Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000254.1 Corchorus olitorius cultivar O-4 contig00254, 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, 833

Length: 1389
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42


Found at i:47 original size:30 final size:30

Alignment explanation


    Indices: 11--604  Score: 818
    Period size: 30  Copynumber: 19.8  Consensus size: 30

          1 GCTTCATCAA

                              *       *   
         11 TAATCCTGTTTGAGGATCGTTGCTTTGTTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                         *    *       *   
         41 TAATCCTGTTTGATGATCTTTGCTTTGTTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

            *                 *       *   
         71 AAATCCTGTTTGAGGATCTTTGCTTTGTTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                              *       *   
        101 TAATCCTGTTTGAGGATCTTTGCTTTGTTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                    *                     
        131 TAATCCTGGTTGAGGATCATTG-TTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                    *                      
        160 TAATCCTGGTTGAGGATCATTG-TTTCATTT
          1 TAATCCTGTTTGAGGATCATTGCTTT-ATTT

                                     *    
        190 TAATCCTGTTTGAGGATCATTGCTTCATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

            *       *                     
        220 CAATCCTGGTTGAGGATCATTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                  *           **          
        250 TAATCCCGTTTGAGGATCGCTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

            *       *                     
        280 CAATCCTGGTTGAGGATCATTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                                     *    
        310 TAATCCTGTTTGAGGATCATTGCTTCATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

            *       *                     
        340 CAATCCTGGTTGAGGATCATTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                              **          
        370 TAATCCTGTTTGAGGATCGCTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

            *       *                     
        400 CAATCCTGATTGAGGATCATTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                              **          
        430 TAATCCTGTTTGAGGATCGCTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                    *         *           
        460 TAATCCTGGTTGAGGATCGTTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                    *                     
        490 TAATCCTGGTTGAGGATCATTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                    *                     
        520 TAATCCTGATTGAGGATCATTGCTTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                    *                     
        550 TAATCCTGATTGAGGATCATTG-TTTATTT
          1 TAATCCTGTTTGAGGATCATTGCTTTATTT

                           *           
        579 TAAATCCTGGTTT-ATGATCATTGCTT
          1 T-AATCCT-GTTTGAGGATCATTGCTT

        605 CAGTTTATTT


Statistics
Matches: 512,  Mismatches: 47, Indels: 9
        0.90            0.08        0.02

Matches are distributed among these distances:
  29   39  0.08
  30  466  0.91
  31    7  0.01

ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47


Consensus pattern (30 bp):   
TAATCCTGTTTGAGGATCATTGCTTTATTT

Found at i:987 original size:28 final size:28

Alignment explanation


    Indices: 945--1015  Score: 90
    Period size: 28  Copynumber: 2.5  Consensus size: 28

        935 TGTAGACACC

                  *        *    *        
        945 CATTTTTGTCATTTTTCACATTTC-GGGG
          1 CATTTTGGTCATTTTGCAC-GTTCAGGGG

                      *                 
        973 CATTTTGGTCGTTTTGCACGTTCAGGGG
          1 CATTTTGGTCATTTTGCACGTTCAGGGG

                           
       1001 CATTTTGGTCATTTT
          1 CATTTTGGTCATTTT

       1016 AGGTTCACTT


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  27    3  0.08
  28   34  0.92

ACGTcount: A:0.13, C:0.17, G:0.23, T:0.48


Consensus pattern (28 bp):   
CATTTTGGTCATTTTGCACGTTCAGGGG
Done.