Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013129.1 Corchorus olitorius cultivar O-4 contig13162, 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: 9544
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34


Found at i:4870 original size:100 final size:100

Alignment explanation


    Indices: 4697--4921  Score: 398
    Period size: 100  Copynumber: 2.2  Consensus size: 100

       4687 CAAAGATACC

                                                                             
       4697 AAAGCCTTGCATCCAAAACTCCTCACCACCATAGCCAACAAAGATACAAGGAGTGGCTTTACTAT
          1 AAAGCCTTGCATCCAAAACTCCTCACCACCATAGCCAACAAAGATACAAGGAGTGGCTTTACTAT

                                               
       4762 CAAGTTTTGATCTTTGTTCCTTAGGAAAATGCAAG
         66 CAAGTTTTGATCTTTGTTCCTTAGGAAAATGCAAG

                                                                             
       4797 AAAGCCTTGCATCCAAAACTCCTCACCACCATAGCCAACAAAGATACAAGGAGTGGCTTTACTAT
          1 AAAGCCTTGCATCCAAAACTCCTCACCACCATAGCCAACAAAGATACAAGGAGTGGCTTTACTAT

              *                      * *       
       4862 CACGTTTTGATCTTTGTTCCTTAGGCACATGCAAG
         66 CAAGTTTTGATCTTTGTTCCTTAGGAAAATGCAAG

                    *                 
       4897 AAAGCCTTACATCCAAATAC-CCTCA
          1 AAAGCCTTGCATCCAAA-ACTCCTCA

       4922 AATGAGCATA


Statistics
Matches: 120,  Mismatches: 4, Indels: 2
        0.95            0.03        0.02

Matches are distributed among these distances:
 100  118  0.98
 101    2  0.02

ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25


Consensus pattern (100 bp):   
AAAGCCTTGCATCCAAAACTCCTCACCACCATAGCCAACAAAGATACAAGGAGTGGCTTTACTAT
CAAGTTTTGATCTTTGTTCCTTAGGAAAATGCAAG

Found at i:6312 original size:41 final size:41

Alignment explanation


    Indices: 6262--6591  Score: 353
    Period size: 41  Copynumber: 8.1  Consensus size: 41

       6252 CTAAAACCAT

                       *            *                
       6262 GGACCAAATTGAATCAAATAGTAACTAAAATCCTAAATCAG
          1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG

                *             *                      
       6303 GGACTAAATTGCATCAAAGAGTAAATAAAATCCTAAATCAG
          1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG

                *                                    
       6344 GGACTAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG
          1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG

                          *                          
       6385 GGACCAAATTGCATTAAATAGTAAATAAAATCCTAAATCAG
          1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG

                          *  *  *      **   *      *  
       6426 GGACCAAATTGCATTAATTAATAAAT-TGAT-TTGAAATTAG
          1 GGACCAAATTGCATCAAATAGTAAATAAAATCCT-AAATCAG

                   ***            *                   
       6466 GGACCAAGCCGCAT-AAATTA-AAAATAAAATCCTAAATCAG
          1 GGACCAAATTGCATCAAA-TAGTAAATAAAATCCTAAATCAG

              * *      *  *  *  *     *              
       6506 GGGCGAAATTGAATTAATTAATAAATGAAATCCTAAATCAG
          1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG

                *      *     *  *     *              
       6547 GGACAAAATTGAATCAATTAATAAATGAAATCCTAAATCAG
          1 GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG

                
       6588 GGAC
          1 GGAC

       6592 TAAGGTGAAA


Statistics
Matches: 249,  Mismatches: 34, Indels: 12
        0.84            0.12        0.04

Matches are distributed among these distances:
  39    7  0.03
  40   39  0.16
  41  203  0.82

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


Consensus pattern (41 bp):   
GGACCAAATTGCATCAAATAGTAAATAAAATCCTAAATCAG

Found at i:6751 original size:19 final size:19

Alignment explanation


    Indices: 6707--6751  Score: 81
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       6697 TACCTGAATT

                  *            
       6707 GGGTCGACCCGCGGTTTCC
          1 GGGTCGGCCCGCGGTTTCC

                               
       6726 GGGTCGGCCCGCGGTTTCC
          1 GGGTCGGCCCGCGGTTTCC

                   
       6745 GGGTCGG
          1 GGGTCGG

       6752 ATCGGGTCGG


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19   25  1.00

ACGTcount: A:0.02, C:0.33, G:0.44, T:0.20


Consensus pattern (19 bp):   
GGGTCGGCCCGCGGTTTCC

Found at i:6871 original size:22 final size:22

Alignment explanation


    Indices: 6846--6897  Score: 68
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       6836 CATGACAGCC

                     **           
       6846 GCCACCATGCCCCACCATCGCT
          1 GCCACCATGAACCACCATCGCT

                                * 
       6868 GCCACCATGAACCACCATCGTT
          1 GCCACCATGAACCACCATCGCT

                    
       6890 GACCACCA
          1 G-CCACCA

       6898 AATTCACTCA


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  22   20  0.77
  23    6  0.23

ACGTcount: A:0.25, C:0.48, G:0.13, T:0.13


Consensus pattern (22 bp):   
GCCACCATGAACCACCATCGCT
Done.