Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008024.1 Corchorus capsularis cultivar CVL-1 contig08045, 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: 8900
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31


Found at i:2191 original size:88 final size:88

Alignment explanation


    Indices: 2042--2221  Score: 324
    Period size: 88  Copynumber: 2.0  Consensus size: 88

       2032 TCGACACAAG

                   *                                                         
       2042 AATTTATTTACGTTTGGCCAAAAGTTCCTGAGCTAACCCTAAAAAGGGTGAACTCAACCCTTTTC
          1 AATTTATGTACGTTTGGCCAAAAGTTCCTGAGCTAACCCTAAAAAGGGTGAACTCAACCCTTTTC

                                   
       2107 AGGTTAACTCAGGAAATTTTCAA
         66 AGGTTAACTCAGGAAATTTTCAA

                               *              *                              
       2130 AATTTATGTACGTTTGGCCCAAAGTTCCTGAGCTGACCCTAAAAAGGGTGAACTCAACCCTTTTC
          1 AATTTATGTACGTTTGGCCAAAAGTTCCTGAGCTAACCCTAAAAAGGGTGAACTCAACCCTTTTC

                          *        
       2195 AGGTTAACTCAGGAGATTTTCAA
         66 AGGTTAACTCAGGAAATTTTCAA

                
       2218 AATT
          1 AATT

       2222 AACCATTTTC


Statistics
Matches: 88,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  88   88  1.00

ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31


Consensus pattern (88 bp):   
AATTTATGTACGTTTGGCCAAAAGTTCCTGAGCTAACCCTAAAAAGGGTGAACTCAACCCTTTTC
AGGTTAACTCAGGAAATTTTCAA

Found at i:2259 original size:5 final size:5

Alignment explanation


    Indices: 2249--2274  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

       2239 AAAATCTTAA

                                           
       2249 TTTTC TTTTC TTTTC TTTTC TTTTC T
          1 TTTTC TTTTC TTTTC TTTTC TTTTC T

       2275 ACCCTAATTC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81


Consensus pattern (5 bp):   
TTTTC

Found at i:3295 original size:33 final size:33

Alignment explanation


    Indices: 3258--3364  Score: 135
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       3248 CGCCTAGCGA

                                 *    *      
       3258 TGGCCGGTTATGGCCGGACATGTCCATGTCGCG
          1 TGGCCGGTTATGGCCGGACATCTCCAAGTCGCG

                    *        *               
       3291 TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCG
          1 TGGCCGGTTATGGCCGGACATCTCCAAGTCGCG

                                *            *
       3324 TGGCCGGTGT-TGGCCGGACTTCTCCAAGTCGCA
          1 TGGCCGGT-TATGGCCGGACATCTCCAAGTCGCG

               *    
       3357 TGGTCGGT
          1 TGGCCGGT

       3365 CACTAGTGCT


Statistics
Matches: 64,  Mismatches: 9, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  33   64  1.00

ACGTcount: A:0.11, C:0.28, G:0.37, T:0.23


Consensus pattern (33 bp):   
TGGCCGGTTATGGCCGGACATCTCCAAGTCGCG

Found at i:4358 original size:16 final size:16

Alignment explanation


    Indices: 4337--4376  Score: 80
    Period size: 16  Copynumber: 2.5  Consensus size: 16

       4327 CCTAACACAA

                            
       4337 AGTCCATGCTAATATG
          1 AGTCCATGCTAATATG

                            
       4353 AGTCCATGCTAATATG
          1 AGTCCATGCTAATATG

                    
       4369 AGTCCATG
          1 AGTCCATG

       4377 GTTCATGAGG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   24  1.00

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


Consensus pattern (16 bp):   
AGTCCATGCTAATATG

Found at i:8723 original size:5 final size:5

Alignment explanation


    Indices: 8713--8746  Score: 59
    Period size: 5  Copynumber: 6.6  Consensus size: 5

       8703 TGGTCGAAAA

                                                    
       8713 TTTAT TTTAT TTTAT TTTAT TTTAT TTATAT TTT
          1 TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT TTT

       8747 TCGATATAAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   5   23  0.82
   6    5  0.18

ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79


Consensus pattern (5 bp):   
TTTAT

Done.