Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021160.1 Corchorus olitorius cultivar O-4 contig21193, 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: 2814
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27


Found at i:564 original size:28 final size:28

Alignment explanation


    Indices: 505--600  Score: 140
    Period size: 28  Copynumber: 3.5  Consensus size: 28

        495 CTTAAAACAA

                 *           * **       
        505 CCAAATTGCCCCTGAATGTGCAAATGA-
          1 CCAAAATGCCCCTGAATATAAAAATGAC

                                        
        532 CCAAAATGCCCCTGAATATAAAAATGAC
          1 CCAAAATGCCCCTGAATATAAAAATGAC

                          *             
        560 CCAAAATGCCCCTGCATATAAAAATGAC
          1 CCAAAATGCCCCTGAATATAAAAATGAC

                         
        588 CCAAAATGCCCCT
          1 CCAAAATGCCCCT

        601 AGATGACCCT


Statistics
Matches: 63,  Mismatches: 5, Indels: 1
        0.91            0.07        0.01

Matches are distributed among these distances:
  27   23  0.37
  28   40  0.63

ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19


Consensus pattern (28 bp):   
CCAAAATGCCCCTGAATATAAAAATGAC

Found at i:1141 original size:69 final size:69

Alignment explanation


    Indices: 1066--1353  Score: 345
    Period size: 69  Copynumber: 4.2  Consensus size: 69

       1056 ACTTGGCTTA

                                       *      * *  *          *              
       1066 TGGAAAAGCC-ACTGTTG-TATGGATGGAACCAATGTTTAAACTGACTCGCATGGAAACGAGTTT
          1 TGGAAAAGCCTACTG-TGCT-TGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTT

                 *
       1129 GACTTA
         64 GACTTG

                    *                          *                             
       1135 TGGAAAAGTCTACATG-GCTTGGATGAAACCAAGGTTTGAACTGACTCGTATGGAAACGAGTTTG
          1 TGGAAAAGCCTAC-TGTGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTG

            *    
       1199 GCTTG
         65 ACTTG

                                    *                                        
       1204 TGGAAAAGCCTA-TGTGACTTGGAAGAAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTG
          1 TGGAAAAGCCTACTGTG-CTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTG

            *    
       1268 GCTTG
         65 ACTTG

                                *     *   *          *                       
       1273 TGGAAAAGCCTAC-GTGGCTCGGATGGAACTAAGGCTTGAATTGACTCGTATGGAAACGAGTTT-
          1 TGGAAAAGCCTACTGT-GCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTG

                  
       1336 AGCTTG
         65 A-CTTG

                        
       1342 TGGAAAAGCCTA
          1 TGGAAAAGCCTA

       1354 TATTGATAAT


Statistics
Matches: 195,  Mismatches: 16, Indels: 16
        0.86            0.07        0.07

Matches are distributed among these distances:
  67    2  0.01
  68    1  0.01
  69  186  0.95
  70    4  0.02
  71    2  0.01

ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26


Consensus pattern (69 bp):   
TGGAAAAGCCTACTGTGCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGA
CTTG

Found at i:1247 original size:138 final size:138

Alignment explanation


    Indices: 1104--1354  Score: 403
    Period size: 138  Copynumber: 1.8  Consensus size: 138

       1094 CCAATGTTTA

                                                   *          *              
       1104 AACTGACTCGCATGGAAACGAGTTTGACTTATGGAAAAGTCTACATGGCTTGGATGAAACCAAGG
          1 AACTGACTCGCATGGAAACGAGTTTGACTTATGGAAAAGCCTACATGGCTCGGATGAAACCAAGG

            *                            *                                   
       1169 TTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGACTTGGAAGAAACC
         66 CTTGAACTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCCTATGTGACTTGGAAGAAACC

                    
       1234 AAGGCTTG
        131 AAGGCTTG

                      *               *   *             *           *   *    
       1242 AACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACGTGGCTCGGATGGAACTAAGG
          1 AACTGACTCGCATGGAAACGAGTTTGACTTATGGAAAAGCCTACATGGCTCGGATGAAACCAAGG

                  *                                         
       1307 CTTGAATTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCCTAT
         66 CTTGAACTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCCTAT

       1355 ATTGATAATT


Statistics
Matches: 102,  Mismatches: 11, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
 138  102  1.00

ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26


Consensus pattern (138 bp):   
AACTGACTCGCATGGAAACGAGTTTGACTTATGGAAAAGCCTACATGGCTCGGATGAAACCAAGG
CTTGAACTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCCTATGTGACTTGGAAGAAACC
AAGGCTTG

Found at i:1365 original size:50 final size:49

Alignment explanation


    Indices: 1311--1475  Score: 267
    Period size: 50  Copynumber: 3.3  Consensus size: 49

       1301 CTAAGGCTTG

                                                              
       1311 AATTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCCTATATTGAT
          1 AATTGACTCGTATGGAAACGAGTTT-GCTTGTGGAAAAGCCTATATTGAT

                  *           *                  *            
       1361 AATTGAATCGTATGGAAATGAGTTTGCCTTGTGGAAAGGCCTATATTGAT
          1 AATTGACTCGTATGGAAACGAGTTTG-CTTGTGGAAAAGCCTATATTGAT

                                                        *     
       1411 AATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGAT
          1 AATTGACTCGTATGGAAACGAGTTT-GCTTGTGGAAAAGCCTATATTGAT

                           
       1461 AATTGACTCGTATGG
          1 AATTGACTCGTATGG

       1476 TGATCGAGTC


Statistics
Matches: 106,  Mismatches: 7, Indels: 4
        0.91            0.06        0.03

Matches are distributed among these distances:
  49    1  0.01
  50  104  0.98
  51    1  0.01

ACGTcount: A:0.30, C:0.12, G:0.26, T:0.33


Consensus pattern (49 bp):   
AATTGACTCGTATGGAAACGAGTTTGCTTGTGGAAAAGCCTATATTGAT

Done.