Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001675.1 Corchorus olitorius cultivar O-4 contig01675, 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, 682

Length: 1138
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21


Found at i:876 original size:41 final size:42

Alignment explanation


    Indices: 777--1100  Score: 349
    Period size: 43  Copynumber: 7.7  Consensus size: 42

        767 TAACCAAAAC

                *                    *      *      *     
        777 GTCCCCAAACACATATATAACACAGGGGCAATTCTAT-TCCAAAA
          1 GTCCTCAAACACATATATAACACAGAGGC-A-CCTATATAC-AAA

                     *                **         *    
        821 GTCCTCAAATACATATATAACACAGATACACCTATATGC-AA
          1 GTCCTCAAACACATATATAACACAGAGGCACCTATATACAAA

                *                    *       *         
        862 GTCCCCAAACAC--ATATAACACAGGGGCACCTTTATTACAAA
          1 GTCCTCAAACACATATATAACACAGAGGCACCTATA-TACAAA

                                                 *    
        903 GTCCTCAAACACATATATAACACAGAGGCACCTATATTC-AA
          1 GTCCTCAAACACATATATAACACAGAGGCACCTATATACAAA

                *                    *      *           
        944 GTCCCCAAACACATATATAACACAGGGGCAATTCTAT-TACAAA
          1 GTCCTCAAACACATATATAACACAGAGGC-A-CCTATATACAAA

                                          **          
        987 GTCCTCAAACACATATATAACACAGAGGCATTTATAT-CAAA
          1 GTCCTCAAACACATATATAACACAGAGGCACCTATATACAAA

                *                    *                  
       1028 GTCCCCAAACACATATATAACACAGGGGCATCTCTAT-TACAAA
          1 GTCCTCAAACACATATATAACACAGAGGCA-C-CTATATACAAA

                                          
       1071 GTCCTCAAACACATATATAACACAGAGGCA
          1 GTCCTCAAACACATATATAACACAGAGGCA

       1101 TTTCTCCTTA


Statistics
Matches: 237,  Mismatches: 31, Indels: 25
        0.81            0.11        0.09

Matches are distributed among these distances:
  39   18  0.08
  40    2  0.01
  41   90  0.38
  42   12  0.05
  43   91  0.38
  44   24  0.10

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (42 bp):   
GTCCTCAAACACATATATAACACAGAGGCACCTATATACAAA

Found at i:987 original size:84 final size:84

Alignment explanation


    Indices: 777--1100  Score: 505
    Period size: 84  Copynumber: 3.9  Consensus size: 84

        767 TAACCAAAAC

                                                  *              *           
        777 GTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAATACATATATAAC
          1 GTCCCCAAACACATATATAACACAGGGGCAATTCTATTAC-AAAGTCCTCAAACACATATATAAC

                 **         *   
        842 ACAGATACACCTATATGCAA
         65 ACAGAGGCACCTATATTCAA

                                           *                                 
        862 GTCCCCAAACAC--ATATAACACAGGGGCACCTT-TATTACAAAGTCCTCAAACACATATATAAC
          1 GTCCCCAAACACATATATAACACAGGGGCA-ATTCTATTACAAAGTCCTCAAACACATATATAAC

                                
        924 ACAGAGGCACCTATATTCAA
         65 ACAGAGGCACCTATATTCAA

                                                                             
        944 GTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAACA
          1 GTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAACA

                    **          
       1009 CAGAGGCATTTATA-TCAAA
         66 CAGAGGCACCTATATTC-AA

                                                                             
       1028 GTCCCCAAACACATATATAACACAGGGGC-ATCTCTATTACAAAGTCCTCAAACACATATATAAC
          1 GTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATATAAC

                     
       1092 ACAGAGGCA
         65 ACAGAGGCA

       1101 TTTCTCCTTA


Statistics
Matches: 224,  Mismatches: 9, Indels: 13
        0.91            0.04        0.05

Matches are distributed among these distances:
  82   52  0.23
  83   27  0.12
  84  133  0.59
  85   12  0.05

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (84 bp):   
GTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATAACA
CAGAGGCACCTATATTCAA

Found at i:1101 original size:43 final size:43

Alignment explanation


    Indices: 777--1101  Score: 368
    Period size: 41  Copynumber: 7.7  Consensus size: 43

        767 TAACCAAAAC

                                     *             *     
        777 GTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTCCAAAA
          1 GTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC-AAA

                *    *                **           *    
        821 GTCCTCAAATACATATATAACACAGATACA-C-CTATATGC-AA
          1 GTCCCCAAACACATATATAACACAGAGGCATCTCTAT-TACAAA

                                     *    *  *         
        862 GTCCCCAAACAC--ATATAACACAGGGGCACCTTTATTACAAA
          1 GTCCCCAAACACATATATAACACAGAGGCATCTCTATTACAAA

                *                         *  *         
        903 GTCCTCAAACACATATATAACACAGAGGCACCTATATT-C-AA
          1 GTCCCCAAACACATATATAACACAGAGGCATCTCTATTACAAA

                                     *                  
        944 GTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAA
          1 GTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTACAAA

                *                                       
        987 GTCCTCAAACACATATATAACACAGAGGCAT-T-TA-TATCAAA
          1 GTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-CAAA

                                     *                 
       1028 GTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAA
          1 GTCCCCAAACACATATATAACACAGAGGCATCTCTATTACAAA

                *                          
       1071 GTCCTCAAACACATATATAACACAGAGGCAT
          1 GTCCCCAAACACATATATAACACAGAGGCAT

       1102 TTCTCCTTAT


Statistics
Matches: 241,  Mismatches: 26, Indels: 29
        0.81            0.09        0.10

Matches are distributed among these distances:
  39   13  0.05
  40    5  0.02
  41   97  0.40
  42   11  0.05
  43   89  0.37
  44   26  0.11

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22


Consensus pattern (43 bp):   
GTCCCCAAACACATATATAACACAGAGGCATCTCTATTACAAA

Done.