Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007241.1 Corchorus olitorius cultivar O-4 contig07266, 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: 1771
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:1070 original size:41 final size:41

Alignment explanation


    Indices: 1024--1155  Score: 210
    Period size: 41  Copynumber: 3.2  Consensus size: 41

       1014 CGACAGATTA

                                *   *                
       1024 AGTCGTTGCGAAATCTTAAACTTTCCGCAACGACTTTTGTT
          1 AGTCGTTGCGAAATCTTAAAGTTTTCGCAACGACTTTTGTT

                    *                      *         
       1065 AGTCGTTGTGAAATCTTAAAGTTTTCGCAACAACTTTTGTT
          1 AGTCGTTGCGAAATCTTAAAGTTTTCGCAACGACTTTTGTT

                    *    *                           
       1106 AGTCGTTGTGAAACCTTAAAGTTTTCGCAACGACTTTTGTT
          1 AGTCGTTGCGAAATCTTAAAGTTTTCGCAACGACTTTTGTT

                     
       1147 AGTCGTTGC
          1 AGTCGTTGC

       1156 TTGATATATT


Statistics
Matches: 84,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  41   84  1.00

ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39


Consensus pattern (41 bp):   
AGTCGTTGCGAAATCTTAAAGTTTTCGCAACGACTTTTGTT

Found at i:1322 original size:131 final size:131

Alignment explanation


    Indices: 1127--1505  Score: 363
    Period size: 131  Copynumber: 2.9  Consensus size: 131

       1117 AACCTTAAAG

                                           *      *          *  *            
       1127 TTTTCGCAACGACTTTTGTTAGTCGTTGCTTGATATATTTTACAAATTGGTTTTCGCAGCGACCT
          1 TTTTCGCAACGAC-TTTGTTAGTCGTTGCTTAATATATGTTACAAATTGATTCTCGCAGCGACCT

             *                        *         * *   *                      
       1192 TGAAAGTCGCTAC-AAAAA-CATAATTACTTTTGAAGCCACAGATTAAGTCGCTGCAAAATCTTA
         65 TAAAAGTCGCTACAAAAAATCATAATCACTTTTGAAACAACAAATTAAGTCGCTGCAAAATCTTA

               
       1255 CTC
        130 -TC

                *                                      *            *        
       1258 TTTTTGCAACGACTATTGTTAGTCGTTGCTTAATATATGTTACTAATTGATTCTCGTAGCGACCT
          1 TTTTCGCAACGACT-TTGTTAGTCGTTGCTTAATATATGTTACAAATTGATTCTCGCAGCGACCT

                   *                                             *  **       
       1323 TAAAAGTTGCTACAAAAAAATCATAATCACTTTTGAAACAACAAATTAAGTCGTTGTGAAATCTT
         65 TAAAAGTCGCTAC-AAAAAATCATAATCACTTTTGAAACAACAAATTAAGTCGCTGCAAAATCTT

               
       1388 ATC
        129 ATC

             *       *       *         *      *   *  *      *   * *    *     
       1391 TATTCGCAATGACTTCTCTTAGTCGTTACTTAATGTATTTTCCAAATTAATTTTTGCAGTGACAC
          1 TTTTCGCAACGACTT-TGTTAGTCGTTGCTTAATATATGTTACAAATTGATTCTCGCAGCGAC-C

              *     * *             *  *        *  *             
       1456 -TGAAAGTTGATA-AAAAAA-CATGATTACTTTTGAGACGACAAATTAAGTCG
         64 TTAAAAGTCGCTACAAAAAATCATAATCACTTTTGAAACAACAAATTAAGTCG

       1506 TTGTGAAATC


Statistics
Matches: 206,  Mismatches: 36, Indels: 13
        0.81            0.14        0.05

Matches are distributed among these distances:
 130   29  0.14
 131   73  0.35
 132    1  0.00
 133   64  0.31
 134   39  0.19

ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36


Consensus pattern (131 bp):   
TTTTCGCAACGACTTTGTTAGTCGTTGCTTAATATATGTTACAAATTGATTCTCGCAGCGACCTT
AAAAGTCGCTACAAAAAATCATAATCACTTTTGAAACAACAAATTAAGTCGCTGCAAAATCTTAT
C
Done.