Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015877.1 Corchorus olitorius cultivar O-4 contig15910, 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: 10220
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:496 original size:16 final size:16

Alignment explanation


    Indices: 420--496  Score: 84
    Period size: 16  Copynumber: 4.8  Consensus size: 16

        410 GTCGGGTTGA

                        *   
        420 TCGGGTTCGGGTCATT
          1 TCGGGTTCGGGTAATT

             *     *         
        436 TTGGGTTTGGGTAATTT
          1 TCGGGTTCGGGTAA-TT

                        **  
        453 TCGGGTTCGGGTCGTT
          1 TCGGGTTCGGGTAATT

                *           
        469 T-GGATTCGGGTAATT
          1 TCGGGTTCGGGTAATT

                         
        484 TCGGGTTCGGGTA
          1 TCGGGTTCGGGTA

        497 CCCAAAATTT


Statistics
Matches: 48,  Mismatches: 11, Indels: 4
        0.76            0.17        0.06

Matches are distributed among these distances:
  15   12  0.25
  16   24  0.50
  17   12  0.25

ACGTcount: A:0.09, C:0.12, G:0.39, T:0.40


Consensus pattern (16 bp):   
TCGGGTTCGGGTAATT

Found at i:544 original size:17 final size:17

Alignment explanation


    Indices: 504--544  Score: 50
    Period size: 16  Copynumber: 2.5  Consensus size: 17

        494 GTACCCAAAA

                             
        504 TTTCGGGTCATTTCTGG
          1 TTTCGGGTCATTTCTGG

            *                 
        521 GTT-GGGTCAGTTTC-GG
          1 TTTCGGGTCA-TTTCTGG

                    
        537 TTTCGGGT
          1 TTTCGGGT

        545 TGGGCGGATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 4
        0.77            0.08        0.15

Matches are distributed among these distances:
  16   10  0.50
  17   10  0.50

ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44


Consensus pattern (17 bp):   
TTTCGGGTCATTTCTGG

Found at i:1735 original size:12 final size:12

Alignment explanation


    Indices: 1718--1743  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1708 GAAGTTGCAG

                        
       1718 GAGCTGGTTTTT
          1 GAGCTGGTTTTT

                        
       1730 GAGCTGGTTTTT
          1 GAGCTGGTTTTT

              
       1742 GA
          1 GA

       1744 TTTCTTGGGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.12, C:0.08, G:0.35, T:0.46


Consensus pattern (12 bp):   
GAGCTGGTTTTT

Found at i:3018 original size:19 final size:19

Alignment explanation


    Indices: 2968--3018  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       2958 TGTGGGATTT

                               
       2968 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
       2986 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
       3005 TTAATAATTAATTA
          1 TTAATAATTAATTA

       3019 ATTTTATCCT


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:3382 original size:13 final size:13

Alignment explanation


    Indices: 3364--3389  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3354 AAGGTAACAA

                         
       3364 CAAAAATCATCAC
          1 CAAAAATCATCAC

                         
       3377 CAAAAATCATCAC
          1 CAAAAATCATCAC

       3390 TCATGCCAAG


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:0.31, G:0.00, T:0.15


Consensus pattern (13 bp):   
CAAAAATCATCAC

Found at i:8888 original size:15 final size:16

Alignment explanation


    Indices: 8858--8897  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       8848 TTACTTTGCT

                            
       8858 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                            
       8874 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTTTAA

               *     
       8889 TTGCTTTCT
          1 TTGTTTTCT

       8898 TTCAACCTCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA
Done.