Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011451.1 Corchorus olitorius cultivar O-4 contig11484, 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: 9923
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:1282 original size:32 final size:32

Alignment explanation


    Indices: 1177--1283  Score: 99
    Period size: 32  Copynumber: 3.3  Consensus size: 32

       1167 ACAACTTCTG

                       *                    
       1177 GTGTCAATTGAGTAAAATTATGACATCTTCAA
          1 GTGTCAATTGAATAAAATTATGACATCTTCAA

                 *          **  *      *    **
       1209 GTGTCTATTGGAA-ATTTATCATGACAACTTCTG
          1 GTGTCAATT-GAATA-AAATTATGACATCTTCAA

               *                            
       1242 GTGCCAATTGAATAAAATTATGACATCTTCAA
          1 GTGTCAATTGAATAAAATTATGACATCTTCAA

            *         
       1274 ATGTCAATTG
          1 GTGTCAATTG

       1284 CAAGATCATG


Statistics
Matches: 54,  Mismatches: 18, Indels: 6
        0.69            0.23        0.08

Matches are distributed among these distances:
  32   32  0.59
  33   22  0.41

ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36


Consensus pattern (32 bp):   
GTGTCAATTGAATAAAATTATGACATCTTCAA

Found at i:1570 original size:36 final size:30

Alignment explanation


    Indices: 1131--1671  Score: 596
    Period size: 30  Copynumber: 17.6  Consensus size: 30

       1121 GAAAGGTAAA

                         *                
       1131 ATCATGACAACTTTTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                 *                      *  *
       1161 ATCATAACAACTTCTGGTGTCAATTGAGTAAA
          1 ATCATGACAACTTCTGGTGTCAATT--GCAAG

              *      *    **     *     *    *
       1193 ATTATGACATCTTCAAGTGTCTATTGGAAATTT
          1 ATCATGACAACTTCTGGTGTCAATT-GCAA--G

                               *        *  *
       1226 ATCATGACAACTTCTGGTGCCAATTGAATAAA
          1 ATCATGACAACTTCTGGTGTCAATTG--CAAG

              *      *    ***             
       1258 ATTATGACATCTTCAAATGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                     *                   *
       1288 ATCATGACAGCTTCTGGTGTCAATTGCAAC
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                   *      *              *
       1318 ATCATGAAAACTTCGGGTGTCAATTGCAAC
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                     *                    
       1348 ATCATGACAGCTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *              *             
       1378 ACCATGACAACTTCTGATGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

            **                            
       1408 GCCATGACAACTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

            **                            
       1438 GCCATGACAACTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

            **                            
       1468 GCCATGACAACTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

            **                            
       1498 GCCATGACAACTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *     *                            
       1528 ACCATGAAAACTTCTGGTGTCAATAGACATAGCAAG
          1 ATCATGACAACTTCTGGTGTCAAT-----T-GCAAG

                              *           
       1564 ATCATGACAACTTCTGGTTTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                                          
       1594 ATCATGACAACTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                          *           *   
       1624 ATCATGACAACTTCCGGTGTCAATTGTAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                      *       
       1654 ATCATGACAATTTCTGGT
          1 ATCATGACAACTTCTGGT

       1672 ATCATTTAGA


Statistics
Matches: 442,  Mismatches: 57, Indels: 24
        0.85            0.11        0.05

Matches are distributed among these distances:
  30  347  0.79
  31    4  0.01
  32   43  0.10
  33   19  0.04
  34    2  0.00
  35    1  0.00
  36   26  0.06

ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Consensus pattern (30 bp):   
ATCATGACAACTTCTGGTGTCAATTGCAAG

Found at i:9897 original size:25 final size:24

Alignment explanation


    Indices: 9864--9920  Score: 80
    Period size: 25  Copynumber: 2.4  Consensus size: 24

       9854 GTGGATTGTA

                        *            
       9864 AAATAAATTGAATAATTAAGACATT
          1 AAATAAATTGAAGAATTAA-ACATT

                     *              
       9889 AAATAAATTTAAGAATTAAACATT
          1 AAATAAATTGAAGAATTAAACATT

                     
       9913 AAA-AAATT
          1 AAATAAATT

       9921 CAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    5  0.17
  24    8  0.27
  25   17  0.57

ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32


Consensus pattern (24 bp):   
AAATAAATTGAAGAATTAAACATT
Done.