Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009362.1 Corchorus capsularis cultivar CVL-1 contig09383, 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: 26281
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:4739 original size:45 final size:45

Alignment explanation


    Indices: 4688--4822  Score: 234
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       4678 TAATAGAGTA

                                            *            
       4688 GTGGAATTACTAAAAGATCCCTACCCCGAATTGATGATAAGCTGG
          1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG

                                                         
       4733 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
          1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG

                                      * *         *      
       4778 GTGGAATTACTAAAAGATCCCTACCCTGGATTAATGATGAGCTGG
          1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG

       4823 AGAAGTAATT


Statistics
Matches: 86,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   86  1.00

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


Consensus pattern (45 bp):   
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG

Found at i:5793 original size:45 final size:45

Alignment explanation


    Indices: 5737--5822  Score: 154
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       5727 TAATAGAATA

                                                         
       5737 GTGGAAATACTAAAAGATCCCTACCCCGAATTAATGATGAGGTGG
          1 GTGGAAATACTAAAAGATCCCTACCCCGAATTAATGATGAGGTGG

                  *                     *            
       5782 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAG
          1 GTGGAAATACTAAAAGATCCCTACCCCGAATTAATGATGAG

       5823 CTGGAGAAGT


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   39  1.00

ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23


Consensus pattern (45 bp):   
GTGGAAATACTAAAAGATCCCTACCCCGAATTAATGATGAGGTGG

Found at i:9551 original size:11 final size:11

Alignment explanation


    Indices: 9537--9574  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       9527 ATTCATAACA

                       
       9537 AATTTATAATT
          1 AATTTATAATT

                       
       9548 AATTTATAATT
          1 AATTTATAATT

                        
       9559 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
       9570 TATTT
          1 AATTT

       9575 TATATAGAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:10596 original size:2 final size:2

Alignment explanation


    Indices: 10589--10639  Score: 59
    Period size: 2  Copynumber: 25.5  Consensus size: 2

      10579 ACATGACATG

                                       *                 *     *           
      10589 AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT GT AT GT AT -T CAT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT

                         
      10631 AT AT AT AT A
          1 AT AT AT AT A

      10640 AAAACCTAAT


Statistics
Matches: 41,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
   1    1  0.02
   2   39  0.95
   3    1  0.02

ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:23615 original size:46 final size:46

Alignment explanation


    Indices: 23548--23641  Score: 179
    Period size: 46  Copynumber: 2.0  Consensus size: 46

      23538 AGTTTTAATT

                                                *         
      23548 ATGTTTCTGCATAAATCTTTGTAAGCTAACTTTTTAGACATGCAAA
          1 ATGTTTCTGCATAAATCTTTGTAAGCTAACTTTTTAAACATGCAAA

                                                          
      23594 ATGTTTCTGCATAAATCTTTGTAAGCTAACTTTTTAAACATGCAAA
          1 ATGTTTCTGCATAAATCTTTGTAAGCTAACTTTTTAAACATGCAAA

              
      23640 AT
          1 AT

      23642 TAAGAAGGTC


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  46   47  1.00

ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39


Consensus pattern (46 bp):   
ATGTTTCTGCATAAATCTTTGTAAGCTAACTTTTTAAACATGCAAA

Found at i:25222 original size:22 final size:22

Alignment explanation


    Indices: 25180--25226  Score: 60
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      25170 AATCAATTCG

                 *          *     
      25180 ATTCACATGTCAGATTGAAGTT
          1 ATTCAAATGTCAGATTAAAGTT

                                   
      25202 ATTCAAATGTCAG-TTAAAAGTT
          1 ATTCAAATGTCAGATT-AAAGTT

               
      25224 ATT
          1 ATT

      25227 GCATGATCTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21    2  0.09
  22   20  0.91

ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38


Consensus pattern (22 bp):   
ATTCAAATGTCAGATTAAAGTT
Done.