Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001020.1 Corchorus capsularis cultivar CVL-1 contig01020, 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: 17326
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:135 original size:31 final size:31

Alignment explanation


    Indices: 93--157  Score: 103
    Period size: 31  Copynumber: 2.1  Consensus size: 31

         83 TTGGGTTATC

                         *                 
         93 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
          1 AGTCTCCAGATCTCTAGATCTTGGATGTTTG

                  *            *           
        124 AGTCTCTAGATCTCTAGATTTTGGATGTTTG
          1 AGTCTCCAGATCTCTAGATCTTGGATGTTTG

               
        155 AGT
          1 AGT

        158 TAGTTCAGTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43


Consensus pattern (31 bp):   
AGTCTCCAGATCTCTAGATCTTGGATGTTTG

Found at i:15150 original size:38 final size:37

Alignment explanation


    Indices: 15101--15228  Score: 195
    Period size: 38  Copynumber: 3.4  Consensus size: 37

      15091 ACAGATTAAC

                                                  
      15101 TAAATTTAAGAGATTTACTTGCCACAAATTCTGCTAAT
          1 TAAATTTAAGAGATTTACTTGCCACAAA-TCTGCTAAT

                               *  *               
      15139 TAAATTTAAGAGATTTACTAGCGACAAAATCTGCTAAT
          1 TAAATTTAAGAGATTTACTTGCCAC-AAATCTGCTAAT

                                                   
      15177 TAAATTTAAGAGATTTA-TTAGCCACAGAATCTGCTAAT
          1 TAAATTTAAGAGATTTACTT-GCCACA-AATCTGCTAAT

                          
      15215 TAAATTTAAGAGAT
          1 TAAATTTAAGAGAT

      15229 AATAATTAGC


Statistics
Matches: 83,  Mismatches: 4, Indels: 6
        0.89            0.04        0.06

Matches are distributed among these distances:
  37    2  0.02
  38   78  0.94
  39    3  0.04

ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34


Consensus pattern (37 bp):   
TAAATTTAAGAGATTTACTTGCCACAAATCTGCTAAT

Found at i:15351 original size:2 final size:2

Alignment explanation


    Indices: 15346--15374  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      15336 TAAGTATGTC

                                                       
      15346 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      15375 GTACTTTTTG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:17296 original size:2 final size:2

Alignment explanation


    Indices: 17289--17326  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      17279 AGTCGCTTGC

                                                                    
      17289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.