Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008726.1 Corchorus capsularis cultivar CVL-1 contig08747, 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: 9788
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:4410 original size:22 final size:22

Alignment explanation


    Indices: 4378--4420  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4368 AGGTTTTTTT

                                  
       4378 TAGTAAACTTGAATAAGAAGAA
          1 TAGTAAACTTGAATAAGAAGAA

                  *              
       4400 TAGTAACCTTGAATAAGAAGA
          1 TAGTAAACTTGAATAAGAAGA

       4421 TTGAATAAGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23


Consensus pattern (22 bp):   
TAGTAAACTTGAATAAGAAGAA

Found at i:4424 original size:13 final size:13

Alignment explanation


    Indices: 4408--4433  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4398 AATAGTAACC

                         
       4408 TTGAATAAGAAGA
          1 TTGAATAAGAAGA

                         
       4421 TTGAATAAGAAGA
          1 TTGAATAAGAAGA

       4434 ATATTAATCT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23


Consensus pattern (13 bp):   
TTGAATAAGAAGA

Found at i:8626 original size:144 final size:144

Alignment explanation


    Indices: 8366--8653  Score: 549
    Period size: 144  Copynumber: 2.0  Consensus size: 144

       8356 TGCACACTAG

                                              *                              
       8366 ATAACTTGATTAGTCACACTAAATAGAATGTTTTGTTATCATCAAAAACACATGAAGTCAACAAA
          1 ATAACTTGATTAGTCACACTAAATAGAATGTTTTCTTATCATCAAAAACACATGAAGTCAACAAA

                                                                             
       8431 AATGACTCTTCCAAAAGAAGAAGGTGAACTTGGGTTTAAAGATATGGAAACCTTCAACAGAGCTC
         66 AATGACTCTTCCAAAAGAAGAAGGTGAACTTGGGTTTAAAGATATGGAAACCTTCAACAGAGCTC

                          
       8496 TATTGGCCAAGCAA
        131 TATTGGCCAAGCAA

                                                                  *          
       8510 ATAACTTGATTAGTCACACTAAATAGAATGTTTTCTTATCATCAAAAACACATGGAGTCAACAAA
          1 ATAACTTGATTAGTCACACTAAATAGAATGTTTTCTTATCATCAAAAACACATGAAGTCAACAAA

                                      *                                      
       8575 AATGACTCTTCCAAAAGAAGAAGGTGGACTTGGGTTTAAAGATATGGAAACCTTCAACAGAGCTC
         66 AATGACTCTTCCAAAAGAAGAAGGTGAACTTGGGTTTAAAGATATGGAAACCTTCAACAGAGCTC

                          
       8640 TATTGGCCAAGCAA
        131 TATTGGCCAAGCAA

       8654 GTCTGGCGTA


Statistics
Matches: 141,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 144  141  1.00

ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26


Consensus pattern (144 bp):   
ATAACTTGATTAGTCACACTAAATAGAATGTTTTCTTATCATCAAAAACACATGAAGTCAACAAA
AATGACTCTTCCAAAAGAAGAAGGTGAACTTGGGTTTAAAGATATGGAAACCTTCAACAGAGCTC
TATTGGCCAAGCAA
Done.