTTTTTTTTGCTTTAAATTA
        131 AAAAAATGGAAAAACTATATTGGAAACGTGAAAAATCCTTC-A-A-TTTTTTTTGCTTTAAATTA

            *           *           *      *          *        *           * 
        511 CATATTTTTTCTAAGTATTTAGGTTAAAATTCCAGAAAAAAATTTTCGGGTAACTTTTTAGCAAA
        193 AATATTTTTTCTGAGTATTT-GGTGAAAATTTCAGAAAAAAAATTTCGGGTCACTTTTTAGCAGA

                          *           *                                     
        576 AATCGTGTACTAACCATCACGGTTTTGTGGGTAAAAACGCGTTTTGTGGGCCCGTCTCAGTTTT
        257 AATC-TGTACTAACTATCACGGTTTTTTGGGTAAAAACGCGTTTTG-GGG-CCGTCTCAGTTTT

            *                                    *             *             
        640 CCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTATATTCATCGAACCATATCTCAGCCACAA
          1 TCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTAAATTCATCGAACCAAATCTCAGCCACAA

              *                          *                      *         *  
        705 TGCATTTAAGGATTTGTTTTTACGAGCATATGAATTTGTTTCGGTTTAATTAGAAATAAATTTGG
         66 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTGTTTCGGTTTAATTAAAAATAAATTAGG

                            *         *                 **                   
        770 AAAAAAATGGAAAAACAATATTGGAAGCGTGAAAAATCCTTCTTTTTTTTTTTTGCTTTAAATTA
        131 -AAAAAATGGAAAAACTATATTGGAAACGTGAAAAATCCTTC--AATTTTTTTTGCTTTAAATTA

                           *                   *            * *              
        835 AATATTTTTTCTGAGAATTATGGTGAAAATTTCATAAAAAAAAATTTCAGATCACTTTTTAGCAG
        193 AATATTTTTTCTGAGTATT-TGGTGAAAATTTCA-GAAAAAAAATTTCGGGTCACTTTTTAGCAG

                          *     *        *     *  * *                        
        900 AAATCATGTACTAATTATCATGGTTTTTTAGGTAATAATGTGTTTTGAGGGTCCGTCTCAGTTTT
        256 AAATC-TGTACTAACTATCACGGTTTTTTGGGTAAAAACGCGTTTTG-GGG-CCGTCTCAGTTTT

                  *              *                          *          *     
        965 TCATGAATTTTGGCAGAAAGCGTCCTTGAAATATCTAAATTCATCGAATCAAATCTCAGTCACAA
          1 TCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTAAATTCATCGAACCAAATCTCAGCCACAA

                                      *  *       *                           
       1030 TGGATTTAAGGATTTGTTTTTACGAGAATTTGAATTTTTTTCGGTTTAATTAAAAATAAATTAGG
         66 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTGTTTCGGTTTAATTAAAAATAAATTAGG

                                                        *           *     *  
       1095 AAAAAATGGAAAAACTATATTGGAAACGTGAAAAATCCTTCAATATTTTTTGCTTTCAATTACAT
        131 AAAAAATGGAAAAACTATATTGGAAACGTGAAAAATCCTTCAATTTTTTTTGCTTTAAATTAAAT

                       
       1160 ATTTTTTCTGA
        196 ATTTTTTCTGA

       1171 ATAAATTAGG


Statistics
Matches: 735,  Mismatches: 101, Indels: 30
        0.85            0.12        0.03

Matches are distributed among these distances:
 315   48  0.07
 316  100  0.14
 317    3  0.00
 318    2  0.00
 319   73  0.10
 321    3  0.00
 322   45  0.06
 323   88  0.12
 324  142  0.19
 325  231  0.31

ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38


Consensus pattern (317 bp):   
TCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTAAATTCATCGAACCAAATCTCAGCCACAA
TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTGTTTCGGTTTAATTAAAAATAAATTAGG
AAAAAATGGAAAAACTATATTGGAAACGTGAAAAATCCTTCAATTTTTTTTGCTTTAAATTAAAT
ATTTTTTCTGAGTATTTGGTGAAAATTTCAGAAAAAAAATTTCGGGTCACTTTTTAGCAGAAATC
TGTACTAACTATCACGGTTTTTTGGGTAAAAACGCGTTTTGGGGCCGTCTCAGTTTT

Found at i:1231 original size:87 final size:87

Alignment explanation


    Indices: 1084--1259  Score: 248
    Period size: 87  Copynumber: 2.0  Consensus size: 87

       1074 TTTAATTAAA

                               *                 *        *                  
       1084 AATAAATTAGGAAAAAATGGAAAAACTATATTGGAAACGTGAAAAATCCTTCAA-TATTTTTTGC
          1 AATAAATTAGGAAAAAATGAAAAAACTATATTGGAAAAGTGAAAAACCCTTCAATTATTTTTTGC

                     *            
       1148 TTTCAATTACATATTTTTTCTG
         66 TTTCAATTAAATATTTTTTCTG

                                               *                       *     
       1170 AATAAATTAGGAAAAAATTGAAAAAACTAT-TATGTAAAAGTGAAAAACCCTTCAATTTTTTTTT
          1 AATAAATTAGGAAAAAA-TGAAAAAACTATAT-TGGAAAAGTGAAAAACCCTTCAA-TTATTTTT

                  *                  
       1234 TGCTTTGAATTAAATATTTTTTCTG
         63 TGCTTTCAATTAAATATTTTTTCTG

             
       1259 A
          1 A

       1260 GTATTGTGAC


Statistics
Matches: 79,  Mismatches: 7, Indels: 5
        0.87            0.08        0.05

Matches are distributed among these distances:
  86   18  0.23
  87   31  0.39
  89   30  0.38

ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39


Consensus pattern (87 bp):   
AATAAATTAGGAAAAAATGAAAAAACTATATTGGAAAAGTGAAAAACCCTTCAATTATTTTTTGC
TTTCAATTAAATATTTTTTCTG
Done.