Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019667.1 Corchorus olitorius cultivar O-4 contig19700, 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: 37170
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:828 original size:2 final size:2

Alignment explanation


    Indices: 821--850  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        811 CAAACTTGAA

                                                        
        821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        851 CTTAATTAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:12081 original size:56 final size:56

Alignment explanation


    Indices: 12013--12124  Score: 206
    Period size: 56  Copynumber: 2.0  Consensus size: 56

      12003 ATAAATTAAA

                                                                    
      12013 TAAGGTTATCAAATCTCTAATATCATCTATCCTAAAAACTATACCATAAATAAACT
          1 TAAGGTTATCAAATCTCTAATATCATCTATCCTAAAAACTATACCATAAATAAACT

                   *                          *                     
      12069 TAAGGTTGTCAAATCTCTAATATCATCTATCCTATAAACTATACCATAAATAAACT
          1 TAAGGTTATCAAATCTCTAATATCATCTATCCTAAAAACTATACCATAAATAAACT

      12125 ACAAACTAAA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  56   54  1.00

ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33


Consensus pattern (56 bp):   
TAAGGTTATCAAATCTCTAATATCATCTATCCTAAAAACTATACCATAAATAAACT

Found at i:25452 original size:38 final size:38

Alignment explanation


    Indices: 25410--25488  Score: 158
    Period size: 38  Copynumber: 2.1  Consensus size: 38

      25400 CCTTTATATG

                                                  
      25410 CCTAATGTTCTTTGCCTTGTATGATATATGGATTCTCC
          1 CCTAATGTTCTTTGCCTTGTATGATATATGGATTCTCC

                                                  
      25448 CCTAATGTTCTTTGCCTTGTATGATATATGGATTCTCC
          1 CCTAATGTTCTTTGCCTTGTATGATATATGGATTCTCC

               
      25486 CCT
          1 CCT

      25489 GTTTGAGTTG


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   41  1.00

ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44


Consensus pattern (38 bp):   
CCTAATGTTCTTTGCCTTGTATGATATATGGATTCTCC

Found at i:31518 original size:8 final size:8

Alignment explanation


    Indices: 31471--31517  Score: 73
    Period size: 8  Copynumber: 6.2  Consensus size: 8

      31461 TAAATTAAGG

                    
      31471 TTAG-CTT
          1 TTAGCCTT

                    
      31478 TTAGCCTT
          1 TTAGCCTT

                    
      31486 TTAGCCTT
          1 TTAGCCTT

                    
      31494 TTAGCCTT
          1 TTAGCCTT

                    
      31502 TTAG-CTT
          1 TTAGCCTT

                    
      31509 TTAG-CTT
          1 TTAGCCTT

              
      31516 TT
          1 TT

      31518 TGCTCCTTTT


Statistics
Matches: 39,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   7   16  0.41
   8   23  0.59

ACGTcount: A:0.13, C:0.19, G:0.13, T:0.55


Consensus pattern (8 bp):   
TTAGCCTT

Found at i:31791 original size:31 final size:31

Alignment explanation


    Indices: 31756--31890  Score: 128
    Period size: 31  Copynumber: 4.4  Consensus size: 31

      31746 TTTGTGCACG

                                    **     
      31756 TGGCATGTCACATGTCACTTTTTGAAACACA
          1 TGGCATGTCACATGTCACTTTTTGGTACACA

                   *   *   *               
      31787 TGGCATGCCACGTGTTACTTTTTGGTACACA
          1 TGGCATGTCACATGTCACTTTTTGGTACACA

                *       *    *             *
      31818 TGGCGTGAT-ACGTGTCGCTTTTTGGTACACG
          1 TGGCATG-TCACATGTCACTTTTTGGTACACA

                *  *        *             *
      31849 TGGCGTGCCACATGTCGCTTTTTGGTACACG
          1 TGGCATGTCACATGTCACTTTTTGGTACACA

              *        
      31880 TGACATGTCAC
          1 TGGCATGTCAC

      31891 GTCTGACATC


Statistics
Matches: 87,  Mismatches: 15, Indels: 4
        0.82            0.14        0.04

Matches are distributed among these distances:
  31   87  1.00

ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33


Consensus pattern (31 bp):   
TGGCATGTCACATGTCACTTTTTGGTACACA

Found at i:35653 original size:26 final size:28

Alignment explanation


    Indices: 35616--35685  Score: 72
    Period size: 31  Copynumber: 2.4  Consensus size: 28

      35606 CTCATCTTAA

                                         
      35616 TTAGTATTATCTT-A-GTAATTTATTAGC
          1 TTAGT-TTATCTTGACGTAATTTATTAGC

                              *            
      35643 TTAGTTTATCTATGGATCTTAATTTATTAGC
          1 TTAGTTTATCT-T-GA-CGTAATTTATTAGC

                  *     
      35674 TTAGTTCATCTT
          1 TTAGTTTATCTT

      35686 CGTTTATCAT


Statistics
Matches: 36,  Mismatches: 2, Indels: 7
        0.80            0.04        0.16

Matches are distributed among these distances:
  26    6  0.17
  27    6  0.17
  29    1  0.03
  30    1  0.03
  31   22  0.61

ACGTcount: A:0.26, C:0.10, G:0.11, T:0.53


Consensus pattern (28 bp):   
TTAGTTTATCTTGACGTAATTTATTAGC
Done.