Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010668.1 Corchorus capsularis cultivar CVL-1 contig10689, 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: 4630
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29


Found at i:798 original size:33 final size:32

Alignment explanation


    Indices: 755--878  Score: 133
    Period size: 33  Copynumber: 3.7  Consensus size: 32

        745 TAGACAAAGG

                                   *    *    
        755 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-A

                **           *     *        
        788 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCCA
          1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCA

                                               
        820 TGTCGCGTGGCCGG-TGATGGCCGGACATGTCCAA
          1 -GTCGCGTGGCCGGTTG-TGGCCGGACATGTCC-A

                                     
        854 GTCGCGTGGCCGGTCTTGTGGCCGG
          1 GTCGCGTGGCCGG--TTGTGGCCGG

        879 TGTTGCGCGG


Statistics
Matches: 76,  Mismatches: 9, Indels: 10
        0.80            0.09        0.11

Matches are distributed among these distances:
  32    3  0.04
  33   63  0.83
  34    1  0.01
  35    7  0.09
  36    2  0.03

ACGTcount: A:0.08, C:0.27, G:0.42, T:0.23


Consensus pattern (32 bp):   
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCA

Found at i:2235 original size:33 final size:33

Alignment explanation


    Indices: 2198--2294  Score: 140
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       2188 AGCGCTAGTG

                    *            *           
       2198 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                                   *       * 
       2231 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                          *    *           
       2264 ACCGGCCACGCGACATGGACATGTCCGGCCA
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCA

       2295 CGCGACATGG


Statistics
Matches: 57,  Mismatches: 7, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  33   57  1.00

ACGTcount: A:0.22, C:0.37, G:0.30, T:0.11


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

Found at i:2295 original size:23 final size:23

Alignment explanation


    Indices: 2265--2318  Score: 108
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       2255 CCGGCCATCA

                                   
       2265 CCGGCCACGCGACATGGACATGT
          1 CCGGCCACGCGACATGGACATGT

                                   
       2288 CCGGCCACGCGACATGGACATGT
          1 CCGGCCACGCGACATGGACATGT

                    
       2311 CCGGCCAC
          1 CCGGCCAC

       2319 AACCGGCCAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   31  1.00

ACGTcount: A:0.20, C:0.39, G:0.30, T:0.11


Consensus pattern (23 bp):   
CCGGCCACGCGACATGGACATGT

Found at i:2498 original size:8 final size:8

Alignment explanation


    Indices: 2485--2518  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       2475 TCTCATCTTG

                    
       2485 AAAAATTC
          1 AAAAATTC

                    
       2493 AAAAATTC
          1 AAAAATTC

                 *   
       2501 AGAAACTTC
          1 A-AAAATTC

                    
       2510 AAAAATTC
          1 AAAAATTC

             
       2518 A
          1 A

       2519 TAGCCGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC
Done.