Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000647.1 Corchorus capsularis cultivar CVL-1 contig00647, 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: 2413
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Found at i:341 original size:199 final size:198

Alignment explanation


    Indices: 1--558  Score: 748
    Period size: 199  Copynumber: 2.8  Consensus size: 198

                                             * *                *            
          1 ATAATTTTTCTTATAGGATTATTATATAATACAATATCAGTGTAAGA-TTTGTACTCCATAAGCG
          1 ATAATTTTTCTTATAGGATTATTATATAATACACTGTCAGTGTAA-ATTTTGAACTCCATAAGCG

             *              *   *                        *     *        *    
         65 GGTTAAGAAGTTGACATATATCTCATTTCATAATTAATTAAATATTTAATAATAATACATCTTCC
         65 GCTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATATAATATTAATACATATTCC

                                              *                             *
        130 CTAAGGGGACACATGTCAACCCTTAAACCTCGCATGTGCAATCTGCTAAAATCCACTGACGGTGT
        130 CTAAGGGGACACATGTCAACCCTTAAACC-CGCACGTGCAATCTGCTAAAATCCACTGACGGTGC

                 
        195 ATTAT
        194 ATTAT

                           *             *                          *     *  
        200 ATAATTTTTCTTATAAGATTATTATATAACACACTGTCAGTGTAAATTTTGAACTCTATAAGTGG
          1 ATAATTTTTCTTATAGGATTATTATATAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGG

            *                             *                                  
        265 TTTAAGAAGTTGACACATACCTCATTTCATCATTAATTAAATATATAATATTAATACATATTCCC
         66 CTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATATAATATTAATACATATTCCC

            *            *                         *         *               
        330 CAAGGGGACACATATCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGCA
        131 TAAGGGGACACATGTCAACCCTTAAACCC-GCACGTGCAATCTGCTAAAATCCACTGACGGTGCA

              * 
        395 TTGT
        195 TTAT

                  *            *      *            *           *             
        399 ATAATTGTTCTTATAGGATAATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGG
          1 ATAATTTTTCTTATAGGATTATTATATAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGG

                        *      **                           *                
        464 CTTAAGAAGTTGGCACATAGTTCATTTCATAATTAATT-AA-ATAT--CATTAATACATATTCCC
         66 CTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATATAATATTAATACATATTCCC

                    *      *                  
        525 TAAGGGGAAACATGTGAACCCTTAAACCCCGCAC
        131 TAAGGGGACACATGTCAACCCTTAAA-CCCGCAC

        559 AGTCAATTTT


Statistics
Matches: 316,  Mismatches: 40, Indels: 10
        0.86            0.11        0.03

Matches are distributed among these distances:
 195   42  0.13
 196    3  0.01
 197    4  0.01
 198    4  0.01
 199  263  0.83

ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34


Consensus pattern (198 bp):   
ATAATTTTTCTTATAGGATTATTATATAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGG
CTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATATAATATTAATACATATTCCC
TAAGGGGACACATGTCAACCCTTAAACCCGCACGTGCAATCTGCTAAAATCCACTGACGGTGCAT
TAT

Found at i:2153 original size:2 final size:2

Alignment explanation


    Indices: 2146--2178  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       2136 ATAATTAATT

                                  *                           
       2146 TA TA TA TA TA TA TA TG T- TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2179 AGTTATTTTT


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:2167 original size:17 final size:17

Alignment explanation


    Indices: 2145--2177  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       2135 GATAATTAAT

                             
       2145 TTATATATATATATATG
          1 TTATATATATATATATG

                            
       2162 TTATATATATATATAT
          1 TTATATATATATATAT

       2178 AAGTTATTTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55


Consensus pattern (17 bp):   
TTATATATATATATATG

Found at i:2170 original size:19 final size:19

Alignment explanation


    Indices: 2146--2184  Score: 69
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2136 ATAATTAATT

                          *    
       2146 TATATATATATATATGTTA
          1 TATATATATATATAAGTTA

                               
       2165 TATATATATATATAAGTTA
          1 TATATATATATATAAGTTA

             
       2184 T
          1 T

       2185 TTTTGAAAAA


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

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51


Consensus pattern (19 bp):   
TATATATATATATAAGTTA

Found at i:2330 original size:2 final size:2

Alignment explanation


    Indices: 2325--2413  Score: 162
    Period size: 2  Copynumber: 44.5  Consensus size: 2

       2315 AAAAAGAAGA

                                                                          
       2325 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                                                           
       2367 AG AG AG AG AG AG AG AG AG AG AG AG TAG A- AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG

                   
       2409 AG AG A
          1 AG AG A


Statistics
Matches: 85,  Mismatches: 0, Indels: 4
        0.96            0.00        0.04

Matches are distributed among these distances:
   1    1  0.01
   2   82  0.96
   3    2  0.02

ACGTcount: A:0.51, C:0.00, G:0.48, T:0.01


Consensus pattern (2 bp):   
AG

Done.