Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024386.1 Corchorus olitorius cultivar O-4 contig24419, 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: 22937
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:7866 original size:43 final size:44

Alignment explanation


    Indices: 7805--7907  Score: 138
    Period size: 43  Copynumber: 2.4  Consensus size: 44

       7795 CATAGTTAGG

                    *    *       *                       
       7805 TTATCAAAGTTTCTTATGGAGTTTATCACAAATTT-AT-AGGTAA
          1 TTATCAAAATTTCATATGGAGGTTATCA-AAATTTAATAAGGTAA

                               *                       *
       7848 TTATCAAAATTTCATATGGTGGTTATCAAAATTTAATAAGGTAT
          1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAAGGTAA

                            
       7892 TTATCAAAATTTCATA
          1 TTATCAAAATTTCATA

       7908 AAATATTCAA


Statistics
Matches: 53,  Mismatches: 5, Indels: 3
        0.87            0.08        0.05

Matches are distributed among these distances:
  42    6  0.11
  43   26  0.49
  44   21  0.40

ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42


Consensus pattern (44 bp):   
TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAAGGTAA

Found at i:7875 original size:22 final size:22

Alignment explanation


    Indices: 7803--7907  Score: 97
    Period size: 22  Copynumber: 4.8  Consensus size: 22

       7793 TTCATAGTTA

                      *    *     *
       7803 GGTTATCAAAGTTTCTTATGGA
          1 GGTTATCAAAATTTCATATGGT

             *                     
       7825 GTTTATCACAAATTT-ATA-GGT
          1 GGTTATCA-AAATTTCATATGGT

            **                    
       7846 AATTATCAAAATTTCATATGGT
          1 GGTTATCAAAATTTCATATGGT

                          *   *   
       7868 GGTTATCAAAATTTAATAAGGT
          1 GGTTATCAAAATTTCATATGGT

            **                
       7890 ATTTATCAAAATTTCATA
          1 GGTTATCAAAATTTCATA

       7908 AAATATTCAA


Statistics
Matches: 67,  Mismatches: 13, Indels: 6
        0.78            0.15        0.07

Matches are distributed among these distances:
  20    6  0.09
  21   11  0.16
  22   45  0.67
  23    5  0.07

ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41


Consensus pattern (22 bp):   
GGTTATCAAAATTTCATATGGT

Found at i:7908 original size:22 final size:22

Alignment explanation


    Indices: 7826--7908  Score: 98
    Period size: 22  Copynumber: 3.8  Consensus size: 22

       7816 TCTTATGGAG

                                   
       7826 TTTATCACAAATTT-AT-AGGTA
          1 TTTATCA-AAATTTCATAAGGTA

            *                *   *
       7847 ATTATCAAAATTTCATATGGTG
          1 TTTATCAAAATTTCATAAGGTA

            *            *        
       7869 GTTATCAAAATTTAATAAGGTA
          1 TTTATCAAAATTTCATAAGGTA

                              
       7891 TTTATCAAAATTTCATAA
          1 TTTATCAAAATTTCATAA

       7909 AATATTCAAT


Statistics
Matches: 51,  Mismatches: 9, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  20    6  0.12
  21    8  0.16
  22   37  0.73

ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41


Consensus pattern (22 bp):   
TTTATCAAAATTTCATAAGGTA

Found at i:7914 original size:22 final size:22

Alignment explanation


    Indices: 7870--7914  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       7860 CATATGGTGG

                             **   
       7870 TTATCAAAATTTAATAAGGTAT
          1 TTATCAAAATTTAATAAAATAT

                        *         
       7892 TTATCAAAATTTCATAAAATAT
          1 TTATCAAAATTTAATAAAATAT

             
       7914 T
          1 T

       7915 CAATCGAAAC


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42


Consensus pattern (22 bp):   
TTATCAAAATTTAATAAAATAT

Found at i:12348 original size:20 final size:20

Alignment explanation


    Indices: 12323--12362  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      12313 TTAGGTTCAA

                                
      12323 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

                                
      12343 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

      12363 GTTTGTAATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35


Consensus pattern (20 bp):   
CTCTCACGGAATGTGAGTTT
Done.