Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022879.1 Corchorus olitorius cultivar O-4 contig22912, 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: 5029
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3050 original size:27 final size:27

Alignment explanation


    Indices: 3020--3160  Score: 201
    Period size: 27  Copynumber: 5.2  Consensus size: 27

       3010 CTTCTTATTC

                  *         *          
       3020 TGGTCAATTGCATGTTTAGGGGCATTT
          1 TGGTCATTTGCATGTTCAGGGGCATTT

                           *           
       3047 TGGTCATTTGCATGTCCAGGGGCATTT
          1 TGGTCATTTGCATGTTCAGGGGCATTT

                        **  *          
       3074 TGGTCATTTGCACATTTAGGGGCATTT
          1 TGGTCATTTGCATGTTCAGGGGCATTT

            *              *           
       3101 GGGTCATTTGCATGTCCAGGGGCATTT
          1 TGGTCATTTGCATGTTCAGGGGCATTT

                         *             
       3128 TGGTCATTTGCATATTCAGGGGCATTT
          1 TGGTCATTTGCATGTTCAGGGGCATTT

                  
       3155 TGGTCA
          1 TGGTCA

       3161 CTTCAAGTAC


Statistics
Matches: 99,  Mismatches: 15, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  27   99  1.00

ACGTcount: A:0.17, C:0.16, G:0.29, T:0.38


Consensus pattern (27 bp):   
TGGTCATTTGCATGTTCAGGGGCATTT

Found at i:3067 original size:128 final size:128

Alignment explanation


    Indices: 2837--3083  Score: 291
    Period size: 128  Copynumber: 1.9  Consensus size: 128

       2827 AAAACAGCTA

                                        *           *    *            * *    
       2837 TAGACACCCATTTTTGTCTTGTACCCTTGAATCAAAATCAGCTTATTTCTTAATTGGTTATTTGC
          1 TAGACACCCATTTTTGTCTTGTACCCTTCAATCAAAATCAACTTACTTCTTAATTGGTCAATTGC

                  *                                      *                 
       2902 ACGCTCGGGGGCATTTTGGTCATTTTACACACTCAGGGGCATTTTTGTCATTTGTACACTCTG
         66 ACGCTCAGGGGCATTTTGGTCATTTTACACACTCAGGGGCATTTTGGTCATTTGTACACTCTG

                                   *      * **       *          *            
       2965 TAGACACCCATTTTTGTCTTGTATCCTTCAGTTTAAATCAATTTACTTCTTATTCTGGTCAATTG
          1 TAGACACCCATTTTTGTCTTGTACCCTTCAATCAAAATCAACTTACTTCTTAAT-TGGTCAATTG

              * * *                    *   **                       
       3030 CATGTTTAGGGGCATTTTGGTCA-TTTGCA-TGTCCAGGGGCATTTTGGTCATTTG
         65 CACGCTCAGGGGCATTTTGGTCATTTTACACACT-CAGGGGCATTTTGGTCATTTG

       3084 CACATTTAGG


Statistics
Matches: 98,  Mismatches: 19, Indels: 4
        0.81            0.16        0.03

Matches are distributed among these distances:
 127    1  0.01
 128   70  0.71
 129   27  0.28

ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42


Consensus pattern (128 bp):   
TAGACACCCATTTTTGTCTTGTACCCTTCAATCAAAATCAACTTACTTCTTAATTGGTCAATTGC
ACGCTCAGGGGCATTTTGGTCATTTTACACACTCAGGGGCATTTTGGTCATTTGTACACTCTG

Found at i:3106 original size:54 final size:54

Alignment explanation


    Indices: 3020--3160  Score: 237
    Period size: 54  Copynumber: 2.6  Consensus size: 54

       3010 CTTCTTATTC

                  *      *                                        
       3020 TGGTCAATTGCATGTTTAGGGGCATTTTGGTCATTTGCATGTCCAGGGGCATTT
          1 TGGTCATTTGCATATTTAGGGGCATTTTGGTCATTTGCATGTCCAGGGGCATTT

                        *              *                          
       3074 TGGTCATTTGCACATTTAGGGGCATTTGGGTCATTTGCATGTCCAGGGGCATTT
          1 TGGTCATTTGCATATTTAGGGGCATTTTGGTCATTTGCATGTCCAGGGGCATTT

                            *                
       3128 TGGTCATTTGCATATTCAGGGGCATTTTGGTCA
          1 TGGTCATTTGCATATTTAGGGGCATTTTGGTCA

       3161 CTTCAAGTAC


Statistics
Matches: 80,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  54   80  1.00

ACGTcount: A:0.17, C:0.16, G:0.29, T:0.38


Consensus pattern (54 bp):   
TGGTCATTTGCATATTTAGGGGCATTTTGGTCATTTGCATGTCCAGGGGCATTT

Found at i:4759 original size:11 final size:11

Alignment explanation


    Indices: 4743--4768  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       4733 AGATAATTTC

                       
       4743 TTTTCTTCTAG
          1 TTTTCTTCTAG

                       
       4754 TTTTCTTCTAG
          1 TTTTCTTCTAG

                
       4765 TTTT
          1 TTTT

       4769 TAGGCAGAGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69


Consensus pattern (11 bp):   
TTTTCTTCTAG
Done.