Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019307.1 Corchorus olitorius cultivar O-4 contig19340, 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: 4955
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33


Found at i:500 original size:25 final size:24

Alignment explanation


    Indices: 464--510  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

        454 TCCTTCTATT

                                    
        464 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
        487 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

        511 AATTTTCTAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Found at i:1267 original size:15 final size:15

Alignment explanation


    Indices: 1247--1278  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1237 CCTTGGGGGT

                           
       1247 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

                           
       1262 TCAAAATCAACAAGC
          1 TCAAAATCAACAAGC

              
       1277 TC
          1 TC

       1279 CACTTAGTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16


Consensus pattern (15 bp):   
TCAAAATCAACAAGC

Found at i:1946 original size:66 final size:66

Alignment explanation


    Indices: 1864--1990  Score: 175
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       1854 AGTGATTCTG

                 *    *                                                      
       1864 AACCTGATTTGAGTGTTGTTTGCAATGACA-TGAAATCTGTTTTAGATGTTGTTAGTGATGATAC
          1 AACCTAATTTAAGTGTTGTTTGCAATGACACT-AAATCTGTTTTAGATGTTGTTAGTGATGATAC

              
       1928 TA
         65 TA

                                  **            *        *       *       
       1930 AACCTAATTTAAGTGTTGTTTGTGATGACACTAAATTTGTTTTAGGTGTTGTTTGTGATGA
          1 AACCTAATTTAAGTGTTGTTTGCAATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGA

       1991 AACAAATTCT


Statistics
Matches: 53,  Mismatches: 7, Indels: 2
        0.85            0.11        0.03

Matches are distributed among these distances:
  66   52  0.98
  67    1  0.02

ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43


Consensus pattern (66 bp):   
AACCTAATTTAAGTGTTGTTTGCAATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGATACT
A

Found at i:1979 original size:33 final size:33

Alignment explanation


    Indices: 1876--2005  Score: 129
    Period size: 33  Copynumber: 3.9  Consensus size: 33

       1866 CCTGATTTGA

                      **                      
       1876 GTGTTGTTTGCAATGACA-TGAAATCTGTTTTAG
          1 GTGTTGTTTGTGATGACACT-AAATCTGTTTTAG

            *       *       *      *  **    *
       1909 ATGTTGTTAGTGATGATACTAAACCTAATTTAA
          1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

                                    *        
       1942 GTGTTGTTTGTGATGACACTAAATTTGTTTTAG
          1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

                            *               
       1975 GTGTTGTTTGTGATGAAAC-AAATTCTGTTTT
          1 GTGTTGTTTGTGATGACACTAAA-TCTGTTTT

       2006 GGATGCTAAT


Statistics
Matches: 76,  Mismatches: 19, Indels: 4
        0.77            0.19        0.04

Matches are distributed among these distances:
  32    3  0.04
  33   72  0.95
  34    1  0.01

ACGTcount: A:0.26, C:0.08, G:0.22, T:0.45


Consensus pattern (33 bp):   
GTGTTGTTTGTGATGACACTAAATCTGTTTTAG

Found at i:3791 original size:21 final size:21

Alignment explanation


    Indices: 3765--3814  Score: 75
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3755 TGCTAGGAGA

                                  
       3765 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                           *     
       3786 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       3807 TCATTGGA
          1 TCATTGGA

       3815 ATTGCCTAAG


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  20    2  0.07
  21   25  0.93

ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:4913 original size:154 final size:154

Alignment explanation


    Indices: 4633--4955  Score: 549
    Period size: 154  Copynumber: 2.1  Consensus size: 154

       4623 AGATTCGTAT

                                                       *                     
       4633 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCACTGAGGTTTGCCAAATCGAAGA
          1 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAGA

                        **   *                                               
       4698 CGATTCGAAACGTCACTGATGGGCCACGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAA
         66 CGATTCGAAACGGAACTAATGGGCCACGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAA

                                    
       4763 AACATCACAGTGGACTAATCTCAA
        131 AACATCACAGTGGACTAATCTCAA

                                                          *                  
       4787 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGGGGTTTGCCAAATCGAAGA
          1 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAGA

                                      *                    *                 
       4852 CGATTC-AAGACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
         66 CGATTCGAA-ACGGAACTAATGGGCCACGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAA

                *                   *
       4916 AAACTTCACAGTGGACTAATCTCAC
        130 AAACATCACAGTGGACTAATCTCAA

                           
       4941 CAAAATGATTATAGT
          1 CAAAATGATTATAGT


Statistics
Matches: 159,  Mismatches: 9, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
 153    2  0.01
 154  157  0.99

ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20


Consensus pattern (154 bp):   
CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAGA
CGATTCGAAACGGAACTAATGGGCCACGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAA
AACATCACAGTGGACTAATCTCAA
Done.