Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000860.1 Corchorus olitorius cultivar O-4 contig00860, 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, 693

Length: 1155
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37


Found at i:998 original size:22 final size:22

Alignment explanation


    Indices: 947--999  Score: 54
    Period size: 22  Copynumber: 2.4  Consensus size: 22

        937 TAACCTCCCT

                    *          *  
        947 TATGAAATCTTAGTAATCACAC
          1 TATGAAATTTTAGTAATCAAAC

             * *                   
        969 TGTTAAATTTT-GATAATCAAAC
          1 TATGAAATTTTAG-TAATCAAAC

                     
        991 TATGAAATT
          1 TATGAAATT

       1000 GTAATGACCT


Statistics
Matches: 24,  Mismatches: 6, Indels: 2
        0.75            0.19        0.06

Matches are distributed among these distances:
  21    1  0.04
  22   23  0.96

ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38


Consensus pattern (22 bp):   
TATGAAATTTTAGTAATCAAAC

Found at i:1047 original size:23 final size:23

Alignment explanation


    Indices: 1017--1095  Score: 108
    Period size: 22  Copynumber: 3.5  Consensus size: 23

       1007 CCTCAGTATG

                          * *      
       1017 AAATTTTGATAAACATTCATATA
          1 AAATTTTGATAAACCTCCATATA

                                   
       1040 AAATTTTGATAAACCTCCA-ATA
          1 AAATTTTGATAAACCTCCATATA

                              *   *
       1062 AAATTTTGAT-AACCTCCTTATG
          1 AAATTTTGATAAACCTCCATATA

                        
       1084 AAATTTTGATAA
          1 AAATTTTGATAA

       1096 TAAAAAATTT


Statistics
Matches: 50,  Mismatches: 4, Indels: 4
        0.86            0.07        0.07

Matches are distributed among these distances:
  21    7  0.14
  22   25  0.50
  23   18  0.36

ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38


Consensus pattern (23 bp):   
AAATTTTGATAAACCTCCATATA

Found at i:1095 original size:44 final size:38

Alignment explanation


    Indices: 1017--1116  Score: 101
    Period size: 38  Copynumber: 2.4  Consensus size: 38

       1007 CCTCAGTATG

                          * *                            
       1017 AAATTTTGATAAACATTCATATAAAATTTTGATAAACCTCCAATA
          1 AAATTTTGAT-AACCTCCATATAAAATTTTGAT-AA--T--AA-A

                             *   *                
       1062 AAATTTTGATAACCTCCTTATGAAATTTTGATAATAAA
          1 AAATTTTGATAACCTCCATATAAAATTTTGATAATAAA

                             
       1100 AAATTTTGATAACCTCC
          1 AAATTTTGATAACCTCC

       1117 CAATGATTTT


Statistics
Matches: 51,  Mismatches: 4, Indels: 7
        0.82            0.06        0.11

Matches are distributed among these distances:
  38   18  0.35
  39    2  0.04
  41    1  0.02
  43    2  0.04
  44   18  0.35
  45   10  0.20

ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37


Consensus pattern (38 bp):   
AAATTTTGATAACCTCCATATAAAATTTTGATAATAAA

Found at i:1133 original size:60 final size:60

Alignment explanation


    Indices: 1039--1151  Score: 149
    Period size: 60  Copynumber: 1.9  Consensus size: 60

       1029 ACATTCATAT

                                                   *                    
       1039 AAAATTTTGATAAACCTCCAATAAAATTTTGATAACCTCCTTATGAAATTTTGATAATAA
          1 AAAATTTTGATAAACCTCCAATAAAATTTTGATAACCTCATTATGAAATTTTGATAATAA

                                    * *           * *              
       1099 AAAATTTTGAT-AACCTCCCAAT-GATTTTTCGATAACTTTATTATGAAATTTTG
          1 AAAATTTTGATAAACCT-CCAATAAAATTTT-GATAACCTCATTATGAAATTTTG

       1152 TTAA


Statistics
Matches: 46,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  59   10  0.22
  60   36  0.78

ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40


Consensus pattern (60 bp):   
AAAATTTTGATAAACCTCCAATAAAATTTTGATAACCTCATTATGAAATTTTGATAATAA
Done.