Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015045.1 Corchorus olitorius cultivar O-4 contig15078, 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: 9585
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28


Found at i:2115 original size:21 final size:21

Alignment explanation


    Indices: 2089--2134  Score: 65
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2079 CAACAAAGAG

                    *    *     * 
       2089 GGAGATGCTTCCTTCCTCCTA
          1 GGAGATGCCTCCTACCTCCCA

                                 
       2110 GGAGATGCCTCCTACCTCCCA
          1 GGAGATGCCTCCTACCTCCCA

                
       2131 GGAG
          1 GGAG

       2135 GCGTCACCTC


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.17, C:0.35, G:0.24, T:0.24


Consensus pattern (21 bp):   
GGAGATGCCTCCTACCTCCCA

Found at i:6190 original size:13 final size:13

Alignment explanation


    Indices: 6172--6197  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       6162 CTTGGCATGA

                         
       6172 GTGATGATTTTTG
          1 GTGATGATTTTTG

                         
       6185 GTGATGATTTTTG
          1 GTGATGATTTTTG

       6198 TTGAGATCTT


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:0.15, C:0.00, G:0.31, T:0.54


Consensus pattern (13 bp):   
GTGATGATTTTTG

Found at i:8034 original size:51 final size:50

Alignment explanation


    Indices: 7933--8034  Score: 111
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       7923 GTTCTTCATA

                                                     * **     
       7933 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT

                                             *                    
       7983 TTTTCTCTTGTTTCA-ATCTTGTCTCCA-GACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCT-CAGGACAAACAAACACTCGTACA-GTGT

             
       8034 T
          1 T

       8035 CTTCATTCAA


Statistics
Matches: 44,  Mismatches: 4, Indels: 7
        0.80            0.07        0.13

Matches are distributed among these distances:
  50    7  0.16
  51   34  0.77
  52    3  0.07

ACGTcount: A:0.24, C:0.23, G:0.13, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Done.