Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006377.1 Corchorus capsularis cultivar CVL-1 contig06398, 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: 2169
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26


Found at i:552 original size:18 final size:18

Alignment explanation


    Indices: 531--568  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        521 GTTGAAGTCA

                              
        531 AGTTAATCAATAAAGTTG
          1 AGTTAATCAATAAAGTTG

                *  *          
        549 AGTTGATTAATAAAGTTG
          1 AGTTAATCAATAAAGTTG

              
        567 AG
          1 AG

        569 GATTATTTTC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34


Consensus pattern (18 bp):   
AGTTAATCAATAAAGTTG

Found at i:1980 original size:26 final size:26

Alignment explanation


    Indices: 1943--2039  Score: 83
    Period size: 26  Copynumber: 3.6  Consensus size: 26

       1933 CCAATAATTA

                                      
       1943 AAGTCCTCAAACACAAGGGCATTTTT
          1 AAGTCCTCAAACACAAGGGCATTTTT

                                           *
       1969 AAGTCC-CTAAACAC-AGAGGCATCTCTCTCA
          1 AAGTCCTC-AAACACAAG-GGCAT-T-T-T-T

                                   ** 
       1999 AAGTCCTCAAACACAAGGGCATTCAT
          1 AAGTCCTCAAACACAAGGGCATTTTT

                            
       2025 AAGTCC-CTAAACACA
          1 AAGTCCTC-AAACACA

       2040 GAGACATCTA


Statistics
Matches: 58,  Mismatches: 4, Indels: 18
        0.73            0.05        0.22

Matches are distributed among these distances:
  25    4  0.07
  26   30  0.52
  27    1  0.02
  28    1  0.02
  29    2  0.03
  30   17  0.29
  31    3  0.05

ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21


Consensus pattern (26 bp):   
AAGTCCTCAAACACAAGGGCATTTTT

Found at i:2020 original size:30 final size:26

Alignment explanation


    Indices: 1940--2021  Score: 87
    Period size: 26  Copynumber: 3.0  Consensus size: 26

       1930 TACCCAATAA

                                      
       1940 TTAAAGTCCTCAAACACAAGGGCATT
          1 TTAAAGTCCTCAAACACAAGGGCATT

              *                          
       1966 TTTAAGTCC-CTAAACAC-AGAGGCATCT
          1 TTAAAGTCCTC-AAACACAAG-GGCAT-T

                                         
       1993 CTCTCAAAGTCCTCAAACACAAGGGCATT
          1 -T-T-AAAGTCCTCAAACACAAGGGCATT

       2022 CATAAGTCCC


Statistics
Matches: 46,  Mismatches: 2, Indels: 13
        0.75            0.03        0.21

Matches are distributed among these distances:
  25    3  0.07
  26   19  0.41
  27    1  0.02
  28    1  0.02
  29    2  0.04
  30   17  0.37
  31    3  0.07

ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23


Consensus pattern (26 bp):   
TTAAAGTCCTCAAACACAAGGGCATT

Found at i:2028 original size:56 final size:56

Alignment explanation


    Indices: 1942--2067  Score: 191
    Period size: 56  Copynumber: 2.2  Consensus size: 56

       1932 CCCAATAATT

                                    **                   *     * *  
       1942 AAAGTCCTCAAACACAAGGGCATTTTTAAGTCCCTAAACACAGAGGCATCTCTCTC
          1 AAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATATC

                                                                    
       1998 AAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATATC
          1 AAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATATC

                           
       2054 AAAGTTCC-CAAACA
          1 AAAG-TCCTCAAACA

       2068 TATATAACAT


Statistics
Matches: 64,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  56   61  0.95
  57    3  0.05

ACGTcount: A:0.39, C:0.28, G:0.13, T:0.21


Consensus pattern (56 bp):   
AAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATATC

Found at i:2166 original size:30 final size:29

Alignment explanation


    Indices: 2113--2169  Score: 87
    Period size: 30  Copynumber: 1.9  Consensus size: 29

       2103 CAATCACAAG

                  *                      
       2113 GGCATCCATACTAAGTCCCTAAACACAGA
          1 GGCATCAATACTAAGTCCCTAAACACAGA

                             *          
       2142 GGCATCAATACTAAAGTTCCTAAACACA
          1 GGCATCAATACT-AAGTCCCTAAACACA


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  29   11  0.44
  30   14  0.56

ACGTcount: A:0.40, C:0.28, G:0.12, T:0.19


Consensus pattern (29 bp):   
GGCATCAATACTAAGTCCCTAAACACAGA

Found at i:2167 original size:100 final size:97

Alignment explanation


    Indices: 1990--2167  Score: 259
    Period size: 100  Copynumber: 1.8  Consensus size: 97

       1980 CACAGAGGCA

                                           *                          *      
       1990 TCTCTCTCAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATATCA
          1 TCTCTCTCAAAGTCCTCAAACACAAGGGCATCCATAAGTCCCTAAACACAGAGACATCAATATCA

                                            
       2055 AAGTTCCCAAACATATATAACATAGGGGCAAC
         66 AAGTTCCCAAACATATATAACATAGGGGCAAC

                 *             *                                    *        
       2087 TCTCTTTCAAAGTCCTCAATCACAAGGGCATCCATACTAAGTCCCTAAACACAGAGGCATCAATA
          1 TCTCTCTCAAAGTCCTCAAACACAAGGGCATCC--A-TAAGTCCCTAAACACAGAGACATCAATA

                       *     
       2152 -CTAAAGTTCCTAAACA
         63 TC-AAAGTTCCCAAACA

       2168 CA


Statistics
Matches: 71,  Mismatches: 6, Indels: 5
        0.87            0.07        0.06

Matches are distributed among these distances:
  97   30  0.42
  99    2  0.03
 100   39  0.55

ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22


Consensus pattern (97 bp):   
TCTCTCTCAAAGTCCTCAAACACAAGGGCATCCATAAGTCCCTAAACACAGAGACATCAATATCA
AAGTTCCCAAACATATATAACATAGGGGCAAC
Done.