Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017201.1 Corchorus olitorius cultivar O-4 contig17234, 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: 7166
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:1462 original size:63 final size:63

Alignment explanation


    Indices: 1363--1489  Score: 245
    Period size: 63  Copynumber: 2.0  Consensus size: 63

       1353 TACTTATAAG

                    *                                                      
       1363 TTATCTTAGCAACCTCTTAAACTTTTTAATAGTCTTCTTGCCAACCTTATAAAGTTCTTTTCA
          1 TTATCTTAACAACCTCTTAAACTTTTTAATAGTCTTCTTGCCAACCTTATAAAGTTCTTTTCA

                                                                           
       1426 TTATCTTAACAACCTCTTAAACTTTTTAATAGTCTTCTTGCCAACCTTATAAAGTTCTTTTCA
          1 TTATCTTAACAACCTCTTAAACTTTTTAATAGTCTTCTTGCCAACCTTATAAAGTTCTTTTCA

             
       1489 T
          1 T

       1490 AATTTTAGAA


Statistics
Matches: 63,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  63   63  1.00

ACGTcount: A:0.28, C:0.22, G:0.06, T:0.45


Consensus pattern (63 bp):   
TTATCTTAACAACCTCTTAAACTTTTTAATAGTCTTCTTGCCAACCTTATAAAGTTCTTTTCA

Found at i:2206 original size:21 final size:20

Alignment explanation


    Indices: 2134--2208  Score: 71
    Period size: 21  Copynumber: 3.6  Consensus size: 20

       2124 AATTTATAGA

                 *      *    *  
       2134 TAAACATATAAGGTTTTAAG
          1 TAAACTTATAAGCTTTTTAG

                                 
       2154 TAAACTATATAAGCTTTTTA-
          1 TAAACT-TATAAGCTTTTTAG

            *                     
       2174 CAAACTTCATAAGCATTTTTAG
          1 TAAACTT-ATAAGC-TTTTTAG

               *         
       2196 TAATCTTATAAGC
          1 TAAACTTATAAGC

       2209 CTTATATTTT


Statistics
Matches: 45,  Mismatches: 6, Indels: 7
        0.78            0.10        0.12

Matches are distributed among these distances:
  19    1  0.02
  20   16  0.36
  21   23  0.51
  22    5  0.11

ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39


Consensus pattern (20 bp):   
TAAACTTATAAGCTTTTTAG

Found at i:4250 original size:37 final size:37

Alignment explanation


    Indices: 4201--4286  Score: 145
    Period size: 37  Copynumber: 2.3  Consensus size: 37

       4191 AATAATTTAT

                          *                *      
       4201 TAAAACTATTTTATTAAGCATTTAAATAAAATCAGTAA
          1 TAAAAC-ATTTTATAAAGCATTTAAATAAAAACAGTAA

                                                 
       4239 TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
          1 TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA

                       
       4276 TAAAACATTTT
          1 TAAAACATTTT

       4287 CCTCAACGGG


Statistics
Matches: 46,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  37   40  0.87
  38    6  0.13

ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35


Consensus pattern (37 bp):   
TAAAACATTTTATAAAGCATTTAAATAAAAACAGTAA

Found at i:5972 original size:40 final size:40

Alignment explanation


    Indices: 5912--5991  Score: 124
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       5902 AAGTAATGGC

                *                        **         
       5912 TTCCTTTTCTTAACTAAATTTTCTTAAAAGCACTTATAAA
          1 TTCCATTTCTTAACTAAATTTTCTTAAAAAAACTTATAAA

                           *                        
       5952 TTCCATTTCTTAACTGAATTTTCTTAAAAAAACTTATAAA
          1 TTCCATTTCTTAACTAAATTTTCTTAAAAAAACTTATAAA

       5992 ATAAAACAGC


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  40   36  1.00

ACGTcount: A:0.38, C:0.16, G:0.03, T:0.44


Consensus pattern (40 bp):   
TTCCATTTCTTAACTAAATTTTCTTAAAAAAACTTATAAA

Found at i:6673 original size:16 final size:16

Alignment explanation


    Indices: 6614--6677  Score: 58
    Period size: 16  Copynumber: 4.0  Consensus size: 16

       6604 GTCTGTTTGG

                            
       6614 TAGGGAGGAAA-GAAA
          1 TAGGGAGGAAAGGAAA

               ***          
       6629 TAGATTGGAAAGGAAA
          1 TAGGGAGGAAAGGAAA

              ***            
       6645 TAACAAGGGAAAGGAAA
          1 TAGGGA-GGAAAGGAAA

                            
       6662 TAGGGAGGAAAGGAAA
          1 TAGGGAGGAAAGGAAA

       6678 GGAAGTCACA


Statistics
Matches: 37,  Mismatches: 10, Indels: 3
        0.74            0.20        0.06

Matches are distributed among these distances:
  15    8  0.22
  16   16  0.43
  17   13  0.35

ACGTcount: A:0.53, C:0.02, G:0.36, T:0.09


Consensus pattern (16 bp):   
TAGGGAGGAAAGGAAA
Done.