Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010818.1 Corchorus olitorius cultivar O-4 contig10850, 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: 4033
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34


Found at i:1584 original size:33 final size:31

Alignment explanation


    Indices: 1478--1623  Score: 123
    Period size: 33  Copynumber: 4.5  Consensus size: 31

       1468 GAGTAATTCT

                         *         *         
       1478 AAATCTGTTTTAGATGTTGTTTGCGAT-AATAC
          1 AAATCTGTTTT-GGTGTTGTTTGTGATGAA-AC

                *  **                     *  
       1510 TAAACCTAATTTGAGTGTTGTTTGTGATGACAC
          1 -AAATCTGTTTTG-GTGTTGTTTGTGATGAAAC

                                             
       1543 TAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
          1 -AAATCTGTTTT-GGTGTTGTTTGTGATGAAAC

                             * **             
       1576 AAATTCTGTTTTGGATGCTAATTGTGATGAAAAC
          1 AAA-TCTGTTTTGG-TGTTGTTTGTGATG-AAAC

                          
       1610 AAATCTGTTTTGGT
          1 AAATCTGTTTTGGT

       1624 TGATCATAGC


Statistics
Matches: 94,  Mismatches: 13, Indels: 13
        0.78            0.11        0.11

Matches are distributed among these distances:
  32    7  0.07
  33   78  0.83
  34    9  0.10

ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42


Consensus pattern (31 bp):   
AAATCTGTTTTGGTGTTGTTTGTGATGAAAC

Found at i:3453 original size:21 final size:21

Alignment explanation


    Indices: 3427--3581  Score: 199
    Period size: 21  Copynumber: 7.4  Consensus size: 21

       3417 TGCTAGAAAT

                                  
       3427 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
       3448 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                               *  
       3469 TCATTGGAGCAA-GTTCCATGC
          1 TCATTGGAG-AAGGTTCCAAGC

                         *      *
       3490 TCATTGGAGAAGGCTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       3511 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       3532 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                 *         *     
       3553 TCATTAGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       3574 TCATTGGA
          1 TCATTGGA

       3582 ATTGCCTAAG


Statistics
Matches: 123,  Mismatches: 10, Indels: 2
        0.91            0.07        0.01

Matches are distributed among these distances:
  20    2  0.02
  21  121  0.98

ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.