Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013894.1 Corchorus capsularis cultivar CVL-1 contig13915, 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: 22359
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:8284 original size:17 final size:18

Alignment explanation


    Indices: 8262--8296  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       8252 TTTAATTACT

                   *          
       8262 ATTAATACTAT-TTATTA
          1 ATTAATAATATATTATTA

                              
       8279 ATTAATAATATATTATTA
          1 ATTAATAATATATTATTA

       8297 TATATATAAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17   10  0.62
  18    6  0.38

ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51


Consensus pattern (18 bp):   
ATTAATAATATATTATTA

Found at i:10688 original size:5 final size:5

Alignment explanation


    Indices: 10678--10705  Score: 56
    Period size: 5  Copynumber: 5.6  Consensus size: 5

      10668 ATTTTAAGGA

                                             
      10678 AATTT AATTT AATTT AATTT AATTT AAT
          1 AATTT AATTT AATTT AATTT AATTT AAT

      10706 CCAAGTGACA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (5 bp):   
AATTT

Found at i:14433 original size:84 final size:84

Alignment explanation


    Indices: 14276--14439  Score: 240
    Period size: 84  Copynumber: 2.0  Consensus size: 84

      14266 AATTACTATC

                          *                    *   *              *    *     
      14276 ACAAAGCTTTTCGATTCTTTCTCCCCAGCCCTTACGCGTGTGCATCGTCGGAAGGGGTCTCACTG
          1 ACAAAGCTTTTCGACTCTTTCTCCCCAGCCCTTACACGTCTGCATCGTCGGAAGCGGTCCCACTG

                      *        
      14341 GTTCCTACACTGCCGGATT
         66 GTTCCTACACAGCCGGATT

                                    *                                    *   
      14360 ACAAAGCTTTTCGACTCTTTCTCCTCAGCCCTTACACGTCTGCATCGTCGGAAGCGGTCCCGCTG
          1 ACAAAGCTTTTCGACTCTTTCTCCCCAGCCCTTACACGTCTGCATCGTCGGAAGCGGTCCCACTG

                            
      14425 GCTT-CTACACAGCCG
         66 G-TTCCTACACAGCCG

      14440 AAAAGGTATT


Statistics
Matches: 71,  Mismatches: 8, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  84   69  0.97
  85    2  0.03

ACGTcount: A:0.17, C:0.34, G:0.21, T:0.28


Consensus pattern (84 bp):   
ACAAAGCTTTTCGACTCTTTCTCCCCAGCCCTTACACGTCTGCATCGTCGGAAGCGGTCCCACTG
GTTCCTACACAGCCGGATT

Found at i:20881 original size:6 final size:6

Alignment explanation


    Indices: 20870--20895  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      20860 TTCTGCTATT

                                          
      20870 CTAGAA CTAGAA CTAGAA CTAGAA CT
          1 CTAGAA CTAGAA CTAGAA CTAGAA CT

      20896 CCTCTGTTCA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.46, C:0.19, G:0.15, T:0.19


Consensus pattern (6 bp):   
CTAGAA

Done.