Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009789.1 Corchorus olitorius cultivar O-4 contig09821, 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: 3740
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:242 original size:135 final size:134

Alignment explanation


    Indices: 1--243  Score: 450
    Period size: 135  Copynumber: 1.8  Consensus size: 134

                                                        *                    
          1 CGTCTCATCTATCCTTCCAAGTGTCTCATCTTTTGCAAGATCCTTAGGGGGTTAAGCAAGGGGCT
          1 CGTCTCATCTATCCTTCCAAGTGTCTCATCTTTTGCAAGATCCTCAGGGGGTTAAGCAAGGGGCT

               *                                                             
         66 ACTTTGTTTTTGCACCTTTGATATGACAAATGAGCCACTGTCATGTTTGCTCTTCTTCTTGTTGT
         66 ACTGTGTTTTTGCACCTTTGATATGACAAATGAGCCACTGTCATGTTTGCTCTTCTTCTTGTTGT

                
        131 TCAA
        131 TCAA

                      *                                                      
        135 CGTCTCATCTTTCCTTCCAAGTGTCTCATCTTTTGCAAGATCCTCAGGGGGTTTAAGCAAGGGGC
          1 CGTCTCATCTATCCTTCCAAGTGTCTCATCTTTTGCAAGATCCTCAGGGGG-TTAAGCAAGGGGC

                                                        
        200 TACTGTGTTTTTGCACCTTTGATATGACAAATGAGCCACTGTCA
         65 TACTGTGTTTTTGCACCTTTGATATGACAAATGAGCCACTGTCA

        244 ACTTTAACTA


Statistics
Matches: 105,  Mismatches: 3, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
 134   49  0.47
 135   56  0.53

ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37


Consensus pattern (134 bp):   
CGTCTCATCTATCCTTCCAAGTGTCTCATCTTTTGCAAGATCCTCAGGGGGTTAAGCAAGGGGCT
ACTGTGTTTTTGCACCTTTGATATGACAAATGAGCCACTGTCATGTTTGCTCTTCTTCTTGTTGT
TCAA

Found at i:696 original size:14 final size:14

Alignment explanation


    Indices: 679--708  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

        669 CAGCTGAGAT

                       *  
        679 ATCTAAATTGAGGA
          1 ATCTAAATTGAAGA

                          
        693 ATCTAAATTGAAGA
          1 ATCTAAATTGAAGA

              
        707 AT
          1 AT

        709 GCAAGAAACA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30


Consensus pattern (14 bp):   
ATCTAAATTGAAGA

Found at i:2716 original size:18 final size:19

Alignment explanation


    Indices: 2695--2738  Score: 63
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       2685 AACGACACCA

                     *         
       2695 GTAAATTCCCT-AACACGT
          1 GTAAATTCCATCAACACGT

                             * 
       2713 GTAAATTCCATCAACACTT
          1 GTAAATTCCATCAACACGT

                   
       2732 GTAAATT
          1 GTAAATT

       2739 TCTCTTCAAC


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18   10  0.43
  19   13  0.57

ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32


Consensus pattern (19 bp):   
GTAAATTCCATCAACACGT

Found at i:2749 original size:21 final size:19

Alignment explanation


    Indices: 2689--2756  Score: 66
    Period size: 18  Copynumber: 3.5  Consensus size: 19

       2679 GAAAATAACG

                 *         *   
       2689 ACACCAGTAAATTCCCT-A
          1 ACACCTGTAAATTCCATCA

                *              
       2707 ACACGTGTAAATTCCATCA
          1 ACACCTGTAAATTCCATCA

                *            *   
       2726 ACACTTGTAAATTTCTCTTCA
          1 ACACCTGTAAA-TTC-CATCA

                      
       2747 ACACCTGTAA
          1 ACACCTGTAA

       2757 CTCCCCACTG


Statistics
Matches: 41,  Mismatches: 6, Indels: 3
        0.82            0.12        0.06

Matches are distributed among these distances:
  18   14  0.34
  19   11  0.27
  20    3  0.07
  21   13  0.32

ACGTcount: A:0.35, C:0.28, G:0.07, T:0.29


Consensus pattern (19 bp):   
ACACCTGTAAATTCCATCA

Found at i:3145 original size:8 final size:8

Alignment explanation


    Indices: 3132--3172  Score: 82
    Period size: 8  Copynumber: 5.1  Consensus size: 8

       3122 TACATACTAT

                    
       3132 TGTTTAGA
          1 TGTTTAGA

                    
       3140 TGTTTAGA
          1 TGTTTAGA

                    
       3148 TGTTTAGA
          1 TGTTTAGA

                    
       3156 TGTTTAGA
          1 TGTTTAGA

                    
       3164 TGTTTAGA
          1 TGTTTAGA

             
       3172 T
          1 T

       3173 ATATATATAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   33  1.00

ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51


Consensus pattern (8 bp):   
TGTTTAGA

Found at i:3178 original size:2 final size:2

Alignment explanation


    Indices: 3171--3227  Score: 55
    Period size: 2  Copynumber: 29.5  Consensus size: 2

       3161 AGATGTTTAG

                                       *  *                 *        *    
       3171 AT AT AT AT AT AT AT AT AT GT TT AT AT AT A- AT TT AT AT GT -T
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

            *                        
       3211 TT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT A

       3228 ATTTAGTATG


Statistics
Matches: 46,  Mismatches: 7, Indels: 4
        0.81            0.12        0.07

Matches are distributed among these distances:
   1    2  0.04
   2   44  0.96

ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54


Consensus pattern (2 bp):   
AT

Done.