Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004759.1 Corchorus capsularis cultivar CVL-1 contig04777, 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: 7534
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26


Found at i:2831 original size:35 final size:35

Alignment explanation


    Indices: 2785--2913  Score: 154
    Period size: 35  Copynumber: 3.7  Consensus size: 35

       2775 ATTTCATCAG

                 *                             
       2785 ATTCAGCACTTGGGGACTCCAACAACCTCTTCCTC
          1 ATTCAACACTTGGGGACTCCAACAACCTCTTCCTC

                                               
       2820 ATTCAACACTTGGGGACTCCAACAACC-CTTCCTC
          1 ATTCAACACTTGGGGACTCCAACAACCTCTTCCTC

                    *  *  *      *           *  
       2854 ATTCAACAGTTAGGTACTCCAGCAA-CTCATTCTTC
          1 ATTCAACACTTGGGGACTCCAACAACCTC-TTCCTC

                  *        *  *      
       2889 ATTCAATACTTGGGGGCTTCAACAA
          1 ATTCAACACTTGGGGACTCCAACAA

       2914 TGAAAATTTC


Statistics
Matches: 79,  Mismatches: 13, Indels: 4
        0.82            0.14        0.04

Matches are distributed among these distances:
  33    1  0.01
  34   29  0.37
  35   49  0.62

ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27


Consensus pattern (35 bp):   
ATTCAACACTTGGGGACTCCAACAACCTCTTCCTC

Found at i:3424 original size:71 final size:72

Alignment explanation


    Indices: 3261--3535  Score: 369
    Period size: 72  Copynumber: 3.8  Consensus size: 72

       3251 CACATGGTCT

                 *                                        *               *  
       3261 TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTGAC
          1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC

                 * 
       3326 ATGATCA
         66 ATGATAA

               *      *                      *                              *
       3333 TC-ACCTTCACTGCGATTGTAGCCGAGGCAGTTTCCACATTT-GCAGTCCTTCGCACAATCCTTC
          1 TCTTCC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA

                    
       3396 CATGATAA
         65 CATGATAA

                           *                                 *               
       3404 TCTTCCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCTTTCGCACAATCCTTA
          1 TCTTCC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA

            **    * 
       3468 TGTGATTA
         65 CATGATAA

             *                                              *            
       3476 TTTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCTTTCGCACAATCC
          1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCC

       3536 ATGCTACTAC


Statistics
Matches: 179,  Mismatches: 20, Indels: 9
        0.86            0.10        0.04

Matches are distributed among these distances:
  71   82  0.46
  72   97  0.54

ACGTcount: A:0.20, C:0.29, G:0.19, T:0.31


Consensus pattern (72 bp):   
TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
ATGATAA

Found at i:3521 original size:143 final size:143

Alignment explanation


    Indices: 3269--3535  Score: 401
    Period size: 143  Copynumber: 1.9  Consensus size: 143

       3259 CTTCTTCTTC

                                                                             
       3269 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTGACATGATCAT
          1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTGACATGATCAT

                                           *       *                         
       3334 CACCTTCACTGCGATTGTAGCCGAGGCAGTTTCCACATTTGCAGTCCTTCGCACAATCCTTCCAT
         66 CACCTTCACTGCGATTGTAGCCGAGGCAGTTCCCACATTGGCAGTCCTTCGCACAATCCTTCCAT

                         
       3399 GATAATCTTCCAT
        131 GATAATCTTCCAT

                  *                               * *             * **    *  
       3412 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCTTTCGCACAATCCTTATGTGATTAT
          1 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTGACATGATCA-

             **      *                                     *            
       3477 TTTCC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTGGCAGTCTTTCGCACAATCC
         65 TCACCTTCACTGCGATTGTAGCCGAGGCAGTTCCCACATTGGCAGTCCTTCGCACAATCC

       3536 ATGCTACTAC


Statistics
Matches: 110,  Mismatches: 13, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
 143  107  0.97
 144    3  0.03

ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30


Consensus pattern (143 bp):   
ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTGACATGATCAT
CACCTTCACTGCGATTGTAGCCGAGGCAGTTCCCACATTGGCAGTCCTTCGCACAATCCTTCCAT
GATAATCTTCCAT

Found at i:4207 original size:16 final size:16

Alignment explanation


    Indices: 4186--4216  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       4176 AACGGAAGGT

                    *       
       4186 TACCGCAGTAGAATGG
          1 TACCGCAGCAGAATGG

                           
       4202 TACCGCAGCAGAATG
          1 TACCGCAGCAGAATG

       4217 TCGCCGCATT


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

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16


Consensus pattern (16 bp):   
TACCGCAGCAGAATGG
Done.