Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010511.1 Corchorus olitorius cultivar O-4 contig10543, 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, 990

Length: 1651
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:773 original size:332 final size:331

Alignment explanation


    Indices: 1--1006  Score: 1017
    Period size: 331  Copynumber: 3.0  Consensus size: 331

                    * *             *                    *  *  *             
          1 CTAAAAACTCATTC-TAGTGCCCCATCTCAGTTTTGCATGACTTTTTGACGACGAGACTACCTTG
          1 CTAAAAACGCGTTCTTAG-GCCCCGTCTCAGTTTTGCATGACTTTCTGGCGCCGAGACT-CCTTG

                                                                     *       
         65 AAATATATATATTCATCTAATCAAATCTCAGCCACATTGGT-TTTAAGGATTTGTATATACGAGT
         64 AAATATATATATTCATCTAATCAAATCTCAGCCACATT-GTATTTAAGGATTTGT-TTTACGAGT

                         *                *        **                        
        129 A-C-GTAAATCATCTTTCGATTTAATATGACATTAATTCTTAAAAAATAGG-AAAACGATATTAG
        127 ATCTG-AAA-CATGTTTCGATTTAATATGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAG

                 *        *        *            *                            
        191 ACA-CATGAAAAG-GCTTTCAATATTTTTGGGCATTAAATTATATA-TTTTTAAGAGTATTTTGA
        190 A-AGCGTGAAAAGCCCTTT-AATCTTTTTGGG--TTGAATTATATATTTTTTAAGAGTATTTTGA

             *                                                   *    *      
        253 CTAAAAATTGAGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAACCGAAGTCGTGTACTAA
        251 CCAAAAATTGAGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTATACTAA

             *              
        318 CGATCACGGTTTTTGC
        316 CCATCACGGTTTTTGC

                    *               *     *         *              *         
        334 CTAAAAACTCGTTCTTAGGCCCCGGCTCAGATTTGCATGATTTTCT-GCGCCGAGTCTCCTTGAA
          1 CTAAAAACGCGTTCTTAGGCCCCGTCTCAGTTTTGCATGACTTTCTGGCGCCGAGACTCCTTGAA

                *                               *        *               *   
        398 ATATGTATATTCATCTAATCAAATCTCAGCCACATTTTATTTAAGAATTTGTTCTTACGAGCATC
         66 ATATATATATTCATCTAATCAAATCTCAGCCACATTGTATTTAAGGATTTGTT-TTACGAGTATC

                 *               *              *    *                       
        463 TGAAAAATGTTTCGATTTAATTTGAAATTAATTC-GGAAAATTAGGAAAAACGATATTAGAAGCG
        130 TGAAACATGTTTCGATTTAATATGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAGAAGCG

            *                                           *     *     *        
        527 CGAAAAGCCCTTTAATCTTTTTGGAGTTGAATTATATATTTTTTCAGAGTGTTTTGGCCAAAAAT
        195 TGAAAAGCCCTTTAATCTTTTTGG-GTTGAATTATATATTTTTTAAGAGTATTTTGACCAAAAAT

                 *    *            *                *                     *  
        592 TGAGGCAAAATATTTTGGGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATTAC
        259 TGAGGAAAAAAATTTTGGGTCA-ATTTTTGCAAAATTTTAACCGAAATCGTATACTAACCATCAC

                      
        657 GGTTTTTTG-
        323 GG-TTTTTGC

                            *       *               *                        
        666 CTAAAAACGCG-T-TTCGCGACCCTGTCTCAGTTTTGCATTA-TTTCTGGCGCCGAGACTCCTTG
          1 CTAAAAACGCGTTCTTAG-G-CCCCGTCTCAGTTTTGCATGACTTTCTGGCGCCGAGACTCCTTG

               *  *             *    *  *     *                              
        728 AAAAATCTATATTCATCTAACCAAAACTTAGCCAAATTGTATTTAAGGATTTGTTTTACGAGTAT
         64 AAATATATATATTCATCTAATCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTACGAGTAT

                 *  *                        *           *                   
        793 CTGAATCACGTTTCGATTTAATCA-GAAATTAAGTCAGAAAAGAAAAGGAAAAACGATATTAGAA
        129 CTGAAACATGTTTCGATTTAAT-ATGAAATTAATTCAGAAAA-AATAGGAAAAACGATATTAGAA

                            *  *   *          *              **        *   * 
        857 GCGTGAAAA-CACCTTCAACCTTCTTGGTGTTGATTTATATA-TTTTTATTAGTATTTTAACTTA
        192 GCGTGAAAAGC-CCTTTAATCTTTTTGG-GTTGAATTATATATTTTTTAAGAGTATTTTGAC-CA

                      **    * * *                    *  *   *   *  *         
        920 AAAA-TGA--TTAAAACTCTCGGGTCAATTTTTGCAAAATTGTAGCCGTAATTGTGTACTAACCA
        254 AAAATTGAGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTATACTAACCA

                         *
        982 TCACGGGTTTTTGG
        319 TCAC-GGTTTTTGC

                       
        996 CTAAAAACGCG
          1 CTAAAAACGCG

       1007 GTATGGGGCC


Statistics
Matches: 564,  Mismatches: 87, Indels: 47
        0.81            0.12        0.07

Matches are distributed among these distances:
 329   42  0.07
 330   49  0.09
 331  204  0.36
 332  165  0.29
 333  101  0.18
 334    3  0.01

ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Consensus pattern (331 bp):   
CTAAAAACGCGTTCTTAGGCCCCGTCTCAGTTTTGCATGACTTTCTGGCGCCGAGACTCCTTGAA
ATATATATATTCATCTAATCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTACGAGTATCT
GAAACATGTTTCGATTTAATATGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAGAAGCGT
GAAAAGCCCTTTAATCTTTTTGGGTTGAATTATATATTTTTTAAGAGTATTTTGACCAAAAATTG
AGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTATACTAACCATCACGGT
TTTTGC
Done.