Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024835.1 Corchorus olitorius cultivar O-4 contig24868, 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: 15822
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30


Found at i:1265 original size:76 final size:76

Alignment explanation


    Indices: 1128--1279  Score: 184
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       1118 ACAAGGACCC

                                                               *           * 
       1128 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       1193 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
       1204 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   *      
       1266 GATGGGCTGTGTCA
         63 GATGGGCAGTGTCA

       1280 TAGCTCATCA


Statistics
Matches: 65,  Mismatches: 8, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   55  0.85
  77    6  0.09

ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:8400 original size:10 final size:9

Alignment explanation


    Indices: 8357--8414  Score: 50
    Period size: 10  Copynumber: 6.4  Consensus size: 9

       8347 TAAAAGTAAC

                     
       8357 TAAGAAAAA
          1 TAAGAAAAA

                *     
       8366 TAAACAAAAA
          1 T-AAGAAAAA

                      
       8376 TAA-AAGAAA
          1 TAAGAA-AAA

                     
       8385 -AAGAAAAA
          1 TAAGAAAAA

                      
       8393 TAACGAAAAA
          1 TAA-GAAAAA

                   * 
       8403 TAA-AAAGA
          1 TAAGAAAAA

                
       8411 TAAG
          1 TAAG

       8415 GGTAAGAAAT


Statistics
Matches: 41,  Mismatches: 2, Indels: 12
        0.75            0.04        0.22

Matches are distributed among these distances:
   8   14  0.34
   9   10  0.24
  10   17  0.41

ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10


Consensus pattern (9 bp):   
TAAGAAAAA

Found at i:8400 original size:16 final size:17

Alignment explanation


    Indices: 8371--8408  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

       8361 AAAAATAAAC

                             
       8371 AAAAATAAAAGAAAAAG
          1 AAAAATAAAAGAAAAAG

                     *      *
       8388 AAAAAT-AACGAAAAAT
          1 AAAAATAAAAGAAAAAG

                 
       8404 AAAAA
          1 AAAAA

       8409 GATAAGGGTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  16   13  0.68
  17    6  0.32

ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08


Consensus pattern (17 bp):   
AAAAATAAAAGAAAAAG

Found at i:10267 original size:33 final size:33

Alignment explanation


    Indices: 10223--10299  Score: 93
    Period size: 33  Copynumber: 2.4  Consensus size: 33

      10213 TTATCACAGC

                               *      *    **
      10223 ATCCAA-TCAGCAAAAGGTTAGTGAGTTGATTG
          1 ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA

                            *                
      10255 ATCCAAGTCAGCAAAATGTCAGTGAGATGATCA
          1 ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA

                   *    
      10288 ATCCAAGCCAGC
          1 ATCCAAGTCAGC

      10300 TGAAGGAATT


Statistics
Matches: 38,  Mismatches: 6, Indels: 1
        0.84            0.13        0.02

Matches are distributed among these distances:
  32    6  0.16
  33   32  0.84

ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22


Consensus pattern (33 bp):   
ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
Done.