Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006169.1 Corchorus capsularis cultivar CVL-1 contig06187, 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: 12286
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32


Found at i:176 original size:50 final size:50

Alignment explanation


    Indices: 4--336  Score: 365
    Period size: 50  Copynumber: 6.7  Consensus size: 50

          1 CCT

                *    *    *   *                               *
          4 AAAAAGCCCTTTCCTGGTTGGAAGG-CCACTGTTTTC-TTATTT-TTTCCA
          1 AAAATGCCCCTTCCCGGTCGGAAGGTCC-CTGTTTTCTTTATTTGTTTCCC

                  *                    *      *      *         
         52 AAAAT-ACCCTTCCCGGTCGGAAGGTCACTGTTTCCTTTATCTGTTTCCTC
          1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCC-C

                *                         *      *            
        102 AAAAAGCCCCTTCCCGGTCGGAAGGTCCCTATTTTCTATATTTGTTTCCC
          1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC

                      *      *                        *      *
        152 AAAATGCCCCATCCCGGCCGGAAGGTCCCTGTTTTCTTTATTCGTTTCCT
          1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC

                                        *   *               * 
        202 AAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTCTTCTTTATTTGTTTCTC
          1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC

                          *   *         *           *          
        252 AAAATGCCCCTTCCTGGTTGGAAGGT-CTTAGTTTTCTTTCTTTG-TTCCC
          1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCT-GTTTTCTTTATTTGTTTCCC

                         *               *       
        301 AAAATGCCCCTTCTCGGTCGGAAGGT-CCAGTTTTCT
          1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCT

        337 CTTCACATTT


Statistics
Matches: 239,  Mismatches: 40, Indels: 12
        0.82            0.14        0.04

Matches are distributed among these distances:
  47   22  0.09
  48   17  0.07
  49   36  0.15
  50  127  0.53
  51   37  0.15

ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37


Consensus pattern (50 bp):   
AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC

Found at i:5150 original size:45 final size:45

Alignment explanation


    Indices: 5086--5175  Score: 171
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       5076 AGGATGTTTC

                                                         
       5086 CCCAAGACCTATAGTTAAATTAACATCAAATTAACATTGGCAGAA
          1 CCCAAGACCTATAGTTAAATTAACATCAAATTAACATTGGCAGAA

                                      *                  
       5131 CCCAAGACCTATAGTTAAATTAACATTAAATTAACATTGGCAGAA
          1 CCCAAGACCTATAGTTAAATTAACATCAAATTAACATTGGCAGAA

       5176 TAAGAAAAGT


Statistics
Matches: 44,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   44  1.00

ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26


Consensus pattern (45 bp):   
CCCAAGACCTATAGTTAAATTAACATCAAATTAACATTGGCAGAA

Found at i:5231 original size:15 final size:15

Alignment explanation


    Indices: 5211--5241  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5201 ATATAGAGAC

                           
       5211 GACATAATCATCAAT
          1 GACATAATCATCAAT

                           
       5226 GACATAATCATCAAT
          1 GACATAATCATCAAT

             
       5241 G
          1 G

       5242 GCCGTTGATG


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

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26


Consensus pattern (15 bp):   
GACATAATCATCAAT

Found at i:5677 original size:84 final size:84

Alignment explanation


    Indices: 5548--5714  Score: 298
    Period size: 84  Copynumber: 2.0  Consensus size: 84

       5538 TTAGTAATAT

                                         *                         *         
       5548 TATTTAGATTAAGCTAGATGATAAACAAATAACCTAGTTAGAGTCCAATTCGAATCTAACATAAT
          1 TATTTAGATTAAGCTAGATGATAAACAAAAAACCTAGTTAGAGTCCAATTCGAATATAACATAAT

                               
       5613 ATAAAACTCTTAAGATAAC
         66 ATAAAACTCTTAAGATAAC

                                             *                               
       5632 TATTTAGATTAAGCTAGATGATAAACAAAAAACTTAGTTAGAGTCCAATTCGAATATAACATAAT
          1 TATTTAGATTAAGCTAGATGATAAACAAAAAACCTAGTTAGAGTCCAATTCGAATATAACATAAT

            *                 
       5697 TTAAAACTCTTAAGATAA
         66 ATAAAACTCTTAAGATAA

       5715 AATAAACAAA


Statistics
Matches: 79,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  84   79  1.00

ACGTcount: A:0.46, C:0.13, G:0.11, T:0.31


Consensus pattern (84 bp):   
TATTTAGATTAAGCTAGATGATAAACAAAAAACCTAGTTAGAGTCCAATTCGAATATAACATAAT
ATAAAACTCTTAAGATAAC
Done.