Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012679.1 Corchorus olitorius cultivar O-4 contig12712, 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: 23158
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31


Found at i:96 original size:9 final size:9

Alignment explanation


    Indices: 82--108  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

         72 CAATAAACAT

                     
         82 CAAAACAAA
          1 CAAAACAAA

                     
         91 CAAAACAAA
          1 CAAAACAAA

                     
        100 CAAAACAAA
          1 CAAAACAAA

        109 GCAACCGTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00


Consensus pattern (9 bp):   
CAAAACAAA

Found at i:9828 original size:28 final size:27

Alignment explanation


    Indices: 9783--9888  Score: 104
    Period size: 28  Copynumber: 3.8  Consensus size: 27

       9773 GGTGTCCCTG

                  *      *         *   
       9783 AAATGATCAAAATACCCCTGGACGTGC
          1 AAATGACCAAAATGCCCCTGGACTTGC

                                 *    * 
       9810 AAGATGACCAAAATGCCCCTGAACTTAC
          1 AA-ATGACCAAAATGCCCCTGGACTTGC

                                ***     
       9838 GAAATGACCAAAATGCCCCTATCCTTGC
          1 -AAATGACCAAAATGCCCCTGGACTTGC

                              *    
       9866 AAAATGACCAAAATGCCCTTGGA
          1 -AAATGACCAAAATGCCCCTGGA

       9889 TCCGAAAAAT


Statistics
Matches: 63,  Mismatches: 14, Indels: 3
        0.79            0.17        0.04

Matches are distributed among these distances:
  27    2  0.03
  28   59  0.94
  29    2  0.03

ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGGACTTGC

Found at i:9897 original size:28 final size:27

Alignment explanation


    Indices: 9813--9907  Score: 86
    Period size: 28  Copynumber: 3.4  Consensus size: 27

       9803 GACGTGCAAG

                                *  *  *  
       9813 ATGACCAAAATGCCCCTGA-ACTTACGAA
          1 ATGACCAAAATGCCCCT-ATCCTGA-AAA

                                    *   
       9841 ATGACCAAAATGCCCCTATCCTTGCAAA
          1 ATGACCAAAATGCCCCTATCC-TGAAAA

                           *             
       9869 ATGACCAAAATGCCCTTGGATCC-GAAAA
          1 ATGACCAAAATGCCCCT--ATCCTGAAAA

                       
       9897 ATGACCAAAAT
          1 ATGACCAAAAT

       9908 AAGGAGTAAA


Statistics
Matches: 57,  Mismatches: 6, Indels: 8
        0.80            0.08        0.11

Matches are distributed among these distances:
  27    1  0.02
  28   51  0.89
  29    1  0.02
  30    4  0.07

ACGTcount: A:0.40, C:0.27, G:0.14, T:0.19


Consensus pattern (27 bp):   
ATGACCAAAATGCCCCTATCCTGAAAA

Found at i:10220 original size:49 final size:50

Alignment explanation


    Indices: 10163--10307  Score: 240
    Period size: 49  Copynumber: 2.9  Consensus size: 50

      10153 TGGGGAATCG

                                                              
      10163 TCTTAAAAGGACCGTCTTCCGC-TATCCTTTGAACTGTCTTCCAATTTAA
          1 TCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTTAA

                                                             *
      10212 TCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTC-TCCAATTTAC
          1 TCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTTAA

               *            *                    *         
      10261 TCTCAAAAGGACCGTCCTCCGCTTATCCTTTGAACTGCCTTCCAATT
          1 TCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATT

      10308 CGTTTTTTCT


Statistics
Matches: 90,  Mismatches: 4, Indels: 3
        0.93            0.04        0.03

Matches are distributed among these distances:
  49   67  0.74
  50   23  0.26

ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35


Consensus pattern (50 bp):   
TCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTTAA

Found at i:11363 original size:9 final size:9

Alignment explanation


    Indices: 11349--11374  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

      11339 TAGGCTGAGT

                     
      11349 TTTTTTTTC
          1 TTTTTTTTC

                     
      11358 TTTTTTTTC
          1 TTTTTTTTC

                    
      11367 TTTTTTTT
          1 TTTTTTTT

      11375 TTAAGCATAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92


Consensus pattern (9 bp):   
TTTTTTTTC
Done.