Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016805.1 Corchorus olitorius cultivar O-4 contig16838, 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: 14135
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31


Found at i:2115 original size:15 final size:16

Alignment explanation


    Indices: 2084--2123  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       2074 TTACTTTGCT

                            
       2084 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                            
       2100 TTGTTTTCTA-TTTAA
          1 TTGTTTTCTAGTTTAA

               *     
       2115 TTGCTTTCT
          1 TTGTTTTCT

       2124 GTCAATCTCT


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

Matches are distributed among these distances:
  15   13  0.57
  16   10  0.43

ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:11029 original size:18 final size:19

Alignment explanation


    Indices: 11001--11043  Score: 79
    Period size: 18  Copynumber: 2.3  Consensus size: 19

      10991 TATTTGAAAA

                               
      11001 TATATATTAAGATAATAAT
          1 TATATATTAAGATAATAAT

                               
      11020 TATA-ATTAAGATAATAAT
          1 TATATATTAAGATAATAAT

                  
      11038 TATATA
          1 TATATA

      11044 AGCAAATAGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  18   18  0.78
  19    5  0.22

ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42


Consensus pattern (19 bp):   
TATATATTAAGATAATAAT

Found at i:13226 original size:27 final size:27

Alignment explanation


    Indices: 13195--13268  Score: 69
    Period size: 28  Copynumber: 2.7  Consensus size: 27

      13185 TCTAGCCTCT

                                       
      13195 AGGGGCAAAACTGTAATTTAGCCAACC
          1 AGGGGCAAAACTGTAATTTAGCCAACC

                 *                  **   
      13222 AGGGGTAAAA-TGGTAATTTTAGCTGACC
          1 AGGGGCAAAACT-GTAA-TTTAGCCAACC

             **        *       
      13250 AATGGCAAAACAGTAATTT
          1 AGGGGCAAAACTGTAATTT

      13269 TGACATCTTA


Statistics
Matches: 37,  Mismatches: 7, Indels: 6
        0.74            0.14        0.12

Matches are distributed among these distances:
  26    1  0.03
  27   16  0.43
  28   20  0.54

ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24


Consensus pattern (27 bp):   
AGGGGCAAAACTGTAATTTAGCCAACC

Found at i:13948 original size:27 final size:26

Alignment explanation


    Indices: 13917--13972  Score: 67
    Period size: 27  Copynumber: 2.1  Consensus size: 26

      13907 TCTCTTCTAT

                 *   *                 
      13917 GGGTAGTTTCGTAATTTAACAACTTAA
          1 GGGTAATTTAGTAATTTAACAAC-TAA

                        *        *    
      13944 GGGTAATTTAGTGATTTAACATCTAA
          1 GGGTAATTTAGTAATTTAACAACTAA

               
      13970 GGG
          1 GGG

      13973 CAAAATGGTC


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  26    6  0.24
  27   19  0.76

ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36


Consensus pattern (26 bp):   
GGGTAATTTAGTAATTTAACAACTAA

Found at i:14059 original size:4 final size:4

Alignment explanation


    Indices: 14041--14082  Score: 66
    Period size: 4  Copynumber: 10.0  Consensus size: 4

      14031 ATTTTACCTA

                                                               
      14041 ATTT ATTTT ATTTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
          1 ATTT A-TTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT

      14083 TTGGGCCAGG


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   4   28  0.76
   5    9  0.24

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (4 bp):   
ATTT

Done.