Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006987.1 Corchorus capsularis cultivar CVL-1 contig07008, 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: 4237
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31


Found at i:350 original size:13 final size:13

Alignment explanation


    Indices: 332--356  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        322 AGATTTAGCC

                         
        332 ATGTTAATATTGA
          1 ATGTTAATATTGA

                        
        345 ATGTTAATATTG
          1 ATGTTAATATTG

        357 TTTGCTTGGC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48


Consensus pattern (13 bp):   
ATGTTAATATTGA

Found at i:1189 original size:30 final size:30

Alignment explanation


    Indices: 1151--1257  Score: 169
    Period size: 30  Copynumber: 3.6  Consensus size: 30

       1141 ATGAAGTAGT

                     *                    
       1151 AGTGGAAGACAACAATGGAAACCAGCAGCA
          1 AGTGGAAGATAACAATGGAAACCAGCAGCA

             *                    *       
       1181 AATGGAAGATAACAATGGAAACGAGCAGCA
          1 AGTGGAAGATAACAATGGAAACCAGCAGCA

                              **          
       1211 AGTGGAAGATAACAATGGGGACCAGCAGCA
          1 AGTGGAAGATAACAATGGAAACCAGCAGCA

                             
       1241 AGTGGAAGATAACAATG
          1 AGTGGAAGATAACAATG

       1258 TTGGAGAGGG


Statistics
Matches: 70,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  30   70  1.00

ACGTcount: A:0.46, C:0.15, G:0.29, T:0.10


Consensus pattern (30 bp):   
AGTGGAAGATAACAATGGAAACCAGCAGCA

Found at i:1526 original size:15 final size:15

Alignment explanation


    Indices: 1500--1560  Score: 95
    Period size: 15  Copynumber: 4.1  Consensus size: 15

       1490 TGTTGGGGTT

                 *         
       1500 GGGCCATCTACTGCA
          1 GGGCCTTCTACTGCA

                   *       
       1515 GGGCCTTTTACTGCA
          1 GGGCCTTCTACTGCA

                           
       1530 GGGCCTTCTACTGCA
          1 GGGCCTTCTACTGCA

                 *         
       1545 GGGCCATCTACTGCA
          1 GGGCCTTCTACTGCA

             
       1560 G
          1 G

       1561 CAAGGATATG


Statistics
Matches: 42,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   42  1.00

ACGTcount: A:0.16, C:0.31, G:0.28, T:0.25


Consensus pattern (15 bp):   
GGGCCTTCTACTGCA

Found at i:2276 original size:15 final size:15

Alignment explanation


    Indices: 2256--2284  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       2246 ACAAGAAACG

                           
       2256 CCCACTGCCCAACAC
          1 CCCACTGCCCAACAC

                          
       2271 CCCACTGCCCAACA
          1 CCCACTGCCCAACA

       2285 ATCATCAGCC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.28, C:0.59, G:0.07, T:0.07


Consensus pattern (15 bp):   
CCCACTGCCCAACAC
Done.