Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006103.1 Corchorus olitorius cultivar O-4 contig06128, 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: 1773
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33


Found at i:342 original size:40 final size:39

Alignment explanation


    Indices: 297--511  Score: 113
    Period size: 38  Copynumber: 5.6  Consensus size: 39

        287 TAAATGCAGG

                               *                     
        297 CCTAAGCAGGTCTTACTTACACGAAAATTCTAAAT-AGAGA
          1 CCTAAGCAGGTCTTACTTAAACG-AAATTCT-AATCAGAGA

                                 *            *   *
        337 CCTAAGCAGGT-TTACTTAAATGAAATTCTAATCGGAGG
          1 CCTAAGCAGGTCTTACTTAAACGAAATTCTAATCAGAGA

                        **   *  *      *     *  *   
        375 CCTAAGCAGGTCCGA-TCAATCGAAAGCTCTAAGCAAAGA
          1 CCTAAGCAGGTCTTACTTAAACGAAA-TTCTAATCAGAGA

                           *                   *   *  
        414 TCCTAAGCAGGT-TTGCTTAAACGGAAATTC-AA-AATGGGA
          1 -CCTAAGCAGGTCTTACTTAAAC-GAAATTCTAATCA-GAGA

                 *         ***      *       * * *  
        453 CCTAAACAGGT-TTAAACAAACGAGATTCTAAGCGGGGA
          1 CCTAAGCAGGTCTTACTTAAACGAAATTCTAATCAGAGA

                          *       
        491 CCTAAGCAGGT-TTTCTTAAAC
          1 CCTAAGCAGGTCTTACTTAAAC

        512 AAAAATTCCA


Statistics
Matches: 130,  Mismatches: 36, Indels: 20
        0.70            0.19        0.11

Matches are distributed among these distances:
  37    9  0.07
  38   67  0.52
  39   22  0.17
  40   28  0.22
  41    4  0.03

ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24


Consensus pattern (39 bp):   
CCTAAGCAGGTCTTACTTAAACGAAATTCTAATCAGAGA

Found at i:379 original size:38 final size:40

Alignment explanation


    Indices: 244--386  Score: 120
    Period size: 40  Copynumber: 3.6  Consensus size: 40

        234 TTAAGCGGGG

                          *              **           
        244 ATTCTAAAT-GAGAACCTAAGCAGGT-TTGTTTAAAC-AAGA
          1 ATTCTAAATAGAG-GCCTAAGCAGGTCTTACTTAAACGAA-A

            *  *                              *      
        283 CTTTTAAAT-GCAGGCCTAAGCAGGTCTTACTTACACGAAA
          1 ATTCTAAATAG-AGGCCTAAGCAGGTCTTACTTAAACGAAA

                         *                     *    
        323 ATTCTAAATAGAGACCTAAGCAGGT-TTACTTAAATG-AA
          1 ATTCTAAATAGAGGCCTAAGCAGGTCTTACTTAAACGAAA

                      *                
        361 ATTCT-AATCGGAGGCCTAAGCAGGTC
          1 ATTCTAAAT-AGAGGCCTAAGCAGGTC

        387 CGATCAATCG


Statistics
Matches: 85,  Mismatches: 13, Indels: 12
        0.77            0.12        0.11

Matches are distributed among these distances:
  37    3  0.04
  38   21  0.25
  39   28  0.33
  40   30  0.35
  41    3  0.04

ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27


Consensus pattern (40 bp):   
ATTCTAAATAGAGGCCTAAGCAGGTCTTACTTAAACGAAA

Found at i:1591 original size:1 final size:1

Alignment explanation


    Indices: 1587--1612  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       1577 TTTTTTAGGC

                                      
       1587 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

       1613 AAGCAGAATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Done.