Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015861.1 Corchorus olitorius cultivar O-4 contig15894, 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: 10272
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:1099 original size:2 final size:2

Alignment explanation


    Indices: 1094--1138  Score: 72
    Period size: 2  Copynumber: 22.5  Consensus size: 2

       1084 TATAGTAGTA

                                                                *     *   
       1094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                
       1136 AT A
          1 AT A

       1139 CTAAAGGCAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44


Consensus pattern (2 bp):   
AT

Found at i:3080 original size:127 final size:127

Alignment explanation


    Indices: 2786--3208  Score: 608
    Period size: 127  Copynumber: 3.4  Consensus size: 127

       2776 TTCTAAATAC

                                 *                                         * 
       2786 AATAGCGGCGTTTCTCAC-A-AAAGACGCCGCTAAATAGTGGCGTTTCTAGAGTAAACGCCGCGA
          1 AATAGCGGCGTTTCTC-CTATGAA-ACGCCGCTAAATAGTGGCGTTTCTAGAGTAAACGCCGCTA

                                *  *           *              **        *    
       2849 TATATAATCTTATCCAAAGAATAAAAAT-TCGGTGAAAC---TAAAAACATTATTTCTTGTTGGG
         64 TATATAATCTTATCCAAAGAGTAGAAATAT-GGTGCAACTGATAAAAACACCATTTCTTGATGGG

                                     *                                      *
       2910 AATAGCGGCGTTTCTCCTATGAAACACCGCTAAATAGTGGCGTTTCTAGAGTAAACGCCGCTATT
          1 AATAGCGGCGTTTCTCCTATGAAACGCCGCTAAATAGTGGCGTTTCTAGAGTAAACGCCGCTATA

                                                                          
       2975 TATAATCTTATCCAAAGAGTAGAAATATGGTGCAACTGATAAAAACACCATTTCTTGATGGG
         66 TATAATCTTATCCAAAGAGTAGAAATATGGTGCAACTGATAAAAACACCATTTCTTGATGGG

                 *          ***         *          *      *                  
       3037 AATAGTGGCGTTTCATAGGA-GAAACGCTGCTAAATAGTTGCGTTTTTAGAGTAAACGCCGCTAT
          1 AATAGCGGCGTTTC-TCCTATGAAACGCCGCTAAATAGTGGCGTTTCTAGAGTAAACGCCGCTAT

                                                                           
       3101 ATATAATCTTATCCAAAGAGTAGAAATATGGTGCAACTGATAAAAACACCATTTCTTGATGGG
         65 ATATAATCTTATCCAAAGAGTAGAAATATGGTGCAACTGATAAAAACACCATTTCTTGATGGG

                                                         
       3164 AATAGCGGCGTTTCTCCTATGAAACGCCGCTAAATAGTGGCGTTT
          1 AATAGCGGCGTTTCTCCTATGAAACGCCGCTAAATAGTGGCGTTT

       3209 AAAGGCAGAA


Statistics
Matches: 266,  Mismatches: 25, Indels: 13
        0.88            0.08        0.04

Matches are distributed among these distances:
 123    1  0.00
 124   87  0.33
 125    3  0.01
 126    2  0.01
 127  171  0.64
 128    2  0.01

ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28


Consensus pattern (127 bp):   
AATAGCGGCGTTTCTCCTATGAAACGCCGCTAAATAGTGGCGTTTCTAGAGTAAACGCCGCTATA
TATAATCTTATCCAAAGAGTAGAAATATGGTGCAACTGATAAAAACACCATTTCTTGATGGG

Found at i:3255 original size:31 final size:32

Alignment explanation


    Indices: 3184--3244  Score: 122
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       3174 TTTCTCCTAT

                                            
       3184 GAAACGCCGCTAAATAGTGGCGTTTAAAGGCA
          1 GAAACGCCGCTAAATAGTGGCGTTTAAAGGCA

                                         
       3216 GAAACGCCGCTAAATAGTGGCGTTTAAAG
          1 GAAACGCCGCTAAATAGTGGCGTTTAAAG

       3245 AGTAAACGCC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   29  1.00

ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20


Consensus pattern (32 bp):   
GAAACGCCGCTAAATAGTGGCGTTTAAAGGCA

Found at i:10261 original size:36 final size:37

Alignment explanation


    Indices: 10167--10272  Score: 126
    Period size: 37  Copynumber: 2.9  Consensus size: 37

      10157 AGTGAAAACT

                *            *                   
      10167 AAAACCTGATGGGAACTCTCCCAATTTAAAAACTTTG
          1 AAAAACTGATGGGAACTTTCCCAATTTAAAAACTTTG

                    *       *          *         
      10204 AAAAACTGGTGGGAACCTTCCCAATTTTAAAAC-TT-
          1 AAAAACTGATGGGAACTTTCCCAATTTAAAAACTTTG

                     *                 *      
      10239 AAAAACTTGTTGGGAACTTTCCCAATTGAAAAAC
          1 AAAAAC-TGATGGGAACTTTCCCAATTTAAAAAC


Statistics
Matches: 59,  Mismatches: 9, Indels: 3
        0.83            0.13        0.04

Matches are distributed among these distances:
  35    6  0.10
  36   25  0.42
  37   28  0.47

ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27


Consensus pattern (37 bp):   
AAAAACTGATGGGAACTTTCCCAATTTAAAAACTTTG
Done.