Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007466.1 Corchorus capsularis cultivar CVL-1 contig07487, 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: 8318
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:301 original size:15 final size:15

Alignment explanation


    Indices: 281--311  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        271 TATATACTAC

                    *      
        281 AAACCCACTAGGCAG
          1 AAACCCACCAGGCAG

                           
        296 AAACCCACCAGGCAG
          1 AAACCCACCAGGCAG

             
        311 A
          1 A

        312 TTTTCATTAC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.42, C:0.35, G:0.19, T:0.03


Consensus pattern (15 bp):   
AAACCCACCAGGCAG

Found at i:2543 original size:29 final size:30

Alignment explanation


    Indices: 2506--2571  Score: 89
    Period size: 29  Copynumber: 2.2  Consensus size: 30

       2496 CGTCATCGGT

                *      *       *          
       2506 CAAACAAGCCCTTGAACT-TCAATTTTGAC
          1 CAAATAAGCCCCTGAACTACCAATTTTGAC

                                          
       2535 CAAATAAGCCCCTGAACTACCAATTTTGAC
          1 CAAATAAGCCCCTGAACTACCAATTTTGAC

              *    
       2565 CAGATAA
          1 CAAATAA

       2572 ACCTTTCTGT


Statistics
Matches: 32,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  29   16  0.50
  30   16  0.50

ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24


Consensus pattern (30 bp):   
CAAATAAGCCCCTGAACTACCAATTTTGAC

Found at i:6411 original size:16 final size:14

Alignment explanation


    Indices: 6392--6433  Score: 50
    Period size: 15  Copynumber: 2.9  Consensus size: 14

       6382 CCCAAATTAA

                          
       6392 AAAAGAAAGAAAAC
          1 AAAAGAAAGAAAAC

                 *          
       6406 AGAAAAAAATGAAAAC
          1 A-AAAGAAA-GAAAAC

                         
       6422 AAAAGAAA-AAAA
          1 AAAAGAAAGAAAA

       6434 AACACAAACG


Statistics
Matches: 24,  Mismatches: 2, Indels: 5
        0.77            0.06        0.16

Matches are distributed among these distances:
  13    4  0.17
  14    1  0.04
  15   12  0.50
  16    7  0.29

ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02


Consensus pattern (14 bp):   
AAAAGAAAGAAAAC

Found at i:6419 original size:20 final size:18

Alignment explanation


    Indices: 6390--6433  Score: 54
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       6380 AGCCCAAATT

                                
       6390 AAAAAAGAAAGA-AAACAGA
          1 AAAAAAGAAA-ACAAA-AGA

                               
       6409 AAAAAATGAAAACAAAAGA
          1 AAAAAA-GAAAACAAAAGA

                  
       6428 AAAAAA
          1 AAAAAA

       6434 AACACAAACG


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  19   16  0.70
  20    7  0.30

ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02


Consensus pattern (18 bp):   
AAAAAAGAAAACAAAAGA

Found at i:7485 original size:16 final size:16

Alignment explanation


    Indices: 7466--7507  Score: 66
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       7456 CGTAATTTTT

                 *       *  
       7466 TTCTTGGTTGAATCTG
          1 TTCTTTGTTGAATATG

                            
       7482 TTCTTTGTTGAATATG
          1 TTCTTTGTTGAATATG

                      
       7498 TTCTTTGTTG
          1 TTCTTTGTTG

       7508 CTTCTCCAAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.12, C:0.10, G:0.21, T:0.57


Consensus pattern (16 bp):   
TTCTTTGTTGAATATG
Done.