Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012843.1 Corchorus olitorius cultivar O-4 contig12876, 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: 31631
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:1819 original size:19 final size:20

Alignment explanation


    Indices: 1789--1852  Score: 76
    Period size: 21  Copynumber: 3.1  Consensus size: 20

       1779 TTAACACTGT

                                 
       1789 TTAGCAACTGTACAGATGAGA
          1 TTAGC-ACTGTACAGATGAGA

                            *   
       1810 TTA-CACTGTACAGATTAGA
          1 TTAGCACTGTACAGATGAGA

                 *             * 
       1829 TTAGGTACTGTACAGATGAAA
          1 TTA-GCACTGTACAGATGAGA

               
       1850 TTA
          1 TTA

       1853 TTAGAGCAGC


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  19   17  0.46
  20    1  0.03
  21   19  0.51

ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30


Consensus pattern (20 bp):   
TTAGCACTGTACAGATGAGA

Found at i:1852 original size:21 final size:19

Alignment explanation


    Indices: 1795--1852  Score: 71
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       1785 CTGTTTAGCA

                               
       1795 ACTGTACAGATGAGATTAC
          1 ACTGTACAGATGAGATTAC

                       *        *
       1814 ACTGTACAGATTAGATTAGGT
          1 ACTGTACAGATGAGATTA--C

                         *    
       1835 ACTGTACAGATGAAATTA
          1 ACTGTACAGATGAGATTA

       1853 TTAGAGCAGC


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   17  0.52
  21   16  0.48

ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29


Consensus pattern (19 bp):   
ACTGTACAGATGAGATTAC

Found at i:3170 original size:31 final size:30

Alignment explanation


    Indices: 3095--3198  Score: 104
    Period size: 31  Copynumber: 3.4  Consensus size: 30

       3085 GCCCCATCAG

                 *          *              
       3095 TCAGGAGTAAAATGTCTTGAATTTGAGAAGT
          1 TCAGGGGTAAAATGTCCTGAATTT-AGAAGT

                 *  *                 *    
       3126 TCAAGAGGCAAAATGTCCTGAATTTAAAAGT
          1 TC-AGGGGTAAAATGTCCTGAATTTAGAAGT

                                           
       3157 TCAGGGGATAAAATGTCCTG-ATTT-GAAGT
          1 TCAGGGG-TAAAATGTCCTGAATTTAGAAGT

                    *    
       3186 TCATGGGGCAAAA
          1 TCA-GGGGTAAAA

       3199 CGTCATTGAT


Statistics
Matches: 61,  Mismatches: 9, Indels: 8
        0.78            0.12        0.10

Matches are distributed among these distances:
  29   11  0.18
  30   12  0.20
  31   20  0.33
  32   18  0.30

ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28


Consensus pattern (30 bp):   
TCAGGGGTAAAATGTCCTGAATTTAGAAGT

Found at i:29031 original size:17 final size:17

Alignment explanation


    Indices: 29002--29037  Score: 56
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      28992 CTCCATCATC

                             
      29002 AAACCACTCAAAGATTA
          1 AAACCACTCAAAGATTA

                              
      29019 AAACC-CTCGAAAGATTA
          1 AAACCACTC-AAAGATTA

              
      29036 AA
          1 AA

      29038 GGAAAATATG


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  16    3  0.17
  17   15  0.83

ACGTcount: A:0.53, C:0.22, G:0.08, T:0.17


Consensus pattern (17 bp):   
AAACCACTCAAAGATTA
Done.