Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005738.1 Corchorus capsularis cultivar CVL-1 contig05756, 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: 2432
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:1681 original size:33 final size:34

Alignment explanation


    Indices: 1644--1717  Score: 125
    Period size: 33  Copynumber: 2.2  Consensus size: 34

       1634 CCGAGTCGTT

                                              
       1644 TGGCCGGTTG-TAGCCGGACATGTCCATGTCGCG
          1 TGGCCGGTTGATAGCCGGACATGTCCATGTCGCG

                        *                     
       1677 TGGCCGG-TGATGGCCGGACATGTCCATGTCGCG
          1 TGGCCGGTTGATAGCCGGACATGTCCATGTCGCG

                    
       1710 TGGCCGGT
          1 TGGCCGGT

       1718 CTTGTGGCCG


Statistics
Matches: 38,  Mismatches: 1, Indels: 3
        0.90            0.02        0.07

Matches are distributed among these distances:
  32    2  0.05
  33   36  0.95

ACGTcount: A:0.11, C:0.27, G:0.39, T:0.23


Consensus pattern (34 bp):   
TGGCCGGTTGATAGCCGGACATGTCCATGTCGCG

Found at i:1956 original size:33 final size:33

Alignment explanation


    Indices: 1909--2027  Score: 166
    Period size: 33  Copynumber: 3.6  Consensus size: 33

       1899 TTCTTTACAC

                                   *         
       1909 CCAAAACATAATTATTTTCAATGTTATGATCAA
          1 CCAAAACATAATTATTTTCAATGCTATGATCAA

                     *       *               
       1942 CCAAAACATGATTATTTGCAATGCTATGATCAA
          1 CCAAAACATAATTATTTTCAATGCTATGATCAA

                    *         *         *    
       1975 CCAAAACAAAATTATTTTTAATGCTATGTTCAA
          1 CCAAAACATAATTATTTTCAATGCTATGATCAA

                    *    *      
       2008 CCAAAACAGAATTGTTTTCA
          1 CCAAAACATAATTATTTTCA

       2028 TCACAATTAG


Statistics
Matches: 75,  Mismatches: 11, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  33   75  1.00

ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34


Consensus pattern (33 bp):   
CCAAAACATAATTATTTTCAATGCTATGATCAA

Found at i:2080 original size:33 final size:33

Alignment explanation


    Indices: 2043--2147  Score: 140
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       2033 ATTAGCATCC

                                *            
       2043 AAAACAGATTTAGTATCATCACAAACAACACTT
          1 AAAACAGATTTAGTATCATCGCAAACAACACTT

                          *    *             
       2076 AAAACAGATTTAGTGTCATTGCAAACAACACTT
          1 AAAACAGATTTAGTATCATCGCAAACAACACTT

               **  *                          
       2109 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
          1 AAAACAGATTTAGTATCATCGCAAACAACACT-T

                  
       2142 AAAACA
          1 AAAACA

       2148 CTCTTTGCAA


Statistics
Matches: 61,  Mismatches: 10, Indels: 2
        0.84            0.14        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   60  0.98

ACGTcount: A:0.46, C:0.19, G:0.10, T:0.26


Consensus pattern (33 bp):   
AAAACAGATTTAGTATCATCGCAAACAACACTT
Done.