Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022725.1 Corchorus olitorius cultivar O-4 contig22758, 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: 19944
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32


Found at i:611 original size:35 final size:35

Alignment explanation


    Indices: 569--688  Score: 186
    Period size: 35  Copynumber: 3.4  Consensus size: 35

        559 GCCAAAGCAG

                                             * 
        569 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTAC
          1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC

              *                   *            
        604 TGAGCCGCGCGGGCCAAGGCCAAGCGCTGGCCTGC
          1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC

                      *               *        
        639 TGGGCCGCGCAGGCCAAGGCCATGCGTTGGCCTGC
          1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC

                      *    
        674 TGGGCCGCGCTGGCC
          1 TGGGCCGCGCGGGCC

        689 TGCTGGGCTG


Statistics
Matches: 77,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  35   77  1.00

ACGTcount: A:0.11, C:0.37, G:0.41, T:0.12


Consensus pattern (35 bp):   
TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC

Found at i:689 original size:18 final size:18

Alignment explanation


    Indices: 627--706  Score: 67
    Period size: 18  Copynumber: 4.5  Consensus size: 18

        617 CCAAGGCCAA

                              
        627 GCGCTGGCCTGCTGGGCC
          1 GCGCTGGCCTGCTGGGCC

                *       **    
        645 GCGCAGG-C--CAAGGCC
          1 GCGCTGGCCTGCTGGGCC

                 *              
        660 ATGCGTTGGCCTGCTGGGCC
          1 --GCGCTGGCCTGCTGGGCC

                             *
        680 GCGCTGGCCTGCTGGGCT
          1 GCGCTGGCCTGCTGGGCC

                *    
        698 GCGCAGGCC
          1 GCGCTGGCC

        707 AGGCCCTAGC


Statistics
Matches: 47,  Mismatches: 10, Indels: 10
        0.70            0.15        0.15

Matches are distributed among these distances:
  15    5  0.11
  17    6  0.13
  18   31  0.66
  20    5  0.11

ACGTcount: A:0.06, C:0.36, G:0.42, T:0.15


Consensus pattern (18 bp):   
GCGCTGGCCTGCTGGGCC

Found at i:4608 original size:31 final size:29

Alignment explanation


    Indices: 4572--4630  Score: 91
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       4562 CTATTCCTTA

                                           
       4572 CTTCCCTGGCAAAAACCAGGAGAAAGTTTTC
          1 CTTCCCT-G-AAAAACCAGGAGAAAGTTTTC

                    *                   
       4603 CTTCCCTGTAAAACCAGGAGAAAGTTTT
          1 CTTCCCTGAAAAACCAGGAGAAAGTTTT

       4631 TTTTCCCCGG


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  29   19  0.70
  30    1  0.04
  31    7  0.26

ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25


Consensus pattern (29 bp):   
CTTCCCTGAAAAACCAGGAGAAAGTTTTC

Found at i:7864 original size:15 final size:15

Alignment explanation


    Indices: 7834--7863  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       7824 CAAGCAAATT

                           
       7834 ATTTATATTTGTAAA
          1 ATTTATATTTGTAAA

                           
       7849 ATTTATATTT-TAAA
          1 ATTTATATTTGTAAA

             
       7863 A
          1 A

       7864 AATGGAGCAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53


Consensus pattern (15 bp):   
ATTTATATTTGTAAA

Found at i:8227 original size:24 final size:24

Alignment explanation


    Indices: 8200--8251  Score: 77
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       8190 ACTTCAGCTA

                       *      *     
       8200 CCTCCAAACCCGAATCCCCCAAAC
          1 CCTCCAAACCCAAATCCCACAAAC

                             *      
       8224 CCTCCAAACCCAAATCCTACAAAC
          1 CCTCCAAACCCAAATCCCACAAAC

                
       8248 CCTC
          1 CCTC

       8252 TAGATAATGC


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.35, C:0.52, G:0.02, T:0.12


Consensus pattern (24 bp):   
CCTCCAAACCCAAATCCCACAAAC

Found at i:11194 original size:56 final size:58

Alignment explanation


    Indices: 11070--11202  Score: 209
    Period size: 56  Copynumber: 2.3  Consensus size: 58

      11060 ACAAAATTCT

                                *                                      
      11070 TCTCCCTTTCAATATATCCTCTCTCTCTCTCCCATCGAATCTCTCCCTCTCTACTAGCC
          1 TCTCCCTTTCAATATA-CCTATCTCTCTCTCCCATCGAATCTCTCCCTCTCTACTAGCC

                                                             *         
      11129 TCTCCCTTTCAATATACC-ATCTCTCTCTCCCATCG-ATCTCTCCCTCTTTACT-GACC
          1 TCTCCCTTTCAATATACCTATCTCTCTCTCCCATCGAATCTCTCCCTCTCTACTAG-CC

                              
      11185 TCTCCCTTTCAATATACC
          1 TCTCCCTTTCAATATACC

      11203 CAGAAAAGTA


Statistics
Matches: 71,  Mismatches: 2, Indels: 5
        0.91            0.03        0.06

Matches are distributed among these distances:
  55    1  0.01
  56   36  0.51
  57   16  0.23
  58    2  0.03
  59   16  0.23

ACGTcount: A:0.17, C:0.43, G:0.03, T:0.38


Consensus pattern (58 bp):   
TCTCCCTTTCAATATACCTATCTCTCTCTCCCATCGAATCTCTCCCTCTCTACTAGCC
Done.