Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006791.1 Corchorus capsularis cultivar CVL-1 contig06812, 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: 23576
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:699 original size:33 final size:33

Alignment explanation


    Indices: 631--700  Score: 88
    Period size: 33  Copynumber: 2.1  Consensus size: 33

        621 GTGGGTTGCA

                          * *        *    *  
        631 CGCGGATTGCGACCTATCATGGTGCCAGTCGCG
          1 CGCGGATTGCGACCGACCATGGTGCAAGTCACG

                                              
        664 CGCGGATTGCGACCGACCATGGTG-AAGGTCACG
          1 CGCGGATTGCGACCGACCATGGTGCAA-GTCACG

                
        697 CGCG
          1 CGCG

        701 ACCCGCGCCC


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  32    1  0.03
  33   31  0.97

ACGTcount: A:0.17, C:0.30, G:0.36, T:0.17


Consensus pattern (33 bp):   
CGCGGATTGCGACCGACCATGGTGCAAGTCACG

Found at i:1477 original size:11 final size:11

Alignment explanation


    Indices: 1461--1485  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       1451 AGCTACTACT

                       
       1461 AATTGATCATA
          1 AATTGATCATA

                       
       1472 AATTGATCATA
          1 AATTGATCATA

               
       1483 AAT
          1 AAT

       1486 CCAGTCAGAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36


Consensus pattern (11 bp):   
AATTGATCATA

Found at i:12726 original size:16 final size:15

Alignment explanation


    Indices: 12689--12727  Score: 51
    Period size: 16  Copynumber: 2.5  Consensus size: 15

      12679 AGGAAAATGA

                           
      12689 GAAGGAAAGAAATAG
          1 GAAGGAAAGAAATAG

            *           *   
      12704 TAAGGAAAGGAAGTAG
          1 GAAGGAAA-GAAATAG

                    
      12720 GAAGGAAA
          1 GAAGGAAA

      12728 TATGAGTTTC


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  15    7  0.35
  16   13  0.65

ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08


Consensus pattern (15 bp):   
GAAGGAAAGAAATAG

Found at i:14051 original size:31 final size:31

Alignment explanation


    Indices: 14013--14071  Score: 100
    Period size: 31  Copynumber: 1.9  Consensus size: 31

      14003 GAAATATATT

                             *             
      14013 TTTTTTTAAAAAAGGTATAATCGAAAAAATA
          1 TTTTTTTAAAAAAGGTACAATCGAAAAAATA

                                   *    
      14044 TTTTTTTAAAAAAGGTACAATCGGAAAA
          1 TTTTTTTAAAAAAGGTACAATCGAAAAA

      14072 TATAAAGTTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   26  1.00

ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34


Consensus pattern (31 bp):   
TTTTTTTAAAAAAGGTACAATCGAAAAAATA

Found at i:19700 original size:2 final size:2

Alignment explanation


    Indices: 19693--19742  Score: 84
    Period size: 2  Copynumber: 25.5  Consensus size: 2

      19683 ATTTCAAGAG

                                                                          
      19693 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

               *         
      19734 AT TT AT AT A
          1 AT AT AT AT A

      19743 CTGTATGGCA


Statistics
Matches: 45,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   44  0.98

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


Consensus pattern (2 bp):   
AT

Found at i:20853 original size:6 final size:6

Alignment explanation


    Indices: 20842--20868  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      20832 TGATTTATAC

                                           
      20842 AAAGTA AAAGTA AAAGTA AAAGTA AAA
          1 AAAGTA AAAGTA AAAGTA AAAGTA AAA

      20869 CCAACATGCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15


Consensus pattern (6 bp):   
AAAGTA

Found at i:21498 original size:96 final size:92

Alignment explanation


    Indices: 21378--21548  Score: 227
    Period size: 96  Copynumber: 1.8  Consensus size: 92

      21368 ACTATTGTAG

                     *                *                   *         *        
      21378 TTTTATTCTGCTAAAAACTCTATTTTTATTCAATTATTAAATCTAATATCTTTATAGTT-TCTTT
          1 TTTTATTCTACTAAAAACTCTATTTTCATTCAATTA--AAATC-AACAT-TTTATAATTAT-TTT

                                            
      21442 ATTTTTACCATTTTACTATTTTTCATATACAA
         61 ATTTTTACCATTTTACTATTTTTCATATACAA

                               *          *       *                          
      21474 TTTTATTCTACTAAAAACTTTATTTTCATTTAATTAAATTCAACATTTTATAATTATTTTATTTT
          1 TTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAAATCAACATTTTATAATTATTTTATTTT

                      
      21539 TACCATTTTA
         66 TACCATTTTA

      21549 ATTTAAAAGG


Statistics
Matches: 67,  Mismatches: 7, Indels: 6
        0.84            0.09        0.08

Matches are distributed among these distances:
  92   26  0.39
  93    5  0.07
  94    4  0.06
  96   32  0.48

ACGTcount: A:0.32, C:0.12, G:0.01, T:0.55


Consensus pattern (92 bp):   
TTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAAATCAACATTTTATAATTATTTTATTTT
TACCATTTTACTATTTTTCATATACAA
Done.