Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012707.1 Corchorus olitorius cultivar O-4 contig12740, 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: 7943
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33


Found at i:2971 original size:22 final size:22

Alignment explanation


    Indices: 2945--3177  Score: 236
    Period size: 22  Copynumber: 10.7  Consensus size: 22

       2935 TGAAACACTT

                                  
       2945 AGTCTGCCCTGAGACGCTTGAA
          1 AGTCTGCCCTGAGACGCTTGAA

                           *  * * 
       2967 AGTCTGCCCTGAGACACTGGGA
          1 AGTCTGCCCTGAGACGCTTGAA

            *              *      
       2989 TGTCTGCCCTGAGACACTTGAA
          1 AGTCTGCCCTGAGACGCTTGAA

                 *              **
       3011 AGTCTACCCTGAGACGCTTGGG
          1 AGTCTGCCCTGAGACGCTTGAA

            *        *            
       3033 TGTCTGCCCCGAGACGC-TGAA
          1 AGTCTGCCCTGAGACGCTTGAA

                 *         *      
       3054 AGTCTACCCTGAGACACTTGAA
          1 AGTCTGCCCTGAGACGCTTGAA

                 *   *    **     *
       3076 AGTCTACCCCGAGATACTTGAG
          1 AGTCTGCCCTGAGACGCTTGAA

                          *     * 
       3098 AGTCTGCCCTGAGATGCTTGGA
          1 AGTCTGCCCTGAGACGCTTGAA

               *     *          * 
       3120 AGTTTGCCCCGAGACGCTTGGA
          1 AGTCTGCCCTGAGACGCTTGAA

                 *     *          
       3142 AGTCTACCCTGTGACGC-TGAA
          1 AGTCTGCCCTGAGACGCTTGAA

                           
       3163 AGTCTGCCCTGAGAC
          1 AGTCTGCCCTGAGAC

       3178 TTAAAAAAGA


Statistics
Matches: 172,  Mismatches: 38, Indels: 3
        0.81            0.18        0.01

Matches are distributed among these distances:
  21   31  0.18
  22  141  0.82

ACGTcount: A:0.22, C:0.28, G:0.27, T:0.23


Consensus pattern (22 bp):   
AGTCTGCCCTGAGACGCTTGAA

Found at i:3136 original size:109 final size:109

Alignment explanation


    Indices: 2945--3177  Score: 297
    Period size: 109  Copynumber: 2.1  Consensus size: 109

       2935 TGAAACACTT

                           *           *   *         *                       
       2945 AGTCTGCCCTGAGACGCTTGAAAGTCTGCCCTGAGACACTGGGATGTCTGCCCTGAGACACTTGA
          1 AGTCTGCCCTGAGACACTTGAAAGTCTACCCCGAGACACTGAGATGTCTGCCCTGAGACACTTGA

                      *           **    *               
       3010 AAGTCTACCCTGAGACGCTTGGGTGTCTGCCCCGAGACGCTGAA
         66 AAGTCTACCCCGAGACGCTTGGAAGTCTACCCCGAGACGCTGAA

                 *                              *                      **    
       3054 AGTCTACCCTGAGACACTTGAAAGTCTACCCCGAGATACTTGAGA-GTCTGCCCTGAGATGCTTG
          1 AGTCTGCCCTGAGACACTTGAAAGTCTACCCCGAGACAC-TGAGATGTCTGCCCTGAGACACTTG

            *    * *                         * *         
       3118 GAAGTTTGCCCCGAGACGCTTGGAAGTCTACCCTGTGACGCTGAA
         65 AAAGTCTACCCCGAGACGCTTGGAAGTCTACCCCGAGACGCTGAA

                           
       3163 AGTCTGCCCTGAGAC
          1 AGTCTGCCCTGAGAC

       3178 TTAAAAAAGA


Statistics
Matches: 105,  Mismatches: 18, Indels: 2
        0.84            0.14        0.02

Matches are distributed among these distances:
 109  101  0.96
 110    4  0.04

ACGTcount: A:0.22, C:0.28, G:0.27, T:0.23


Consensus pattern (109 bp):   
AGTCTGCCCTGAGACACTTGAAAGTCTACCCCGAGACACTGAGATGTCTGCCCTGAGACACTTGA
AAGTCTACCCCGAGACGCTTGGAAGTCTACCCCGAGACGCTGAA

Found at i:4444 original size:12 final size:12

Alignment explanation


    Indices: 4427--4451  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       4417 TTGATTCACT

                        
       4427 TTTGATTTGAAC
          1 TTTGATTTGAAC

                        
       4439 TTTGATTTGAAC
          1 TTTGATTTGAAC

             
       4451 T
          1 T

       4452 GCTTCTTTTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52


Consensus pattern (12 bp):   
TTTGATTTGAAC
Done.