Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022039.1 Corchorus olitorius cultivar O-4 contig22072, 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: 4949
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:965 original size:21 final size:21

Alignment explanation


    Indices: 939--983  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        929 TCCGGCCATG

                           *     
        939 GCCCGGCCAGCCGAGTCACCT
          1 GCCCGGCCAGCCGAGCCACCT

                     *   *       
        960 GCCCGGCCATCCGCGCCACCT
          1 GCCCGGCCAGCCGAGCCACCT

               
        981 GCC
          1 GCC

        984 TAGTGAAGCT


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.11, C:0.53, G:0.27, T:0.09


Consensus pattern (21 bp):   
GCCCGGCCAGCCGAGCCACCT

Found at i:1005 original size:35 final size:35

Alignment explanation


    Indices: 959--1029  Score: 124
    Period size: 35  Copynumber: 2.0  Consensus size: 35

        949 CCGAGTCACC

                                         *     
        959 TGCCCGGCCATCCGCGCCACCTGCCTAGTGAAGCT
          1 TGCCCGGCCATCCGCGCCACCTGCCTAGTCAAGCT

                              *                
        994 TGCCCGGCCATCCGCGCCGCCTGCCTAGTCAAGCT
          1 TGCCCGGCCATCCGCGCCACCTGCCTAGTCAAGCT

             
       1029 T
          1 T

       1030 CAACCGCGCC


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  35   34  1.00

ACGTcount: A:0.13, C:0.44, G:0.25, T:0.18


Consensus pattern (35 bp):   
TGCCCGGCCATCCGCGCCACCTGCCTAGTCAAGCT

Found at i:1185 original size:22 final size:22

Alignment explanation


    Indices: 1160--1201  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1150 CCGCGCCACT

                      *           
       1160 ACCAAGCCACTACCGGCCATTC
          1 ACCAAGCCACCACCGGCCATTC

                *   *           
       1182 ACCATGCCTCCACCGGCCAT
          1 ACCAAGCCACCACCGGCCAT

       1202 GCCCGTGCCA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.24, C:0.48, G:0.14, T:0.14


Consensus pattern (22 bp):   
ACCAAGCCACCACCGGCCATTC

Found at i:4519 original size:39 final size:40

Alignment explanation


    Indices: 4443--4524  Score: 121
    Period size: 44  Copynumber: 2.0  Consensus size: 40

       4433 TTTCTTTCTT

                                                        
       4443 ATTTGTCGTAGATTTAGATTTAATTTACTTGTTTTGTTTCTACC
          1 ATTTGTCGTAGATTTAGATTTAATTTAC----TTTGTTTCTACC

                                                   
       4487 ATTTGTCGTAGATTTAGATTTAATTTAC-TTGTTTCTAC
          1 ATTTGTCGTAGATTTAGATTTAATTTACTTTGTTTCTAC

       4525 TTGTTTTGTT


Statistics
Matches: 38,  Mismatches: 0, Indels: 5
        0.88            0.00        0.12

Matches are distributed among these distances:
  39   10  0.26
  44   28  0.74

ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54


Consensus pattern (40 bp):   
ATTTGTCGTAGATTTAGATTTAATTTACTTTGTTTCTACC

Found at i:4789 original size:32 final size:31

Alignment explanation


    Indices: 4715--4778  Score: 101
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       4705 TTTGGCGCCG

                  *      *                 
       4715 TTGCCGGGGAAGGGAAACTTTCTCCTAGTTT
          1 TTGCCGAGGAAGGAAAACTTTCTCCTAGTTT

                                      *    
       4746 TTGCCGAGGAAGGAAAACTTTCTCCTGGTTT
          1 TTGCCGAGGAAGGAAAACTTTCTCCTAGTTT

              
       4777 TT
          1 TT

       4779 TTCCGCGGAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34


Consensus pattern (31 bp):   
TTGCCGAGGAAGGAAAACTTTCTCCTAGTTT
Done.