Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005142.1 Corchorus capsularis cultivar CVL-1 contig05160, 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, 699

Length: 1165
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32


Found at i:1106 original size:321 final size:319

Alignment explanation


    Indices: 8--1108  Score: 1072
    Period size: 321  Copynumber: 3.4  Consensus size: 319

          1 CGGTGAT

                                 *          *         *                  *   
          8 TTTGTTAGATGAATATAGATAATTCAAGAAGTTTTTCTGCCATAAATCATGCGAAACTAAGCCGG
          1 TTTGTT-GATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAAC-AAGACGG

                                    *                               *        
         73 GGCTCCGAAACACGTTTTTAGCCCCAAAACCGTCATGGTTAGTACACGATTTCGGCTAAAAACTG
         64 GGCTCCGAAACACGTTTTTAGCCCAAAAACCGTCATGGTTAGTACACGATTTCGGCCAAAAACTG

                                                                             
        138 AGTCGAATTTCTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACACCA
        129 AGTCGAATTT-TTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACACCA

                                                                       **    
        203 AAAAGATTGACGGATCTTTTCAGAC-CTT-T-ACT-TCGTTTTTCCATTTTTTCCTAAAAAAATT
        193 AAAAGATTGACGGAT-TTTT-A-ACGCTTCTAACTATCGTTTTTCCATTTTTT--TAAATTAATT

                              *   *       *          *    *  *   *     **    
        264 TCTAATTAAATAGAATCAGGATACAGATACCCGTAAAAA-ATGTCCCTATATCTAATGCTCTTGA
        253 TCTAATTAAATAGAATCAAGATTCAGATACTCGTAAAAACAAGTCCTTAAATCCAATGCGATTGA

              
        328 G-
        318 GA

                           *       *              *                     *    
        329 --T-TTGATGAATATTGATATTTTAA-AGAGTC-TTCACGCCAAAAATCATGC-AAA-ATTGAGC
          1 TTTGTTGATGAATATAGATATTTCAAGA-AGTCTTTC-TGCCAAAAATCATGCGAAACA-AGA-C

             *        **  *        *   *         *                           
        387 TAGGGCTCCGGCACGCGTTTTTTTG-CAAAAAACCGTGATGGTTAGTACACGATTTCGGCTATAA
         62 -GGGGCTCCGAAACACG-TTTTTAGCCCAAAAACCGTCATGGTTAGTACACGATTTCGGC-----

                            **    * *         *   *              *          *
        451 TTTTGCAAAAAACTGACCCGAAATGTTTTTCCT-CAATTTTTGCCACAATACTGAGAAAAAATTT
        120 -----C-AAAAACTGAGTCGAATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAA-TA

               *       *             *  **    *                    *         
        515 TATGATTCAACGCCAAAAA-ATTGAAGGGGTTTTCACGCTTCTAA-TATCGTTTTCCCATTTTTA
        178 TATAATTCAACACCAAAAAGATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTT-

               *    *              *   *                          *          
        578 TTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATC
        242 TT-AAATTAATTTCTAATTAAATAGAATCAAGATTCAGATACTCGTAAAAACAAGTCCTTAAATC

             *   * **  *  
        643 CGATGTGGCTGTGA
        306 CAATGCGATTGAGA

                                               *          *           *  *   
        657 TCTTGTTGATGAATATAGATATTTCAAGAAGTCTTGCTGCCAAAAACCATGCGAAACTGAGCCGG
          1 T-TTGTTGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAAC-AAGACGG

                       *                                             *       
        722 GGCTCCGAAACGCGTTTTTAGCCTC-AAAACCGTCATGGTTAGTACACGATTTCGGCTAAAAACT
         64 GGCTCCGAAACACGTTTTTAGCC-CAAAAACCGTCATGGTTAGTACACGATTTCGGCCAAAAACT

                                                                           * 
        786 GAGTCGAATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACACTA
        128 GAGTCGAATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACACCA

                                                                             
        851 AAAAGATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTTTTAAATTAATTTCTAA
        193 AAAAGATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTTTTAAATTAATTTCTAA

                           *          *             *   *                 
        916 TTAAATAGAATCAAGTTTCAGATACTTGTAAAAACAAGTCATTACATCCAATGCGATTGAGA
        258 TTAAATAGAATCAAGATTCAGATACTCGTAAAAACAAGTCCTTAAATCCAATGCGATTGAGA

                            *          * *               *                   
        978 TTTGGTTAGATGAATAGAGATATTTCAGGGAGTCTTTCTGCCAAATATCATGCGAAACACAGACG
          1 TTT-GTT-GATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACA-AGACG

             **                   *        *   *   *         *               
       1043 GAAC-CTCGAAACACGTTTTTAACCCAAAAATCGTGAT-TTTAGTACACAATTTCGGCCAAAAAC
         63 GGGCTC-CGAAACACGTTTTTAGCCCAAAAACCGTCATGGTTAGTACACGATTTCGGCCAAAAAC

               
       1106 TGA
        127 TGA

       1109 TCTGAAAATT


Statistics
Matches: 621,  Mismatches: 114, Indels: 90
        0.75            0.14        0.11

Matches are distributed among these distances:
 314    1  0.00
 315    1  0.00
 316    8  0.01
 317   76  0.12
 318    8  0.01
 319    1  0.00
 320    2  0.00
 321  133  0.21
 322  123  0.20
 323   19  0.03
 324    3  0.00
 325    7  0.01
 326   87  0.14
 327   42  0.07
 328   14  0.02
 331    7  0.01
 332   81  0.13
 333    7  0.01
 334    1  0.00

ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32


Consensus pattern (319 bp):   
TTTGTTGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCGAAACAAGACGGGG
CTCCGAAACACGTTTTTAGCCCAAAAACCGTCATGGTTAGTACACGATTTCGGCCAAAAACTGAG
TCGAATTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAA
AGATTGACGGATTTTTAACGCTTCTAACTATCGTTTTTCCATTTTTTTAAATTAATTTCTAATTA
AATAGAATCAAGATTCAGATACTCGTAAAAACAAGTCCTTAAATCCAATGCGATTGAGA
Done.