Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021332.1 Corchorus olitorius cultivar O-4 contig21365, 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: 2275
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Found at i:22 original size:2 final size:2

Alignment explanation


    Indices: 15--41  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

          5 GTTCCAATCA

                                                    
         15 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

         42 GATACTTATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:229 original size:16 final size:16

Alignment explanation


    Indices: 204--234  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        194 GCCATGGAAC

                            
        204 AAAAAAAAAAAAGAAG
          1 AAAAAAAAAAAAGAAG

                 *         
        220 AAAAAGAAAAAAGAA
          1 AAAAAAAAAAAAGAA

        235 AACAGAAGAT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (16 bp):   
AAAAAAAAAAAAGAAG

Found at i:1121 original size:109 final size:110

Alignment explanation


    Indices: 935--1179  Score: 325
    Period size: 109  Copynumber: 2.2  Consensus size: 110

        925 CACGCCCATA

                           *     *            *        *                     
        935 ACGCCGCCATATATAATGAAGGC-GAGCCGAGGATGTTTCCTCGATTTCACTATATATGGCGGCG
          1 ACGCCGCCATATATAGTGAA-ACTGAGCCGAGGAAGTTTCCTCAATTTCACTATATATGGCGGCG

                    *              *                 *     
        999 TCTGAGCTGTGAAACGCCACTAACCTAGCGGCGTCT-CACAGCTCAG
         65 TCTGAGCTCTGAAACGCCACTAAACTAGCGGCGT-TGCACACCTCAG

                                 *                         *   *             
       1045 ACGCCGCCATATATAGTGAAATTGAGCC-AGGAAGTTTCCTCAATTTTACTCTATATGGCGGCGT
          1 ACGCCGCCATATATAGTGAAACTGAGCCGAGGAAGTTTCCTCAATTTCACTATATATGGCGGCGT

                                   *      *    *         
       1109 CTGAGCTCTGAAACGCCACTAAAGTAGCGGTGTTGTACACCTCAG
         66 CTGAGCTCTGAAACGCCACTAAACTAGCGGCGTTGCACACCTCAG

                             *        
       1154 ACGCCGCCATATATAGTAAAACTGAG
          1 ACGCCGCCATATATAGTGAAACTGAG

       1180 GAAACTTCCT


Statistics
Matches: 118,  Mismatches: 15, Indels: 5
        0.86            0.11        0.04

Matches are distributed among these distances:
 108    1  0.01
 109   93  0.79
 110   24  0.20

ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24


Consensus pattern (110 bp):   
ACGCCGCCATATATAGTGAAACTGAGCCGAGGAAGTTTCCTCAATTTCACTATATATGGCGGCGT
CTGAGCTCTGAAACGCCACTAAACTAGCGGCGTTGCACACCTCAG

Found at i:1355 original size:32 final size:32

Alignment explanation


    Indices: 1311--1409  Score: 137
    Period size: 32  Copynumber: 3.1  Consensus size: 32

       1301 TTAGAAATTA

                   *            *   *        
       1311 TATATAGCGGCG-TTTCGTTTAGTGGACGCCGC
          1 TATATAGGGGCGTTTTC-TTCAGTAGACGCCGC

               *                            
       1343 TATGTAGGGGCGTTTTCTTCAGTAGACGCCGC
          1 TATATAGGGGCGTTTTCTTCAGTAGACGCCGC

              *                             
       1375 TAAATAGGGGCGTTTTCTTCAGTAGACGCCGC
          1 TATATAGGGGCGTTTTCTTCAGTAGACGCCGC

               
       1407 TAT
          1 TAT

       1410 TTTTCCAGCA


Statistics
Matches: 59,  Mismatches: 7, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  32   55  0.93
  33    4  0.07

ACGTcount: A:0.18, C:0.21, G:0.29, T:0.31


Consensus pattern (32 bp):   
TATATAGGGGCGTTTTCTTCAGTAGACGCCGC
Done.