Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024730.1 Corchorus olitorius cultivar O-4 contig24763, 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: 17974
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:669 original size:16 final size:16

Alignment explanation


    Indices: 648--683  Score: 72
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        638 CCAGCAACAA

                            
        648 CAGCTATGTTTGTCAG
          1 CAGCTATGTTTGTCAG

                            
        664 CAGCTATGTTTGTCAG
          1 CAGCTATGTTTGTCAG

                
        680 CAGC
          1 CAGC

        684 AAGCTTGATA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   20  1.00

ACGTcount: A:0.19, C:0.22, G:0.25, T:0.33


Consensus pattern (16 bp):   
CAGCTATGTTTGTCAG

Found at i:2575 original size:23 final size:22

Alignment explanation


    Indices: 2549--2600  Score: 61
    Period size: 23  Copynumber: 2.3  Consensus size: 22

       2539 CTAATTAACG

                                    
       2549 AATGTTA-ATTAATTGTTAATGTT
          1 AATGTTAGATTAA-T-TTAATGTT

                                   
       2572 AATGTTAGGATTAATTTAATGTT
          1 AATGTTA-GATTAATTTAATGTT

             *    
       2595 ATTGTT
          1 AATGTT

       2601 TCAAAATTTG


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  23   20  0.77
  24    1  0.04
  25    5  0.19

ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52


Consensus pattern (22 bp):   
AATGTTAGATTAATTTAATGTT

Found at i:5101 original size:32 final size:32

Alignment explanation


    Indices: 5053--5147  Score: 111
    Period size: 32  Copynumber: 3.0  Consensus size: 32

       5043 TGATTGAGGA

                   *   *     *               
       5053 CAAAATTTCAACTCATTTAATGCAAAT-AAGGC
          1 CAAAATTCCAATTCATTAAATGCAAATCAA-GC

                                 *          
       5085 CAAAATTCCAATTCATTAAATACAAATCAAGC
          1 CAAAATTCCAATTCATTAAATGCAAATCAAGC

                   *    *             *    
       5117 CAAAATTGCAATCCATTAAATGCAAAACAAG
          1 CAAAATTCCAATTCATTAAATGCAAATCAAG

       5148 ATAAAATTAC


Statistics
Matches: 54,  Mismatches: 8, Indels: 2
        0.84            0.12        0.03

Matches are distributed among these distances:
  32   52  0.96
  33    2  0.04

ACGTcount: A:0.48, C:0.20, G:0.07, T:0.24


Consensus pattern (32 bp):   
CAAAATTCCAATTCATTAAATGCAAATCAAGC

Found at i:5154 original size:32 final size:32

Alignment explanation


    Indices: 5051--5183  Score: 94
    Period size: 32  Copynumber: 4.2  Consensus size: 32

       5041 ATTGATTGAG

                     *          *            *
       5051 GACAAAATTTCAA-CTCATTTAATGCAAATA-AG
          1 GACAAAATTACAATC-CATTAAATGCAAA-ACAA

             *       *    *        *    *   
       5083 GCCAAAATTCCAATTCATTAAATACAAATCAA
          1 GACAAAATTACAATCCATTAAATGCAAAACAA

             *       *                      
       5115 GCCAAAATTGCAATCCATTAAATGCAAAACAA
          1 GACAAAATTACAATCCATTAAATGCAAAACAA

              *          *                   
       5147 GATAAAATTACAACCCATT-AATCGCAAAA-AA
          1 GACAAAATTACAATCCATTAAAT-GCAAAACAA

             *    
       5178 GCCAAA
          1 GACAAA

       5184 TTTGCAACGG


Statistics
Matches: 81,  Mismatches: 17, Indels: 7
        0.77            0.16        0.07

Matches are distributed among these distances:
  31    9  0.11
  32   72  0.89

ACGTcount: A:0.50, C:0.20, G:0.08, T:0.22


Consensus pattern (32 bp):   
GACAAAATTACAATCCATTAAATGCAAAACAA

Found at i:12109 original size:15 final size:15

Alignment explanation


    Indices: 12089--12118  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      12079 AGAAAACTAA

                     *     
      12089 CAACCTGTTTGAAAC
          1 CAACCTGTTGGAAAC

                           
      12104 CAACCTGTTGGAAAC
          1 CAACCTGTTGGAAAC

      12119 AGAGATAATA


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23


Consensus pattern (15 bp):   
CAACCTGTTGGAAAC

Found at i:17497 original size:32 final size:32

Alignment explanation


    Indices: 17456--17516  Score: 106
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      17446 TGTAAAACTT

                                             
      17456 TTGAATCGACTATTATA-CCTTTATTTTTCTAA
          1 TTGAATCGACTATTATATCC-TTATTTTTCTAA

                                         
      17488 TTGAATCGACTATTATATCCTTATTTTTC
          1 TTGAATCGACTATTATATCCTTATTTTTC

      17517 AAACATATTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  32   26  0.93
  33    2  0.07

ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51


Consensus pattern (32 bp):   
TTGAATCGACTATTATATCCTTATTTTTCTAA
Done.