Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018214.1 Corchorus olitorius cultivar O-4 contig18247, 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: 4624
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34


Found at i:1250 original size:76 final size:76

Alignment explanation


    Indices: 1128--1272  Score: 179
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       1118 CTATGACATA

                             *                                            *  
       1128 GCCCATCTGGGTGATCAGGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCCAGCTGGA
          1 GCCCATCTGGGTGATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCCAGCTAGA

                       
       1193 GTCGTGACACT
         66 GTCGTGACACT

                        **                            *              *     * 
       1204 GCCCATCTGGGTTCTCAAGC-AAACCACATGGGTGC-TCAAGGC-AACCATGTGGGCGCCCAGGT
          1 GCCCATCTGGGTGATCAAGCGAAA-CACATGGGT-CTTC-AGACAAACCATGTGGGCACCCAGCT

                   
       1266 AGAGTCG
         63 AGAGTCG

       1273 GGGTCCTTGT


Statistics
Matches: 59,  Mismatches: 7, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    3  0.05
  76   52  0.88
  77    4  0.07

ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18


Consensus pattern (76 bp):   
GCCCATCTGGGTGATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCCAGCTAGA
GTCGTGACACT

Found at i:1256 original size:21 final size:21

Alignment explanation


    Indices: 1206--1256  Score: 50
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1196 GTGACACTGC

                *     *          
       1206 CCATCTGGGTTCTCAAGCAAA
          1 CCATATGGGTGCTCAAGCAAA

               *                  
       1227 CCACATGGGTGCTCAAGGC-AA
          1 CCATATGGGTGCTCAA-GCAAA

                *    
       1248 CCATGTGGG
          1 CCATATGGG

       1257 CGCCCAGGTA


Statistics
Matches: 24,  Mismatches: 5, Indels: 2
        0.77            0.16        0.06

Matches are distributed among these distances:
  21   22  0.92
  22    2  0.08

ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20


Consensus pattern (21 bp):   
CCATATGGGTGCTCAAGCAAA
Done.