Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012320.1 Corchorus capsularis cultivar CVL-1 contig12341, 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: 23074
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:9660 original size:29 final size:31

Alignment explanation


    Indices: 9620--9690  Score: 85
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       9610 CTTGCTCAAT

                                            
       9620 TTGAGGCC-AAACCTTTAAAG-AGA-ACCAAA
          1 TTGA-GCCTAAACCTTTAAAGAAGACACCAAA

                        *    *    *        
       9649 TTGAGCCTAAACGTTTACAGAATACACCAAA
          1 TTGAGCCTAAACCTTTAAAGAAGACACCAAA

                       
       9680 TTGAGCCTAAA
          1 TTGAGCCTAAA

       9691 TCAAACAGAA


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  28    3  0.08
  29   14  0.39
  30    2  0.06
  31   17  0.47

ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21


Consensus pattern (31 bp):   
TTGAGCCTAAACCTTTAAAGAAGACACCAAA

Found at i:9701 original size:30 final size:30

Alignment explanation


    Indices: 9643--9701  Score: 75
    Period size: 31  Copynumber: 1.9  Consensus size: 30

       9633 TTTAAAGAGA

                                **         
       9643 ACCAAATTGAGCCTAAACGTTTACAGAATAC
          1 ACCAAATTGAGCCTAAACG-AAACAGAATAC

                                         
       9674 ACCAAATTGAGCCTAAATC-AAACAGAAT
          1 ACCAAATTGAGCCTAAA-CGAAACAGAAT

       9702 TTTGGATGTG


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  30    7  0.28
  31   17  0.68
  32    1  0.04

ACGTcount: A:0.46, C:0.22, G:0.12, T:0.20


Consensus pattern (30 bp):   
ACCAAATTGAGCCTAAACGAAACAGAATAC

Found at i:14722 original size:89 final size:85

Alignment explanation


    Indices: 14450--14764  Score: 418
    Period size: 89  Copynumber: 3.7  Consensus size: 85

      14440 TAAAATTTTA

                        *        *            *      *                       
      14450 ATTTTAAGGGTAAATTTTAAAGTTAAAATA-TTAATTCTCTTGGGTTTTAGAAAAAAAAAAGTTT
          1 ATTTTAAGGGTATATTTTAAACTTAAAATATTTATTTC-CTAGGGTTTTAGAAAAAAAAAAGTTT

            * *  *         *     
      14514 TGTCCTAAA-AAAAATAAATT
         65 AGCCCCAAATAAAAAGAAATT

             *     *  *        *                 *                           
      14534 AGTTTAATGGCATATTTTAGACTTAAAATATTTATTTTCTAGGGTTTTAGAAAAAAAAAAGTTTA
          1 ATTTTAAGGGTATATTTTAAACTTAAAATATTTATTTCCTAGGGTTTTAGAAAAAAAAAAGTTTA

                                 
      14599 GCCCCAAATAGAAAAGAAATT
         66 GCCCCAAATA-AAAAGAAATT

                                                                             
      14620 ATTTTAAGGGTATATTTTAAACTTAAAATATTTATTTCCTAGGGTTTTAGAAAGAAAAAAAAAGT
          1 ATTTTAAGGGTATATTTTAAACTTAAAATATTTATTTCCTAGGGTTTTAG--A-AAAAAAAAAGT

                                   *
      14685 TTAGCCCCAAATTAAAAAGAAATG
         63 TTAGCCCCAAA-TAAAAAGAAATT

                                       *             *              
      14709 ATTTTAAGGGTATATTTTAAACTTAAAGTATTTATTTCCTATGGTTTTAGAAAAAA
          1 ATTTTAAGGGTATATTTTAAACTTAAAATATTTATTTCCTAGGGTTTTAGAAAAAA

      14765 TCAAAGATAA


Statistics
Matches: 203,  Mismatches: 21, Indels: 12
        0.86            0.09        0.05

Matches are distributed among these distances:
  84   55  0.27
  85    6  0.03
  86   59  0.29
  87    1  0.00
  88    1  0.00
  89   79  0.39
  90    2  0.01

ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37


Consensus pattern (85 bp):   
ATTTTAAGGGTATATTTTAAACTTAAAATATTTATTTCCTAGGGTTTTAGAAAAAAAAAAGTTTA
GCCCCAAATAAAAAGAAATT

Found at i:22875 original size:25 final size:26

Alignment explanation


    Indices: 22823--22877  Score: 69
    Period size: 24  Copynumber: 2.2  Consensus size: 26

      22813 TATTTTGTCT

                       *       *      
      22823 TTTTCTTTAATTTTCAAAATTTTCAA
          1 TTTTCTTTAATCTTCAAAACTTTCAA

                                      
      22849 TTTTC-TTAATCTTC-AAACTTTCAA
          1 TTTTCTTTAATCTTCAAAACTTTCAA

            *    
      22873 ATTTC
          1 TTTTC

      22878 AATCATTCAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  24   13  0.50
  25    8  0.31
  26    5  0.19

ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55


Consensus pattern (26 bp):   
TTTTCTTTAATCTTCAAAACTTTCAA
Done.