Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007561.1 Corchorus capsularis cultivar CVL-1 contig07582, 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: 15077
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1898 original size:24 final size:24

Alignment explanation


    Indices: 1823--1891  Score: 86
    Period size: 24  Copynumber: 2.9  Consensus size: 24

       1813 GATGATCCAC

                    **              
       1823 ATGATGCTATTTTAGATGCTGTTA
          1 ATGATGCTGGTTTAGATGCTGTTA

                  *            *     
       1847 ATGATGTTGGTTT-GAATGATGTTA
          1 ATGATGCTGGTTTAG-ATGCTGTTA

                                 
       1871 ATGATGCTGGTTTAGATGCTG
          1 ATGATGCTGGTTTAGATGCTG

       1892 AAAATGAGCC


Statistics
Matches: 37,  Mismatches: 6, Indels: 4
        0.79            0.13        0.09

Matches are distributed among these distances:
  23    1  0.03
  24   35  0.95
  25    1  0.03

ACGTcount: A:0.23, C:0.06, G:0.28, T:0.43


Consensus pattern (24 bp):   
ATGATGCTGGTTTAGATGCTGTTA

Found at i:4416 original size:21 final size:21

Alignment explanation


    Indices: 4392--4432  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4382 ACAGCTGAAA

                                 
       4392 CAAACCCTACAAACATGCCAG
          1 CAAACCCTACAAACATGCCAG

                    *           
       4413 CAAACCCTCCAAACATGCCA
          1 CAAACCCTACAAACATGCCA

       4433 ACAGACCTGC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.41, C:0.41, G:0.07, T:0.10


Consensus pattern (21 bp):   
CAAACCCTACAAACATGCCAG

Found at i:7262 original size:30 final size:30

Alignment explanation


    Indices: 7226--7304  Score: 151
    Period size: 30  Copynumber: 2.7  Consensus size: 30

       7216 AATAAAACGT

                                          
       7226 GCTTTATTGCCCCCTTTTTTTTTGGCCATC
          1 GCTTTATTGCCCCCTTTTTTTTTGGCCATC

                                          
       7256 GCTTTATTGCCCCCTTTTTTTTTGGCCATC
          1 GCTTTATTGCCCCCTTTTTTTTTGGCCATC

                                
       7286 GCTTTATTG-CCCCTTTTTT
          1 GCTTTATTGCCCCCTTTTTT

       7305 AAACGGTAAA


Statistics
Matches: 49,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  29   10  0.20
  30   39  0.80

ACGTcount: A:0.06, C:0.29, G:0.13, T:0.52


Consensus pattern (30 bp):   
GCTTTATTGCCCCCTTTTTTTTTGGCCATC

Found at i:12986 original size:30 final size:30

Alignment explanation


    Indices: 12952--13009  Score: 91
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      12942 ATGAAAGATA

                                           
      12952 AATTATTTTAAGAAG-CTAAAAAGAAAAAAG
          1 AATTATTTTAAGAAGTC-AAAAAGAAAAAAG

                        *               
      12982 AATTATTTTAAGGAGTCAAAAAGAAAAA
          1 AATTATTTTAAGAAGTCAAAAAGAAAAA

      13010 GTTCAACGAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  30   25  0.96
  31    1  0.04

ACGTcount: A:0.59, C:0.03, G:0.14, T:0.24


Consensus pattern (30 bp):   
AATTATTTTAAGAAGTCAAAAAGAAAAAAG

Found at i:13411 original size:73 final size:75

Alignment explanation


    Indices: 13269--13426  Score: 184
    Period size: 73  Copynumber: 2.1  Consensus size: 75

      13259 TTTATAAATC

                     *                     *                        *        
      13269 TTTA-GGGGACCAAATTATAAACTTTTCATTTTTTTTTTCAATTGGAATGCATATATATGAAAGA
          1 TTTAGGGGGGCCAAATTATAAACTTTTCA-TATTTTTTTCAATTGGAATGCATATACATGAAAGA

                        
      13333 ATTCTTGGCAA-
         65 ATTCTTGG-AAG

                                                        *                *   
      13344 TTT-GGGGGGCCAAATTATAAA-TTTTCCA-ATTTTTTTC-ATTTGAAGTGCATATACATGCAAG
          1 TTTAGGGGGGCCAAATTATAAACTTTT-CATATTTTTTTCAATTGGAA-TGCATATACATGAAAG

             *          
      13405 ATTTCTTGGAAG
         64 AATTCTTGGAAG

                      
      13417 TTTAGGGGGG
          1 TTTAGGGGGG

      13427 TCATGACCCC


Statistics
Matches: 72,  Mismatches: 6, Indels: 11
        0.81            0.07        0.12

Matches are distributed among these distances:
  72    8  0.11
  73   33  0.46
  74   10  0.14
  75   21  0.29

ACGTcount: A:0.30, C:0.11, G:0.20, T:0.40


Consensus pattern (75 bp):   
TTTAGGGGGGCCAAATTATAAACTTTTCATATTTTTTTCAATTGGAATGCATATACATGAAAGAA
TTCTTGGAAG

Found at i:14389 original size:73 final size:74

Alignment explanation


    Indices: 14261--14417  Score: 244
    Period size: 73  Copynumber: 2.1  Consensus size: 74

      14251 TTGTCTTTTC

                       *                              *                  *   
      14261 ACACTTTTCGGGTGACTAAAAAGTCCCTCTATGAGTTTCCCATATTCCTTTTCCTTCTACCCTTT
          1 ACACTTTTCGGATGACTAAAAAGTCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCATTT

                     
      14326 TTCGTAATT
         66 TTCGTAATT

                                        *            *                       
      14335 ACACTTTTCGGATGACTAAAAAGT-CCTTTATGAGTTTCCCCCATTCCTTTTCCTTCTACCATTT
          1 ACACTTTTCGGATGACTAAAAAGTCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCATTT

                     
      14399 TTCGTAATT
         66 TTCGTAATT

            *         
      14408 GCACATTTTC
          1 ACAC-TTTTC

      14418 CTTCCTTAAT


Statistics
Matches: 76,  Mismatches: 6, Indels: 2
        0.90            0.07        0.02

Matches are distributed among these distances:
  73   48  0.63
  74   28  0.37

ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42


Consensus pattern (74 bp):   
ACACTTTTCGGATGACTAAAAAGTCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCATTT
TTCGTAATT
Done.