Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010857.1 Corchorus capsularis cultivar CVL-1 contig10878, 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: 28717
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:979 original size:13 final size:13

Alignment explanation


    Indices: 961--986  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        951 ATTATTTTCT

                         
        961 ATTTCTACTACTA
          1 ATTTCTACTACTA

                         
        974 ATTTCTACTACTA
          1 ATTTCTACTACTA

        987 CTAATTTAAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46


Consensus pattern (13 bp):   
ATTTCTACTACTA

Found at i:3989 original size:193 final size:188

Alignment explanation


    Indices: 3644--3990  Score: 509
    Period size: 193  Copynumber: 1.8  Consensus size: 188

       3634 TTTAAATTTA

                                 *                                           
       3644 CATTAAAACCCCAAAAAGCTATAAACATTATAATCCAACCATTGGCTTAACCGGTGCCCTCAGGC
          1 CATTAAAACCCCAAAAAGCTAAAAACATTATAATCCAACCATTGGCTTAACCGGTGCCCTCAGGC

                *               *      *                        *            
       3709 ACCCTTTAGCCAAACTCTAATAATTAATAATTATCAACACAAAAACTAAAAGTTACATTCAATTG
         66 ACCCGTTAGCCAAACTCTAACAATTAAAAATTATCAACACAAAAACTAAAAGCTACATTCAATTG

                                                                      
       3774 CATTAATTACATGCAATAATTATAGAATTAGTAGGGTTTTAGGGTTTTTGGCCTTTTG
        131 CATTAATTACATGCAATAATTATAGAATTAGTAGGGTTTTAGGGTTTTTGGCCTTTTG

                                                  *            *        *    
       3832 CATTAAAACCCCAAAAAGCTAAAAAC-TTATAATCCAATCATTGGCTTAACGGGTGCCC-GAGGG
          1 CATTAAAACCCCAAAAAGCTAAAAACATTATAATCCAACCATTGGCTTAACCGGTGCCCTCA-GG

               **                                    *                       
       3895 CACTGGTTAGCCAAACTCTAACAATTACTCAAAAACTATATTAACACAAAAACTAAAAGCTACAT
         65 CACCCGTTAGCCAAACTCTAACAA-T--T-AAAAA-T-TATCAACACAAAAACTAAAAGCTACAT

             *                             
       3960 TTAATTGCATTAATTACATGCAATAATTATA
        124 TCAATTGCATTAATTACATGCAATAATTATA

       3991 ATGATAAATC


Statistics
Matches: 140,  Mismatches: 12, Indels: 9
        0.87            0.07        0.06

Matches are distributed among these distances:
 186    1  0.01
 187   52  0.37
 188   26  0.19
 190    1  0.01
 191    4  0.03
 192    1  0.01
 193   55  0.39

ACGTcount: A:0.40, C:0.20, G:0.12, T:0.29


Consensus pattern (188 bp):   
CATTAAAACCCCAAAAAGCTAAAAACATTATAATCCAACCATTGGCTTAACCGGTGCCCTCAGGC
ACCCGTTAGCCAAACTCTAACAATTAAAAATTATCAACACAAAAACTAAAAGCTACATTCAATTG
CATTAATTACATGCAATAATTATAGAATTAGTAGGGTTTTAGGGTTTTTGGCCTTTTG

Found at i:20079 original size:6 final size:6

Alignment explanation


    Indices: 20068--20094  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      20058 TAGACCTTCT

                                           
      20068 AATTAA AATTAA AATTAA AATTAA AAT
          1 AATTAA AATTAA AATTAA AATTAA AAT

      20095 CAGCTATTAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (6 bp):   
AATTAA

Found at i:27424 original size:15 final size:16

Alignment explanation


    Indices: 27396--27426  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

      27386 AAAACAAAAA

                            
      27396 TTTCCATGATTCCTCC
          1 TTTCCATGATTCCTCC

                            
      27412 TTTCCAT-ATTCCTCC
          1 TTTCCATGATTCCTCC

      27427 ATCACCCATA


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

Matches are distributed among these distances:
  15    8  0.53
  16    7  0.47

ACGTcount: A:0.13, C:0.39, G:0.03, T:0.45


Consensus pattern (16 bp):   
TTTCCATGATTCCTCC
Done.