Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020627.1 Corchorus olitorius cultivar O-4 contig20660, 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: 12139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:39 original size:25 final size:23

Alignment explanation


    Indices: 1--48  Score: 60
    Period size: 25  Copynumber: 2.0  Consensus size: 23

                     *               
          1 TAAATTGAATAATTAAGACATTAAA
          1 TAAATTGAAGAATT-A-ACATTAAA

                  *                
         26 TAAATTTAAGAATTAACATTAAA
          1 TAAATTGAAGAATTAACATTAAA

         49 AAACTTCAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  23    8  0.38
  24    1  0.05
  25   12  0.57

ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33


Consensus pattern (23 bp):   
TAAATTGAAGAATTAACATTAAA

Found at i:832 original size:14 final size:17

Alignment explanation


    Indices: 813--848  Score: 51
    Period size: 17  Copynumber: 2.3  Consensus size: 17

        803 ATTAAATTAG

                             
        813 TAAAAT-GGT-TA-AAA
          1 TAAAATAGGTATATAAA

                             
        827 TAAAATAGGTATATAAA
          1 TAAAATAGGTATATAAA

                 
        844 TAAAA
          1 TAAAA

        849 AATAGAGTTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  14    6  0.32
  15    3  0.16
  16    2  0.11
  17    8  0.42

ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28


Consensus pattern (17 bp):   
TAAAATAGGTATATAAA

Found at i:5479 original size:13 final size:14

Alignment explanation


    Indices: 5461--5491  Score: 55
    Period size: 13  Copynumber: 2.3  Consensus size: 14

       5451 ACCTTACTCG

                          
       5461 AAAAAAAAAA-GAA
          1 AAAAAAAAAAGGAA

                          
       5474 AAAAAAAAAAGGAA
          1 AAAAAAAAAAGGAA

                
       5488 AAAA
          1 AAAA

       5492 TGAGAAGCAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   10  0.59
  14    7  0.41

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (14 bp):   
AAAAAAAAAAGGAA

Found at i:5480 original size:14 final size:14

Alignment explanation


    Indices: 5461--5491  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       5451 ACCTTACTCG

                          
       5461 AAAAAAAAAAGAAA
          1 AAAAAAAAAAGAAA

                     *    
       5475 AAAAAAAAAGGAAA
          1 AAAAAAAAAAGAAA

               
       5489 AAA
          1 AAA

       5492 TGAGAAGCAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (14 bp):   
AAAAAAAAAAGAAA
Done.