Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009003.1 Corchorus capsularis cultivar CVL-1 contig09024, 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, 1000

Length: 3152
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35


Found at i:58 original size:32 final size:31

Alignment explanation


    Indices: 24--225  Score: 148
    Period size: 29  Copynumber: 6.6  Consensus size: 31

         14 AACAATAATT

                  *                        *
         24 GTGTGCTTCTCCCGCACATCATATTAATATTT
          1 GTGTGCATCTCCCGCACA-CATATTAATATTC

                 * *                    *   
         56 GTGTGAACCTCCCGCACACTATATTAATGTTC
          1 GTGTGCATCTCCCGCACAC-ATATTAATATTC

                * *       *                
         88 GTGTACTTCTCCCGTACAC-TA-TAATATTC
          1 GTGTGCATCTCCCGCACACATATTAATATTC

            *                      *       
        117 ATGTGCATCTCCCGCACAC-T-TGAATATTC
          1 GTGTGCATCTCCCGCACACATATTAATATTC

            *     *     *          * *       
        146 ATGTGCGTCTCCTGCACACCATACTGATACTT-
          1 GTGTGCATCTCCCGCACA-CATATTAATA-TTC

                *         *         *      
        178 GTGTACATCTCCCGTACAC-TA-TCATATTC
          1 GTGTGCATCTCCCGCACACATATTAATATTC

            *                  
        207 ATGTGCATCTCCCGCACAC
          1 GTGTGCATCTCCCGCACAC

        226 TTTTTCTATC


Statistics
Matches: 133,  Mismatches: 30, Indels: 17
        0.74            0.17        0.09

Matches are distributed among these distances:
  28    2  0.02
  29   66  0.50
  30    5  0.04
  31    3  0.02
  32   55  0.41
  33    2  0.02

ACGTcount: A:0.23, C:0.30, G:0.13, T:0.33


Consensus pattern (31 bp):   
GTGTGCATCTCCCGCACACATATTAATATTC

Found at i:994 original size:85 final size:85

Alignment explanation


    Indices: 887--1124  Score: 440
    Period size: 85  Copynumber: 2.8  Consensus size: 85

        877 CCTTCATAAT

                          *  *                                               
        887 TTGGCTTTCTCTTCTTCCAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
          1 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT

                                
        952 TATGATAACTTTGCAGACCA
         66 TATGATAACTTTGCAGACCA

                                                                    *        
        972 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAAAGATTCTT
          1 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT

            *                   
       1037 CATGATAACTTTGCAGACCA
         66 TATGATAACTTTGCAGACCA

                                                                             
       1057 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
          1 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT

               
       1122 TAT
         66 TAT

       1125 AATTGGGATA


Statistics
Matches: 147,  Mismatches: 6, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  85  147  1.00

ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41


Consensus pattern (85 bp):   
TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
TATGATAACTTTGCAGACCA

Found at i:1162 original size:21 final size:21

Alignment explanation


    Indices: 1136--1179  Score: 88
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1126 ATTGGGATAA

                                 
       1136 CTTTGCAGACCATTATTTTTC
          1 CTTTGCAGACCATTATTTTTC

                                 
       1157 CTTTGCAGACCATTATTTTTC
          1 CTTTGCAGACCATTATTTTTC

              
       1178 CT
          1 CT

       1180 CTTTTTTTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48


Consensus pattern (21 bp):   
CTTTGCAGACCATTATTTTTC
Done.