Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000014.1 Corchorus capsularis cultivar CVL-1 contig00014, 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: 19116
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:2768 original size:94 final size:95

Alignment explanation


    Indices: 2625--2813  Score: 283
    Period size: 94  Copynumber: 2.0  Consensus size: 95

       2615 AGAGTAAGAC

                              *                                              
       2625 ATCAATTTGTACGAAATGTCAGAATTTCCTTCATAAAGTTGAATTTCGTCAAAAA-ATTAAATGG
          1 ATCAATTTGTACGAAATGCCAGAATTTCCTTCATAAAGTTGAATTTCGTCAAAAATATTAAATGG

                               *           
       2689 GCTGCAG-AATGAACACTATACAAGACCAAG
         66 GCTGC-GTAATGAACACTAGACAAGACCAAG

                       *        *  *        *                                
       2719 ATCAATTTGTATGAAATGCCCGATTTTCCTTCGTAAAGTTGAATTTCGTCAAAAATATTAAATGG
          1 ATCAATTTGTACGAAATGCCAGAATTTCCTTCATAAAGTTGAATTTCGTCAAAAATATTAAATGG

                   *       *              
       2784 GCTGCGTTATGAACATTAGACAAGACCAAG
         66 GCTGCGTAATGAACACTAGACAAGACCAAG

       2814 TCCAATTATG


Statistics
Matches: 85,  Mismatches: 8, Indels: 3
        0.89            0.08        0.03

Matches are distributed among these distances:
  94   51  0.60
  95   34  0.40

ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30


Consensus pattern (95 bp):   
ATCAATTTGTACGAAATGCCAGAATTTCCTTCATAAAGTTGAATTTCGTCAAAAATATTAAATGG
GCTGCGTAATGAACACTAGACAAGACCAAG

Found at i:7193 original size:27 final size:26

Alignment explanation


    Indices: 7163--7225  Score: 72
    Period size: 28  Copynumber: 2.3  Consensus size: 26

       7153 AAAAACTATC

                          *            
       7163 TTTATATTTTTTTGGCCAAAATCTGGA
          1 TTTA-ATTTTTTTGACCAAAATCTGGA

                          * *           
       7190 TTTAAAATTTTTTTTATCAAAATCTGGA
          1 TTT--AATTTTTTTGACCAAAATCTGGA

                    
       7218 TTTAATTT
          1 TTTAATTT

       7226 ATTATCTTAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 5
        0.79            0.08        0.13

Matches are distributed among these distances:
  26    5  0.16
  27    3  0.10
  28   22  0.71
  29    1  0.03

ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52


Consensus pattern (26 bp):   
TTTAATTTTTTTGACCAAAATCTGGA

Found at i:7199 original size:28 final size:28

Alignment explanation


    Indices: 7168--7222  Score: 83
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       7158 CTATCTTTAT

                     *                  
       7168 ATTTTTTTGGCCAAAATCTGGATTTAAA
          1 ATTTTTTTGACCAAAATCTGGATTTAAA

                    * *                
       7196 ATTTTTTTTATCAAAATCTGGATTTAA
          1 ATTTTTTTGACCAAAATCTGGATTTAA

       7223 TTTATTATCT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  28   24  1.00

ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47


Consensus pattern (28 bp):   
ATTTTTTTGACCAAAATCTGGATTTAAA

Found at i:14998 original size:4 final size:4

Alignment explanation


    Indices: 14989--15015  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

      14979 TGGTTGACAC

                                             
      14989 TAAT TAAT TAAT TAAT TAAT TAAT TAA
          1 TAAT TAAT TAAT TAAT TAAT TAAT TAA

      15016 CCAAAAAGCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (4 bp):   
TAAT

Done.