Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016180.1 Corchorus olitorius cultivar O-4 contig16213, 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: 4896
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:513 original size:21 final size:22

Alignment explanation


    Indices: 456--514  Score: 68
    Period size: 22  Copynumber: 2.7  Consensus size: 22

        446 TAAGCTTTAC

                   *         *    
        456 TATTTTAGAT-ATAATATATAA
          1 TATTTTAAATAATAATAAATAA

                                    
        477 TATTGTTAAATAAATAATAAAT-A
          1 TATT-TTAAAT-AATAATAAATAA

                           
        500 TATTTTAAATAATAA
          1 TATTTTAAATAATAA

        515 ATCATGAGTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  21    9  0.27
  22   11  0.33
  23    5  0.15
  24    8  0.24

ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44


Consensus pattern (22 bp):   
TATTTTAAATAATAATAAATAA

Found at i:1282 original size:48 final size:48

Alignment explanation


    Indices: 1226--1318  Score: 177
    Period size: 48  Copynumber: 1.9  Consensus size: 48

       1216 AACCTAATAA

                                              *             
       1226 ATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTGGACCT
          1 ATAAGCACACATACCAAATAATACAAAATGCAATAAACTATTGGACCT

                                                         
       1274 ATAAGCACACATACCAAATAATACAAAATGCAATAAACTATTGGA
          1 ATAAGCACACATACCAAATAATACAAAATGCAATAAACTATTGGA

       1319 TTTAAAGAAA


Statistics
Matches: 44,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  48   44  1.00

ACGTcount: A:0.51, C:0.19, G:0.10, T:0.20


Consensus pattern (48 bp):   
ATAAGCACACATACCAAATAATACAAAATGCAATAAACTATTGGACCT

Found at i:3065 original size:12 final size:12

Alignment explanation


    Indices: 3048--3076  Score: 58
    Period size: 12  Copynumber: 2.4  Consensus size: 12

       3038 ATCCTTCTAC

                        
       3048 TATTTTTGTATA
          1 TATTTTTGTATA

                        
       3060 TATTTTTGTATA
          1 TATTTTTGTATA

                 
       3072 TATTT
          1 TATTT

       3077 GAGATTATGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69


Consensus pattern (12 bp):   
TATTTTTGTATA

Found at i:4231 original size:15 final size:15

Alignment explanation


    Indices: 4211--4241  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       4201 GAGCACACAG

                           
       4211 TTCATAGAGTCTAAC
          1 TTCATAGAGTCTAAC

                           
       4226 TTCATAGAGTCTAAC
          1 TTCATAGAGTCTAAC

             
       4241 T
          1 T

       4242 GTATATTCCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35


Consensus pattern (15 bp):   
TTCATAGAGTCTAAC
Done.