Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008696.1 Corchorus capsularis cultivar CVL-1 contig08717, 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: 4146
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:1312 original size:15 final size:15

Alignment explanation


    Indices: 1280--1330  Score: 59
    Period size: 15  Copynumber: 3.4  Consensus size: 15

       1270 TATGTTTGGT

                 *   *     
       1280 AGGAACGAAGTAGGG
          1 AGGAAAGAAATAGGG

                         * 
       1295 AGGAAAGAAATAGTG
          1 AGGAAAGAAATAGGG

                            
       1310 AGGAAAGAAAGT-GGG
          1 AGGAAAGAAA-TAGGG

                  
       1325 AGGAAA
          1 AGGAAA

       1331 ATGCAATTTT


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

Matches are distributed among these distances:
  15   30  0.97
  16    1  0.03

ACGTcount: A:0.49, C:0.02, G:0.41, T:0.08


Consensus pattern (15 bp):   
AGGAAAGAAATAGGG

Found at i:2768 original size:21 final size:22

Alignment explanation


    Indices: 2744--2792  Score: 73
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       2734 AAAAATTCTT

                     *            
       2744 TATTTTAAATAA-ATATTTTTA
          1 TATTTTAAAAAATATATTTTTA

                                 *
       2765 TATTTTAAAAAATATATTTTTT
          1 TATTTTAAAAAATATATTTTTA

                  
       2787 TATTTT
          1 TATTTT

       2793 TTAATTCCAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  21   11  0.44
  22   14  0.56

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (22 bp):   
TATTTTAAAAAATATATTTTTA

Found at i:2786 original size:24 final size:24

Alignment explanation


    Indices: 2750--2796  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2740 TCTTTATTTT

                                    
       2750 AAATAAATATTTTTATATTTTAAA
          1 AAATAAATATTTTTATATTTTAAA

                 *  *       *      
       2774 AAATATATTTTTTTATTTTTTAA
          1 AAATAAATATTTTTATATTTTAA

       2797 TTCCATGTGG


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (24 bp):   
AAATAAATATTTTTATATTTTAAA

Found at i:3171 original size:16 final size:17

Alignment explanation


    Indices: 3150--3184  Score: 63
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       3140 TTTTTTTTTC

                             
       3150 TTCTTT-CCTATTTCCT
          1 TTCTTTCCCTATTTCCT

                             
       3166 TTCTTTCCCTATTTCCT
          1 TTCTTTCCCTATTTCCT

              
       3183 TT
          1 TT

       3185 TCATGCAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  16    6  0.33
  17   12  0.67

ACGTcount: A:0.06, C:0.31, G:0.00, T:0.63


Consensus pattern (17 bp):   
TTCTTTCCCTATTTCCT

Found at i:3981 original size:26 final size:26

Alignment explanation


    Indices: 3951--4001  Score: 93
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       3941 GAGACGGGTC

                               *      
       3951 GCGCGCGTCCCGCACCATGGCTGGTT
          1 GCGCGCGTCCCGCACCATGACTGGTT

                                     
       3977 GCGCGCGTCCCGCACCATGACTGGT
          1 GCGCGCGTCCCGCACCATGACTGGT

       4002 CGCGATCCGC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.10, C:0.39, G:0.33, T:0.18


Consensus pattern (26 bp):   
GCGCGCGTCCCGCACCATGACTGGTT
Done.