Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015492.1 Corchorus capsularis cultivar CVL-1 contig15513, 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: 17786
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30


Found at i:1119 original size:27 final size:28

Alignment explanation


    Indices: 1090--1149  Score: 75
    Period size: 33  Copynumber: 2.0  Consensus size: 28

       1080 TGGCCACAAG

                                             
       1090 ACCGGCCACGCGACATGGACATGTCCGACCATC
          1 ACCGGCCACGCGACATGGACATGTCCG-----C

                                       
       1123 ACCGGCCACGCGACATGGACATGTCCG
          1 ACCGGCCACGCGACATGGACATGTCCG

       1150 GCTACAACCG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   27  1.00

ACGTcount: A:0.23, C:0.38, G:0.27, T:0.12


Consensus pattern (28 bp):   
ACCGGCCACGCGACATGGACATGTCCGC

Found at i:2123 original size:9 final size:8

Alignment explanation


    Indices: 2103--2136  Score: 59
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       2093 CACCTTCTTG

                    
       2103 AAAAATTC
          1 AAAAATTC

                    
       2111 AAAAATTC
          1 AAAAATTC

                     
       2119 AAAAACTTC
          1 AAAAA-TTC

                    
       2128 AAAAATTC
          1 AAAAATTC

             
       2136 A
          1 A

       2137 TACCCAATTC


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

Matches are distributed among these distances:
   8   17  0.68
   9    8  0.32

ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24


Consensus pattern (8 bp):   
AAAAATTC

Found at i:2128 original size:17 final size:16

Alignment explanation


    Indices: 2103--2136  Score: 59
    Period size: 17  Copynumber: 2.1  Consensus size: 16

       2093 CACCTTCTTG

                            
       2103 AAAAATTCAAAAATTC
          1 AAAAATTCAAAAATTC

                             
       2119 AAAAACTTCAAAAATTC
          1 AAAAA-TTCAAAAATTC

             
       2136 A
          1 A

       2137 TACCCAATTC


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    5  0.29
  17   12  0.71

ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24


Consensus pattern (16 bp):   
AAAAATTCAAAAATTC

Found at i:9586 original size:25 final size:25

Alignment explanation


    Indices: 9552--9702  Score: 178
    Period size: 25  Copynumber: 5.7  Consensus size: 25

       9542 TATAAGTAGC

                           *         
       9552 GGCGTCTAGACGCCGGTAAAATAGT
          1 GGCGTCTAGACGCCGCTAAAATAGT

                                      
       9577 GGCGTCTAGACGCC-CTAAAAATAGT
          1 GGCGTCTAGACGCCGCT-AAAATAGT

                       *        *    
       9602 GGCGTCTAGACACCGCTAAAGTAGT
          1 GGCGTCTAGACGCCGCTAAAATAGT

                   *                 
       9627 GGCGTCTTGACGCCGCTAAAATAGT
          1 GGCGTCTAGACGCCGCTAAAATAGT

                                             
       9652 GGCGTCCTGAAGTCCTAACGCCGCTAAAATAGT
          1 GGCGT-CT--AG-----ACGCCGCTAAAATAGT

                              
       9685 GGCGTCTAGACGCCGCTA
          1 GGCGTCTAGACGCCGCTA

       9703 TATGCAAATT


Statistics
Matches: 109,  Mismatches: 7, Indels: 20
        0.80            0.05        0.15

Matches are distributed among these distances:
  24    1  0.01
  25   78  0.72
  26    4  0.04
  28    1  0.01
  30    2  0.02
  32    2  0.02
  33   21  0.19

ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21


Consensus pattern (25 bp):   
GGCGTCTAGACGCCGCTAAAATAGT

Found at i:17174 original size:13 final size:13

Alignment explanation


    Indices: 17156--17190  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      17146 AATCTAAATC

                   *     
      17156 TAAAGCAGATTAA
          1 TAAAGCAAATTAA

                         
      17169 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
      17182 TAAAGCAAA
          1 TAAAGCAAA

      17191 CAATAATTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20


Consensus pattern (13 bp):   
TAAAGCAAATTAA
Done.