Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005651.1 Corchorus capsularis cultivar CVL-1 contig05669, 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: 2084
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24


Found at i:1068 original size:67 final size:68

Alignment explanation


    Indices: 804--1292  Score: 758
    Period size: 67  Copynumber: 7.3  Consensus size: 68

        794 AGGACCAAAC

                                *                       *                    
        804 AAACGATCCTTGAATCGT-AGACTTAAGCGAGACGAACGTCTCCTTTGAGACCGTTTTGCTAAAA
          1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAA

               
        868 TGA
         66 TGA

                                                           *         *       
        871 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTAAGACCGTTTGGCTAAAA
          1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAA

               
        936 TGA
         66 TGA

                                                           *         *       
        939 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTAAGACCGTTTGGCTAAAA
          1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAA

               
       1004 TGA
         66 TGA

                                *                         *                 *
       1007 AAACGATCCTTGAATCGT-AGACTTAAGCGAGACGAACGTCTCCCTCGAGACCGTTTTGCTAAAG
          1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAA

               
       1071 TG-
         66 TGA

                 *                 *              *      **                * 
       1073 -AACGGTCCTTGAATCGTAAAACATAAGCGAGACGAACATCTCCCGCGAGACCGTTTTGCTAAGA
          1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAA

               
       1137 T-A
         66 TGA

                                                                           * 
       1139 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAGA
          1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAA

               
       1204 T-A
         66 TGA

                                                                      *    * 
       1206 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTACTAAGA
          1 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAA

               
       1271 T-A
         66 TGA

                       *        
       1273 AAACGATCCTTAAATCGTAA
          1 AAACGATCCTTGAATCGTAA

       1293 GTTCGAGATT


Statistics
Matches: 395,  Mismatches: 23, Indels: 8
        0.93            0.05        0.02

Matches are distributed among these distances:
  65   16  0.04
  66   41  0.10
  67  207  0.52
  68  131  0.33

ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24


Consensus pattern (68 bp):   
AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAA
TGA

Found at i:1233 original size:200 final size:202

Alignment explanation


    Indices: 804--1292  Score: 768
    Period size: 200  Copynumber: 2.4  Consensus size: 202

        794 AGGACCAAAC

                                                       *                     
        804 AAACGATCCTTGAATCGTAGACTTAAGCGAGACGAACGTCTCCTTTGAGACCGTTTTGCTAAAAT
          1 AAACGATCCTTGAATCGTAGACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAAT

                                     *              *      **                
        869 GAAAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTAAGACCGTTTGGCTAA
         66 G-AAACGATCCTTGAATCGTAAAACATAAGCGAGACGAACATCTCCCGCAAGACCGTTTGGCTAA

                                                                             
        934 AATGAAAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTAAGACCGTTTGGC
        130 AATGAAAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTAAGACCGTTTGGC

                    
        999 TAAAATGA
        195 TAAAATGA

                                                         *                 * 
       1007 AAACGATCCTTGAATCGTAGACTTAAGCGAGACGAACGTCTCCCTCGAGACCGTTTTGCTAAAGT
          1 AAACGATCCTTGAATCGTAGACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAAT

                  *                                         *         *     *
       1072 G-AACGGTCCTTGAATCGTAAAACATAAGCGAGACGAACATCTCCCGCGAGACCGTTTTGCTAAG
         66 GAAACGATCCTTGAATCGTAAAACATAAGCGAGACGAACATCTCCCGCAAGACCGTTTGGCTAAA

                                                               *         *   
       1136 AT-AAAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCT
        131 ATGAAAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTAAGACCGTTTGGCT

              *    
       1200 AAGAT-A
        196 AAAATGA

                                *                                     *    * 
       1206 AAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTACTAAGA
          1 AAACGATCCTTGAATCGT-AGACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAA

             *           *        
       1271 TAAAACGATCCTTAAATCGTAA
         65 TGAAACGATCCTTGAATCGTAA

       1293 GTTCGAGATT


Statistics
Matches: 262,  Mismatches: 22, Indels: 6
        0.90            0.08        0.02

Matches are distributed among these distances:
 199   19  0.07
 200  106  0.40
 201   74  0.28
 203   63  0.24

ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24


Consensus pattern (202 bp):   
AAACGATCCTTGAATCGTAGACTTAAGCGAGACGAACGTCTCCCTTGAGACCGTTTTGCTAAAAT
GAAACGATCCTTGAATCGTAAAACATAAGCGAGACGAACATCTCCCGCAAGACCGTTTGGCTAAA
ATGAAAACGATCCTTGAATCGTAAAACTTAAGCGAGACGAACGTCTCCCTTAAGACCGTTTGGCT
AAAATGA
Done.