Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013319.1 Corchorus olitorius cultivar O-4 contig13352, 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: 14197
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35


Found at i:6668 original size:27 final size:28

Alignment explanation


    Indices: 6630--6777  Score: 160
    Period size: 28  Copynumber: 5.3  Consensus size: 28

       6620 TCACCTAGGT

                                 **     
       6630 GGGCATTTTAGTC-TTTTGCATGTTCAG
          1 GGGCATTTTAGTCATTTTGCACATTCAG

                                 **     
       6657 GGGCATTTTAGTCA-TTTGCATGTTCAG
          1 GGGCATTTTAGTCATTTTGCACATTCAG

               *                         
       6684 GGGTATTTT-GTTCATTTTGCACATTCAG
          1 GGGCATTTTAG-TCATTTTGCACATTCAG

                  *  *                    
       6712 GGGCATGTTGGTCATTTCTGCACA-TCTAG
          1 GGGCATTTTAGTCATTT-TGCACATTC-AG

               *     *                  
       6741 GGGTATTTTTGTCATTTTGCACATTCAG
          1 GGGCATTTTAGTCATTTTGCACATTCAG

                     
       6769 GGGCATTTT
          1 GGGCATTTT

       6778 GCACATTCAG


Statistics
Matches: 105,  Mismatches: 9, Indels: 13
        0.83            0.07        0.10

Matches are distributed among these distances:
  26    1  0.01
  27   37  0.35
  28   42  0.40
  29   25  0.24

ACGTcount: A:0.17, C:0.16, G:0.25, T:0.43


Consensus pattern (28 bp):   
GGGCATTTTAGTCATTTTGCACATTCAG

Found at i:6784 original size:28 final size:27

Alignment explanation


    Indices: 6630--6778  Score: 151
    Period size: 27  Copynumber: 5.4  Consensus size: 27

       6620 TCACCTAGGT

                                 **     
       6630 GGGCATTTTAGTC-TTTTGCATGTTCAG
          1 GGGCATTTT-GTCATTTTGCACATTCAG

                                 **     
       6657 GGGCATTTTAGTCA-TTTGCATGTTCAG
          1 GGGCATTTT-GTCATTTTGCACATTCAG

               *                        
       6684 GGGTATTTTGTTCATTTTGCACATTCAG
          1 GGGCATTTTG-TCATTTTGCACATTCAG

                     *                    
       6712 GGGCATGTTGGTCATTTCTGCACA-TCTAG
          1 GGGCAT-TTTGTCATTT-TGCACATTC-AG

               *                        
       6741 GGGTATTTTTGTCATTTTGCACATTCAG
          1 GGGCA-TTTTGTCATTTTGCACATTCAG

                      
       6769 GGGCATTTTG
          1 GGGCATTTTG

       6779 CACATTCAGG


Statistics
Matches: 106,  Mismatches: 8, Indels: 16
        0.82            0.06        0.12

Matches are distributed among these distances:
  26    1  0.01
  27   42  0.40
  28   36  0.34
  29   26  0.25
  30    1  0.01

ACGTcount: A:0.17, C:0.15, G:0.26, T:0.42


Consensus pattern (27 bp):   
GGGCATTTTGTCATTTTGCACATTCAG

Found at i:6803 original size:19 final size:19

Alignment explanation


    Indices: 6753--6796  Score: 88
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       6743 GTATTTTTGT

                               
       6753 CATTTTGCACATTCAGGGG
          1 CATTTTGCACATTCAGGGG

                               
       6772 CATTTTGCACATTCAGGGG
          1 CATTTTGCACATTCAGGGG

                  
       6791 CATTTT
          1 CATTTT

       6797 AGTCATTTTA


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

Matches are distributed among these distances:
  19   25  1.00

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


Consensus pattern (19 bp):   
CATTTTGCACATTCAGGGG

Found at i:7157 original size:57 final size:57

Alignment explanation


    Indices: 7088--7205  Score: 236
    Period size: 57  Copynumber: 2.1  Consensus size: 57

       7078 ATCTACTTGG

                                                                     
       7088 ATTACTTCCCATTGCTAGGTAGAAATAGATTTGCATTTTCTTTAGCTAGTAACTAGT
          1 ATTACTTCCCATTGCTAGGTAGAAATAGATTTGCATTTTCTTTAGCTAGTAACTAGT

                                                                     
       7145 ATTACTTCCCATTGCTAGGTAGAAATAGATTTGCATTTTCTTTAGCTAGTAACTAGT
          1 ATTACTTCCCATTGCTAGGTAGAAATAGATTTGCATTTTCTTTAGCTAGTAACTAGT

                
       7202 ATTA
          1 ATTA

       7206 TGGCATTGCT


Statistics
Matches: 61,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  57   61  1.00

ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41


Consensus pattern (57 bp):   
ATTACTTCCCATTGCTAGGTAGAAATAGATTTGCATTTTCTTTAGCTAGTAACTAGT

Found at i:9356 original size:41 final size:41

Alignment explanation


    Indices: 9311--9400  Score: 126
    Period size: 41  Copynumber: 2.2  Consensus size: 41

       9301 TCAATTTGCC

                                 *       *           
       9311 CCCTGATTGAGGTTAACATTTCTTAATTGGTTCAATTTCGT
          1 CCCTGATTGAGGTTAACATTTATTAATTGATTCAATTTCGT

                          * *       *             *  
       9352 CCCTGATTGAGGTTGATATTTATTTATTGATTCAATTTTGT
          1 CCCTGATTGAGGTTAACATTTATTAATTGATTCAATTTCGT

                    
       9393 CCCTGATT
          1 CCCTGATT

       9401 TAAGATTTTA


Statistics
Matches: 43,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  41   43  1.00

ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47


Consensus pattern (41 bp):   
CCCTGATTGAGGTTAACATTTATTAATTGATTCAATTTCGT
Done.