Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020329.1 Corchorus olitorius cultivar O-4 contig20362, 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: 3467
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32


Found at i:1435 original size:136 final size:136

Alignment explanation


    Indices: 1186--1682  Score: 682
    Period size: 136  Copynumber: 3.7  Consensus size: 136

       1176 TAATTTTATC

                *           *          *                             *       
       1186 TTCACAGAATCTAACCCTATCTCAATCTAACCGTTGGATTAAAAGTGAGATTCAAATATGACCGT
          1 TTCATAGAATCTAACCTTATCTCAATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGT

                                                                             
       1251 TAATTTGAATCGTTATCTCTTCCACACAATATCCAAGATATGTCAGAAAATCTAACACAATAGCC
         66 TAATTTGAATCGTTATCTCTTCCACACAATATCCAAGATATGTCAGAAAATCTAACACAATAGCC

                  
       1316 AATAAT
        131 AATAAT

                                                                             
       1322 TTCATAGAATCTAACCTTATCTCATAT-CAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCG
          1 TTCATAGAATCTAACCTTATCTCA-ATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCG

                                                                             
       1386 TTAATTTGAATCGTTATCTCTTCCACACAATATCCAAGATATGTCAGAAAATCTAACACAATAGC
         65 TTAATTTGAATCGTTATCTCTTCCACACAATATCCAAGATATGTCAGAAAATCTAACACAATAGC

                   
       1451 CAATAAT
        130 CAATAAT

                *                 *                                          
       1458 TTCAAAGAATCTAACCTTATCTTAATCCAACCGTTGGA-TAAAAGTTG-GATTCAAATGTGACCG
          1 TTCATAGAATCTAACCTTATCTCAATCCAACCGTTGGATTAAAAG-TGAGATTCAAATGTGACCG

              *  ***  *                                   *     *        *  *
       1521 TTGATGAAAAAC-TTATCTCTTCCACACAATATCCAAGATATGTCAAAAAATATAACACAACAGT
         65 TTAATTTGAATCGTTATCTCTTCCACACAATATCCAAGATATGTCAGAAAATCTAACACAATAGC

                   
       1585 CAATAA-
        130 CAATAAT

            *       *   *   **                        *           *          
       1591 ATCGATGATAATTTAATATTATCTCAATCCAACCGTTGGATTCAAAGTGAGATTGAAATGTGACC
          1 TTC-AT-AGAATCTAACCTTATCTCAATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACC

                *        *    * *       
       1656 GTT-GTTTGAATCCTTATATGTTCCACA
         64 GTTAATTTGAATCGTTATCTCTTCCACA

       1683 AATTGTGCCT


Statistics
Matches: 322,  Mismatches: 31, Indels: 16
        0.87            0.08        0.04

Matches are distributed among these distances:
 133    2  0.01
 134   55  0.17
 135   65  0.20
 136  198  0.61
 137    2  0.01

ACGTcount: A:0.38, C:0.20, G:0.12, T:0.31


Consensus pattern (136 bp):   
TTCATAGAATCTAACCTTATCTCAATCCAACCGTTGGATTAAAAGTGAGATTCAAATGTGACCGT
TAATTTGAATCGTTATCTCTTCCACACAATATCCAAGATATGTCAGAAAATCTAACACAATAGCC
AATAAT

Found at i:3049 original size:21 final size:21

Alignment explanation


    Indices: 3008--3083  Score: 116
    Period size: 21  Copynumber: 3.5  Consensus size: 21

       2998 TTTTAAATTT

                          *       *
       3008 ATTTAAGTTGTAATTTTAACTTT
          1 ATTTAAGTTGT--TATTAACTTA

                                 
       3031 ATTTAAGTTGTTATTAACTTA
          1 ATTTAAGTTGTTATTAACTTA

                                 
       3052 ATTTAAGTTGTTATTAACTTA
          1 ATTTAAGTTGTTATTAACTTA

                       
       3073 ATTTAAGTTGT
          1 ATTTAAGTTGT

       3084 AATTTTAAGT


Statistics
Matches: 51,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
  21   40  0.78
  23   11  0.22

ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54


Consensus pattern (21 bp):   
ATTTAAGTTGTTATTAACTTA

Found at i:3096 original size:23 final size:21

Alignment explanation


    Indices: 2997--3083  Score: 111
    Period size: 21  Copynumber: 4.0  Consensus size: 21

       2987 TTTATTTTGT

                   *  *          
       2997 TTTTTAAATTTATTTAAGTTG
          1 TTTTTAACTTAATTTAAGTTG

                        *          
       3018 TAATTTTAACTTTATTTAAGTTG
          1 T--TTTTAACTTAATTTAAGTTG

              *                  
       3041 TTATTAACTTAATTTAAGTTG
          1 TTTTTAACTTAATTTAAGTTG

              *                  
       3062 TTATTAACTTAATTTAAGTTG
          1 TTTTTAACTTAATTTAAGTTG

             
       3083 T
          1 T

       3084 AATTTTAAGT


Statistics
Matches: 61,  Mismatches: 3, Indels: 4
        0.90            0.04        0.06

Matches are distributed among these distances:
  21   41  0.67
  23   20  0.33

ACGTcount: A:0.31, C:0.03, G:0.09, T:0.56


Consensus pattern (21 bp):   
TTTTTAACTTAATTTAAGTTG

Found at i:3276 original size:12 final size:12

Alignment explanation


    Indices: 3259--3303  Score: 54
    Period size: 12  Copynumber: 3.6  Consensus size: 12

       3249 ATTATTCAAT

                        
       3259 ATATAAATGTAA
          1 ATATAAATGTAA

                    **  
       3271 ATATAAATCAAA
          1 ATATAAATGTAA

                          
       3283 ATATAAATTGTGAA
          1 ATATAAA-TGT-AA

                   
       3297 ATATAAA
          1 ATATAAA

       3304 AAAGGATTAT


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  12   17  0.63
  13    1  0.04
  14    9  0.33

ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31


Consensus pattern (12 bp):   
ATATAAATGTAA
Done.