Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016056.1 Corchorus olitorius cultivar O-4 contig16089, 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: 5822
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32


Found at i:8 original size:2 final size:2

Alignment explanation


    Indices: 2--38  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

          1 T

                                                                   
          2 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         39 GCTGAACACT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:713 original size:2 final size:2

Alignment explanation


    Indices: 669--694  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

        659 TTGACTGTAT

                                                  
        669 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

        695 AATCTATGGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:896 original size:53 final size:53

Alignment explanation


    Indices: 835--993  Score: 318
    Period size: 53  Copynumber: 3.0  Consensus size: 53

        825 TCAACATACT

                                                                 
        835 TTTATCATATAAAAAATTCTCACTGCATAGCATAGATTAAGCTTTTATTTTTC
          1 TTTATCATATAAAAAATTCTCACTGCATAGCATAGATTAAGCTTTTATTTTTC

                                                                 
        888 TTTATCATATAAAAAATTCTCACTGCATAGCATAGATTAAGCTTTTATTTTTC
          1 TTTATCATATAAAAAATTCTCACTGCATAGCATAGATTAAGCTTTTATTTTTC

                                                                 
        941 TTTATCATATAAAAAATTCTCACTGCATAGCATAGATTAAGCTTTTATTTTTC
          1 TTTATCATATAAAAAATTCTCACTGCATAGCATAGATTAAGCTTTTATTTTTC

        994 CATATTTTCA


Statistics
Matches: 106,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  53  106  1.00

ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43


Consensus pattern (53 bp):   
TTTATCATATAAAAAATTCTCACTGCATAGCATAGATTAAGCTTTTATTTTTC

Found at i:2123 original size:156 final size:155

Alignment explanation


    Indices: 1839--2150  Score: 561
    Period size: 156  Copynumber: 2.0  Consensus size: 155

       1829 GGTGAGAGAT

                                  *                                          
       1839 TTAGGCTTGTAGAGTTTGACATTAGGATATGAAACTTAGAAATCCTTTGTATGTAGTTTCACGAT
          1 TTAGGCTTGTAGAGTTTGACATGAGGATATGAAACTTAGAAATCCTTTGTATGTAGTTTCACGAT

                                                                             
       1904 ACATTTTTTTGCAGTATCTCACATTAAATGCAATAAGTTAATTGCATTTTCCTTTATGGACAGTT
         66 ACATTTTTTTGCAGTATCTCACATTAAATGCAATAAGTTAATTGCATTTTCCTTTATGGACAGTT

                     *               
       1969 GTAATTAATTTGAGTTGGTACATGG
        131 GTAATTAATATGAGTTGGTACATGG

                                            ***                              
       1994 TTAGGCTTGTAGAGTTTGACATGAGAGATATGTTTCTTAGAAATCCTTTGTATGTAGTTTCACGA
          1 TTAGGCTTGTAGAGTTTGACATGAG-GATATGAAACTTAGAAATCCTTTGTATGTAGTTTCACGA

                                                                       *     
       2059 TACATTTTTTTGCAGTATCTCACATTAAATGCAATAAGTTAATTGCATTTTCCTTTATGTACAGT
         65 TACATTTTTTTGCAGTATCTCACATTAAATGCAATAAGTTAATTGCATTTTCCTTTATGGACAGT

                                      
       2124 TGTAATTAATATGAGTTGGTACATGG
        130 TGTAATTAATATGAGTTGGTACATGG

             
       2150 T
          1 T

       2151 CAACACCTCG


Statistics
Matches: 150,  Mismatches: 6, Indels: 1
        0.96            0.04        0.01

Matches are distributed among these distances:
 155   24  0.16
 156  126  0.84

ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41


Consensus pattern (155 bp):   
TTAGGCTTGTAGAGTTTGACATGAGGATATGAAACTTAGAAATCCTTTGTATGTAGTTTCACGAT
ACATTTTTTTGCAGTATCTCACATTAAATGCAATAAGTTAATTGCATTTTCCTTTATGGACAGTT
GTAATTAATATGAGTTGGTACATGG
Done.