Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007637.1 Corchorus capsularis cultivar CVL-1 contig07658, 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: 2741
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30


Found at i:1698 original size:31 final size:30

Alignment explanation


    Indices: 1660--1766  Score: 90
    Period size: 31  Copynumber: 3.5  Consensus size: 30

       1650 TTTGGCTAAT

                                           
       1660 TGTTCAAATAAGGGCCTAATGTTTGACAAAA
          1 TGTTCAAATAAGGGCCTAATGTTTG-CAAAA

                       *  *  *  *    *  **
       1691 TGTTCAAATAAAGGTCTGATCTTT-TAATT
          1 TGTTCAAATAAGGGCCTAATGTTTGCAAAA

              **                           
       1720 TGACCAAATAAGGGCCTAATGTTTGCCAAAA
          1 TGTTCAAATAAGGGCCTAATGTTTG-CAAAA

             **             
       1751 TACTCAAATAAGGGCC
          1 TGTTCAAATAAGGGCC

       1767 CCATCTTTGA


Statistics
Matches: 55,  Mismatches: 19, Indels: 4
        0.71            0.24        0.05

Matches are distributed among these distances:
  29   20  0.36
  31   35  0.64

ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30


Consensus pattern (30 bp):   
TGTTCAAATAAGGGCCTAATGTTTGCAAAA

Found at i:1758 original size:60 final size:60

Alignment explanation


    Indices: 1664--1794  Score: 181
    Period size: 60  Copynumber: 2.2  Consensus size: 60

       1654 GCTAATTGTT

                                        **           * **      *        
       1664 CAAATAAGGGCCTAATGTTTGACAAAATGTTCAAATAAAGGTCTGATCTTTTAATTTGAC
          1 CAAATAAGGGCCTAATGTTTGACAAAATACTCAAATAAAGGCCCCATCTTTGAATTTGAC

                                 *                *                   * 
       1724 CAAATAAGGGCCTAATGTTTGCCAAAATACTCAAATAAGGGCCCCATCTTTGAATTTGGC
          1 CAAATAAGGGCCTAATGTTTGACAAAATACTCAAATAAAGGCCCCATCTTTGAATTTGAC

                       
       1784 CAAATAAGGGC
          1 CAAATAAGGGC

       1795 TTGTCTCACA


Statistics
Matches: 62,  Mismatches: 9, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  60   62  1.00

ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28


Consensus pattern (60 bp):   
CAAATAAGGGCCTAATGTTTGACAAAATACTCAAATAAAGGCCCCATCTTTGAATTTGAC

Found at i:1866 original size:31 final size:31

Alignment explanation


    Indices: 1828--1898  Score: 133
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       1818 GACACCAGGT

                                           
       1828 CCTTATTTGAGCATTTTCGATAACGTTAGAC
          1 CCTTATTTGAGCATTTTCGATAACGTTAGAC

                                         * 
       1859 CCTTATTTGAGCATTTTCGATAACGTTAGGC
          1 CCTTATTTGAGCATTTTCGATAACGTTAGAC

                     
       1890 CCTTATTTG
          1 CCTTATTTG

       1899 GCCAAATTAA


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  31   39  1.00

ACGTcount: A:0.23, C:0.20, G:0.17, T:0.41


Consensus pattern (31 bp):   
CCTTATTTGAGCATTTTCGATAACGTTAGAC

Found at i:1925 original size:60 final size:59

Alignment explanation


    Indices: 1856--2023  Score: 237
    Period size: 60  Copynumber: 2.8  Consensus size: 59

       1846 GATAACGTTA

                                                         *              
       1856 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
          1 GACCCTTATTTGAGCATTTT-GATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCG

                         *       *     *                                
       1916 GACCCTTATTTGAACATTTTTTATAACATTAGGCCCTTATTTGGCAAAATTAAAAGATCG
          1 GACCCTTATTTGAGCA-TTTTGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCG

             * *                   *                        
       1976 GGCTCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGAGCAA
          1 GACCCTTATTTGAGCATTTTGA-TAACGTTAGGCCCTTATTTG-GCAA

       2024 TTAGCCTAAG


Statistics
Matches: 95,  Mismatches: 10, Indels: 5
        0.86            0.09        0.05

Matches are distributed among these distances:
  59    5  0.05
  60   82  0.86
  61    8  0.08

ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35


Consensus pattern (59 bp):   
GACCCTTATTTGAGCATTTTGATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCG

Found at i:1956 original size:31 final size:31

Alignment explanation


    Indices: 1918--2022  Score: 56
    Period size: 31  Copynumber: 3.5  Consensus size: 31

       1908 AAAGATCGGA

                       *      **           
       1918 CCCTTATTTGAACATTTTTTATAACATTAGG
          1 CCCTTATTTGAGCATTTTCGATAACATTAGG

                           **     *  *  **  
       1949 CCCTTATTTG-GCAAAATT--AAAAGATCGGG
          1 CCCTTATTTGAGC-ATTTTCGATAACATTAGG

             *                    *   *     
       1978 CTCTTATTTGAGCATTTT-GACAAACGTTAGG
          1 CCCTTATTTGAGCATTTTCGA-TAACATTAGG

                          
       2009 CCCTTATTTGAGCA
          1 CCCTTATTTGAGCA

       2023 ATTAGCCTAA


Statistics
Matches: 55,  Mismatches: 15, Indels: 8
        0.71            0.19        0.10

Matches are distributed among these distances:
  29   19  0.35
  30    4  0.07
  31   32  0.58

ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37


Consensus pattern (31 bp):   
CCCTTATTTGAGCATTTTCGATAACATTAGG
Done.