Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002320.1 Corchorus capsularis cultivar CVL-1 contig02326, 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, 664

Length: 1107
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:210 original size:31 final size:30

Alignment explanation


    Indices: 172--339  Score: 123
    Period size: 31  Copynumber: 5.6  Consensus size: 30

        162 TTAGGTTAAT

                                           
        172 TGCTCAAATAAGGGCCTAACGTTTGCTAAAA
          1 TGCTCAAATAAGGGCCTAAC-TTTGCTAAAA

                          *    *         **
        203 TGCTCAAATAAGGGTCTGATCTTT--TAATT
          1 TGCTCAAATAAGGGCCT-AACTTTGCTAAAA

                                       *    
        232 TGAC-CAAATAAGGGCCTAACATTTGCCAAAA
          1 TG-CTCAAATAAGGGCCTAAC-TTTGCTAAAA

                             * *         **
        263 TGCTCAAATAAGGGCCCCATCTTTG--AATT
          1 TGCTCAAATAAGGG-CCTAACTTTGCTAAAA

                            *    *     *    
        292 TGGC-CAAATAAGGGCATAATGTTTGCAAAAA
          1 T-GCTCAAATAAGGGCCTAA-CTTTGCTAAAA

                             
        323 TGCTCAAATAAGGGCCT
          1 TGCTCAAATAAGGGCCT

        340 GTCTCACGTG


Statistics
Matches: 105,  Mismatches: 20, Indels: 24
        0.70            0.13        0.16

Matches are distributed among these distances:
  28    4  0.04
  29   37  0.35
  30    6  0.06
  31   52  0.50
  32    6  0.06

ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27


Consensus pattern (30 bp):   
TGCTCAAATAAGGGCCTAACTTTGCTAAAA

Found at i:263 original size:60 final size:60

Alignment explanation


    Indices: 176--338  Score: 236
    Period size: 60  Copynumber: 2.7  Consensus size: 60

        166 GTTAATTGCT

                                  *                  * **      *        
        176 CAAATAAGGGCCTAACGTTTGCTAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGAC
          1 CAAATAAGGGCCTAACGTTTGCAAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC

                            *     *                                   * 
        236 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
          1 CAAATAAGGGCCTAACGTTTGCAAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC

                       *   *                           
        296 CAAATAAGGGCATAATGTTTGCAAAAATGCTCAAATAAGGGCC
          1 CAAATAAGGGCCTAACGTTTGCAAAAATGCTCAAATAAGGGCC

        339 TGTCTCACGT


Statistics
Matches: 92,  Mismatches: 11, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  60   92  1.00

ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26


Consensus pattern (60 bp):   
CAAATAAGGGCCTAACGTTTGCAAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC

Found at i:410 original size:31 final size:31

Alignment explanation


    Indices: 372--440  Score: 120
    Period size: 31  Copynumber: 2.2  Consensus size: 31

        362 CACCAGACCT

                    *                      
        372 TTATTTGAGCATTTTCGATAACGTTAGGCCC
          1 TTATTTGAACATTTTCGATAACGTTAGGCCC

                                          *
        403 TTATTTGAACATTTTCGATAACGTTAGGCCT
          1 TTATTTGAACATTTTCGATAACGTTAGGCCC

                   
        434 TTATTTG
          1 TTATTTG

        441 GCCAAATTAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  31   36  1.00

ACGTcount: A:0.23, C:0.16, G:0.17, T:0.43


Consensus pattern (31 bp):   
TTATTTGAACATTTTCGATAACGTTAGGCCC
Done.