Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011160.1 Corchorus capsularis cultivar CVL-1 contig11181, 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: 38764
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:17469 original size:1 final size:1

Alignment explanation


    Indices: 17463--17499  Score: 74
    Period size: 1  Copynumber: 37.0  Consensus size: 1

      17453 GATCCTGCAG

                                                 
      17463 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      17500 GAAAGCGAGG


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

Matches are distributed among these distances:
   1   36  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:18607 original size:15 final size:15

Alignment explanation


    Indices: 18587--18617  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      18577 CTACAAATGT

                           
      18587 TATTTTGCACATGGG
          1 TATTTTGCACATGGG

                           
      18602 TATTTTGCACATGGG
          1 TATTTTGCACATGGG

             
      18617 T
          1 T

      18618 GTACAAATAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42


Consensus pattern (15 bp):   
TATTTTGCACATGGG

Found at i:23713 original size:1 final size:1

Alignment explanation


    Indices: 23707--23738  Score: 64
    Period size: 1  Copynumber: 32.0  Consensus size: 1

      23697 TTTATAAATG

                                            
      23707 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      23739 CCCCACAGAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   31  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:34138 original size:32 final size:34

Alignment explanation


    Indices: 34073--34139  Score: 93
    Period size: 34  Copynumber: 2.0  Consensus size: 34

      34063 ATTATAAAAC

                                    *   *     
      34073 TAATAAAAATAATTTATTATATATTATATATATA
          1 TAATAAAAATAATTTATTATATATCATAAATATA

                   *                          
      34107 TAATAAATATAATTTA-TAT-TATCATAAATATA
          1 TAATAAAAATAATTTATTATATATCATAAATATA

             
      34139 T
          1 T

      34140 TTTATATATA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  32   12  0.40
  33    3  0.10
  34   15  0.50

ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46


Consensus pattern (34 bp):   
TAATAAAAATAATTTATTATATATCATAAATATA

Found at i:34143 original size:21 final size:22

Alignment explanation


    Indices: 34091--34155  Score: 87
    Period size: 21  Copynumber: 3.0  Consensus size: 22

      34081 ATAATTTATT

                   *              
      34091 ATATATTATATATATATAATAA
          1 ATATATTTTATATATATAATAA

                 *           *    
      34113 ATATAATTTATAT-TATCATAA
          1 ATATATTTTATATATATAATAA

                                  
      34134 ATATATTTTATATATAATAATA
          1 ATATATTTTATATAT-ATAATA

      34156 TAATCGGTCG


Statistics
Matches: 36,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  21   19  0.53
  22   12  0.33
  23    5  0.14

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48


Consensus pattern (22 bp):   
ATATATTTTATATATATAATAA
Done.