Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000701.1 Corchorus olitorius cultivar O-4 contig00701, 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: 6422
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36


Found at i:916 original size:38 final size:38

Alignment explanation


    Indices: 643--957  Score: 269
    Period size: 38  Copynumber: 8.3  Consensus size: 38

        633 CTAAACTGAA

                 *  *       *           *          
        643 AACTGTTGGAAGATGATCTGTTTCCAGTGAA-CTTTGAT
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATC-TTGAT

                   ***              *    *        
        681 AACTGCTTTGAGATGACCTGTTTCTAGTCGATCTTGAT
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT

             *     ***       *          **        
        719 ATCTGCTTTGAGATGACATGTTTCCAGTTGATCTTGAT
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT

                *       *            *            
        757 AACTTCTGAAAGGTGACCTGTTTCCGGTCAATCTTGAT
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT

                   ***          *        *        
        795 AACTGCTTTGAGATGACCTGCTTCCAGTCGATCTTGAT
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT

                   ***       *          **        
        833 AACTGCTTTGAGATGACTTGTTTCCAGTTGATCTTGAT
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT

                                 *                 
        871 AACTGCTGAAAGATGACCTGTCTCCAGTCAA-CTTTGAT
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAATC-TTGAT

                          *          *              
        909 AACTGCTGAAAGATTA-CTAGTTTCTAGTCAA-CTTTGAT
          1 AACTGCTGAAAGATGACCT-GTTTCCAGTCAATC-TTGAT

                       
        947 AACTGCTGAAA
          1 AACTGCTGAAA

        958 AGACATGTTC


Statistics
Matches: 231,  Mismatches: 43, Indels: 6
        0.82            0.15        0.02

Matches are distributed among these distances:
  37    3  0.01
  38  227  0.98
  39    1  0.00

ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36


Consensus pattern (38 bp):   
AACTGCTGAAAGATGACCTGTTTCCAGTCAATCTTGAT

Found at i:953 original size:114 final size:114

Alignment explanation


    Indices: 643--915  Score: 422
    Period size: 114  Copynumber: 2.4  Consensus size: 114

        633 CTAAACTGAA

                 *  *       *           *                                    
        643 AACTGTTGGAAGATGATCTGTTTCCAGTGAACTTTGATAACTGCTTTGAGATGACCTGTTTCTAG
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTTTGAGATGACCTGTTTCTAG

                        *                                    
        708 TCGATCTTGATATCTGCTTTGAGATGACATGTTTCCAGTTGATCTTGAT
         66 TCGATCTTGATAACTGCTTTGAGATGACATGTTTCCAGTTGATCTTGAT

                *       *            *                                 *   * 
        757 AACTTCTGAAAGGTGACCTGTTTCCGGTCAA-TCTTGATAACTGCTTTGAGATGACCTGCTTCCA
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATAACTGCTTTGAGATGACCTGTTTCTA

                                         *                    
        821 GTCGATCTTGATAACTGCTTTGAGATGACTTGTTTCCAGTTGATCTTGAT
         65 GTCGATCTTGATAACTGCTTTGAGATGACATGTTTCCAGTTGATCTTGAT

                                 *                       
        871 AACTGCTGAAAGATGACCTGTCTCCAGTCAACTTTGATAACTGCT
          1 AACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCT

        916 GAAAGATTAC


Statistics
Matches: 142,  Mismatches: 15, Indels: 4
        0.88            0.09        0.02

Matches are distributed among these distances:
 113    1  0.01
 114  140  0.99
 115    1  0.01

ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37


Consensus pattern (114 bp):   
AACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTTTGAGATGACCTGTTTCTAG
TCGATCTTGATAACTGCTTTGAGATGACATGTTTCCAGTTGATCTTGAT

Found at i:4023 original size:34 final size:35

Alignment explanation


    Indices: 3944--4039  Score: 113
    Period size: 36  Copynumber: 2.7  Consensus size: 35

       3934 AAAAACTGAA

                         *    *   *            *
       3944 TGGGAACTTTCCCTATTTTAAACCTTAAAAACTTGT
          1 TGGGAACTTTCCCAATTTAAAAAC-TAAAAACTTGG

                                         *     
       3980 TGGGAACTTTCCCAATTTAAAAACTAAAATC-TGG
          1 TGGGAACTTTCCCAATTTAAAAACTAAAAACTTGG

                         *            
       4014 TGGGAACTTTCCCGATTTGAAAAACT
          1 TGGGAACTTTCCCAATTT-AAAAACT

       4040 TCAAAGACTG


Statistics
Matches: 53,  Mismatches: 6, Indels: 3
        0.85            0.10        0.05

Matches are distributed among these distances:
  34   19  0.36
  35   13  0.25
  36   21  0.40

ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33


Consensus pattern (35 bp):   
TGGGAACTTTCCCAATTTAAAAACTAAAAACTTGG
Done.