Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008984.1 Corchorus olitorius cultivar O-4 contig09012, 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, 616

Length: 1028
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31


Found at i:230 original size:33 final size:33

Alignment explanation


    Indices: 177--257  Score: 83
    Period size: 33  Copynumber: 2.5  Consensus size: 33

        167 CTGTTTTAGA

                     *   * *                  
        177 TGTTGTTTGCGATAATACTAAACCTAATTTGA-G
          1 TGTTGTTTGTGATGACACTAAACCT-ATTTGAGG

                                  *  *   *   
        210 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
          1 TGTTGTTTGTGATGACACTAAACCTATTTGAGG

                *          
        243 TGTTTTTTGTGATGA
          1 TGTTGTTTGTGATGA

        258 AACAAATTCT


Statistics
Matches: 40,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  32    4  0.10
  33   36  0.90

ACGTcount: A:0.23, C:0.09, G:0.22, T:0.46


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACTAAACCTATTTGAGG

Found at i:269 original size:33 final size:31

Alignment explanation


    Indices: 204--305  Score: 105
    Period size: 33  Copynumber: 3.1  Consensus size: 31

        194 CTAAACCTAA

                      *          *           
        204 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT
          1 TTTG-GTGTTATTTGTGATGAAAC-AAATCTGT

                      *                      
        237 TTTAGGTGTTTTTTGTGATGAAACAAATTCTGT
          1 TTT-GGTGTTATTTGTGATGAAACAAA-TCTGT

                    *  *                     
        270 TTTGGATGCTAATTGTGATGAAAACAAATCTGT
          1 TTTGG-TGTTATTTGTGATG-AAACAAATCTGT

               
        303 TTT
          1 TTT

        306 CATTGATCAT


Statistics
Matches: 60,  Mismatches: 5, Indels: 8
        0.82            0.07        0.11

Matches are distributed among these distances:
  32    5  0.08
  33   47  0.78
  34    8  0.13

ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45


Consensus pattern (31 bp):   
TTTGGTGTTATTTGTGATGAAACAAATCTGT

Found at i:948 original size:154 final size:154

Alignment explanation


    Indices: 666--1021  Score: 563
    Period size: 154  Copynumber: 2.3  Consensus size: 154

        656 ATCTAAAACA

                                                                             
        666 ACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA
          1 ACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA

                                                                             
        731 GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAACTGTTCCAAATGAGCTA
         66 GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAACTGTTCCAAATGAGCTA

                      *       *      
        796 -AGAACTTCATAGGGGACTAATCTC
        131 GA-AACTTCACAGGGGACAAATCTC

             *                  *             *          *                   
        820 ATCAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGA
          1 ACCAAAATGATTATAGTTAGTCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA

              *            **           *                    *               
        884 AGGCGATTCAAAACGTCACTAATGGGCCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
         65 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAACTGTTCCAAATGAGCT

                         *           
        949 AGAAACTTCACAGTGGACAAATCTC
        130 AGAAACTTCACAGGGGACAAATCTC

                                                  *         
        974 ACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGGAAAGCATTG
          1 ACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTG

       1022 GGGGTTT


Statistics
Matches: 182,  Mismatches: 17, Indels: 6
        0.89            0.08        0.03

Matches are distributed among these distances:
 153    1  0.01
 154  179  0.98
 155    2  0.01

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22


Consensus pattern (154 bp):   
ACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA
GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAACTGTTCCAAATGAGCTA
GAAACTTCACAGGGGACAAATCTC
Done.