Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011566.1 Corchorus olitorius cultivar O-4 contig11599, 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: 2101
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31


Found at i:77 original size:21 final size:21

Alignment explanation


    Indices: 52--101  Score: 82
    Period size: 21  Copynumber: 2.4  Consensus size: 21

         42 GGCAAGAAGT

                                 
         52 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGA

                           *    *
         73 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGA

                    
         94 TCATTGGA
          1 TCATTGGA

        102 ATTGCCTAAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGA

Found at i:1918 original size:33 final size:32

Alignment explanation


    Indices: 1845--1944  Score: 114
    Period size: 33  Copynumber: 3.1  Consensus size: 32

       1835 GCTATGATCA

                                        ** * 
       1845 ACCAAAACAG-ATTTGTTTTCATCACAATTAGC
          1 ACCAAAACAGAATTTG-TTTCATCACAAACAAC

                                             
       1877 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
          1 A-CCAAAACAGAATTTGTTTCATCACAAACAAC

                               *              
       1910 ACCTAAAACA-AATTTAGTGTCATCACAAACAAC
          1 ACC-AAAACAGAATTT-GTTTCATCACAAACAAC

              
       1943 AC
          1 AC

       1945 TGAAATTAGG


Statistics
Matches: 60,  Mismatches: 4, Indels: 7
        0.85            0.06        0.10

Matches are distributed among these distances:
  32    8  0.13
  33   47  0.78
  34    5  0.08

ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25


Consensus pattern (32 bp):   
ACCAAAACAGAATTTGTTTCATCACAAACAAC

Found at i:1959 original size:33 final size:33

Alignment explanation


    Indices: 1881--2010  Score: 122
    Period size: 33  Copynumber: 3.9  Consensus size: 33

       1871 ATTAGCATCC

                           *                  
       1881 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT

                  *                          
       1914 AAAACAAATTTAGTGTCATCACAAACAACA-CT
          1 AAAACAGATTTAGTGTCATCACAAACAACACCT

                **  *      *       *       *  
       1946 GAAATTAGGTTTAGTATCATCACTAACAACATCT
          1 -AAAACAGATTTAGTGTCATCACAAACAACACCT

                *               *           
       1980 AAAATAGATTTCA-TGTCATTACAAACAACAC
          1 AAAACAGATTT-AGTGTCATCACAAACAACAC

       2011 TCAAATCAGG


Statistics
Matches: 79,  Mismatches: 14, Indels: 8
        0.78            0.14        0.08

Matches are distributed among these distances:
  32    6  0.08
  33   70  0.89
  34    3  0.04

ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26


Consensus pattern (33 bp):   
AAAACAGATTTAGTGTCATCACAAACAACACCT

Found at i:1968 original size:66 final size:66

Alignment explanation


    Indices: 1896--2022  Score: 175
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       1886 AGAATTTGTT

                                                               *    *        
       1896 TCATCACAAACAACACCTAAAACAAATTT-AGTGTCATCACAAACAACACTGAAATTAGGTTTAG
          1 TCATCACAAACAACACCTAAAACAAATTTCA-TGTCATCACAAACAACACTCAAATCAGGTTTAG

              
       1960 TA
         65 TA

                   *       *      * *            *                       
       1962 TCATCACTAACAACATCTAAAATAGATTTCATGTCATTACAAACAACACTCAAATCAGGTT
          1 TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTT

       2023 CAGAATTACT


Statistics
Matches: 53,  Mismatches: 7, Indels: 2
        0.85            0.11        0.03

Matches are distributed among these distances:
  66   52  0.98
  67    1  0.02

ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26


Consensus pattern (66 bp):   
TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTTTAGT
A
Done.