Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019789.1 Corchorus olitorius cultivar O-4 contig19822, 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: 16634
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29


Found at i:3892 original size:72 final size:72

Alignment explanation


    Indices: 3775--3916  Score: 266
    Period size: 72  Copynumber: 2.0  Consensus size: 72

       3765 AAAGACAAGC

                                                          *                  
       3775 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGTTATGAGATCATTGGATAT
          1 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT

                   
       3840 CCTGCTG
         66 CCTGCTG

                     *                                                       
       3847 CAAGGTGTGGACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
          1 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT

                 
       3912 CCTGC
         66 CCTGC

       3917 ACGGTGGCGT


Statistics
Matches: 68,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  72   68  1.00

ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24


Consensus pattern (72 bp):   
CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
CCTGCTG

Found at i:9223 original size:19 final size:18

Alignment explanation


    Indices: 9201--9240  Score: 55
    Period size: 17  Copynumber: 2.2  Consensus size: 18

       9191 GAGTGAAAAC

                               
       9201 TGAGTGCAAAAACAGAGAG
          1 TGAG-GCAAAAACAGAGAG

                    *         
       9220 TGA-GCAAGAACAGAGAG
          1 TGAGGCAAAAACAGAGAG

                
       9237 TGAG
          1 TGAG

       9241 CAAGAGTGAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  17   16  0.84
  19    3  0.16

ACGTcount: A:0.45, C:0.10, G:0.35, T:0.10


Consensus pattern (18 bp):   
TGAGGCAAAAACAGAGAG

Found at i:9231 original size:17 final size:17

Alignment explanation


    Indices: 9206--9245  Score: 71
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       9196 AAAACTGAGT

                *            
       9206 GCAAAAACAGAGAGTGA
          1 GCAAGAACAGAGAGTGA

                             
       9223 GCAAGAACAGAGAGTGA
          1 GCAAGAACAGAGAGTGA

                  
       9240 GCAAGA
          1 GCAAGA

       9246 GTGAGTCGTG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  17   22  1.00

ACGTcount: A:0.50, C:0.12, G:0.33, T:0.05


Consensus pattern (17 bp):   
GCAAGAACAGAGAGTGA

Found at i:12864 original size:20 final size:18

Alignment explanation


    Indices: 12825--12860  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      12815 CTAGCGCTAA

                          *   
      12825 AACTAGAAGAAAAACTAG
          1 AACTAGAAGAAAAAATAG

                              
      12843 AACTAGAAGAGAAAAATA
          1 AACTAGAAGA-AAAAATA

      12861 AGAAGAGAAA


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

Matches are distributed among these distances:
  18   10  0.62
  19    6  0.38

ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11


Consensus pattern (18 bp):   
AACTAGAAGAAAAAATAG

Found at i:13463 original size:9 final size:9

Alignment explanation


    Indices: 13449--13474  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

      13439 TTGAAATAAT

                     
      13449 TCTTCAAAG
          1 TCTTCAAAG

                     
      13458 TCTTCAAAG
          1 TCTTCAAAG

                    
      13467 TCTTCAAA
          1 TCTTCAAA

      13475 TTATCTTCAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35


Consensus pattern (9 bp):   
TCTTCAAAG
Done.