Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009308.1 Corchorus capsularis cultivar CVL-1 contig09329, 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: 24733
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:6006 original size:12 final size:13

Alignment explanation


    Indices: 5989--6021  Score: 50
    Period size: 12  Copynumber: 2.5  Consensus size: 13

       5979 ATAAAGGGCC

                         
       5989 AAAATTAA-TAAT
          1 AAAATTAATTAAT

                         
       6001 AAAATTAATTAAT
          1 AAAATTAATTAAT

                    
       6014 AATAATTA
          1 AA-AATTA

       6022 TTTTGGAAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12    8  0.42
  13    6  0.32
  14    5  0.26

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (13 bp):   
AAAATTAATTAAT

Found at i:6941 original size:156 final size:156

Alignment explanation


    Indices: 6563--6933  Score: 412
    Period size: 156  Copynumber: 2.4  Consensus size: 156

       6553 TCATCTCAAA

                   * *             *           *              *    **       *
       6563 CAGACTTCGTATGAAAAACTTATACTAGTTTTTCAGTTAAGGACAATTTGGGGTGTCAAACCTAC
          1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAAACCTAG

               * *    *      *                             *      *          
       6628 TTCTCTATGCTAGAGAGGTCGGTTTTACTTAGAATTTTTGCCATAGCTTCATGGGGATAATCTAA
         66 TTCACCATGCAAGAGAGCTCGGTTTTACTTAGAATTTTTGCCATAGCCTCATGGAGATAATCTAA

                                       
       6693 GTCTACTGGTGGAAAATCAACTTCATT
        131 GTCTACTGGT-GAAAATCAACTTCATT

             *  *                                            *    *          
       6720 -GGAGTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAA-TTCAGGGAGAGAAACCTA
          1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGA-GGTGAGAAACCTA

                           *                *        *                   * * 
       6783 GTTCACCAT-CAAGGGGAGCTCGGTTTTACTTGGAATTTTTTCCATAGCCTCATGGAGATAGTGT
         65 GTTCACCATGCAA-GAGAGCTCGGTTTTACTTAGAATTTTTGCCATAGCCTCATGGAGATAATCT

                  *            *   *       
       6847 AAGTC-CCTTGGT-AAAGTTTCAGC-TCATT
        129 AAGTCTAC-TGGTGAAA--ATCAACTTCATT

                                                                       
       6875 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAA
          1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAA

       6934 GTCTAGTTTA


Statistics
Matches: 177,  Mismatches: 30, Indels: 15
        0.80            0.14        0.07

Matches are distributed among these distances:
 154    3  0.02
 155   10  0.06
 156  161  0.91
 157    3  0.02

ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33


Consensus pattern (156 bp):   
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAAACCTAG
TTCACCATGCAAGAGAGCTCGGTTTTACTTAGAATTTTTGCCATAGCCTCATGGAGATAATCTAA
GTCTACTGGTGAAAATCAACTTCATT

Found at i:11487 original size:19 final size:20

Alignment explanation


    Indices: 11445--11487  Score: 52
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      11435 AAAAAAGAGA

                               *
      11445 AAAAAAAAAAGAAAAGCCTT
          1 AAAAAAAAAAGAAAAGCCTG

                    *  *        
      11465 AAAAAAAAGAGTAAAG-CTG
          1 AAAAAAAAAAGAAAAGCCTG

                
      11484 AAAA
          1 AAAA

      11488 CGAAATATAT


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  19    6  0.30
  20   14  0.70

ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09


Consensus pattern (20 bp):   
AAAAAAAAAAGAAAAGCCTG

Found at i:18183 original size:3 final size:3

Alignment explanation


    Indices: 18175--18204  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

      18165 ATCTTAAGTT

                              *                    
      18175 ATG ATG ATG ATG ATT ATG ATG ATG ATG ATG
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG

      18205 TGTCCGATTC


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37


Consensus pattern (3 bp):   
ATG

Found at i:18193 original size:15 final size:15

Alignment explanation


    Indices: 18173--18203  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      18163 TAATCTTAAG

                           
      18173 TTATGATGATGATGA
          1 TTATGATGATGATGA

                           
      18188 TTATGATGATGATGA
          1 TTATGATGATGATGA

             
      18203 T
          1 T

      18204 GTGTCCGATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42


Consensus pattern (15 bp):   
TTATGATGATGATGA

Found at i:20635 original size:2 final size:2

Alignment explanation


    Indices: 20628--20652  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      20618 TTCTTTCATT

                                                 
      20628 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

      20653 GTTGGGTTTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.