Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011005.1 Corchorus capsularis cultivar CVL-1 contig11026, 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: 9678
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38


Found at i:92 original size:3 final size:3

Alignment explanation


    Indices: 84--133  Score: 100
    Period size: 3  Copynumber: 16.7  Consensus size: 3

         74 CAAACTGATT

                                                                           
         84 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

              
        132 TT
          1 TT

        134 GTTGTTGTTG


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   47  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:138 original size:3 final size:3

Alignment explanation


    Indices: 132--160  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

        122 ATTATTATTA

                                                  
        132 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
          1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT

        161 TTTTTATTGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69


Consensus pattern (3 bp):   
TTG

Found at i:7036 original size:13 final size:14

Alignment explanation


    Indices: 7017--7048  Score: 57
    Period size: 13  Copynumber: 2.4  Consensus size: 14

       7007 ATAAACTCTC

                          
       7017 CAAAACAGAGCAAA
          1 CAAAACAGAGCAAA

                          
       7031 -AAAACAGAGCAAA
          1 CAAAACAGAGCAAA

                 
       7044 CAAAA
          1 CAAAA

       7049 AAGCTTAAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  13   13  0.76
  14    4  0.24

ACGTcount: A:0.69, C:0.19, G:0.12, T:0.00


Consensus pattern (14 bp):   
CAAAACAGAGCAAA

Found at i:7082 original size:22 final size:21

Alignment explanation


    Indices: 7056--7102  Score: 58
    Period size: 23  Copynumber: 2.1  Consensus size: 21

       7046 AAAAAGCTTA

                *                  
       7056 AAAAAAAAAAGAAAACAGAGCAG
          1 AAAAGAAAAA-AAAACAGAG-AG

                          *      
       7079 AAAAGAAAAAAAAAGAGAGAG
          1 AAAAGAAAAAAAAACAGAGAG

               
       7100 AAA
          1 AAA

       7103 TCCTGGAAAG


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21    5  0.23
  22    8  0.36
  23    9  0.41

ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00


Consensus pattern (21 bp):   
AAAAGAAAAAAAAACAGAGAG
Done.