Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001951.1 Corchorus capsularis cultivar CVL-1 contig01953, 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, 902

Length: 1504
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34


Found at i:67 original size:9 final size:9

Alignment explanation


    Indices: 50--87  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

         40 TCATCTTTTT

                     
         50 TTTTTCTTC
          1 TTTTTCTTC

              *      
         59 TTCTTCTTC
          1 TTTTTCTTC

                     
         68 TTTTTCTT-
          1 TTTTTCTTC

                     
         76 TTTTTCTTC
          1 TTTTTCTTC

               
         85 TTT
          1 TTT

         88 AAAGGTTTTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
   8    8  0.31
   9   18  0.69

ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79


Consensus pattern (9 bp):   
TTTTTCTTC

Found at i:70 original size:23 final size:23

Alignment explanation


    Indices: 43--86  Score: 72
    Period size: 23  Copynumber: 1.9  Consensus size: 23

         33 GGCGGGTTCA

                                    
         43 TCTTTTT-TTTTTCTTCTTCTTCT
          1 TCTTTTTCTTTTT-TTCTTCTTCT

                                 
         66 TCTTTTTCTTTTTTTCTTCTT
          1 TCTTTTTCTTTTTTTCTTCTT

         87 TAAAGGTTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  23   15  0.75
  24    5  0.25

ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80


Consensus pattern (23 bp):   
TCTTTTTCTTTTTTTCTTCTTCT

Found at i:990 original size:33 final size:33

Alignment explanation


    Indices: 940--1016  Score: 111
    Period size: 33  Copynumber: 2.4  Consensus size: 33

        930 AGAGAAGAGA

                         *              **   
        940 AGGAAAAAAAA-CTCTTTCTATCGCCTCTGATC
          1 AGGAAAAAAAATCCCTTTCTATCGCCTCCAATC

                                             
        972 AGGAAAAAAAATCCCTTTCTATCGCCTCCAATC
          1 AGGAAAAAAAATCCCTTTCTATCGCCTCCAATC

            *           
       1005 TGGAAAAAAAAT
          1 AGGAAAAAAAAT

       1017 TAATTATTTC


Statistics
Matches: 40,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  32   11  0.28
  33   29  0.73

ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25


Consensus pattern (33 bp):   
AGGAAAAAAAATCCCTTTCTATCGCCTCCAATC

Found at i:1112 original size:22 final size:22

Alignment explanation


    Indices: 1084--1127  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1074 TAATTATCAT

                                  
       1084 CGTTCTTTTACAAAGTTTCTAC
          1 CGTTCTTTTACAAAGTTTCTAC

                                  
       1106 CGTTCTTTTACAAAGTTTCTAC
          1 CGTTCTTTTACAAAGTTTCTAC

       1128 AAGTCAACAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45


Consensus pattern (22 bp):   
CGTTCTTTTACAAAGTTTCTAC

Found at i:1469 original size:22 final size:22

Alignment explanation


    Indices: 1444--1492  Score: 64
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       1434 TTCCTTAGGG

                    *           *  
       1444 AGGTT-AACAAAATTTCATAGAA
          1 AGGTTAAAAAAAATTT-ATAAAA

                                  
       1466 AGGTTAAAAAAAATTTATAAAA
          1 AGGTTAAAAAAAATTTATAAAA

                 
       1488 AGGTT
          1 AGGTT

       1493 CTCGAAATTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  22   15  0.62
  23    9  0.38

ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29


Consensus pattern (22 bp):   
AGGTTAAAAAAAATTTATAAAA
Done.