Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002149.1 Corchorus capsularis cultivar CVL-1 contig02153, 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, 645

Length: 1076
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41


Found at i:978 original size:18 final size:18

Alignment explanation


    Indices: 955--989  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        945 ATCATTATTG

                              
        955 ATTATTATATGATAATTA
          1 ATTATTATATGATAATTA

                             
        973 ATTATTATATGATAATT
          1 ATTATTATATGATAATT

        990 CATTTTTGAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51


Consensus pattern (18 bp):   
ATTATTATATGATAATTA

Found at i:1012 original size:21 final size:21

Alignment explanation


    Indices: 988--1062  Score: 69
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        978 TATATGATAA

                                 
        988 TTCATTTTTGAAATTTAGAAT
          1 TTCATTTTTGAAATTTAGAAT

                           *           *
       1009 TTCATCATTATTGATTATTATATGATAA
          1 TTCAT--TT-TTGA-AATT-TA-GA-AT

                                 
       1037 TTCATTTTTGAAATTTAGAAT
          1 TTCATTTTTGAAATTTAGAAT

                 
       1058 TTCAT
          1 TTCAT

       1063 CATTATTGAT


Statistics
Matches: 43,  Mismatches: 4, Indels: 14
        0.70            0.07        0.23

Matches are distributed among these distances:
  21   11  0.26
  22    2  0.05
  23    4  0.09
  24    7  0.16
  25    7  0.16
  26    4  0.09
  27    2  0.05
  28    6  0.14

ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52


Consensus pattern (21 bp):   
TTCATTTTTGAAATTTAGAAT

Found at i:1017 original size:24 final size:24

Alignment explanation


    Indices: 989--1071  Score: 82
    Period size: 24  Copynumber: 3.4  Consensus size: 24

        979 ATATGATAAT

                 *                  
        989 TCATTTTTGAAATTTAGAATTTCA
          1 TCATTATTGAAATTTAGAATTTCA

                       *           *    
       1013 TCATTATTGATTATTATATGATAATTCA
          1 TCATTATTGA-AATT-TA-GA-ATTTCA

                                    
       1041 T--TT-TTGAAATTTAGAATTTCA
          1 TCATTATTGAAATTTAGAATTTCA

                      
       1062 TCATTATTGA
          1 TCATTATTGA

       1072 TTATT


Statistics
Matches: 47,  Mismatches: 5, Indels: 14
        0.71            0.08        0.21

Matches are distributed among these distances:
  21    6  0.13
  22    2  0.04
  23    4  0.09
  24   16  0.34
  25    7  0.15
  26    4  0.09
  27    2  0.04
  28    6  0.13

ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51


Consensus pattern (24 bp):   
TCATTATTGAAATTTAGAATTTCA

Found at i:1031 original size:49 final size:49

Alignment explanation


    Indices: 973--1076  Score: 208
    Period size: 49  Copynumber: 2.1  Consensus size: 49

        963 ATGATAATTA

                                                             
        973 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

                                                             
       1022 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

                  
       1071 ATTATT
          1 ATTATT


Statistics
Matches: 55,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   55  1.00

ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52


Consensus pattern (49 bp):   
ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
Done.