Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009522.1 Corchorus olitorius cultivar O-4 contig09554, 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: 2762
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:1279 original size:16 final size:16

Alignment explanation


    Indices: 1245--1394  Score: 155
    Period size: 16  Copynumber: 9.4  Consensus size: 16

       1235 CGGACTCGGA

                     *   *  
       1245 CGGGTTCGGATA-CTT
          1 CGGGTTCGGGTATTTT

                       *    
       1260 CGGGTTCGGGTTTTTT
          1 CGGGTTCGGGTATTTT

                   *        
       1276 CGGGTTCAGGTATTTT
          1 CGGGTTCGGGTATTTT

                       *    
       1292 CGGGTTCGGGTTTTTT
          1 CGGGTTCGGGTATTTT

                   *        
       1308 CGGGTTCAGGTATTTT
          1 CGGGTTCGGGTATTTT

                          ** 
       1324 CGGGTTCGGGT-TAAGT
          1 CGGGTTCGGGTAT-TTT

                            
       1340 CGGGTTCGGGTATTTT
          1 CGGGTTCGGGTATTTT

                *             
       1356 CGGGCTC-GG-ATTATGT
          1 CGGGTTCGGGTATT-T-T

                            
       1372 CGGGTTCGGGTATTTT
          1 CGGGTTCGGGTATTTT

             *     
       1388 CAGGTTC
          1 CGGGTTC

       1395 AGTCTCGGGT


Statistics
Matches: 111,  Mismatches: 17, Indels: 13
        0.79            0.12        0.09

Matches are distributed among these distances:
  14    3  0.03
  15   14  0.13
  16   87  0.78
  17    4  0.04
  18    3  0.03

ACGTcount: A:0.09, C:0.15, G:0.36, T:0.41


Consensus pattern (16 bp):   
CGGGTTCGGGTATTTT

Found at i:1296 original size:32 final size:32

Alignment explanation


    Indices: 1258--1394  Score: 184
    Period size: 32  Copynumber: 4.3  Consensus size: 32

       1248 GTTCGGATAC

                          * *               
       1258 TTCGGGTTCGGGTTTTTTCGGGTTCAGGTATT
          1 TTCGGGTTCGGGTTATGTCGGGTTCAGGTATT

                          * *               
       1290 TTCGGGTTCGGGTTTTTTCGGGTTCAGGTATT
          1 TTCGGGTTCGGGTTATGTCGGGTTCAGGTATT

                           *         *      
       1322 TTCGGGTTCGGGTTAAGTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTTATGTCGGGTTCAGGTATT

                  *    *             *      
       1354 TTCGGGCTCGGATTATGTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTTATGTCGGGTTCAGGTATT

               *     
       1386 TTCAGGTTC
          1 TTCGGGTTC

       1395 AGTCTCGGGT


Statistics
Matches: 96,  Mismatches: 9, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  32   96  1.00

ACGTcount: A:0.08, C:0.14, G:0.36, T:0.42


Consensus pattern (32 bp):   
TTCGGGTTCGGGTTATGTCGGGTTCAGGTATT

Found at i:1582 original size:13 final size:12

Alignment explanation


    Indices: 1559--1605  Score: 51
    Period size: 13  Copynumber: 3.8  Consensus size: 12

       1549 AAGTTTATTG

                        
       1559 ATAATATATAAT
          1 ATAATATATAAT

                         
       1571 ATAATAATATAAT
          1 ATAAT-ATATAAT

                *     * 
       1584 ATAACAT-TATT
          1 ATAATATATAAT

                       
       1595 ATCAATATATA
          1 AT-AATATATA

       1606 TAAAGATTTA


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  11    5  0.17
  12   11  0.38
  13   13  0.45

ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40


Consensus pattern (12 bp):   
ATAATATATAAT

Found at i:1894 original size:31 final size:31

Alignment explanation


    Indices: 1859--1930  Score: 78
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       1849 TAAATTATTG

                            *                
       1859 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
          1 CAAATTAAAA-AAATAAAAGTC-TTAAATTAAA

                     *                      
       1890 CAAA-TAATTAAAATAAAAGTCTTAAATTAAA
          1 CAAATTAA-AAAAATAAAAGTCTTAAATTAAA

                      
       1921 CAAATTAAAA
          1 CAAATTAAAA

       1931 GCTGATAGAC


Statistics
Matches: 34,  Mismatches: 3, Indels: 8
        0.76            0.07        0.18

Matches are distributed among these distances:
  30    7  0.21
  31   23  0.68
  32    4  0.12

ACGTcount: A:0.62, C:0.08, G:0.03, T:0.26


Consensus pattern (31 bp):   
CAAATTAAAAAAATAAAAGTCTTAAATTAAA

Found at i:2393 original size:23 final size:23

Alignment explanation


    Indices: 2367--2410  Score: 61
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       2357 CGGGTTCAGG

                    *              
       2367 CTCGGGTCGGGATCGGGCTCGAT
          1 CTCGGGTCAGGATCGGGCTCGAT

                   *   *         
       2390 CTCGGGTTAGGTTCGGGCTCG
          1 CTCGGGTCAGGATCGGGCTCG

       2411 GGCTACCTCG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.07, C:0.25, G:0.43, T:0.25


Consensus pattern (23 bp):   
CTCGGGTCAGGATCGGGCTCGAT
Done.