Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013524.1 Corchorus olitorius cultivar O-4 contig13557, 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: 26334
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34


Found at i:2747 original size:16 final size:16

Alignment explanation


    Indices: 2726--2772  Score: 53
    Period size: 14  Copynumber: 3.0  Consensus size: 16

       2716 GTTATTTATG

                            
       2726 CTTTATTTTCAATTTC
          1 CTTTATTTTCAATTTC

                         *  
       2742 CTTTATTTT--ATGTC
          1 CTTTATTTTCAATTTC

               *             
       2756 CTTAATTTTCAAGTTTC
          1 CTTTATTTTCAA-TTTC

       2773 ATTAATAAAC


Statistics
Matches: 25,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  14   12  0.48
  16   10  0.40
  17    3  0.12

ACGTcount: A:0.19, C:0.17, G:0.04, T:0.60


Consensus pattern (16 bp):   
CTTTATTTTCAATTTC

Found at i:3066 original size:15 final size:15

Alignment explanation


    Indices: 3046--3080  Score: 61
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       3036 TAGGATAGAA

                           
       3046 AATTGTTTGTTTTTG
          1 AATTGTTTGTTTTTG

                           
       3061 AATTGTTTGTTTTTG
          1 AATTGTTTGTTTTTG

            *    
       3076 GATTG
          1 AATTG

       3081 ATTATTCCCC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63


Consensus pattern (15 bp):   
AATTGTTTGTTTTTG

Found at i:16502 original size:19 final size:18

Alignment explanation


    Indices: 16478--16513  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      16468 TGAAGATTTA

                               
      16478 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      16497 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      16514 ATAATTTCAA


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:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:17835 original size:22 final size:22

Alignment explanation


    Indices: 17793--17835  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      17783 CTTTTAATTA

                           **     
      17793 ATTGTTTTCTTTAATTTTCTTG
          1 ATTGTTTTCTTTAATAGTCTTG

                                  
      17815 ATTGTTTTC-TTAGATAGTCTT
          1 ATTGTTTTCTTTA-ATAGTCTT

      17836 AATTACTAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    3  0.17
  22   15  0.83

ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63


Consensus pattern (22 bp):   
ATTGTTTTCTTTAATAGTCTTG

Found at i:23446 original size:16 final size:17

Alignment explanation


    Indices: 23412--23446  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      23402 TGTGCATGCG

                        *    
      23412 TTGGGCCTTAGTTTCCT
          1 TTGGGCCTTAGTGTCCT

                             
      23429 TTGGGCCTTA-TGTCCT
          1 TTGGGCCTTAGTGTCCT

              
      23445 TT
          1 TT

      23447 CATTATGTAG


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

Matches are distributed among these distances:
  16    7  0.41
  17   10  0.59

ACGTcount: A:0.06, C:0.23, G:0.23, T:0.49


Consensus pattern (17 bp):   
TTGGGCCTTAGTGTCCT
Done.