Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013727.1 Corchorus capsularis cultivar CVL-1 contig13748, 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: 5498
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:1835 original size:59 final size:60

Alignment explanation


    Indices: 1750--1885  Score: 184
    Period size: 60  Copynumber: 2.3  Consensus size: 60

       1740 GGCTAATTGC

                       *    *                         * *       *       
       1750 TCAAATAAGGGACTAATGTTTACCAAAAT-CTCAAATAAGGGTCTGATCTTTTAATTTGG
          1 TCAAATAAGGGCCTAACGTTTACCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGG

                                 *        *               *             
       1809 TCAAATAAGGGCCTAACGTTTGCCAAAATGTTCAAATAAGGGCCCGGTCTTTGAATTTGG
          1 TCAAATAAGGGCCTAACGTTTACCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGG

            *                
       1869 CCAAATAAGGGCCTAAC
          1 TCAAATAAGGGCCTAAC

       1886 CAAAATGTTC


Statistics
Matches: 67,  Mismatches: 9, Indels: 1
        0.87            0.12        0.01

Matches are distributed among these distances:
  59   26  0.39
  60   41  0.61

ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29


Consensus pattern (60 bp):   
TCAAATAAGGGCCTAACGTTTACCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGG

Found at i:1866 original size:60 final size:58

Alignment explanation


    Indices: 1750--1906  Score: 180
    Period size: 60  Copynumber: 2.7  Consensus size: 58

       1740 GGCTAATTGC

                       *                  *           * *       *       
       1750 TCAAATAAGGGACTAATGTTTACCAAAAT-CTCAAATAAGGGTCTGATCTTTTAATTTGG
          1 TCAAATAAGGGCCTAA-GTTT-CCAAAATGTTCAAATAAGGGCCCGATCTTTGAATTTGG

                                                          *             
       1809 TCAAATAAGGGCCTAACGTTTGCCAAAATGTTCAAATAAGGGCCCGGTCTTTGAATTTGG
          1 TCAAATAAGGGCCTAA-GTTT-CCAAAATGTTCAAATAAGGGCCCGATCTTTGAATTTGG

            *                                         
       1869 CCAAATAAGGGCCTAA----CCAAAATGTTCAAATAAGGGCC
          1 TCAAATAAGGGCCTAAGTTTCCAAAATGTTCAAATAAGGGCC

       1907 TATCTCATAC


Statistics
Matches: 88,  Mismatches: 9, Indels: 7
        0.85            0.09        0.07

Matches are distributed among these distances:
  54   22  0.25
  59   26  0.30
  60   40  0.45

ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27


Consensus pattern (58 bp):   
TCAAATAAGGGCCTAAGTTTCCAAAATGTTCAAATAAGGGCCCGATCTTTGAATTTGG

Found at i:1973 original size:31 final size:31

Alignment explanation


    Indices: 1938--2069  Score: 128
    Period size: 31  Copynumber: 4.3  Consensus size: 31

       1928 TGAAACCAGA

                              *            
       1938 CCCTTATTTGAGCATTTTTGATAACGTTAGG
          1 CCCTTATTTGAGCATTTTCGATAACGTTAGG

                       *       *           
       1969 CCCTTATTTGACCATTTTCAATAACGTTAGG
          1 CCCTTATTTGAGCATTTTCGATAACGTTAGG

                           **        * * *   
       2000 CCCTTATTTG-GCAAAATT--A-AAAGATCGAG
          1 CCCTTATTTGAGC-ATTTTCGATAACGTTAG-G

                     *               *     
       2029 CCCTTATTTAAGCATTTTCGATAACATTAGG
          1 CCCTTATTTGAGCATTTTCGATAACGTTAGG

                      
       2060 CCCTTATTTG
          1 CCCTTATTTG

       2070 GCCAAATTAA


Statistics
Matches: 78,  Mismatches: 17, Indels: 12
        0.73            0.16        0.11

Matches are distributed among these distances:
  28    5  0.06
  29   14  0.18
  30    3  0.04
  31   52  0.67
  32    4  0.05

ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38


Consensus pattern (31 bp):   
CCCTTATTTGAGCATTTTCGATAACGTTAGG

Found at i:2037 original size:60 final size:60

Alignment explanation


    Indices: 1968--2106  Score: 217
    Period size: 60  Copynumber: 2.3  Consensus size: 60

       1958 ATAACGTTAG

                        *             *                                  
       1968 GCCCTTATTTGACCATTTTCAATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCGA-
          1 GCCCTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGGCAAAATTAAAAGATC-AT

                      *         *                       *               
       2028 GCCCTTATTTAAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAT
          1 GCCCTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGGCAAAATTAAAAGATCAT

                               
       2088 GCCCTTATTTGAGCATTTT
          1 GCCCTTATTTGAGCATTTT

       2107 GACAAATGTT


Statistics
Matches: 72,  Mismatches: 6, Indels: 2
        0.90            0.08        0.03

Matches are distributed among these distances:
  59    1  0.01
  60   71  0.99

ACGTcount: A:0.29, C:0.20, G:0.14, T:0.36


Consensus pattern (60 bp):   
GCCCTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGGCAAAATTAAAAGATCAT

Found at i:2126 original size:60 final size:58

Alignment explanation


    Indices: 1968--2128  Score: 182
    Period size: 60  Copynumber: 2.7  Consensus size: 58

       1958 ATAACGTTAG

                        *      *                                        
       1968 GCCCTTATTTGACCATTTTCAATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCGA
          1 GCCCTTATTTGAGCATTTTGAA-AA-GTTAGGCCCTTATTTGGCAAAATTAAAAGATCGA

                      *                                  *               
       2028 GCCCTTATTTAAGCATTTTCGATAACA-TTAGGCCCTTATTTGGCCAAATTAAAAGATC-A
          1 GCCCTTATTTGAGCATTTT-GA-AA-AGTTAGGCCCTTATTTGGCAAAATTAAAAGATCGA

                                           *  *       
       2087 TGCCCTTATTTGAGCATTTTGACAAATGTTAAGCTCTTATTT
          1 -GCCCTTATTTGAGCATTTTGA-AAA-GTTAGGCCCTTATTT

       2129 AAACAATTGA


Statistics
Matches: 87,  Mismatches: 8, Indels: 12
        0.81            0.07        0.11

Matches are distributed among these distances:
  58    1  0.01
  59    5  0.06
  60   77  0.89
  61    2  0.02
  62    2  0.02

ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37


Consensus pattern (58 bp):   
GCCCTTATTTGAGCATTTTGAAAAGTTAGGCCCTTATTTGGCAAAATTAAAAGATCGA
Done.