Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007423.1 Corchorus capsularis cultivar CVL-1 contig07444, 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: 10341
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:1121 original size:17 final size:17

Alignment explanation


    Indices: 1096--1132  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       1086 TGTTTGGTTG

                      *      
       1096 GAGGAGTAGGGAGGGGT
          1 GAGGAGTAGGAAGGGGT

                *            
       1113 GAGGGGTAGGAAGGGGT
          1 GAGGAGTAGGAAGGGGT

               
       1130 GAG
          1 GAG

       1133 CTCCACCCCT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.24, C:0.00, G:0.65, T:0.11


Consensus pattern (17 bp):   
GAGGAGTAGGAAGGGGT

Found at i:1395 original size:15 final size:16

Alignment explanation


    Indices: 1365--1407  Score: 50
    Period size: 18  Copynumber: 2.6  Consensus size: 16

       1355 CTTTGATACA

                  *           
       1365 ATATTTATAATAATAATT
          1 ATATTTTTAATAAT--TT

              *             
       1383 ATTTTTTTAATAATTT
          1 ATATTTTTAATAATTT

                     
       1399 ATATTTTTA
          1 ATATTTTTA

       1408 TTTCTTTCTC


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  16   10  0.45
  18   12  0.55

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (16 bp):   
ATATTTTTAATAATTT

Found at i:1866 original size:15 final size:15

Alignment explanation


    Indices: 1831--1881  Score: 66
    Period size: 15  Copynumber: 3.4  Consensus size: 15

       1821 TTTCTAAAAT

                     *   * 
       1831 CCCTCCCAAACCCTC
          1 CCCTCCCAACCCCAC

             *             
       1846 CTCTCCCAACCCCAC
          1 CCCTCCCAACCCCAC

                   *       
       1861 CCCTCCCCACCCCAC
          1 CCCTCCCAACCCCAC

                  
       1876 CCCTCC
          1 CCCTCC

       1882 TTTAGTTGAA


Statistics
Matches: 31,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  15   31  1.00

ACGTcount: A:0.16, C:0.73, G:0.00, T:0.12


Consensus pattern (15 bp):   
CCCTCCCAACCCCAC

Found at i:5073 original size:67 final size:67

Alignment explanation


    Indices: 4963--5094  Score: 212
    Period size: 67  Copynumber: 2.0  Consensus size: 67

       4953 TGCTTGAAAC

                                                  *          * *      *      
       4963 GCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGCTTCTACCATTTTTTCCT
          1 GCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAAGTAATGGTGCTCCCACCATTATTTCCT

              
       5028 AT
         66 AT

                                                                             
       5030 GCATTGTCTTTATATGTAATTTTAGCA-TTGAGATGTAAGTAATGGTGCTCCCACCATTATTTCC
          1 GCATTGTCTTTATATGTAATTTTAGCATTTG-GATGTAAGTAATGGTGCTCCCACCATTATTTCC

             
       5094 T
         65 T

       5095 TAGTTGTTAT


Statistics
Matches: 60,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  66    3  0.05
  67   57  0.95

ACGTcount: A:0.23, C:0.15, G:0.16, T:0.45


Consensus pattern (67 bp):   
GCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAAGTAATGGTGCTCCCACCATTATTTCCT
AT

Found at i:7849 original size:11 final size:11

Alignment explanation


    Indices: 7806--7843  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       7796 TTCCTATATA

                *      
       7806 AAATAAATTAT
          1 AAATTAATTAT

                        
       7817 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
       7828 AAATTAATTAT
          1 AAATTAATTAT

                 
       7839 AAATT
          1 AAATT

       7844 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

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


Consensus pattern (11 bp):   
AAATTAATTAT
Done.