Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009547.1 Corchorus olitorius cultivar O-4 contig09579, 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: 6397
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:1188 original size:46 final size:46

Alignment explanation


    Indices: 1100--1191  Score: 139
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       1090 TACAAACATG

                                  *            ***        
       1100 CAAAATCATGAAGTTCAAGTTTTAGGTTTTGAAGATTTTTTTTTTT
          1 CAAAATCATGAAGTTCAAGTTTAAGGTTTTGAAGAAAGTTTTTTTT

                   *                                      
       1146 CAAAATCGTGAAGTTCAAGTTTAAGGTTTTGAAGAAAGTTTTTTTT
          1 CAAAATCATGAAGTTCAAGTTTAAGGTTTTGAAGAAAGTTTTTTTT

       1192 GGCTAGCCCA


Statistics
Matches: 41,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  46   41  1.00

ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46


Consensus pattern (46 bp):   
CAAAATCATGAAGTTCAAGTTTAAGGTTTTGAAGAAAGTTTTTTTT

Found at i:1503 original size:22 final size:22

Alignment explanation


    Indices: 1473--1691  Score: 155
    Period size: 22  Copynumber: 10.0  Consensus size: 22

       1463 TCTAACGTAG

                                   
       1473 AAATATTGATAACCACACTATGA
          1 AAAT-TTGATAACCACACTATGA

                        ** **     
       1496 AAATTTGATAACTTCGTTATG-
          1 AAATTTGATAACCACACTATGA

                   *                
       1517 AAATTTCAATAACCTA-A-TATGA
          1 AAATTT-GATAACC-ACACTATGA

                     *        *   
       1539 AAATTTGATCACCACACTGTGA
          1 AAATTTGATAACCACACTATGA

              *                   
       1561 AATTTTGATAACCACACTATGA
          1 AAATTTGATAACCACACTATGA

              *          *  * *   
       1583 AATTTTGATAACCTCAATGTGA
          1 AAATTTGATAACCACACTATGA

              *        *     *    
       1605 AATTTTGATAATCACACAAT-A
          1 AAATTTGATAACCACACTATGA

                *  *     *        
       1626 AAA-CTGGTAACCGCACTATGA
          1 AAATTTGATAACCACACTATGA

                                    
       1647 AAATTTTGATAACCACA-TCATG-
          1 AAA-TTTGATAACCACACT-ATGA

                          * *      
       1669 AAATTTCGATAACCTCCCTATGA
          1 AAATTT-GATAACCACACTATGA

       1692 GAATGAAACT


Statistics
Matches: 151,  Mismatches: 33, Indels: 24
        0.73            0.16        0.12

Matches are distributed among these distances:
  20   12  0.08
  21   26  0.17
  22   96  0.64
  23   17  0.11

ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31


Consensus pattern (22 bp):   
AAATTTGATAACCACACTATGA

Found at i:1520 original size:44 final size:44

Alignment explanation


    Indices: 1472--1684  Score: 186
    Period size: 43  Copynumber: 4.9  Consensus size: 44

       1462 TTCTAACGTA

                 *                              *  ** * 
       1472 GAAATATTGATAACCACACTATGAAAATTTGATAACTTCGTTAT
          1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATGT

                   **                         *   *  *   
       1516 GAAATTTCAATAACCTA-A-TATGAAAATTTGATCACCACACTGT
          1 GAAATTTTGATAACC-ACACTATGAAAATTTGATAACCTCAATGT

                                      *                 
       1559 GAAATTTTGATAACCACACTATGAAATTTTGATAACCTCAATGT
          1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATGT

                         *     *        *  *     *  * * 
       1603 GAAATTTTGATAATCACACAAT-AAAA-CTGGTAACCGCACTAT
          1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATGT

                                                      
       1645 GAAAATTTTGATAACCACA-TCATG-AAATTTCGATAACCTC
          1 G-AAATTTTGATAACCACACT-ATGAAAATTT-GATAACCTC

       1685 CCTATGAGAA


Statistics
Matches: 133,  Mismatches: 28, Indels: 15
        0.76            0.16        0.09

Matches are distributed among these distances:
  42   13  0.10
  43   57  0.43
  44   55  0.41
  45    8  0.06

ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31


Consensus pattern (44 bp):   
GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATGT

Found at i:1582 original size:65 final size:66

Alignment explanation


    Indices: 1473--1691  Score: 178
    Period size: 65  Copynumber: 3.3  Consensus size: 66

       1463 TCTAACGTAG

                                               ** **                         
       1473 AAATATTGATAACCACACTATGAAAATTTGATAACTTCGTTATGAAATTTCAATAACCT-AATAT
          1 AAAT-TTGATAACCACACTATGAAAATTTGATAACCACACTATGAAATTTCAATAACCTCAATAT

              
       1537 GA
         65 GA

                     *        *     *                        **           *  
       1539 AAATTTGATCACCACACTGTGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCAATGTG
          1 AAATTTGATAACCACACTATGAAAATTTGATAACCACACTATGAAATTTCAATAACCTCAATATG

             
       1604 A
         66 A

              *        *     *        *  *     *              **      *      
       1605 AATTTTGATAATCACACAAT-AAAA-CTGGTAACCGCACTATGAAAATTTTGATAACCAC-ATCA
          1 AAATTTGATAACCACACTATGAAAATTTGATAACCACACTATG-AAATTTCAATAACCTCAAT-A

               
       1667 TG-
         64 TGA

                          * *      
       1669 AAATTTCGATAACCTCCCTATGA
          1 AAATTT-GATAACCACACTATGA

       1692 GAATGAAACT


Statistics
Matches: 122,  Mismatches: 26, Indels: 10
        0.77            0.16        0.06

Matches are distributed among these distances:
  64   21  0.17
  65   75  0.61
  66   26  0.21

ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31


Consensus pattern (66 bp):   
AAATTTGATAACCACACTATGAAAATTTGATAACCACACTATGAAATTTCAATAACCTCAATATG
A
Done.