Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023303.1 Corchorus olitorius cultivar O-4 contig23336, 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: 7884
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32


Found at i:3610 original size:134 final size:132

Alignment explanation


    Indices: 3236--3614  Score: 494
    Period size: 134  Copynumber: 2.8  Consensus size: 132

       3226 TTTCTCTTTG

                                *                                            
       3236 AAACGCCGCTAAATTAGAATGATTGGTGGGAAAATTCCCCCCAAAATAATTCAAGAAAAAGTTAA
          1 AAACGCCGCTAAATTAGAATAATTGGTGGGAAAATTCCCCCCAAAATAATTCAAGAAAAAGTTAA

                         *                    *              *               
       3301 AAGATAAACTAAACCATTTAGCGGCGTTTTGATAATGGAAACGCCACTATTTAGTGGCGTTTCAT
         66 AAGATAAACTAAAACATTTAGCGGCGTTTTG-TATTGGAAACGCCACTAATTAGTGGCGTTTCAT

               
       3366 ATA
        130 ATA

                         *      *                     *            *   **    
       3369 AAGACGCCGCT-ATTTAGAAAAATTGGTGGGAAAAATTTTCCTCCCAAAATAATTAAAGGGAAAG
          1 AA-ACGCCGCTAAATTAGAATAATTGGTGGG-AAAA--TTCCCCCCAAAATAATTCAAGAAAAAG

               *        *                        *  *                        
       3433 TTAGAA-ATAAAGTAAAACATTTAGCGGCGTTGTT-TGTTAGAAACGCCACTAATTAGTGGCGTT
         62 TTAAAAGATAAACTAAAACATTTAGCGGCGTT-TTGTATTGGAAACGCCACTAATTAGTGGCGTT

              * *  *
       3496 TCCTGTGC
        126 TCATAT-A

                                                                             
       3504 AAACGCCGCTAAATTAGAATAATTGGTGGGAAAATTCCCCCCAAAATAATTCAAGAAAAAGTTAA
          1 AAACGCCGCTAAATTAGAATAATTGGTGGGAAAATTCCCCCCAAAATAATTCAAGAAAAAGTTAA

                         *        *                       
       3569 AAGATAAACTAAATCATTTAGCAGCGTTTTGGTATTGGAAACGCCA
         66 AAGATAAACTAAAACATTTAGCGGCGTTTT-GTATTGGAAACGCCA

       3615 TTATTGAGTG


Statistics
Matches: 207,  Mismatches: 29, Indels: 19
        0.81            0.11        0.07

Matches are distributed among these distances:
 132   30  0.14
 133   40  0.19
 134   65  0.31
 135   42  0.20
 136   30  0.14

ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26


Consensus pattern (132 bp):   
AAACGCCGCTAAATTAGAATAATTGGTGGGAAAATTCCCCCCAAAATAATTCAAGAAAAAGTTAA
AAGATAAACTAAAACATTTAGCGGCGTTTTGTATTGGAAACGCCACTAATTAGTGGCGTTTCATA
TA

Found at i:4150 original size:32 final size:32

Alignment explanation


    Indices: 4109--4191  Score: 130
    Period size: 32  Copynumber: 2.6  Consensus size: 32

       4099 AAACAAGCCA

                              *             
       4109 AAATAGCGGCGTTTCGGTTCGGAAACGCCACT
          1 AAATAGCGGCGTTTCGGTACGGAAACGCCACT

                                 *        * 
       4141 AAATAGCGGCGTTTCGGTACGTAAACGCCATT
          1 AAATAGCGGCGTTTCGGTACGGAAACGCCACT

                       *       
       4173 AAATAGCGGCGCTTCGGTA
          1 AAATAGCGGCGTTTCGGTA

       4192 TTTTGAAATC


Statistics
Matches: 47,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  32   47  1.00

ACGTcount: A:0.27, C:0.23, G:0.28, T:0.23


Consensus pattern (32 bp):   
AAATAGCGGCGTTTCGGTACGGAAACGCCACT

Found at i:7455 original size:14 final size:14

Alignment explanation


    Indices: 7436--7463  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       7426 TGCATTATTA

                          
       7436 TAAACTAACAACAC
          1 TAAACTAACAACAC

                          
       7450 TAAACTAACAACAC
          1 TAAACTAACAACAC

       7464 ACAATTTGGC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14


Consensus pattern (14 bp):   
TAAACTAACAACAC
Done.