Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000706.1 Corchorus olitorius cultivar O-4 contig00706, 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, 684

Length: 1141
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36


Found at i:775 original size:86 final size:86

Alignment explanation


    Indices: 645--893  Score: 378
    Period size: 86  Copynumber: 2.9  Consensus size: 86

        635 TTTGCATGTT

                      * *             *              *                       
        645 CAGGGGCATTTTTGTCA-T-TTGCACGTCCAGGGGCATTTTAGTCATCTTGCACATCCAGGGGCA
          1 CAGGGGCATTATGGTCATTCTTGCACATCCAGGGGCATTTTGGTCATCTTGCACATCCAGGGGCA

                                 
        708 TTATGGTCATTTTCGCACCTC
         66 TTATGGTCATTTTCGCACCTC

                                                    *                        
        729 CAGGGGCATTATGGTCATTCTTGCACATCCAGGGGCATTTCGGTCATTCTTGCACATCCA-GGGC
          1 CAGGGGCATTATGGTCATTCTTGCACATCCAGGGGCATTTTGGTCA-TCTTGCACATCCAGGGGC

                  *               
        793 ATTATGATCATTTTCGCACCTC
         65 ATTATGGTCATTTTCGCACCTC

                                      *                    *                 
        815 CAGGGGCATTATGGTCATTCTTGCACCTCCAGGGGCATTTTGGTCATTTGTGCACATCCAGGGGC
          1 CAGGGGCATTATGGTCATTCTTGCACATCCAGGGGCATTTTGGTCATCT-TGCACATCCAGGGGC

               *          
        880 ATTTTGGTCATTTT
         65 ATTATGGTCATTTT

        894 TGCAGGTTCT


Statistics
Matches: 149,  Mismatches: 11, Indels: 7
        0.89            0.07        0.04

Matches are distributed among these distances:
  84   15  0.10
  85    3  0.02
  86  102  0.68
  87   29  0.19

ACGTcount: A:0.18, C:0.24, G:0.24, T:0.33


Consensus pattern (86 bp):   
CAGGGGCATTATGGTCATTCTTGCACATCCAGGGGCATTTTGGTCATCTTGCACATCCAGGGGCA
TTATGGTCATTTTCGCACCTC

Found at i:897 original size:29 final size:29

Alignment explanation


    Indices: 645--926  Score: 311
    Period size: 29  Copynumber: 9.9  Consensus size: 29

        635 TTTGCATGTT

                        *             *  
        645 CAGGGGCATTTTTGTCA--TTTGCACGTC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                        *      *         
        672 CAGGGGCATTTTAGTCA-TCTTGCACATC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                      *          *    *  
        700 CAGGGGCATTATGGTCATTTTCGCACCTC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                      *        *         
        729 CAGGGGCATTATGGTCATTCTTGCACATC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                       *       *         
        758 CAGGGGCATTTCGGTCATTCTTGCACATC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                      *  *       *    *  
        787 CA-GGGCATTATGATCATTTTCGCACCTC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                      *        *      *  
        815 CAGGGGCATTATGGTCATTCTTGCACCTC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                                *        
        844 CAGGGGCATTTTGGTCATTTGTGCACATC
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

                                     ** *
        873 CAGGGGCATTTTGGTCATTTTTGCAGGTT
          1 CAGGGGCATTTTGGTCATTTTTGCACATC

             *             **        
        902 CTGGGGCATTTTGGTTGTTTTTGCA
          1 CAGGGGCATTTTGGTCATTTTTGCA

        927 TACTTTAAGC


Statistics
Matches: 219,  Mismatches: 33, Indels: 4
        0.86            0.13        0.02

Matches are distributed among these distances:
  27   16  0.07
  28   45  0.21
  29  158  0.72

ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35


Consensus pattern (29 bp):   
CAGGGGCATTTTGGTCATTTTTGCACATC

Found at i:897 original size:115 final size:115

Alignment explanation


    Indices: 645--897  Score: 356
    Period size: 115  Copynumber: 2.2  Consensus size: 115

        635 TTTGCATGTT

                        *             *             *                        
        645 CAGGGGCATTTTTGTCA--TTTGCACGTCCAGGGGCATTTTAGTCATCTTGCACATCCAGGGGCA
          1 CAGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTGAGTCATCTTGCACATCCAGGGGCA

                                                              
        708 TTATGGTCATTTTCGCACCTCCAGGGGCATTATGGTCATTCTTGCACATC
         66 TTATGGTCATTTTCGCACCTCCAGGGGCATTATGGTCATTCTTGCACATC

                       *       *                            *       *        
        758 CAGGGGCATTTCGGTCATTCTTGCACATCCA-GGGCATTATGA-TCATTTTCGCACCTCCAGGGG
          1 CAGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATT-TGAGTCATCTT-GCACATCCAGGGG

                                              *                   
        821 CATTATGGTCATTCTT-GCACCTCCAGGGGCATTTTGGTCATT-TGTGCACATC
         64 CATTATGGTCATT-TTCGCACCTCCAGGGGCATTATGGTCATTCT-TGCACATC

                                     
        873 CAGGGGCATTTTGGTCATTTTTGCA
          1 CAGGGGCATTTTGGTCATTTTTGCA

        898 GGTTCTGGGG


Statistics
Matches: 124,  Mismatches: 10, Indels: 10
        0.86            0.07        0.07

Matches are distributed among these distances:
 113   15  0.12
 114   14  0.11
 115   93  0.75
 116    2  0.02

ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33


Consensus pattern (115 bp):   
CAGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTGAGTCATCTTGCACATCCAGGGGCA
TTATGGTCATTTTCGCACCTCCAGGGGCATTATGGTCATTCTTGCACATC

Found at i:1096 original size:15 final size:15

Alignment explanation


    Indices: 1076--1109  Score: 68
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       1066 GTACTATTTA

                           
       1076 CATTAGTCATGTTTG
          1 CATTAGTCATGTTTG

                           
       1091 CATTAGTCATGTTTG
          1 CATTAGTCATGTTTG

                
       1106 CATT
          1 CATT

       1110 TTGGACTATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47


Consensus pattern (15 bp):   
CATTAGTCATGTTTG
Done.