Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006823.1 Corchorus olitorius cultivar O-4 contig06848, 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, 784

Length: 1307
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36


Found at i:627 original size:123 final size:127

Alignment explanation


    Indices: 382--636  Score: 365
    Period size: 131  Copynumber: 2.0  Consensus size: 127

        372 ATTTAAGAAA

                   *                           *                *            
        382 TATATTTGAAAAATACTAATATATATAAGTTTTTTGATTAAAATAGTAAAATTGTAAAAATAAAA
          1 TATATTTAAAAAATACTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---A

                                 *                                     *     
        447 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAACTTTTAGTTGAGTAAAACTGTAAAA
         63 TA-GTATAAGGATATTAGATTCAATTAAATAAAAATAGAACTTTTAGTTGAGTAAAACTATAAAA

             
        512 G
        127 G

                          *                                                  
        513 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
          1 TATATTTAAAAAATACTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG

                                          *    **                         
        576 TA-AA-GATATTAGATTCAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
         66 TATAAGGATATTAGATTCAATTAAATAAAAATAGAACTTTTAGTTGAGTAAAACTATAAAAG

             
        636 T
          1 T

        637 TTAAACAATG


Statistics
Matches: 115,  Mismatches: 9, Indels: 8
        0.87            0.07        0.06

Matches are distributed among these distances:
 123   52  0.45
 124    2  0.02
 125    2  0.02
 127    2  0.02
 131   57  0.50

ACGTcount: A:0.49, C:0.02, G:0.11, T:0.37


Consensus pattern (127 bp):   
TATATTTAAAAAATACTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
TATAAGGATATTAGATTCAATTAAATAAAAATAGAACTTTTAGTTGAGTAAAACTATAAAAG

Found at i:662 original size:123 final size:127

Alignment explanation


    Indices: 390--644  Score: 302
    Period size: 123  Copynumber: 2.0  Consensus size: 127

        380 AATATATTTG

                  *    * *             *                *                    
        390 AAAAATACTAATATATATAAGTTTTTTGATTAAAATAGTAAAATTGTAAAAATAAAATAGGTATA
          1 AAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-GTATA

                         *                                     *          ***
        455 AGGATATTAGATTTAATTAAATAAAAATAGAACTTTTAGTTGAGTAAAACTGTAAAAGTATATTT
         62 AGGATATTAGATTCAATTAAATAAAAATAGAACTTTTAGTTGAGTAAAACTATAAAAGTATAAAC

             
        520 A
        127 A

                       * *                                                   
        521 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-AA-GA
          1 AAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGA

                                  *    **                          *      
        582 TATTAGATTCAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAAACA
         66 TATTAGATTCAATTAAATAAAAATAGAACTTTTAGTTGAGTAAAACTATAAAAGTATAAACA

             
        644 A
          1 A

        645 TGGCATTTAA


Statistics
Matches: 112,  Mismatches: 12, Indels: 8
        0.85            0.09        0.06

Matches are distributed among these distances:
 123   56  0.50
 124    2  0.02
 125    2  0.02
 127    2  0.02
 131   50  0.45

ACGTcount: A:0.51, C:0.03, G:0.11, T:0.36


Consensus pattern (127 bp):   
AAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGA
TATTAGATTCAATTAAATAAAAATAGAACTTTTAGTTGAGTAAAACTATAAAAGTATAAACA
Done.