Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005649.1 Corchorus capsularis cultivar CVL-1 contig05667, 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: 2024
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30


Found at i:62 original size:21 final size:22

Alignment explanation


    Indices: 14--66  Score: 65
    Period size: 21  Copynumber: 2.5  Consensus size: 22

          4 AGCAAAAGTG

                 *                
         14 GTAATTAGT-AAGAGTAAATAA
          1 GTAATCAGTAAAGAGTAAATAA

                                 *
         35 GTAATCAGTAAAGAGTAAA-AG
          1 GTAATCAGTAAAGAGTAAATAA

              *        
         56 GTGATCAGTAA
          1 GTAATCAGTAA

         67 TTCAAAAGAG


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  21   19  0.68
  22    9  0.32

ACGTcount: A:0.49, C:0.04, G:0.23, T:0.25


Consensus pattern (22 bp):   
GTAATCAGTAAAGAGTAAATAA

Found at i:145 original size:13 final size:13

Alignment explanation


    Indices: 129--175  Score: 51
    Period size: 13  Copynumber: 3.5  Consensus size: 13

        119 GGTAATAAAT

                         
        129 AAAAGAGAGTAAG
          1 AAAAGAGAGTAAG

                     * *  
        142 AAAAGAGTAATTAG
          1 AAAAGAG-AGTAAG

                          
        156 TAAAA-AGAGTAAG
          1 -AAAAGAGAGTAAG

                   
        169 AAAAGAG
          1 AAAAGAG

        176 TAAAAATGAT


Statistics
Matches: 27,  Mismatches: 4, Indels: 6
        0.73            0.11        0.16

Matches are distributed among these distances:
  12    4  0.15
  13   13  0.48
  14    6  0.22
  15    4  0.15

ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13


Consensus pattern (13 bp):   
AAAAGAGAGTAAG

Found at i:145 original size:29 final size:28

Alignment explanation


    Indices: 120--182  Score: 94
    Period size: 27  Copynumber: 2.3  Consensus size: 28

        110 GTAAAAAGTG

                                        
        120 GTAATAAATAAAAGAGAGTAAGAAAAGA
          1 GTAATAAATAAAAGAGAGTAAGAAAAGA

                 * *                    
        148 GTAATTAGTAAAA-AGAGTAAGAAAAGA
          1 GTAATAAATAAAAGAGAGTAAGAAAAGA

                     
        175 GTAA-AAAT
          1 GTAATAAAT

        183 GATAAAAGTA


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  26    2  0.06
  27   18  0.58
  28   11  0.35

ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17


Consensus pattern (28 bp):   
GTAATAAATAAAAGAGAGTAAGAAAAGA

Found at i:1761 original size:26 final size:26

Alignment explanation


    Indices: 1731--1782  Score: 86
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1721 ACTATTGGAA

                                      
       1731 ATCGAAATTGTTGGTGTTCTTTCACG
          1 ATCGAAATTGTTGGTGTTCTTTCACG

                        **            
       1757 ATCGAAATTGTTTTTGTTCTTTCACG
          1 ATCGAAATTGTTGGTGTTCTTTCACG

       1783 TTTTTTTGTC


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.19, C:0.15, G:0.19, T:0.46


Consensus pattern (26 bp):   
ATCGAAATTGTTGGTGTTCTTTCACG
Done.