Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015700.1 Corchorus capsularis cultivar CVL-1 contig15721, 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: 10119
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--75  Score: 150
    Period size: 2  Copynumber: 37.5  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                             
         43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         76 ATATATATAT


Statistics
Matches: 73,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   73  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:80 original size:2 final size:2

Alignment explanation


    Indices: 75--100  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

         65 TCTCTCTCTC

                                                  
         75 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

        101 CACCAAAAAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:1124 original size:31 final size:31

Alignment explanation


    Indices: 992--1130  Score: 161
    Period size: 31  Copynumber: 4.5  Consensus size: 31

        982 TCCTTTTGTG

                    *         *  *      ** 
        992 CACGTGGCATGCCACATGCCATTTTTTGAAA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

              *     *      *               
       1023 CATGTGGCATGCCACGTGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

                       *  **               
       1054 CACGTGGCGTGACATGTGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

              *                            
       1085 CATGTGGCGTGCCACATGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

                      *    
       1116 CACGTGGCGTTCCAC
          1 CACGTGGCGTGCCAC

       1131 GTCGGACATT


Statistics
Matches: 92,  Mismatches: 16, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  31   92  1.00

ACGTcount: A:0.18, C:0.24, G:0.25, T:0.32


Consensus pattern (31 bp):   
CACGTGGCGTGCCACATGTCACTTTTTGGTA

Found at i:2896 original size:30 final size:30

Alignment explanation


    Indices: 2860--2961  Score: 80
    Period size: 30  Copynumber: 3.3  Consensus size: 30

       2850 GGCTGGTCAT

                                          
       2860 ATGGCCGGTGTTGCGCGGCTTCTCCAAGCA
          1 ATGGCCGGTGTTGCGCGGCTTCTCCAAGCA

                      *      **     ** **    
       2890 ATGGCCGGTCATATGCGATGCTT-GGCTGGTCA
          1 ATGGCCGGT-GT-TGCGCGGCTTCTCCAAG-CA

                          *             *  
       2922 AGTGGCCGGTGTTGTGCGGCTTCTCCAAACA
          1 A-TGGCCGGTGTTGCGCGGCTTCTCCAAGCA

                     
       2953 ATGGCCGGT
          1 ATGGCCGGT

       2962 CATATGCGAT


Statistics
Matches: 51,  Mismatches: 16, Indels: 10
        0.66            0.21        0.13

Matches are distributed among these distances:
  30   17  0.33
  31   13  0.25
  32   13  0.25
  33    8  0.16

ACGTcount: A:0.15, C:0.25, G:0.34, T:0.25


Consensus pattern (30 bp):   
ATGGCCGGTGTTGCGCGGCTTCTCCAAGCA

Found at i:2931 original size:63 final size:63

Alignment explanation


    Indices: 2849--2975  Score: 220
    Period size: 63  Copynumber: 2.0  Consensus size: 63

       2839 ACCGGTCAAG

                                                  *                        
       2849 TGGCTGGTCATATGGCCGGTGTTGCGCGGCTTCTCCAAGCAATGGCCGGTCATATGCGATGCT
          1 TGGCTGGTCATATGGCCGGTGTTGCGCGGCTTCTCCAAACAATGGCCGGTCATATGCGATGCT

                                     *                                      
       2912 TGGCTGGTCA-AGTGGCCGGTGTTGTGCGGCTTCTCCAAACAATGGCCGGTCATATGCGATGCT
          1 TGGCTGGTCATA-TGGCCGGTGTTGCGCGGCTTCTCCAAACAATGGCCGGTCATATGCGATGCT

             
       2975 T
          1 T

       2976 CCAACTCCAT


Statistics
Matches: 61,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  62    1  0.02
  63   60  0.98

ACGTcount: A:0.15, C:0.24, G:0.33, T:0.28


Consensus pattern (63 bp):   
TGGCTGGTCATATGGCCGGTGTTGCGCGGCTTCTCCAAACAATGGCCGGTCATATGCGATGCT

Found at i:4981 original size:53 final size:53

Alignment explanation


    Indices: 4880--4981  Score: 132
    Period size: 53  Copynumber: 1.9  Consensus size: 53

       4870 CACGTGTCAG

                                 * **                 *          
       4880 TTTTTGGTACACGTGGCGTGATATGTGTCACTTTTTGATACATATGGCACGAC
          1 TTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGATACACATGGCACGAC

                       *        *                *     *     
       4933 TTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACCTGGCA
          1 TTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGATACACATGGCA

       4982 TGCCACGTCG


Statistics
Matches: 41,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  53   41  1.00

ACGTcount: A:0.19, C:0.20, G:0.25, T:0.37


Consensus pattern (53 bp):   
TTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGATACACATGGCACGAC
Done.