Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012202.1 Corchorus capsularis cultivar CVL-1 contig12223, 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: 42972
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:13679 original size:45 final size:45

Alignment explanation


    Indices: 13612--13698  Score: 140
    Period size: 45  Copynumber: 1.9  Consensus size: 45

      13602 GATTACTTCT

                                         *               
      13612 CCAGCTCATCATTAATCGGGGGTAGGGATTTTTTAGTAATTCCAC
          1 CCAGCTCATCATTAATCGGGGGTAGGGATCTTTTAGTAATTCCAC

                  *                                    
      13657 CCAGCTTATCATTAATTC-GGGGTAGGGATCTTTTAGTAATTC
          1 CCAGCTCATCATTAA-TCGGGGGTAGGGATCTTTTAGTAATTC

      13699 GACTACTCTA


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  45   37  0.95
  46    2  0.05

ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36


Consensus pattern (45 bp):   
CCAGCTCATCATTAATCGGGGGTAGGGATCTTTTAGTAATTCCAC

Found at i:30866 original size:23 final size:23

Alignment explanation


    Indices: 30840--30896  Score: 62
    Period size: 23  Copynumber: 2.5  Consensus size: 23

      30830 TAGTTTGTTA

                                    
      30840 CATTTTTTTTTATTC-TTTTGATT
          1 CATTTTTTTTTA-TCATTTTGATT

                  **  *            
      30863 CATTTTGATTGATCATTTTGATT
          1 CATTTTTTTTTATCATTTTGATT

             *         
      30886 CTTTTTTTTTT
          1 CATTTTTTTTT

      30897 TTAATTTATT


Statistics
Matches: 26,  Mismatches: 7, Indels: 2
        0.74            0.20        0.06

Matches are distributed among these distances:
  22    2  0.08
  23   24  0.92

ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70


Consensus pattern (23 bp):   
CATTTTTTTTTATCATTTTGATT

Found at i:30880 original size:13 final size:14

Alignment explanation


    Indices: 30857--30885  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

      30847 TTTTATTCTT

                          
      30857 TTGATTCATTTTGA
          1 TTGATTCATTTTGA

                          
      30871 TTGA-TCATTTTGA
          1 TTGATTCATTTTGA

              
      30884 TT
          1 TT

      30886 CTTTTTTTTT


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

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59


Consensus pattern (14 bp):   
TTGATTCATTTTGA

Found at i:31111 original size:31 final size:31

Alignment explanation


    Indices: 31070--31155  Score: 109
    Period size: 31  Copynumber: 2.8  Consensus size: 31

      31060 ACGGAGTCCG

                 *                         
      31070 ACGTGGCACCTTTTGGAACACGTGGCGTCAC
          1 ACGTGTCACCTTTTGGAACACGTGGCGTCAC

            *                    *      ** 
      31101 CCGTGTCACCTTTTGGAACACATGGCGTGTC
          1 ACGTGTCACCTTTTGGAACACGTGGCGTCAC

              *             *       
      31132 ACATGTCACCTTTTGGTACACGTG
          1 ACGTGTCACCTTTTGGAACACGTG

      31156 ACGTGCCACC


Statistics
Matches: 46,  Mismatches: 9, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  31   46  1.00

ACGTcount: A:0.19, C:0.28, G:0.26, T:0.28


Consensus pattern (31 bp):   
ACGTGTCACCTTTTGGAACACGTGGCGTCAC

Found at i:31165 original size:24 final size:24

Alignment explanation


    Indices: 31138--31188  Score: 93
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      31128 TGTCACATGT

                                    
      31138 CACCTTTTGGTACACGTGACGTGC
          1 CACCTTTTGGTACACGTGACGTGC

                              *     
      31162 CACCTTTTGGTACACGTGGCGTGC
          1 CACCTTTTGGTACACGTGACGTGC

               
      31186 CAC
          1 CAC

      31189 GTGTCATTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.16, C:0.31, G:0.25, T:0.27


Consensus pattern (24 bp):   
CACCTTTTGGTACACGTGACGTGC

Found at i:37034 original size:22 final size:22

Alignment explanation


    Indices: 37009--37054  Score: 92
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      36999 TCCTCTGCCT

                                  
      37009 TGTTGATCCCAATTGTCATCGG
          1 TGTTGATCCCAATTGTCATCGG

                                  
      37031 TGTTGATCCCAATTGTCATCGG
          1 TGTTGATCCCAATTGTCATCGG

              
      37053 TG
          1 TG

      37055 AAGTATATGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37


Consensus pattern (22 bp):   
TGTTGATCCCAATTGTCATCGG

Found at i:39657 original size:16 final size:15

Alignment explanation


    Indices: 39632--39661  Score: 51
    Period size: 16  Copynumber: 1.9  Consensus size: 15

      39622 TCCTTACTGG

                           
      39632 AAAAAAAAAAGAAAC
          1 AAAAAAAAAAGAAAC

                           
      39647 AAAAAAGAAAAGAAA
          1 AAAAAA-AAAAGAAA

      39662 ACCCTCTACC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00


Consensus pattern (15 bp):   
AAAAAAAAAAGAAAC
Done.