Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012030.1 Corchorus capsularis cultivar CVL-1 contig12051, 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: 19613
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:547 original size:13 final size:14

Alignment explanation


    Indices: 526--557  Score: 50
    Period size: 13  Copynumber: 2.4  Consensus size: 14

        516 TTTCTTGATT

                          
        526 GATTT-CTTAGTTA
          1 GATTTACTTAGTTA

                          
        539 -ATTTACTTAGTTA
          1 GATTTACTTAGTTA

                  
        552 GATTTA
          1 GATTTA

        558 ATTAAAATTC


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  12    4  0.24
  13    8  0.47
  14    5  0.29

ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53


Consensus pattern (14 bp):   
GATTTACTTAGTTA

Found at i:2597 original size:14 final size:15

Alignment explanation


    Indices: 2578--2610  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       2568 AGATTAGAAG

                           
       2578 AATATG-AGCACAAA
          1 AATATGAAGCACAAA

                     *     
       2592 AATATGAAGGACAAA
          1 AATATGAAGCACAAA

                
       2607 AATA
          1 AATA

       2611 GGAGATAAAG


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

Matches are distributed among these distances:
  14    6  0.35
  15   11  0.65

ACGTcount: A:0.61, C:0.09, G:0.15, T:0.15


Consensus pattern (15 bp):   
AATATGAAGCACAAA

Found at i:7649 original size:6 final size:6

Alignment explanation


    Indices: 7638--7662  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       7628 AGCAAACGAG

                                         
       7638 ATCTAA ATCTAA ATCTAA ATCTAA A
          1 ATCTAA ATCTAA ATCTAA ATCTAA A

       7663 GCAGAATTAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32


Consensus pattern (6 bp):   
ATCTAA

Found at i:11419 original size:13 final size:13

Alignment explanation


    Indices: 11401--11425  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      11391 AGTTTTGCGT

                         
      11401 TATCTATGTTGTG
          1 TATCTATGTTGTG

                        
      11414 TATCTATGTTGT
          1 TATCTATGTTGT

      11426 TGCTAGGGTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.08, G:0.20, T:0.56


Consensus pattern (13 bp):   
TATCTATGTTGTG

Found at i:17054 original size:20 final size:20

Alignment explanation


    Indices: 17010--17057  Score: 62
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      17000 CTTTCCTTTA

                                
      17010 GTTTTGTTTTTATTTTTCGT
          1 GTTTTGTTTTTATTTTTCGT

            *          *        
      17030 ATTTTGTTTTTGTTTTT-GT
          1 GTTTTGTTTTTATTTTTCGT

                     
      17049 GGTTTTGTT
          1 -GTTTTGTT

      17058 AATTTTTCAG


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  19    2  0.08
  20   22  0.92

ACGTcount: A:0.04, C:0.02, G:0.19, T:0.75


Consensus pattern (20 bp):   
GTTTTGTTTTTATTTTTCGT
Done.