Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014535.1 Corchorus olitorius cultivar O-4 contig14568, 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: 8386
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:554 original size:36 final size:36

Alignment explanation


    Indices: 507--593  Score: 123
    Period size: 30  Copynumber: 2.6  Consensus size: 36

        497 GTGGTCTTCT

                                                
        507 TAATGATGTTGGGTTAGGGTTAGGTGATGGTATTTA
          1 TAATGATGTTGGGTTAGGGTTAGGTGATGGTATTTA

                                                
        543 TAATGA---T--GTT-GGGTTAGGTGATGGTATTTA
          1 TAATGATGTTGGGTTAGGGTTAGGTGATGGTATTTA

               *                 
        573 TAAGGATGTTGGGTTAGGGTT
          1 TAATGATGTTGGGTTAGGGTT

        594 TCAAGAGGGT


Statistics
Matches: 44,  Mismatches: 1, Indels: 12
        0.77            0.02        0.21

Matches are distributed among these distances:
  30   25  0.57
  31    3  0.07
  33    2  0.05
  35    3  0.07
  36   11  0.25

ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41


Consensus pattern (36 bp):   
TAATGATGTTGGGTTAGGGTTAGGTGATGGTATTTA

Found at i:559 original size:30 final size:30

Alignment explanation


    Indices: 523--590  Score: 127
    Period size: 30  Copynumber: 2.3  Consensus size: 30

        513 TGTTGGGTTA

                                   *      
        523 GGGTTAGGTGATGGTATTTATAATGATGTT
          1 GGGTTAGGTGATGGTATTTATAAGGATGTT

                                          
        553 GGGTTAGGTGATGGTATTTATAAGGATGTT
          1 GGGTTAGGTGATGGTATTTATAAGGATGTT

                    
        583 GGGTTAGG
          1 GGGTTAGG

        591 GTTTCAAGAG


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   37  1.00

ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40


Consensus pattern (30 bp):   
GGGTTAGGTGATGGTATTTATAAGGATGTT

Found at i:7687 original size:58 final size:57

Alignment explanation


    Indices: 7617--7777  Score: 225
    Period size: 58  Copynumber: 2.8  Consensus size: 57

       7607 CCTGGACGCG

                             * *                                  *    
       7617 AAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCGAAATGCCCCTAG-AGGGGTAA
          1 AAATGACCAAAATGCCCTTGGATGTGC-AAAATGACCGAAATGCCCCTAGAAGGCGT-A

                                                                *     
       7675 AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCCCTAGATATGCGTA
          1 AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCCCTAGA-AGGCGTA

                                    *         * *        
       7733 AAATGACCAAAATGCCCTTGGATGCGCAAAATGATCAAAATGCCC
          1 AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCC

       7778 TTGGCTTCGC


Statistics
Matches: 94,  Mismatches: 7, Indels: 4
        0.90            0.07        0.04

Matches are distributed among these distances:
  57   22  0.23
  58   68  0.72
  59    4  0.04

ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18


Consensus pattern (57 bp):   
AAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCCCTAGAAGGCGTA

Found at i:7706 original size:28 final size:28

Alignment explanation


    Indices: 7590--7777  Score: 182
    Period size: 29  Copynumber: 6.6  Consensus size: 28

       7580 ATGCAAAAAA

                   *                 *  
       7590 AAAATGATCAAAATGCCCCTGGA--CGC
          1 AAAATGACCAAAATGCCCCTGGATGTGC

            *                   *       
       7616 GAAATGACCAAAATGCCCCTAGATGTGC
          1 AAAATGACCAAAATGCCCCTGGATGTGC

                      *          *  * *  *
       7644 AAAAATGACCGAAATGCCCCTAGAGGGGTA
          1 -AAAATGACCAAAATGCCCCTGGATGTG-C

                              *         
       7674 AAAATGACCAAAATGCCCTTGGATGTGC
          1 AAAATGACCAAAATGCCCCTGGATGTGC

                     *          *   *   
       7702 AAAATGACCGAAATGCCCCTAGATATGC
          1 AAAATGACCAAAATGCCCCTGGATGTGC

                                *      *  
       7730 GTAAAATGACCAAAATGCCCTTGGATGCGC
          1 --AAAATGACCAAAATGCCCCTGGATGTGC

                   *          
       7760 AAAATGATCAAAATGCCC
          1 AAAATGACCAAAATGCCC

       7778 TTGGCTTCGC


Statistics
Matches: 131,  Mismatches: 25, Indels: 10
        0.79            0.15        0.06

Matches are distributed among these distances:
  26   20  0.15
  28   43  0.33
  29   45  0.34
  30   23  0.18

ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGGATGTGC

Found at i:7764 original size:86 final size:84

Alignment explanation


    Indices: 7589--7781  Score: 235
    Period size: 86  Copynumber: 2.3  Consensus size: 84

       7579 TATGCAAAAA

                               *       *                       *             
       7589 AAAAATGATCAAAATGCCCCTGGACGCGAAATGACCAAAATGCCCCTAGATGTGCAAAAATGACC
          1 AAAAATGATCAAAATGCCCTTGGACGCAAAATGACCAAAATGCCCCTAGATATGCAAAAATGACC

            *               *  
       7654 GAAATGCCCCTAGAGGGGT
         66 AAAATGCCCCTAGAGGCGT

                    *                 *           *                   *      
       7673 AAAAATGACCAAAATGCCCTTGGATGTGCAAAATGACCGAAATGCCCCTAGATATGCGTAAAATG
          1 AAAAATGATCAAAATGCCCTTGGA--CGCAAAATGACCAAAATGCCCCTAGATATGC-AAAAATG

                        * *  *    
       7738 ACCAAAATGCCCTTGGATGCG-
         63 ACCAAAATGCCCCTAGAGGCGT

            *                      
       7759 CAAAATGATCAAAATGCCCTTGG
          1 AAAAATGATCAAAATGCCCTTGG

       7782 CTTCGCAAAA


Statistics
Matches: 92,  Mismatches: 14, Indels: 4
        0.84            0.13        0.04

Matches are distributed among these distances:
  84   22  0.24
  86   48  0.52
  87   22  0.24

ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18


Consensus pattern (84 bp):   
AAAAATGATCAAAATGCCCTTGGACGCAAAATGACCAAAATGCCCCTAGATATGCAAAAATGACC
AAAATGCCCCTAGAGGCGT

Done.