Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008885.1 Corchorus capsularis cultivar CVL-1 contig08906, 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: 10681
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:884 original size:15 final size:16

Alignment explanation


    Indices: 864--897  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        854 GATTGCTTTC

                         *  
        864 TTAGTTA-ATTTACTT
          1 TTAGTTAGATTTAATT

                            
        879 TTAGTTAGATTTAATT
          1 TTAGTTAGATTTAATT

               
        895 TTA
          1 TTA

        898 ATTCTTCTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59


Consensus pattern (16 bp):   
TTAGTTAGATTTAATT

Found at i:1940 original size:29 final size:28

Alignment explanation


    Indices: 1866--1940  Score: 75
    Period size: 29  Copynumber: 2.6  Consensus size: 28

       1856 AACTTGGAAA

                            *           
       1866 AAAAATAAAAAG-TAAGGAAAAATTAAC
          1 AAAAATAAAAAGATAAAGAAAAATTAAC

                *                         
       1893 AAAACTAAAAATTGA-AAAGAAAAA-TAAC
          1 AAAAATAAAAA--GATAAAGAAAAATTAAC

                                
       1921 GAAAAATATAAAAGATAAAG
          1 -AAAAATA-AAAAGATAAAG

       1941 GTAAGAAATT


Statistics
Matches: 39,  Mismatches: 3, Indels: 10
        0.75            0.06        0.19

Matches are distributed among these distances:
  27   10  0.26
  28    6  0.15
  29   19  0.49
  30    4  0.10

ACGTcount: A:0.71, C:0.04, G:0.11, T:0.15


Consensus pattern (28 bp):   
AAAAATAAAAAGATAAAGAAAAATTAAC

Found at i:3598 original size:20 final size:21

Alignment explanation


    Indices: 3573--3625  Score: 63
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       3563 ACTAGCGCTG

                               * 
       3573 GGCG-CCCATGTGATTTGCTT
          1 GGCGACCCATGTGATTTGCCT

                *        *       
       3593 GGCGCCCCATGTGGTTTGCCT
          1 GGCGACCCATGTGATTTGCCT

            *           
       3614 CGCGACCCATGT
          1 GGCGACCCATGT

       3626 ATTCCAGTGC


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  20    4  0.14
  21   24  0.86

ACGTcount: A:0.09, C:0.32, G:0.30, T:0.28


Consensus pattern (21 bp):   
GGCGACCCATGTGATTTGCCT

Found at i:4835 original size:38 final size:37

Alignment explanation


    Indices: 4775--4870  Score: 122
    Period size: 38  Copynumber: 2.6  Consensus size: 37

       4765 ATCTAAGACC

                 *      *    *                   
       4775 AAATAGGACGTTGGAAATAAAGACAAAAAACAAAATT
          1 AAATAAGACGTTCGAAACAAAGACAAAAAACAAAATT

                                          *        
       4812 AAATACA-ACGATTCGAAACAAAGACAAAAGACAAAATT
          1 AAATA-AGACG-TTCGAAACAAAGACAAAAAACAAAATT

                        *        
       4850 AAATAAGACGTTGGAAACAAA
          1 AAATAAGACGTTCGAAACAAA

       4871 AGGCCAAATT


Statistics
Matches: 51,  Mismatches: 5, Indels: 6
        0.82            0.08        0.10

Matches are distributed among these distances:
  37   19  0.37
  38   32  0.63

ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15


Consensus pattern (37 bp):   
AAATAAGACGTTCGAAACAAAGACAAAAAACAAAATT

Found at i:5119 original size:24 final size:24

Alignment explanation


    Indices: 5091--5138  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5081 TTATATATAA

                                    
       5091 TATATAGTATAGATTATAAATTCG
          1 TATATAGTATAGATTATAAATTCG

                                    
       5115 TATATAGTATAGATTATAAATTCG
          1 TATATAGTATAGATTATAAATTCG

       5139 ACTAAAGTTC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42


Consensus pattern (24 bp):   
TATATAGTATAGATTATAAATTCG
Done.