Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024863.1 Corchorus olitorius cultivar O-4 contig24896, 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: 11316
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:4668 original size:26 final size:28

Alignment explanation


    Indices: 4624--4676  Score: 74
    Period size: 27  Copynumber: 2.0  Consensus size: 28

       4614 AAAACTTATA

                    *                   
       4624 TTTTAACAGTGGCATATTTA-AAATATT
          1 TTTTAACAATGGCATATTTAGAAATATT

                  *                    
       4651 TTTTAATAATGGCA-ATTTAGAAATAT
          1 TTTTAACAATGGCATATTTAGAAATAT

       4677 ATTTGAAAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  26    5  0.22
  27   18  0.78

ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43


Consensus pattern (28 bp):   
TTTTAACAATGGCATATTTAGAAATATT

Found at i:5632 original size:88 final size:91

Alignment explanation


    Indices: 5479--5648  Score: 274
    Period size: 88  Copynumber: 1.9  Consensus size: 91

       5469 TAATAAGGAC

                                                               *             
       5479 AATTTAGAAATATATTTTTTTAAAAAAAAAGGTACAATAGGAAAACATAAAGTTTCCCCTTATTC
          1 AATTTAGAAATATA-TTTTTT-AAAAAAAAGGTACAATAGGAAAACATAAACTTTCCCCTTATTC

                                        
       5544 GTGCTTTTATA-TAGTATAGATTATGGA
         64 GTGCTTTTATATTAGTATAGATTATGGA

                                       *        *                            
       5571 AATTTAGAAATATA-TTTTT-AAAAAAGGGTACAATCGGAAAACATAAACTTTCCCCTTATTCGT
          1 AATTTAGAAATATATTTTTTAAAAAAAAGGTACAATAGGAAAACATAAACTTTCCCCTTATTCGT

                           
       5634 GCTTTTATATTAGTA
         66 GCTTTTATATTAGTA

       5649 CTTAAAGGAA


Statistics
Matches: 74,  Mismatches: 3, Indels: 5
        0.90            0.04        0.06

Matches are distributed among these distances:
  88   50  0.68
  89    5  0.07
  90    5  0.07
  92   14  0.19

ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37


Consensus pattern (91 bp):   
AATTTAGAAATATATTTTTTAAAAAAAAGGTACAATAGGAAAACATAAACTTTCCCCTTATTCGT
GCTTTTATATTAGTATAGATTATGGA

Found at i:8736 original size:20 final size:20

Alignment explanation


    Indices: 8711--8762  Score: 70
    Period size: 20  Copynumber: 2.6  Consensus size: 20

       8701 TTCTTTTTTT

                                
       8711 TTTCTTTTTCTTCCTTTCCC
          1 TTTCTTTTTCTTCCTTTCCC

                   *     *    * 
       8731 TTTCTTTCTCTTCTTTTCTC
          1 TTTCTTTTTCTTCCTTTCCC

                         
       8751 TTT-TTTTTCTTC
          1 TTTCTTTTTCTTC

       8763 TACTGGGCCT


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  19    8  0.29
  20   20  0.71

ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71


Consensus pattern (20 bp):   
TTTCTTTTTCTTCCTTTCCC

Found at i:8762 original size:39 final size:39

Alignment explanation


    Indices: 8686--8762  Score: 111
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       8676 TCCTTCTTAT

                 *                * *              
       8686 TTTCCTTTTCTTTCTTTCTTTTTTTTTTCTTTTTCTTCC
          1 TTTCCCTTTCTTTCTTTCTTTTCTCTTTCTTTTTCTTCC

                                                   
       8725 TTTCCCTTTCTTTCTCTTCTTTTCTCTTT-TTTTTCTTC
          1 TTTCCCTTTCTTTCT-TTCTTTTCTCTTTCTTTTTCTTC

       8763 TACTGGGCCT


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  39   23  0.68
  40   11  0.32

ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74


Consensus pattern (39 bp):   
TTTCCCTTTCTTTCTTTCTTTTCTCTTTCTTTTTCTTCC
Done.