Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021604.1 Corchorus olitorius cultivar O-4 contig21637, 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: 6881
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33


Found at i:1415 original size:28 final size:28

Alignment explanation


    Indices: 1383--1589  Score: 299
    Period size: 28  Copynumber: 7.4  Consensus size: 28

       1373 AGTGCACTCG

                         *            * 
       1383 AAATGACCAAAATACCCCTGGACATGTA
          1 AAATGACCAAAATGCCCCTGGACATGAA

                               *        
       1411 AAATGACCAAAATGCCCCTAGACATGAA
          1 AAATGACCAAAATGCCCCTGGACATGAA

                               *      **
       1439 AAATGACCAAAATGCCCCTAGACATGTC
          1 AAATGACCAAAATGCCCCTGGACATGAA

                                       *
       1467 AAATGACCAAAATGCCCCTGGACATGAC
          1 AAATGACCAAAATGCCCCTGGACATGAA

                              *   *     
       1495 AAATGACCAAAATGCCCCAGGATATGAA
          1 AAATGACCAAAATGCCCCTGGACATGAA

                                  *  *  
       1523 AAATGACCAAAATGCCCCTGGATATTAA
          1 AAATGACCAAAATGCCCCTGGACATGAA

                              *         
       1551 AAATGACCAAAATGCCCCAGGACAT-AA
          1 AAATGACCAAAATGCCCCTGGACATGAA

                        
       1578 AAATGACCAAAA
          1 AAATGACCAAAA

       1590 AGAGAAGTAA


Statistics
Matches: 165,  Mismatches: 14, Indels: 1
        0.92            0.08        0.01

Matches are distributed among these distances:
  27   14  0.08
  28  151  0.92

ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15


Consensus pattern (28 bp):   
AAATGACCAAAATGCCCCTGGACATGAA

Found at i:1911 original size:50 final size:50

Alignment explanation


    Indices: 1811--2136  Score: 598
    Period size: 50  Copynumber: 6.5  Consensus size: 50

       1801 CGATCAACTT

                   *               *                           
       1811 CTTCGAATTGTCTTCCAATTCAAACTTACAAAGGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTA-AAAGGACCGTCTTCCGCTTATC

                                                              
       1862 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                                *             
       1912 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCTTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                           *                  
       1962 CTTCGAACTGTCTTCCAATTCAATCTTAAAATGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                                              
       2012 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                     *                        
       2062 CTTCGAACTGTCTTCCAATTCAATCATAAAAGGACCGTCTTCCGCTTATC
          1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                     
       2112 CTTCGAACTGTCTTCCAATTCAATC
          1 CTTCGAACTGTCTTCCAATTCAATC

       2137 CTGATATCCG


Statistics
Matches: 268,  Mismatches: 7, Indels: 1
        0.97            0.03        0.00

Matches are distributed among these distances:
  50  242  0.90
  51   26  0.10

ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34


Consensus pattern (50 bp):   
CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

Found at i:2001 original size:27 final size:26

Alignment explanation


    Indices: 1871--2104  Score: 77
    Period size: 27  Copynumber: 9.3  Consensus size: 26

       1861 CCTTCGAACT

                                       
       1871 GTCTTCCAATTCAATCTTAAAAGGACC
          1 GTCTTCCAATTCAATCTTAAAA-GACC

                   **           **    *
       1898 GTCTTCCGCTT--ATCCTT-CGA-ACT
          1 GTCTTCCAATTCAAT-CTTAAAAGACC

                                       
       1921 GTCTTCCAATTCAATCTTAAAAGGACC
          1 GTCTTCCAATTCAATCTTAAAA-GACC

            *      **           **    *
       1948 TTCTTCCGCTT--ATCCTT-CGA-ACT
          1 GTCTTCCAATTCAAT-CTTAAAAGACC

                                       
       1971 GTCTTCCAATTCAATCTTAAAATGACC
          1 GTCTTCCAATTCAATCTTAAAA-GACC

                   **           **    *
       1998 GTCTTCCGCTT--ATCCTT-CGA-ACT
          1 GTCTTCCAATTCAAT-CTTAAAAGACC

                                       
       2021 GTCTTCCAATTCAATCTTAAAAGGACC
          1 GTCTTCCAATTCAATCTTAAAA-GACC

                   **           **    *
       2048 GTCTTCCGCTT--ATCCTT-CGA-ACT
          1 GTCTTCCAATTCAAT-CTTAAAAGACC

                            *          
       2071 GTCTTCCAATTCAATCATAAAAGGACC
          1 GTCTTCCAATTCAATCTTAAAA-GACC

                   
       2098 GTCTTCC
          1 GTCTTCC

       2105 GCTTATCCTT


Statistics
Matches: 140,  Mismatches: 43, Indels: 48
        0.61            0.19        0.21

Matches are distributed among these distances:
  23   43  0.31
  24   11  0.08
  25   24  0.17
  26   12  0.09
  27   50  0.36

ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34


Consensus pattern (26 bp):   
GTCTTCCAATTCAATCTTAAAAGACC

Done.