Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009574.1 Corchorus olitorius cultivar O-4 contig09606, 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: 7418
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:103 original size:43 final size:43

Alignment explanation


    Indices: 56--161  Score: 194
    Period size: 43  Copynumber: 2.5  Consensus size: 43

         46 AAAGCTTATC

                       *                               
         56 AAGCTTTGCCCTTACAAAATATAAATTGACAAAATCATATATG
          1 AAGCTTTGCCCGTACAAAATATAAATTGACAAAATCATATATG

                                                       
         99 AAGCTTTGCCCGTACAAAATATAAATTGACAAAATCATATATG
          1 AAGCTTTGCCCGTACAAAATATAAATTGACAAAATCATATATG

               *                
        142 AAGATTTGCCCGTACAAAAT
          1 AAGCTTTGCCCGTACAAAAT

        162 CATTTAAAAT


Statistics
Matches: 61,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  43   61  1.00

ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28


Consensus pattern (43 bp):   
AAGCTTTGCCCGTACAAAATATAAATTGACAAAATCATATATG

Found at i:415 original size:24 final size:23

Alignment explanation


    Indices: 385--440  Score: 67
    Period size: 24  Copynumber: 2.3  Consensus size: 23

        375 GTTTTGGGGA

                       *            
        385 TTTTTTCTAAAGGATATATACATT
          1 TTTTTTCTAAAAGA-ATATACATT

                                *   
        409 TTTTTTCATAAAAGAATATATATT
          1 TTTTTTC-TAAAAGAATATACATT

               *    
        433 TTTATTCT
          1 TTTTTTCT

        441 TTTAGTTTTC


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  23    1  0.04
  24   21  0.75
  25    6  0.21

ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54


Consensus pattern (23 bp):   
TTTTTTCTAAAAGAATATACATT

Found at i:465 original size:16 final size:15

Alignment explanation


    Indices: 440--473  Score: 50
    Period size: 16  Copynumber: 2.2  Consensus size: 15

        430 ATTTTTATTC

                           
        440 TTTTAGTTTTCAATT
          1 TTTTAGTTTTCAATT

                       *    
        455 TTTTCAGTTTTTAATT
          1 TTTT-AGTTTTCAATT

               
        471 TTT
          1 TTT

        474 CAAAAATATA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    4  0.24
  16   13  0.76

ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71


Consensus pattern (15 bp):   
TTTTAGTTTTCAATT

Found at i:2914 original size:6 final size:6

Alignment explanation


    Indices: 2903--2940  Score: 76
    Period size: 6  Copynumber: 6.3  Consensus size: 6

       2893 ATTCGACTAT

                                                        
       2903 TATACA TATACA TATACA TATACA TATACA TATACA TA
          1 TATACA TATACA TATACA TATACA TATACA TATACA TA

       2941 CTAAATATTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   32  1.00

ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34


Consensus pattern (6 bp):   
TATACA

Done.