Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013055.1 Corchorus olitorius cultivar O-4 contig13088, 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: 7178
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:1722 original size:2 final size:2

Alignment explanation


    Indices: 1715--1744  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1705 AGTTATAGAT

                                             *          
       1715 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1745 ATTCCCATCA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:4821 original size:124 final size:126

Alignment explanation


    Indices: 4511--4829  Score: 459
    Period size: 126  Copynumber: 2.5  Consensus size: 126

       4501 CCCCATGCAA

                                                                 **   *      
       4511 ATGGAAC-CAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACGCACTACATATT
          1 ATGGAACTC-GTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCATATT

                                                                          
       4575 TATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATACATAGCATCTCACTCTATAT
         65 TATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATACATAGCATCTCACTCTATAT

                 *  * *                             *     *                  
       4637 ATGGAGCTAGGGTTTGTCGAAACTTTTCCTAACATATGTCATTATAGACGACATACTGCATATTT
          1 ATGGAACTCGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCATATTT

                                                                           
       4702 ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCA-A-A-A-CATCTCACTCTGTATAT
         66 ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATACATAGCATCTCACTC--TATAT

                         *   *                *              *     *         
       4761 ATGGAACTCGTGTGTGTTGAAACTTTTCCTAACACATGTCGTTATAAACAACATATTGCATATTT
          1 ATGGAACTCGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCATATTT

                
       4826 ATCT
         66 ATCT

       4830 TACACCTACT


Statistics
Matches: 172,  Mismatches: 18, Indels: 8
        0.87            0.09        0.04

Matches are distributed among these distances:
 122   10  0.06
 123    1  0.01
 124   65  0.38
 125    1  0.01
 126   95  0.55

ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36


Consensus pattern (126 bp):   
ATGGAACTCGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCATATTT
ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATACATAGCATCTCACTCTATAT

Found at i:6018 original size:10 final size:10

Alignment explanation


    Indices: 6003--6041  Score: 78
    Period size: 10  Copynumber: 3.9  Consensus size: 10

       5993 GGAAAATTCC

                      
       6003 CAAATAAAAT
          1 CAAATAAAAT

                      
       6013 CAAATAAAAT
          1 CAAATAAAAT

                      
       6023 CAAATAAAAT
          1 CAAATAAAAT

                     
       6033 CAAATAAAA
          1 CAAATAAAA

       6042 AACGAGGGAG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   29  1.00

ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18


Consensus pattern (10 bp):   
CAAATAAAAT

Found at i:6315 original size:54 final size:56

Alignment explanation


    Indices: 6248--6354  Score: 157
    Period size: 54  Copynumber: 1.9  Consensus size: 56

       6238 TGATAACTTG

                    *       *                                        
       6248 GATCATCATCAACAACTAGCAGCTGAT-C-CTGGTCAG-CAAGAGGCAGCAAGGGAC
          1 GATCATCAACAACAACCAGCAGCTGATCCACTGGTC-GCCAAGAGGCAGCAAGGGAC

                                                                 
       6302 GATCATCAACAACAACCAGCAGCTGATCCAGCTGGTCGCCAAGAGGCAGCAAG
          1 GATCATCAACAACAACCAGCAGCTGATCCA-CTGGTCGCCAAGAGGCAGCAAG

       6355 TGAACTGCCA


Statistics
Matches: 47,  Mismatches: 2, Indels: 5
        0.87            0.04        0.09

Matches are distributed among these distances:
  54   25  0.53
  55    1  0.02
  56    1  0.02
  57   20  0.43

ACGTcount: A:0.34, C:0.28, G:0.25, T:0.13


Consensus pattern (56 bp):   
GATCATCAACAACAACCAGCAGCTGATCCACTGGTCGCCAAGAGGCAGCAAGGGAC
Done.