Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011071.1 Corchorus olitorius cultivar O-4 contig11104, 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, 899

Length: 1499
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22


Found at i:1369 original size:20 final size:20

Alignment explanation


    Indices: 1339--1499  Score: 154
    Period size: 20  Copynumber: 8.8  Consensus size: 20

       1329 TCCCGAGTGT

                                
       1339 CAAG-GCCGAGTGCCATCGG
          1 CAAGTGCCGAGTGCCATCGG

                 *              
       1358 CAAGTCCCGAGTGCCATCGG
          1 CAAGTGCCGAGTGCCATCGG

               * *              
       1378 CAACTCCCGAGTGCCAT---
          1 CAAGTGCCGAGTGCCATCGG

                    *           
       1395 ---G-GCCTAGTGCCATCGG
          1 CAAGTGCCGAGTGCCATCGG

                                
       1411 CAAGTGCCGAGTG----C--
          1 CAAGTGCCGAGTGCCATCGG

                    *           
       1425 CAAG-GCCTAGTGCCATCGG
          1 CAAGTGCCGAGTGCCATCGG

                                
       1444 CAAGTGCCGAGTGCCATCGG
          1 CAAGTGCCGAGTGCCATCGG

                  *             
       1464 CAAGTGTCGAGTGCCATCGG
          1 CAAGTGCCGAGTGCCATCGG

                 *          
       1484 CAAGTCCCGAGTGCCA
          1 CAAGTGCCGAGTGCCA


Statistics
Matches: 116,  Mismatches: 11, Indels: 29
        0.74            0.07        0.19

Matches are distributed among these distances:
  13   17  0.15
  14    4  0.03
  16    1  0.01
  17    1  0.01
  19    9  0.08
  20   84  0.72

ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16


Consensus pattern (20 bp):   
CAAGTGCCGAGTGCCATCGG

Found at i:1386 original size:53 final size:53

Alignment explanation


    Indices: 1317--1499  Score: 228
    Period size: 53  Copynumber: 3.5  Consensus size: 53

       1307 GTTGCCAAGC

                                 *                        *      
       1317 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGTGCCATCGGCAAGTCCCGAGT
          1 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT

                       *            *    *                       
       1370 GCCATCGGCAACTCCCGAGTGCCATGGCCTAGTGCCATCGGCAAGTGCCGAGT
          1 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT

                 *    *   *        *                          *     
       1423 GCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGTGCCATCGGCAAGTGTCGAGT
          1 GCCATCGG-CAAGTCCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAAGTGCCGAGT

                                    
       1476 GCCATCGGCAAGTCCCGAGTGCCA
          1 GCCATCGGCAAGTCCCGAGTGCCA


Statistics
Matches: 107,  Mismatches: 17, Indels: 11
        0.79            0.13        0.08

Matches are distributed among these distances:
  51    1  0.01
  52    7  0.07
  53   92  0.86
  54    6  0.06
  55    1  0.01

ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16


Consensus pattern (53 bp):   
GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT

Found at i:1409 original size:33 final size:33

Alignment explanation


    Indices: 1367--1460  Score: 161
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       1357 GCAAGTCCCG

                          * *                
       1367 AGTGCCATCGGCAACTCCCGAGTGCCATGGCCT
          1 AGTGCCATCGGCAAGTGCCGAGTGCCATGGCCT

                                       *     
       1400 AGTGCCATCGGCAAGTGCCGAGTGCCAAGGCCT
          1 AGTGCCATCGGCAAGTGCCGAGTGCCATGGCCT

                                        
       1433 AGTGCCATCGGCAAGTGCCGAGTGCCAT
          1 AGTGCCATCGGCAAGTGCCGAGTGCCAT

       1461 CGGCAAGTGT


Statistics
Matches: 57,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  33   57  1.00

ACGTcount: A:0.20, C:0.32, G:0.31, T:0.17


Consensus pattern (33 bp):   
AGTGCCATCGGCAAGTGCCGAGTGCCATGGCCT
Done.