Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017317.1 Corchorus olitorius cultivar O-4 contig17350, 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: 14124
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:3095 original size:19 final size:18

Alignment explanation


    Indices: 3071--3106  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3061 TGAAGACTTA

                               
       3071 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       3090 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       3107 ATTATCTCAA


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:7274 original size:116 final size:116

Alignment explanation


    Indices: 7070--7304  Score: 461
    Period size: 116  Copynumber: 2.0  Consensus size: 116

       7060 GTCTGGATTC

                                                                             
       7070 ACCGTCGTAGAAAACAAGGAAGGAGAGCTAGTTCCTCAAAGACTGCAGAATGGATGGAGAGTATG
          1 ACCGTCGTAGAAAACAAGGAAGGAGAGCTAGTTCCTCAAAGACTGCAGAATGGATGGAGAGTATG

               *                                               
       7135 CATTGACTACAGAAAATTAATCTTTGCCACAAGGAAGGACCACTTTCCACT
         66 CATCGACTACAGAAAATTAATCTTTGCCACAAGGAAGGACCACTTTCCACT

                                                                             
       7186 ACCGTCGTAGAAAACAAGGAAGGAGAGCTAGTTCCTCAAAGACTGCAGAATGGATGGAGAGTATG
          1 ACCGTCGTAGAAAACAAGGAAGGAGAGCTAGTTCCTCAAAGACTGCAGAATGGATGGAGAGTATG

                                                               
       7251 CATCGACTACAGAAAATTAATCTTTGCCACAAGGAAGGACCACTTTCCACT
         66 CATCGACTACAGAAAATTAATCTTTGCCACAAGGAAGGACCACTTTCCACT

               
       7302 ACC
          1 ACC

       7305 ATTCATTGAC


Statistics
Matches: 118,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 116  118  1.00

ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20


Consensus pattern (116 bp):   
ACCGTCGTAGAAAACAAGGAAGGAGAGCTAGTTCCTCAAAGACTGCAGAATGGATGGAGAGTATG
CATCGACTACAGAAAATTAATCTTTGCCACAAGGAAGGACCACTTTCCACT

Found at i:10702 original size:21 final size:22

Alignment explanation


    Indices: 10673--10726  Score: 67
    Period size: 23  Copynumber: 2.5  Consensus size: 22

      10663 TCGACTAGGG

                                   
      10673 AATTGTCGAC-CAA-AGGAAGCA
          1 AATTGTCGACTCAAGA-GAAGCA

                *                  
      10694 AATTATCGACTCAAGTAGAAGCA
          1 AATTGTCGACTCAAG-AGAAGCA

                      
      10717 AATTGTCGAC
          1 AATTGTCGAC

      10727 AAGTAGCTAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  21    9  0.32
  22    3  0.11
  23   15  0.54
  24    1  0.04

ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20


Consensus pattern (22 bp):   
AATTGTCGACTCAAGAGAAGCA

Found at i:10731 original size:21 final size:22

Alignment explanation


    Indices: 10688--10732  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 22

      10678 TCGACCAAAG

                                   
      10688 GAAGCAAATTATCGACTCAAGTA
          1 GAAGCAAATTATCGAC-CAAGTA

                      *           
      10711 GAAGCAAATTGTCGA-CAAGTA
          1 GAAGCAAATTATCGACCAAGTA

             
      10732 G
          1 G

      10733 CTAAGAAAGG


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    7  0.33
  23   14  0.67

ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20


Consensus pattern (22 bp):   
GAAGCAAATTATCGACCAAGTA

Found at i:13275 original size:19 final size:18

Alignment explanation


    Indices: 13251--13286  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      13241 TGAAGACTTA

                               
      13251 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      13270 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      13287 ATTATCTCAA


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.