Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017707.1 Corchorus olitorius cultivar O-4 contig17740, 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: 30274
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:11459 original size:32 final size:28

Alignment explanation


    Indices: 11415--11479  Score: 76
    Period size: 32  Copynumber: 2.2  Consensus size: 28

      11405 GTAATCTAAA

                                   *        
      11415 GTCCTCTAATTAGGGCTTTTTTTTTTTGGGCC
          1 GTCCTCTAATTA-GG--TTTTTTCTTT-GGCC

                   *                    
      11447 GTCCTCTGATTAGGTTTTTTCTTTGGCC
          1 GTCCTCTAATTAGGTTTTTTCTTTGGCC

                 
      11475 GTCCT
          1 GTCCT

      11480 TGTTATATTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  28    9  0.29
  29    9  0.29
  31    2  0.06
  32   11  0.35

ACGTcount: A:0.08, C:0.22, G:0.22, T:0.49


Consensus pattern (28 bp):   
GTCCTCTAATTAGGTTTTTTCTTTGGCC

Found at i:19423 original size:7 final size:7

Alignment explanation


    Indices: 19411--19438  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

      19401 AAACACATCT

                   
      19411 CATAATC
          1 CATAATC

                   
      19418 CATAATC
          1 CATAATC

                   
      19425 CATAATC
          1 CATAATC

                   
      19432 CATAATC
          1 CATAATC

      19439 TCCCTGAATC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29


Consensus pattern (7 bp):   
CATAATC

Found at i:22127 original size:13 final size:13

Alignment explanation


    Indices: 22109--22136  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      22099 CTCTTCCTAA

                         
      22109 AAAAAAAAAAACG
          1 AAAAAAAAAAACG

                         
      22122 AAAAAAAAAAACG
          1 AAAAAAAAAAACG

              
      22135 AA
          1 AA

      22137 CTCTACCCTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00


Consensus pattern (13 bp):   
AAAAAAAAAAACG

Done.