Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017954.1 Corchorus olitorius cultivar O-4 contig17987, 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: 22098
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:2249 original size:19 final size:20

Alignment explanation


    Indices: 2207--2264  Score: 64
    Period size: 19  Copynumber: 2.9  Consensus size: 20

       2197 TTGACATTGT

                                 
       2207 TTAGCAACTGTACAGATGAAA
          1 TTAGC-ACTGTACAGATGAAA

                            * * 
       2228 TTA-CACTGTACAGATTAGA
          1 TTAGCACTGTACAGATGAAA

                 *            
       2247 TTAGGTACTGTACAGATG
          1 TTA-GCACTGTACAGATG

       2265 CGATATGAGA


Statistics
Matches: 31,  Mismatches: 4, Indels: 4
        0.79            0.10        0.10

Matches are distributed among these distances:
  19   16  0.52
  20    1  0.03
  21   14  0.45

ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29


Consensus pattern (20 bp):   
TTAGCACTGTACAGATGAAA

Found at i:11673 original size:35 final size:35

Alignment explanation


    Indices: 11627--11697  Score: 115
    Period size: 35  Copynumber: 2.0  Consensus size: 35

      11617 TATATTCTAT

                           *  *        *       
      11627 ACACCCATCTCCGGCGTCCTTTAGTGTTGGGTTCG
          1 ACACCCATCTCCGGCCTCATTTAGTGTCGGGTTCG

                                               
      11662 ACACCCATCTCCGGCCTCATTTAGTGTCGGGTTCG
          1 ACACCCATCTCCGGCCTCATTTAGTGTCGGGTTCG

             
      11697 A
          1 A

      11698 GTATTGTGAA


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

Matches are distributed among these distances:
  35   33  1.00

ACGTcount: A:0.14, C:0.32, G:0.24, T:0.30


Consensus pattern (35 bp):   
ACACCCATCTCCGGCCTCATTTAGTGTCGGGTTCG

Found at i:12049 original size:57 final size:56

Alignment explanation


    Indices: 11941--12050  Score: 125
    Period size: 57  Copynumber: 1.9  Consensus size: 56

      11931 TGGCCAATTC

                 *            *     *  *                * *         
      11941 AGGCCTATAAAAGCCCAATGATTGTTTTATTAGCCCAACAAAAGTATGAATTACAG
          1 AGGCCCATAAAAGCCCAAAGATTGGTTCATTAGCCCAACAAAAGAAAGAATTACAG

                                                                    
      11997 AGGCCCATAAAGAGCCCAAAGATTGGTTCATTAGCGCCCAA-AAAA-AAAGAATTA
          1 AGGCCCATAAA-AGCCCAAAGATTGGTTCATTA--GCCCAACAAAAGAAAGAATTA

      12051 GGGGAAGATT


Statistics
Matches: 45,  Mismatches: 6, Indels: 5
        0.80            0.11        0.09

Matches are distributed among these distances:
  56   10  0.22
  57   25  0.56
  58    4  0.09
  59    6  0.13

ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22


Consensus pattern (56 bp):   
AGGCCCATAAAAGCCCAAAGATTGGTTCATTAGCCCAACAAAAGAAAGAATTACAG
Done.