Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001624.1 Corchorus capsularis cultivar CVL-1 contig01624, 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: 3714
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26


Found at i:175 original size:29 final size:30

Alignment explanation


    Indices: 143--199  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 30

        133 TTTACCCCCC

                                          
        143 GAACTTCAATCTT-GGACATTTTGCCCCTT
          1 GAACTTCAATCTTGGGACATTTTGCCCCTT

                      *       *         
        172 GAACTTCAATTTTGGGACGTTTTGCCCC
          1 GAACTTCAATCTTGGGACATTTTGCCCC

        200 CTCAACCTAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  29   12  0.48
  30   13  0.52

ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37


Consensus pattern (30 bp):   
GAACTTCAATCTTGGGACATTTTGCCCCTT

Found at i:197 original size:30 final size:29

Alignment explanation


    Indices: 128--200  Score: 92
    Period size: 29  Copynumber: 2.5  Consensus size: 29

        118 GTAGCATTTA

                    *                    
        128 GACGTTTTACCCCCCGAACTTCAATCTTG
          1 GACGTTTTGCCCCCCGAACTTCAATCTTG

               *         **          *    
        157 GACATTTTGCCCCTTGAACTTCAATTTTGG
          1 GACGTTTTGCCCCCCGAACTTCAATCTT-G

                          
        187 GACGTTTTGCCCCC
          1 GACGTTTTGCCCCC

        201 TCAACCTAAC


Statistics
Matches: 36,  Mismatches: 7, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  29   23  0.64
  30   13  0.36

ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34


Consensus pattern (29 bp):   
GACGTTTTGCCCCCCGAACTTCAATCTTG

Found at i:451 original size:29 final size:30

Alignment explanation


    Indices: 393--469  Score: 102
    Period size: 29  Copynumber: 2.6  Consensus size: 30

        383 CGGAACCGTT

                 *      *                 
        393 AAGTTGAGGGGGTAAAACGTCCCAAAATTG
          1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG

                             *       *    
        423 AAGTTCAGGGGGCAAAATGT-CCAAGATTG
          1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG

                  *           
        452 AAGTTCGGGGGGCAAAAC
          1 AAGTTCAGGGGGCAAAAC

        470 ATCTAAACGC


Statistics
Matches: 41,  Mismatches: 6, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  29   24  0.59
  30   17  0.41

ACGTcount: A:0.35, C:0.14, G:0.32, T:0.18


Consensus pattern (30 bp):   
AAGTTCAGGGGGCAAAACGTCCCAAAATTG

Found at i:3640 original size:2 final size:2

Alignment explanation


    Indices: 3633--3714  Score: 155
    Period size: 2  Copynumber: 40.5  Consensus size: 2

       3623 ATAAATTAAA

                                                                          
       3633 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                                                       
       3675 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG ACG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG A


Statistics
Matches: 79,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
   2   77  0.97
   3    2  0.03

ACGTcount: A:0.50, C:0.01, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.