Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011682.1 Corchorus capsularis cultivar CVL-1 contig11703, 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: 8136
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31


Found at i:2094 original size:32 final size:32

Alignment explanation


    Indices: 1977--2153  Score: 282
    Period size: 32  Copynumber: 5.5  Consensus size: 32

       1967 AGCCACGCGG

                *                           *
       1977 AGCCTCCCCACTAGGACGGCTCTGCCACGGCGG
          1 AGCCGCCCCACTAGGACGGCTCTGCCACGGC-T

                *                           *
       2010 AGCCTCCCCACTAGGACGGCTCTGCCACGGCGG
          1 AGCCGCCCCACTAGGACGGCTCTGCCACGGC-T

                *                           
       2043 AGCCTCCCCACTAGGACGGCTCTGCCACGGCT
          1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT

                          *                 
       2075 AGCCGCCCCACTAGTACGGCTCTGCCACGGCT
          1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT

                                            
       2107 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
          1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT

                           
       2139 AGCCGCCCCACTAGG
          1 AGCCGCCCCACTAGG

       2154 GTGGCAAGGC


Statistics
Matches: 140,  Mismatches: 4, Indels: 1
        0.97            0.03        0.01

Matches are distributed among these distances:
  32   76  0.54
  33   64  0.46

ACGTcount: A:0.16, C:0.44, G:0.28, T:0.13


Consensus pattern (32 bp):   
AGCCGCCCCACTAGGACGGCTCTGCCACGGCT

Found at i:2244 original size:33 final size:33

Alignment explanation


    Indices: 2202--2284  Score: 103
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       2192 TTGTACCGGT

                        *     *   *          
       2202 GCCGCCCCAGGGGGGCGATCTATCCATGGTAGG
          1 GCCGCCCCAGGGAGGCGACCTAGCCATGGTAGG

                             *   *          *
       2235 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
          1 GCCGCCCCAGGGAGGCGACCTAGCCATGGTAGG

                       *     
       2268 GCCGCCCCAGGAAGGCG
          1 GCCGCCCCAGGGAGGCG

       2285 GCTTGGCCAT


Statistics
Matches: 43,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  33   43  1.00

ACGTcount: A:0.14, C:0.34, G:0.41, T:0.11


Consensus pattern (33 bp):   
GCCGCCCCAGGGAGGCGACCTAGCCATGGTAGG

Found at i:2285 original size:33 final size:33

Alignment explanation


    Indices: 2225--2296  Score: 117
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       2215 GGCGATCTAT

                                 *           
       2225 CCATGGTAGGGCCGCCCCAGGGAGGCGGCCTGG
          1 CCATGGTAGGGCCGCCCCAGGAAGGCGGCCTGG

                     *                   *   
       2258 CCATGGTAGTGCCGCCCCAGGAAGGCGGCTTGG
          1 CCATGGTAGGGCCGCCCCAGGAAGGCGGCCTGG

                  
       2291 CCATGG
          1 CCATGG

       2297 CTCAGCCGCC


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  33   36  1.00

ACGTcount: A:0.14, C:0.32, G:0.42, T:0.12


Consensus pattern (33 bp):   
CCATGGTAGGGCCGCCCCAGGAAGGCGGCCTGG

Found at i:2305 original size:33 final size:32

Alignment explanation


    Indices: 2225--2311  Score: 113
    Period size: 33  Copynumber: 2.6  Consensus size: 32

       2215 GGCGATCTAT

                                 *           
       2225 CCATGGTAGGGCCGCCCCAGGGAGGCGGCCTGG
          1 CCATGGTA-GGCCGCCCCAGGAAGGCGGCCTGG

                                         *   
       2258 CCATGGTAGTGCCGCCCCAGGAAGGCGGCTTGG
          1 CCATGGTAG-GCCGCCCCAGGAAGGCGGCCTGG

                                  
       2291 CCATGGCTCA-GCCGCCCCAGG
          1 CCATGG-T-AGGCCGCCCCAGG

       2312 GGGACGGCAC


Statistics
Matches: 49,  Mismatches: 2, Indels: 6
        0.86            0.04        0.11

Matches are distributed among these distances:
  32    1  0.02
  33   46  0.94
  34    1  0.02
  35    1  0.02

ACGTcount: A:0.14, C:0.36, G:0.39, T:0.11


Consensus pattern (32 bp):   
CCATGGTAGGCCGCCCCAGGAAGGCGGCCTGG

Found at i:2453 original size:32 final size:32

Alignment explanation


    Indices: 2402--2471  Score: 79
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       2392 CCCACCGGGA

                *         *         *        
       2402 CGGCCTGCCCTGGCTAAGCCGCCCCA-TGAGGG
          1 CGGCTTGCCCTGGCGAAGCCGCCCAAGTG-GGG

                     *          *           
       2434 CGGCTTGCCGTGGCGAAGCCTCCCAAGTGGGG
          1 CGGCTTGCCCTGGCGAAGCCGCCCAAGTGGGG

                  
       2466 CGGCTT
          1 CGGCTT

       2472 CGCCACGGTA


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  32   30  0.94
  33    2  0.06

ACGTcount: A:0.11, C:0.36, G:0.37, T:0.16


Consensus pattern (32 bp):   
CGGCTTGCCCTGGCGAAGCCGCCCAAGTGGGG

Found at i:3956 original size:17 final size:17

Alignment explanation


    Indices: 3911--3957  Score: 60
    Period size: 17  Copynumber: 2.7  Consensus size: 17

       3901 AAATCAGTTC

                             
       3911 TAATTAATATTTATTAT
          1 TAATTAATATTTATTAT

              *               
       3928 TATTTCAATATTTATT-T
          1 TAATT-AATATTTATTAT

                         
       3945 TAATTGAATATTT
          1 TAATT-AATATTT

       3958 GTGATCTCTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  17   16  0.62
  18   10  0.38

ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60


Consensus pattern (17 bp):   
TAATTAATATTTATTAT
Done.