Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011861.1 Corchorus olitorius cultivar O-4 contig11894, 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: 3050
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:2291 original size:23 final size:22

Alignment explanation


    Indices: 2259--2340  Score: 67
    Period size: 23  Copynumber: 3.4  Consensus size: 22

       2249 TTTTAGAAAA

                                   
       2259 ACGCAAAAACTTTTTTTTTTATG
          1 ACGC-AAAACTTTTTTTTTTATG

                          *            
       2282 ACGCAGAAACAAAAATTTTTTTTTATG
          1 ACGCA-AAAC----TTTTTTTTTTATG

                    *               
       2309 ACGCAAAAATATTTTTTTTT-TCG
          1 ACGCAAAACT-TTTTTTTTTAT-G

                     
       2332 ACGCAAAAC
          1 ACGCAAAAC

       2341 ACAAAACTCT


Statistics
Matches: 48,  Mismatches: 4, Indels: 14
        0.73            0.06        0.21

Matches are distributed among these distances:
  22    2  0.04
  23   26  0.54
  26    3  0.06
  27   17  0.35

ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39


Consensus pattern (22 bp):   
ACGCAAAACTTTTTTTTTTATG

Found at i:2300 original size:27 final size:26

Alignment explanation


    Indices: 2270--2357  Score: 94
    Period size: 27  Copynumber: 3.3  Consensus size: 26

       2260 CGCAAAAACT

                                       
       2270 TTTTTTTTTATGACGCAGAAACAAAAA
          1 TTTTTTTTTATGACGCA-AAACAAAAA

                                    * 
       2297 TTTTTTTTTATGACGC--AA-AAATA
          1 TTTTTTTTTATGACGCAAAACAAAAA

                                        
       2320 TTTTTTTTT-TCGACGCAAAACACAAAA
          1 TTTTTTTTTAT-GACGCAAAACA-AAAA

                       
       2347 CTCTTTTTTTT
          1 -T-TTTTTTTT

       2358 TCTTTGACGC


Statistics
Matches: 52,  Mismatches: 2, Indels: 12
        0.79            0.03        0.18

Matches are distributed among these distances:
  22    1  0.02
  23   18  0.35
  24    2  0.04
  25    2  0.04
  26    1  0.02
  27   19  0.37
  28    1  0.02
  29    8  0.15

ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45


Consensus pattern (26 bp):   
TTTTTTTTTATGACGCAAAACAAAAA

Found at i:2313 original size:50 final size:52

Alignment explanation


    Indices: 2259--2357  Score: 136
    Period size: 50  Copynumber: 1.9  Consensus size: 52

       2249 TTTTAGAAAA

                                                                   
       2259 ACGCAAAAACT-TTTTTTTTTAT-GACGCAGAAACA-AAAA-T-TTTTTTTTATG
          1 ACGCAAAAA-TATTTTTTTTT-TCGACGCA-AAACACAAAACTCTTTTTTTTATG

                                                             
       2309 ACGCAAAAATATTTTTTTTTTCGACGCAAAACACAAAACTCTTTTTTTT
          1 ACGCAAAAATATTTTTTTTTTCGACGCAAAACACAAAACTCTTTTTTTT

       2358 TCTTTGACGC


Statistics
Matches: 44,  Mismatches: 0, Indels: 8
        0.85            0.00        0.15

Matches are distributed among these distances:
  49    7  0.16
  50   28  0.64
  51    1  0.02
  52    8  0.18

ACGTcount: A:0.35, C:0.15, G:0.08, T:0.41


Consensus pattern (52 bp):   
ACGCAAAAATATTTTTTTTTTCGACGCAAAACACAAAACTCTTTTTTTTATG
Done.