Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015795.1 Corchorus capsularis cultivar CVL-1 contig15816, 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: 8577
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34


Found at i:542 original size:29 final size:29

Alignment explanation


    Indices: 500--559  Score: 120
    Period size: 29  Copynumber: 2.1  Consensus size: 29

        490 GCGTGCTAGC

                                         
        500 GTGAGCATGCTAAATTAAGCTAGTAACTA
          1 GTGAGCATGCTAAATTAAGCTAGTAACTA

                                         
        529 GTGAGCATGCTAAATTAAGCTAGTAACTA
          1 GTGAGCATGCTAAATTAAGCTAGTAACTA

              
        558 GT
          1 GT

        560 AATGAATTAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28


Consensus pattern (29 bp):   
GTGAGCATGCTAAATTAAGCTAGTAACTA

Found at i:3917 original size:34 final size:34

Alignment explanation


    Indices: 3878--3943  Score: 96
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       3868 TGAAAGCAAC

                               *              
       3878 TGAAGAAAGACCGCCCTGGGTCAATTGAAATTAT
          1 TGAAGAAAGACCGCCCTGGATCAATTGAAATTAT

                  *     *  *                
       3912 TGAAGAGAGACCTCCTTGGATCAATTGAAATT
          1 TGAAGAAAGACCGCCCTGGATCAATTGAAATT

       3944 TACTGAATGG


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  34   28  1.00

ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26


Consensus pattern (34 bp):   
TGAAGAAAGACCGCCCTGGATCAATTGAAATTAT

Found at i:5635 original size:17 final size:16

Alignment explanation


    Indices: 5613--5646  Score: 50
    Period size: 17  Copynumber: 2.1  Consensus size: 16

       5603 TCAAAAACCA

                   *         
       5613 TTTTTGAGAAATCATTT
          1 TTTTTGAAAAATC-TTT

                            
       5630 TTTTTGAAAAATCTTT
          1 TTTTTGAAAAATCTTT

             
       5646 T
          1 T

       5647 AAAATAATAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    4  0.25
  17   12  0.75

ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56


Consensus pattern (16 bp):   
TTTTTGAAAAATCTTT

Found at i:7384 original size:19 final size:18

Alignment explanation


    Indices: 7360--7395  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7350 TGAAGATTTC

                               
       7360 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       7379 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       7396 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.