Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006003.1 Corchorus capsularis cultivar CVL-1 contig06021, 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: 3139
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.33


Found at i:1235 original size:4 final size:4

Alignment explanation


    Indices: 1226--1256  Score: 62
    Period size: 4  Copynumber: 7.8  Consensus size: 4

       1216 GTCTTTGGAT

                                                  
       1226 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT

       1257 TTGCCTAAGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   27  1.00

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTTA

Found at i:1995 original size:19 final size:19

Alignment explanation


    Indices: 1956--1991  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       1946 TTTTTAAGTA

                  *            
       1956 AAAAATGTAATATATAAAT
          1 AAAAATATAATATATAAAT

                              
       1975 AAAAATATAATAT-TAAA
          1 AAAAATATAATATATAAA

       1992 ATAATTAATA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    4  0.25
  19   12  0.75

ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31


Consensus pattern (19 bp):   
AAAAATATAATATATAAAT

Found at i:2204 original size:16 final size:15

Alignment explanation


    Indices: 2150--2206  Score: 51
    Period size: 15  Copynumber: 3.7  Consensus size: 15

       2140 AATGATATTT

                  *        *
       2150 AAGAATGTATTTTTTA
          1 AAGAATATA-TTTTTG

               *  *        
       2166 AAGGATTTATTTTTG
          1 AAGAATATATTTTTG

                           
       2181 AAGAATATATTTTTG
          1 AAGAATATATTTTTG

             *         
       2196 ATGATATATAT
          1 AAGA-ATATAT

       2207 GGTGTGGATA


Statistics
Matches: 34,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  15   21  0.62
  16   13  0.38

ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49


Consensus pattern (15 bp):   
AAGAATATATTTTTG

Found at i:2796 original size:20 final size:20

Alignment explanation


    Indices: 2771--2810  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       2761 AAATAGTGAA

                                
       2771 TTACTAAATACCGCCCCCTT
          1 TTACTAAATACCGCCCCCTT

                  **            
       2791 TTACTAGCTACCGCCCCCTT
          1 TTACTAAATACCGCCCCCTT

       2811 CTTGGACTAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.20, C:0.42, G:0.07, T:0.30


Consensus pattern (20 bp):   
TTACTAAATACCGCCCCCTT
Done.