Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009819.1 Corchorus capsularis cultivar CVL-1 contig09840, 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: 12181
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:803 original size:2 final size:2

Alignment explanation


    Indices: 796--820  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        786 TTCTTTTAAA

                                                 
        796 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

        821 AAATAAAATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:2859 original size:26 final size:24

Alignment explanation


    Indices: 2797--2865  Score: 84
    Period size: 26  Copynumber: 2.8  Consensus size: 24

       2787 AAATTGCCAG

                     *              
       2797 GGGCATTTTTGTCATTTTCCTCAA
          1 GGGCATTTTGGTCATTTTCCTCAA

               *                   *  
       2821 GGGTATTTTGGTCATTTTCACTTTAA
          1 GGGCATTTTGGTCATTTTC-C-TCAA

             *                 
       2847 GTGCATTTTGGTCATTTTC
          1 GGGCATTTTGGTCATTTTC

       2866 GTAAGGGACT


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
  24   17  0.45
  25    1  0.03
  26   20  0.53

ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49


Consensus pattern (24 bp):   
GGGCATTTTGGTCATTTTCCTCAA

Found at i:8800 original size:15 final size:16

Alignment explanation


    Indices: 8773--8803  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

       8763 GTTATATCGA

                            
       8773 AAAATATAAAAAAAAT
          1 AAAATATAAAAAAAAT

                            
       8789 AAAATA-AAAAAAAAT
          1 AAAATATAAAAAAAAT

       8804 TCGACCAGAA


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

Matches are distributed among these distances:
  15    9  0.60
  16    6  0.40

ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (16 bp):   
AAAATATAAAAAAAAT

Found at i:10263 original size:66 final size:66

Alignment explanation


    Indices: 10181--10323  Score: 250
    Period size: 66  Copynumber: 2.2  Consensus size: 66

      10171 TTGAAAAGAG

                                                                   * *       
      10181 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATGACACTAAAT
          1 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT

             
      10246 C
         66 C

                                                   *                         
      10247 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTTAGTGTTGTTTGCAATAAAACTAAAT
          1 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT

             
      10312 C
         66 C

                  *    
      10313 TGTTTTGGATG
          1 TGTTTTAGATG

      10324 CTAATTGTGA


Statistics
Matches: 73,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  66   73  1.00

ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43


Consensus pattern (66 bp):   
TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
C

Found at i:10309 original size:33 final size:34

Alignment explanation


    Indices: 10183--10310  Score: 163
    Period size: 33  Copynumber: 3.9  Consensus size: 34

      10173 GAAAAGAGTG

                             *                
      10183 TTTTAGATGTTGTTTGCGATGATACTAAACCTAA
          1 TTTTAGATGTTGTTTGCAATGATACTAAACCTAA

               *                  *      *   *
      10217 TTTGAG-TGTTGTTTGCAATGACACTAAATCT-G
          1 TTTTAGATGTTGTTTGCAATGATACTAAACCTAA

                             *                
      10249 TTTTAGATGTTGTTTGCGATGATACTAAACCTAA
          1 TTTTAGATGTTGTTTGCAATGATACTAAACCTAA

                                * *      
      10283 TTTTAG-TGTTGTTTGCAATAAAACTAAA
          1 TTTTAGATGTTGTTTGCAATGATACTAAA

      10311 TCTGTTTTGG


Statistics
Matches: 79,  Mismatches: 13, Indels: 5
        0.81            0.13        0.05

Matches are distributed among these distances:
  32    5  0.06
  33   63  0.80
  34   11  0.14

ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41


Consensus pattern (34 bp):   
TTTTAGATGTTGTTTGCAATGATACTAAACCTAA

Found at i:10373 original size:33 final size:33

Alignment explanation


    Indices: 10336--10423  Score: 113
    Period size: 33  Copynumber: 2.7  Consensus size: 33

      10326 AATTGTGATG

                                             
      10336 AAAACAATTCTGTTTTGGTTGAGCATAGCATTA
          1 AAAACAATTCTGTTTTGGTTGAGCATAGCATTA

                      *           **        *
      10369 AAAACAATTCAGTTTTGGTTGATTATAGCATTG
          1 AAAACAATTCTGTTTTGGTTGAGCATAGCATTA

            *   *   *             
      10402 CAAATAATCCTGTTTTGGTTGA
          1 AAAACAATTCTGTTTTGGTTGA

      10424 TAGCATTGAA


Statistics
Matches: 47,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  33   47  1.00

ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39


Consensus pattern (33 bp):   
AAAACAATTCTGTTTTGGTTGAGCATAGCATTA

Done.