Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011951.1 Corchorus olitorius cultivar O-4 contig11984, 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: 7157
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37


Found at i:2073 original size:15 final size:15

Alignment explanation


    Indices: 2055--2085  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2045 TATAGCTTGA

                           
       2055 TCTTGACAAGCTGCC
          1 TCTTGACAAGCTGCC

                      *    
       2070 TCTTGACAAGTTGCC
          1 TCTTGACAAGCTGCC

             
       2085 T
          1 T

       2086 TCAAATAATT


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

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.19, C:0.29, G:0.19, T:0.32


Consensus pattern (15 bp):   
TCTTGACAAGCTGCC

Found at i:2545 original size:156 final size:156

Alignment explanation


    Indices: 2252--2565  Score: 547
    Period size: 156  Copynumber: 2.0  Consensus size: 156

       2242 AAATAAATTA

                *              *     *                                      *
       2252 TTCGGCTCATTCGACCCAAGGCTAGGCTATGCGATTCATGAATTTAATACGGTGGTTAATCTAAT
          1 TTCGACTCATTCGACCCAAAGCTAGCCTATGCGATTCATGAATTTAATACGGTGGTTAATCTAAA

                                                                             
       2317 ATTATTGGTTTCCCTTGTGATATACTCTATATTAGTTATAGAATTAAGTCATAATAGCATTGGAA
         66 ATTATTGGTTTCCCTTGTGATATACTCTATATTAGTTATAGAATTAAGTCATAATAGCATTGGAA

                                *     
       2382 AGACAATTCTCTCATCAATCGGATGG
        131 AGACAATTCTCTCATCAATCAGATGG

                                 *                                           
       2408 TTCGACTCATTCGACCCAAAGTTAGCCTATGCGATTCATGAATTTAATACGGTGGTTAATCTAAA
          1 TTCGACTCATTCGACCCAAAGCTAGCCTATGCGATTCATGAATTTAATACGGTGGTTAATCTAAA

                         *                                   *               
       2473 ATTATTGGTTTCCTTTGTGATATACTCTATATTAGTTATAGAATTAAGTTATAATAGCATTGGAA
         66 ATTATTGGTTTCCCTTGTGATATACTCTATATTAGTTATAGAATTAAGTCATAATAGCATTGGAA

              *                       
       2538 AGGCAATTCTCTCATCAATCAGATGG
        131 AGACAATTCTCTCATCAATCAGATGG

              
       2564 TT
          1 TT

       2566 GCATGAAGTA


Statistics
Matches: 149,  Mismatches: 9, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 156  149  1.00

ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36


Consensus pattern (156 bp):   
TTCGACTCATTCGACCCAAAGCTAGCCTATGCGATTCATGAATTTAATACGGTGGTTAATCTAAA
ATTATTGGTTTCCCTTGTGATATACTCTATATTAGTTATAGAATTAAGTCATAATAGCATTGGAA
AGACAATTCTCTCATCAATCAGATGG

Found at i:4946 original size:23 final size:23

Alignment explanation


    Indices: 4916--4974  Score: 100
    Period size: 23  Copynumber: 2.6  Consensus size: 23

       4906 GAGAAATTGC

                                   
       4916 CAATGTTGAATGTGAAATCTAAT
          1 CAATGTTGAATGTGAAATCTAAT

              *                  * 
       4939 CAGTGTTGAATGTGAAATCTATT
          1 CAATGTTGAATGTGAAATCTAAT

                         
       4962 CAATGTTGAATGT
          1 CAATGTTGAATGT

       4975 TATGGTAAAT


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   33  1.00

ACGTcount: A:0.34, C:0.08, G:0.20, T:0.37


Consensus pattern (23 bp):   
CAATGTTGAATGTGAAATCTAAT
Done.