Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023903.1 Corchorus olitorius cultivar O-4 contig23936, 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: 2282
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:1172 original size:22 final size:22

Alignment explanation


    Indices: 1144--1210  Score: 80
    Period size: 26  Copynumber: 2.9  Consensus size: 22

       1134 CATCTAGCTA

                                  
       1144 CAACATAAGCATAGTAATGTTT
          1 CAACATAAGCATAGTAATGTTT

              *                       
       1166 CATCATATTGCAGCATAGTAATGTTT
          1 CAACATA----AGCATAGTAATGTTT

                      *        
       1192 CAACATAAGCCTAGTAATG
          1 CAACATAAGCATAGTAATG

       1211 CCTACATTTC


Statistics
Matches: 38,  Mismatches: 3, Indels: 8
        0.78            0.06        0.16

Matches are distributed among these distances:
  22   17  0.45
  26   21  0.55

ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31


Consensus pattern (22 bp):   
CAACATAAGCATAGTAATGTTT

Found at i:1430 original size:50 final size:50

Alignment explanation


    Indices: 1376--1573  Score: 168
    Period size: 50  Copynumber: 3.9  Consensus size: 50

       1366 AAATTAAGGC

                     *                                         
       1376 TTTGAGTAAGAGATTGAA-CTTTTAATCAATTTGTAAATAAAGATTGGATT
          1 TTTGAGTAAAAGATTGAACCTTTTAAT-AATTTGTAAATAAAGATTGGATT

                 *            *              * *           *   
       1426 TTTGATTAAAAGA-TGAAACTTTTAAGTAATTTATGAATAAAGATTGAATT
          1 TTTGAGTAAAAGATTGAACCTTTTAA-TAATTTGTAAATAAAGATTGGATT

              **   *          *             *  *                  
       1476 TTAAAGTGAAA-ATTGAAGCTTTTAAGTAATTCGTGAATAAAGATTGGATTTTT
          1 TTTGAGTAAAAGATTGAACCTTTTAA-TAATTTGTAAATAAAGATTGGA---TT

               * *         *                       *     
       1529 TTTTATTAAAAGATTAAACCTTTTAATTAATTTGTAAATGAAGAT
          1 TTTGAGTAAAAGATTGAACCTTTTAA-TAATTTGTAAATAAAGAT

       1574 GAAATTTTTG


Statistics
Matches: 118,  Mismatches: 23, Indels: 10
        0.78            0.15        0.07

Matches are distributed among these distances:
  49    5  0.04
  50   76  0.64
  51    1  0.01
  53    9  0.08
  54   27  0.23

ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41


Consensus pattern (50 bp):   
TTTGAGTAAAAGATTGAACCTTTTAATAATTTGTAAATAAAGATTGGATT

Found at i:2208 original size:44 final size:43

Alignment explanation


    Indices: 2131--2282  Score: 150
    Period size: 44  Copynumber: 3.5  Consensus size: 43

       2121 ATTGTTTTCC

                   *          *    *   **               
       2131 CTCTTTCCAAAAATGCCCATTCCCGGTCAGAAGGTCCCTGTTTT
          1 CTCTTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCCT-TTTT

                   *                                    
       2175 CTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGT--CTTTATT
          1 CTCTTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTTT-TT

            *                                             
       2217 GTCTTTTCAAAAAAATGCCCCTTCCTGGTTGGAAGG--CCTTTATT
          1 CTC-TTTC-AAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTTT-TT

            *                     
       2261 GTCTTTTCAAAAAATGCCCCTT
          1 CTC-TTTCAAAAAATGCCCCTT


Statistics
Matches: 98,  Mismatches: 6, Indels: 9
        0.87            0.05        0.08

Matches are distributed among these distances:
  41    2  0.02
  42    6  0.06
  43   18  0.18
  44   72  0.73

ACGTcount: A:0.22, C:0.27, G:0.16, T:0.36


Consensus pattern (43 bp):   
CTCTTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTTTTT
Done.