Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006270.1 Corchorus olitorius cultivar O-4 contig06295, 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, 712

Length: 1188
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38


Found at i:698 original size:331 final size:326

Alignment explanation


    Indices: 17--1081  Score: 1160
    Period size: 331  Copynumber: 3.2  Consensus size: 326

          7 TTTAAAAATC

                        *  * *    *      *                                   
         17 TGTTTTTACGAGCATTTGAATCATGTTTCAATTTAATTAGAAATTAATTTGAAAAAAAATAGGAA
          1 TGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTG-AAAAAAATAGGAA

                                                                             
         82 AAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAG
         65 AAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAG

                * **                   *                *         *          
        147 TATTGTGGCTAAAAATTGA-GAAAAATATTTCGGGTCAATTTTTTCAAAATTTTTGCCGAAATCG
        130 TATTTTAACTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCG

                                 *         **  *   *   *   **         *      
        211 TGT--ACCATCATGGTTTTTTAGCTAAAAACATGTACAGGGGCCCTAGGTCAGTTTTGGATGATT
        195 TGTACACCATCATGG-TTTTTGGCTAAAAACGCGTTCAGAGGCAC-AACTCAGTTTTGCATGATT

                   *      *                  *   *                           
        274 TTTGGCGGCAAGACCCCTTAAATTTTGGATGATTTATATATATATCATCTAACCAAATCTCAGCC
        258 TTTGGCGCCAAGACTCC-------TT-GA--A-ATATCTATAT-TCATCTAA-CAAATCTCAGCC

                              
        339 ACATTGTATTTAAGGATT
        310 ACATTG-ATTTAAGGATT

                         *                                                   
        357 TGTTTTTACGAGTTTCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTTGAAATAAAATAGGA
          1 TGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAATTAA-TTTGAAA-AAAATAGGA

                *           *         * *  *   *                             
        422 AAAATGATATTAGAAGTGTGAAAAAGGCTTTTAATTTTTTTGGCGTTGAATTATATATTATTTAT
         64 AAAACGATATTAGAAGCGTG-AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATT-TTTAT

                     *    *    **                                            
        487 GAGTATTTTCACTAGAAATCAAGGAAAAATCTTTCGGGTCAATTTTTACAAAA-TTTAGCCGAAA
        127 GAGTATTTTAACTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAA

                                  *                *     * *                 
        551 TCGTGTACACCATCATGGTTTTCGGCTAAAAACGCGTTCCGAGGCGCGACTCAGTTTTGCATGAT
        192 TCGTGTACACCATCATGGTTTTTGGCTAAAAACGCGTTCAGAGGCACAACTCAGTTTTGCATGAT

                  *                                                          
        616 TTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACGAAATCTCAGCCACATTAGATTT
        257 TTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAAC-AAATCTCAGCCACATT-GATTT

                   
        681 AAGGATT
        320 AAGGATT

                        *                          *         * *             
        688 TGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAATAGGAAA
          1 TGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATAGGAAA

               *        *    *                     ***                       
        753 AACAATATTAGATGCGTTAAAAGCCCTTCAATCTTTTTGATATTGAATTATATATTTTTTATGAG
         66 AACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAG

                                    **      *  *                     *      *
        818 TATTTTAAC-AAAAATTTGAGGAATTATCTTTTGGATCAATTTTTACAAAATTTTAGTCGAAATT
        130 TATTTTAACTAAAAA-TTGAGGAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATC

                                               *                  *          
        882 GTGTACTACCATCATGGGTTTTTGGCTAAAAACGCATT-AGAGGGCCACAACTCTGTTTTGCATG
        194 GTGTAC-ACCATCAT-GGTTTTTGGCTAAAAACGCGTTCAGA-GG-CACAACTCAGTTTTGCATG

                 *   ** *         *        *                                 
        946 ATTTTCGGCATCGAGACTCCTTAAAATATCTTTATTCATCTAATCAAATCTCAGCCACATTGGAT
        255 ATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAA-CAAATCTCAGCCACATT-GAT

                     
       1011 TTAAGG-TT
        318 TTAAGGATT

              *     *         *                                          *   
       1019 TGCTTTTATGTA-TATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TT-AAAAAAATATGAA
          1 TGTTTTTACG-AGTATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATAGGAA

             
       1081 A
         65 A

       1082 CAAAAATTTG


Statistics
Matches: 620,  Mismatches: 87, Indels: 47
        0.82            0.12        0.06

Matches are distributed among these distances:
 327    4  0.01
 328   74  0.12
 329   55  0.09
 330   17  0.03
 331  143  0.23
 332   87  0.14
 333    2  0.00
 335    2  0.00
 336    2  0.00
 340   44  0.07
 341   31  0.05
 342   34  0.05
 343   66  0.11
 344   49  0.08
 345   10  0.02

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


Consensus pattern (326 bp):   
TGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATAGGAAA
AACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGT
ATTTTAACTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGT
GTACACCATCATGGTTTTTGGCTAAAAACGCGTTCAGAGGCACAACTCAGTTTTGCATGATTTTT
GGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAATCTCAGCCACATTGATTTAAGGAT
T
Done.