Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023860.1 Corchorus olitorius cultivar O-4 contig23893, 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, 630

Length: 1051
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Found at i:752 original size:322 final size:319

Alignment explanation


    Indices: 167--982  Score: 1084
    Period size: 322  Copynumber: 2.5  Consensus size: 319

        157 GTTTTTTTTT

                   *                  *              *    *         *       *
        167 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAATCAAACCCTTAAATCCAATGTGGT
          1 ATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGC

              *  *      *   *                        *               *      *
        232 TGAGACTTGGTTAGATGAATATAGATATTTTTAAGGAGCCTTTTTGCCAAAAAT-ATTCAAAACC
         66 TGGGATTTGGTTCGATAAATATAGATA-TTTTAAGGAG--TCTTTGCCAAAAATCATACAAAACT

                          *     *         *                       *          
        296 GAGCTGGGG-CCCGAAACGCATTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTAAGCTA
        128 GAGC-GGGGACCCGGAACGCGTTTTTAG-CAAAAAACCGTGATGGTTAGTACACAATTTAAGCTA

                                         **                                  
        360 AAAACTGAGTCGAAATTTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
        191 AAAACTGAGTCGAAATTTTTTTTTCTGAAACTTTTGCCACAATACTCAGAAAAAATATATAATTC

                                        *                           *       
        425 AACGCCAAAAAGAATGACACGCTTTTCATGCTTATAATATCATTTTTCCATTTTTTCGGAATTA
        256 AACGCCAAAAAGAATGACACGCTTTTCACGCTTATAATATCATTTTTCCATTTTTTAGGAATTA

                               *           *    *           *                
        489 ATTTCTATTTAAATCGAAATAAGATTCAGATACTCGAAAAAACAAATCGTTAAATCGAATGTGGC
          1 ATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGC

                                          *                          *       
        554 TGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTGCAACAAAAAATCATGCAAAACT
         66 TGGGATTTGGTTCGATAAATATAGATATTTTAAGGAGTCTTTGC--C-AAAAATCATACAAAACT

                      *        *                  *                    *     
        619 GAGTCGGGGAGCCGGAACGGGTTTTTAGCAAAAAACCGCGATGGTTAGTACACAATTTAGGCTAA
        128 GAG-CGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACAATTTAAGCTAA

                         *                               *                   
        684 AAACTGAGTCGAATTTTTTTTTTCTGAAACTTTTGCCACAATACTTAG-AAAAATATATAATTCA
        192 AAACTGAGTCGAAATTTTTTTTTCTGAAACTTTTGCCACAATACTCAGAAAAAATATATAATTCA

                        *    **             *                              
        748 ACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTAGGAATTA
        257 ACGCCAAAAAGAATGACACGCTTTTCACGCTTATAATATCATTTTTCCATTTTTTAGGAATTA

            *                                                   *           *
        811 TTTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATAT-GCAATGTGA
          1 ATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCG-AATGTGG

                       *                        *                            
        875 CTGGGATTTGGATCGA-AGAATATAGATATTTTAAGAAGTCTTTACGCCAAAAATCATACAAAAC
         65 CTGGGATTTGGTTCGATA-AATATAGATATTTTAAGGAGTCTTT--GCCAAAAATCATACAAAAC

                                        *               
        939 TGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACCGTGATG
        127 TGAG-CGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATG

        983 TACACGATTT


Statistics
Matches: 432,  Mismatches: 52, Indels: 21
        0.86            0.10        0.04

Matches are distributed among these distances:
 319    6  0.01
 321   66  0.15
 322  251  0.58
 323   92  0.21
 324   17  0.04

ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31


Consensus pattern (319 bp):   
ATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGC
TGGGATTTGGTTCGATAAATATAGATATTTTAAGGAGTCTTTGCCAAAAATCATACAAAACTGAG
CGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACAATTTAAGCTAAAAAC
TGAGTCGAAATTTTTTTTTCTGAAACTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC
CAAAAAGAATGACACGCTTTTCACGCTTATAATATCATTTTTCCATTTTTTAGGAATTA
Done.