Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023783.1 Corchorus olitorius cultivar O-4 contig23816, 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: 17107
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:10525 original size:4 final size:4

Alignment explanation


    Indices: 10516--10555  Score: 52
    Period size: 4  Copynumber: 11.0  Consensus size: 4

      10506 CATGAGTAGA

                                                                  
      10516 AAAT AAAT -AAT -AAT -AAT -AAT AAAT AAAT AAAT AAAT AAAT
          1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT

      10556 TAGCTAAATG


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   3   12  0.34
   4   23  0.66

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (4 bp):   
AAAT

Found at i:14505 original size:19 final size:19

Alignment explanation


    Indices: 14481--14518  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      14471 CTGAATTCAA

                               
      14481 AAAACTGGTTGGTTCCTTG
          1 AAAACTGGTTGGTTCCTTG

                               
      14500 AAAACTGGTTGGTTCCTTG
          1 AAAACTGGTTGGTTCCTTG

      14519 CAGTATCTCA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37


Consensus pattern (19 bp):   
AAAACTGGTTGGTTCCTTG

Found at i:16354 original size:59 final size:59

Alignment explanation


    Indices: 16265--16384  Score: 240
    Period size: 59  Copynumber: 2.0  Consensus size: 59

      16255 CATTCTCTAG

                                                                       
      16265 CTAAAATTGAGCTGGATAATCGTGTGGTGCAGGACTATTCCTCCTGGTGTTTGTAATCT
          1 CTAAAATTGAGCTGGATAATCGTGTGGTGCAGGACTATTCCTCCTGGTGTTTGTAATCT

                                                                       
      16324 CTAAAATTGAGCTGGATAATCGTGTGGTGCAGGACTATTCCTCCTGGTGTTTGTAATCT
          1 CTAAAATTGAGCTGGATAATCGTGTGGTGCAGGACTATTCCTCCTGGTGTTTGTAATCT

              
      16383 CT
          1 CT

      16385 GATTATTGAC


Statistics
Matches: 61,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  59   61  1.00

ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36


Consensus pattern (59 bp):   
CTAAAATTGAGCTGGATAATCGTGTGGTGCAGGACTATTCCTCCTGGTGTTTGTAATCT

Found at i:16462 original size:82 final size:82

Alignment explanation


    Indices: 16325--16475  Score: 250
    Period size: 82  Copynumber: 1.8  Consensus size: 82

      16315 TTGTAATCTC

                                                       *  *             *    
      16325 TAAAATTGAGCTGGATAATCGTGTGGTGCAGGACTATTCCTCCTGGTGTTTGTAATCTCTGATTA
          1 TAAAATTGAGCTGGATAATCGTGTGGTGCAGGACTATTCCTCCCGGCGTTTGTAATCTCTAATTA

                             
      16390 TTGACCCATTCTCTAGT
         66 TTGACCCATTCTCTAGT

                      *                                                      
      16407 TAAAATTGAGTTGGATAATCGTGTGGTGC-GGAACTATTCCTCCCGGCGTTTGTAATCTCTAATT
          1 TAAAATTGAGCTGGATAATCGTGTGGTGCAGG-ACTATTCCTCCCGGCGTTTGTAATCTCTAATT

                 
      16471 ATTGA
         65 ATTGA

      16476 TTAATGAAAG


Statistics
Matches: 64,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  81    2  0.03
  82   62  0.97

ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37


Consensus pattern (82 bp):   
TAAAATTGAGCTGGATAATCGTGTGGTGCAGGACTATTCCTCCCGGCGTTTGTAATCTCTAATTA
TTGACCCATTCTCTAGT

Found at i:16659 original size:18 final size:18

Alignment explanation


    Indices: 16625--16660  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      16615 AGTAGTTTTT

                     *  *     
      16625 GGTAGTTTTTTTTAAATG
          1 GGTAGTTTTGTTAAAATG

                              
      16643 GGTAGTTTTGTTAAAATG
          1 GGTAGTTTTGTTAAAATG

      16661 ATATAAATAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50


Consensus pattern (18 bp):   
GGTAGTTTTGTTAAAATG
Done.