Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010062.1 Corchorus capsularis cultivar CVL-1 contig10083, 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: 13579
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30


Found at i:2190 original size:67 final size:67

Alignment explanation


    Indices: 2061--2203  Score: 186
    Period size: 67  Copynumber: 2.2  Consensus size: 67

       2051 TCAATGTTTT

                               *                     *      *        *       
       2061 TCACATAAACATTTGAAGCCTGCAATTTGGAACAAATTAAGGCATATATACAATGATTAAAAAAA
          1 TCACATAAACATTTGAAGCATGCAATTTGGAACAAATTAAGACATATAAACAATGATAAAAAAAA

              
       2126 AA
         66 AA

                      *                                             *  *     
       2128 TCACATAAACCTTTGAAGCATGCAATTTGGAACAAATTAAGACATAT--ACAAT--CAATAAAAA
          1 TCACATAAACATTTGAAGCATGCAATTTGGAACAAATTAAGACATATAAACAATGATAAAAAAAA

              
       2189 AA
         66 AA

                  *      
       2191 TCACATCAACATT
          1 TCACATAAACATT

       2204 GTTATGATTT


Statistics
Matches: 68,  Mismatches: 8, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  63   19  0.28
  65    5  0.07
  67   44  0.65

ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25


Consensus pattern (67 bp):   
TCACATAAACATTTGAAGCATGCAATTTGGAACAAATTAAGACATATAAACAATGATAAAAAAAA
AA

Found at i:13049 original size:31 final size:30

Alignment explanation


    Indices: 13008--13083  Score: 98
    Period size: 30  Copynumber: 2.5  Consensus size: 30

      12998 GCTAAATATC

                 *                    *    
      13008 TAAAAAAATCCCTTATGTTTTGTTTTTGGGA
          1 TAAAATAATCCCTTATGTTTT-TTTTCGGGA

                       *                  
      13039 TAAAATAATCCATTATGTTTTTTTTCGGGA
          1 TAAAATAATCCCTTATGTTTTTTTTCGGGA

            *   *          
      13069 CAAATTAATCCCTTA
          1 TAAAATAATCCCTTA

      13084 CATTTCAAAA


Statistics
Matches: 39,  Mismatches: 6, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  30   20  0.51
  31   19  0.49

ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43


Consensus pattern (30 bp):   
TAAAATAATCCCTTATGTTTTTTTTCGGGA

Found at i:13276 original size:30 final size:31

Alignment explanation


    Indices: 13202--13276  Score: 100
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      13192 CCACATCAGC

                  *  *                     
      13202 AAGGGACTAATTTGTCCCAAACAAAAAACAT
          1 AAGGGATTATTTTGTCCCAAACAAAAAACAT

                                            
      13233 AAGGGATTATTTTGTCCCAAA-AGAAAAACAT
          1 AAGGGATTATTTTGTCCCAAACA-AAAAACAT

                    *     
      13264 AA-GGATTTTTTTG
          1 AAGGGATTATTTTG

      13277 ATATTTAGTC


Statistics
Matches: 40,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  30   11  0.28
  31   29  0.73

ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28


Consensus pattern (31 bp):   
AAGGGATTATTTTGTCCCAAACAAAAAACAT
Done.