Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012194.1 Corchorus capsularis cultivar CVL-1 contig12215, 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: 14084
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:5334 original size:116 final size:116

Alignment explanation


    Indices: 5130--5357  Score: 456
    Period size: 116  Copynumber: 2.0  Consensus size: 116

       5120 TTTGAGATTA

                                                                             
       5130 AAAATATACAGCAAAAGAATTGAGATCAATAATACCGAAACCGACGTACCACAGAAGCATATATT
          1 AAAATATACAGCAAAAGAATTGAGATCAATAATACCGAAACCGACGTACCACAGAAGCATATATT

                                                               
       5195 TTTAAAGATGAATAATATATGTTGCATATATTTTAAGACTAGTAATATCTC
         66 TTTAAAGATGAATAATATATGTTGCATATATTTTAAGACTAGTAATATCTC

                                                                             
       5246 AAAATATACAGCAAAAGAATTGAGATCAATAATACCGAAACCGACGTACCACAGAAGCATATATT
          1 AAAATATACAGCAAAAGAATTGAGATCAATAATACCGAAACCGACGTACCACAGAAGCATATATT

                                                           
       5311 TTTAAAGATGAATAATATATGTTGCATATATTTTAAGACTAGTAATA
         66 TTTAAAGATGAATAATATATGTTGCATATATTTTAAGACTAGTAATA

       5358 CCGAAAGACC


Statistics
Matches: 112,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 116  112  1.00

ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28


Consensus pattern (116 bp):   
AAAATATACAGCAAAAGAATTGAGATCAATAATACCGAAACCGACGTACCACAGAAGCATATATT
TTTAAAGATGAATAATATATGTTGCATATATTTTAAGACTAGTAATATCTC

Found at i:9609 original size:30 final size:29

Alignment explanation


    Indices: 9573--9631  Score: 91
    Period size: 30  Copynumber: 2.0  Consensus size: 29

       9563 GAGTTTTTGA

                         *                
       9573 CCAAACCATTGTAGTTCTTAAAAATAATTC
          1 CCAAACCATTGTACTT-TTAAAAATAATTC

                                  *      
       9603 CCAAACCATTGTACTTTTAAAATTAATTC
          1 CCAAACCATTGTACTTTTAAAAATAATTC

       9632 TCATTCTCTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  29   12  0.44
  30   15  0.56

ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36


Consensus pattern (29 bp):   
CCAAACCATTGTACTTTTAAAAATAATTC

Found at i:13554 original size:2 final size:2

Alignment explanation


    Indices: 13547--13574  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      13537 AAATGCATTG

                                                     
      13547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13575 CTTTTTGAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Done.