Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013783.1 Corchorus capsularis cultivar CVL-1 contig13804, 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: 6047
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:1681 original size:293 final size:293

Alignment explanation


    Indices: 1140--1725  Score: 1039
    Period size: 293  Copynumber: 2.0  Consensus size: 293

       1130 AGTTGACAGG

                         *                                                   
       1140 TTTACACCCAAATTGATTTCTTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCATC
          1 TTTACACCCAAATCGATTTCTTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCATC

                         *                                                   
       1205 TTGTAGAGTCCTAGCAAGCAACTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGATCTTGA
         66 TTGTAGAGTCCTAACAAGCAACTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGATCTTGA

                                                              *              
       1270 GAATTCAATTGCAGGTCTAATTGAGTGCTCAAGGCCGACGAAAGAGGAGGGATAGCTTTGTGAAG
        131 GAATTCAATTGCAGGTCTAATTGAGTGCTCAAGGCCGACGAAAGAGGAGGAATAGCTTTGTGAAG

                  *              *                                       *   
       1335 GTCATCGACATACAAGTCTAGGAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCAAATGGT
        196 GTCATCAACATACAAGTCTAGAAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCAAAGGGT

                      *                      
       1400 GGATTTCAATCTAATACAACTAGATTCGTATCA
        261 GGATTTCAATATAATACAACTAGATTCGTATCA

                *     *                                                      
       1433 TTTATACCCATATCGATTTCTTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCATC
          1 TTTACACCCAAATCGATTTCTTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCATC

                                 *                                           
       1498 TTGTAGAGTCCTAACAAGCAATTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGATCTTGA
         66 TTGTAGAGTCCTAACAAGCAACTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGATCTTGA

                                         *        *                          
       1563 GAATTCAATTGCAGGTCTAATTGAGTGCTTAAGGCCGATGAAAGAGGAGGAATAGGC-TTGTGAA
        131 GAATTCAATTGCAGGTCTAATTGAGTGCTCAAGGCCGACGAAAGAGGAGGAATA-GCTTTGTGAA

                                                                             
       1627 GGTCATCAACATACAAGTCTAGAAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCAAAGGG
        195 GGTCATCAACATACAAGTCTAGAAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCAAAGGG

                   *                          
       1692 TGGATTTGAATATAATACAACTAGATTCGTATCA
        260 TGGATTTCAATATAATACAACTAGATTCGTATCA

       1726 CCTTATATTT


Statistics
Matches: 279,  Mismatches: 13, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
 293  277  0.99
 294    2  0.01

ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33


Consensus pattern (293 bp):   
TTTACACCCAAATCGATTTCTTTGGCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCATC
TTGTAGAGTCCTAACAAGCAACTAGGTTGAGATAACTTAGTTGTTTGTGAATCTTGTGATCTTGA
GAATTCAATTGCAGGTCTAATTGAGTGCTCAAGGCCGACGAAAGAGGAGGAATAGCTTTGTGAAG
GTCATCAACATACAAGTCTAGAAGTTGAAGAAGTTCAAGTCGACTTTGGTGGATATTCAAAGGGT
GGATTTCAATATAATACAACTAGATTCGTATCA

Found at i:4388 original size:33 final size:33

Alignment explanation


    Indices: 4346--4424  Score: 149
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       4336 AATCGAGGGT

                                           * 
       4346 CGGTTGTGGCCGGTTGGTGCGCCAAGCAATGGC
          1 CGGTTGTGGCCGGTTGGTGCGCCAAGCAATGCC

                                             
       4379 CGGTTGTGGCCGGTTGGTGCGCCAAGCAATGCC
          1 CGGTTGTGGCCGGTTGGTGCGCCAAGCAATGCC

                         
       4412 CGGTTGTGGCCGG
          1 CGGTTGTGGCCGG

       4425 ACATGTCCAT


Statistics
Matches: 45,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  33   45  1.00

ACGTcount: A:0.10, C:0.25, G:0.43, T:0.22


Consensus pattern (33 bp):   
CGGTTGTGGCCGGTTGGTGCGCCAAGCAATGCC

Found at i:4476 original size:33 final size:33

Alignment explanation


    Indices: 4418--4514  Score: 104
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       4408 TGCCCGGTTG

                       *    *   *            
       4418 TGGCCGGACATGTCCATGTCTCGTGGCCGGTGA
          1 TGGCCGGACATCTCCAAGTCGCGTGGCCGGTGA

                           **          *    *
       4451 TGGCCGGACATCTCCGGGTCGCGTGGCTGGTGT
          1 TGGCCGGACATCTCCAAGTCGCGTGGCCGGTGA

                   * *            *        
       4484 TGGCCGGGCTTCTCCAAGTCGCATGGCCGGT
          1 TGGCCGGACATCTCCAAGTCGCGTGGCCGGT

       4515 CACTCGCGCA


Statistics
Matches: 52,  Mismatches: 12, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  33   52  1.00

ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24


Consensus pattern (33 bp):   
TGGCCGGACATCTCCAAGTCGCGTGGCCGGTGA
Done.