Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015181.1 Corchorus olitorius cultivar O-4 contig15214, 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: 41220
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:462 original size:27 final size:27

Alignment explanation


    Indices: 424--485  Score: 115
    Period size: 27  Copynumber: 2.3  Consensus size: 27

        414 CCTTGCATCG

                *                      
        424 AAAAATTTCAGATCTCGGGTCAAATTT
          1 AAAACTTTCAGATCTCGGGTCAAATTT

                                       
        451 AAAACTTTCAGATCTCGGGTCAAATTT
          1 AAAACTTTCAGATCTCGGGTCAAATTT

                    
        478 AAAACTTT
          1 AAAACTTT

        486 GACTGGAAAG


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   34  1.00

ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34


Consensus pattern (27 bp):   
AAAACTTTCAGATCTCGGGTCAAATTT

Found at i:2091 original size:22 final size:22

Alignment explanation


    Indices: 2061--2114  Score: 63
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       2051 ACATTAAAAA

                          *       
       2061 TGGGTCGTGCTGCATCGGCACG
          1 TGGGTCGTGCTGCACCGGCACG

                *    *  **        
       2083 TGGGACGTGTTGTGCCGGCACG
          1 TGGGTCGTGCTGCACCGGCACG

                      
       2105 TGGGTCGTGC
          1 TGGGTCGTGC

       2115 CATGCCGTGT


Statistics
Matches: 25,  Mismatches: 7, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.07, C:0.24, G:0.44, T:0.24


Consensus pattern (22 bp):   
TGGGTCGTGCTGCACCGGCACG

Found at i:2120 original size:22 final size:22

Alignment explanation


    Indices: 2076--2121  Score: 56
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       2066 CGTGCTGCAT

                            ***   
       2076 CGGCACGTGGGACGTGTTGTGC
          1 CGGCACGTGGGACGTGCCATGC

                       *          
       2098 CGGCACGTGGGTCGTGCCATGC
          1 CGGCACGTGGGACGTGCCATGC

              
       2120 CG
          1 CG

       2122 TGTCATTTTA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.09, C:0.28, G:0.43, T:0.20


Consensus pattern (22 bp):   
CGGCACGTGGGACGTGCCATGC

Found at i:11298 original size:24 final size:24

Alignment explanation


    Indices: 11266--11314  Score: 98
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      11256 ATATCCTCAT

                                    
      11266 GACTAATTCAGAATCCAATTAACC
          1 GACTAATTCAGAATCCAATTAACC

                                    
      11290 GACTAATTCAGAATCCAATTAACC
          1 GACTAATTCAGAATCCAATTAACC

             
      11314 G
          1 G

      11315 TGTCTCGAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24


Consensus pattern (24 bp):   
GACTAATTCAGAATCCAATTAACC

Found at i:11407 original size:21 final size:21

Alignment explanation


    Indices: 11381--11424  Score: 88
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      11371 TTTCTTCTAT

                                 
      11381 TTGACTTAATTAGGCATTTGG
          1 TTGACTTAATTAGGCATTTGG

                                 
      11402 TTGACTTAATTAGGCATTTGG
          1 TTGACTTAATTAGGCATTTGG

              
      11423 TT
          1 TT

      11425 TATTGTTATT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45


Consensus pattern (21 bp):   
TTGACTTAATTAGGCATTTGG

Found at i:24589 original size:21 final size:21

Alignment explanation


    Indices: 24565--24628  Score: 69
    Period size: 21  Copynumber: 3.1  Consensus size: 21

      24555 GCTGTTCGAA

                *                
      24565 TAATCTCATCTGTACAGTACC
          1 TAATATCATCTGTACAGTACC

                * *             *
      24586 TAATTTAATCTGTACAGT--G
          1 TAATATCATCTGTACAGTACC

                            *    
      24605 TAATATCATCTGTACATTACC
          1 TAATATCATCTGTACAGTACC

               
      24626 TAA
          1 TAA

      24629 ACAGTGTCAA


Statistics
Matches: 34,  Mismatches: 7, Indels: 4
        0.76            0.16        0.09

Matches are distributed among these distances:
  19   15  0.44
  21   19  0.56

ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38


Consensus pattern (21 bp):   
TAATATCATCTGTACAGTACC

Found at i:32554 original size:23 final size:23

Alignment explanation


    Indices: 32528--32576  Score: 98
    Period size: 23  Copynumber: 2.1  Consensus size: 23

      32518 TTACATGTTC

                                   
      32528 ATATAAAAGATATAATCATGGAA
          1 ATATAAAAGATATAATCATGGAA

                                   
      32551 ATATAAAAGATATAATCATGGAA
          1 ATATAAAAGATATAATCATGGAA

               
      32574 ATA
          1 ATA

      32577 GTTTCGAATT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   26  1.00

ACGTcount: A:0.57, C:0.04, G:0.12, T:0.27


Consensus pattern (23 bp):   
ATATAAAAGATATAATCATGGAA
Done.