Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002341.1 Corchorus capsularis cultivar CVL-1 contig02347, 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, 684

Length: 1141
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:29 original size:21 final size:21

Alignment explanation


    Indices: 5--79  Score: 69
    Period size: 21  Copynumber: 3.2  Consensus size: 21

          1 ATAA

                                 
          5 TTCATTTTTGAAATTTAGAAT
          1 TTCATTTTTGAAATTTAGAAT

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

                                 
         54 TTCATTTTTGAAATTTAGAAT
          1 TTCATTTTTGAAATTTAGAAT

                 
         75 TTCAT
          1 TTCAT

         80 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:34 original size:24 final size:24

Alignment explanation


    Indices: 6--88  Score: 82
    Period size: 24  Copynumber: 3.4  Consensus size: 24

          1 ATAAT

                 *                  
          6 TCATTTTTGAAATTTAGAATTTCA
          1 TCATTATTGAAATTTAGAATTTCA

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

                                    
         58 T--TT-TTGAAATTTAGAATTTCA
          1 TCATTATTGAAATTTAGAATTTCA

                      
         79 TCATTATTGA
          1 TCATTATTGA

         89 TTATTATATG


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:58 original size:25 final size:25

Alignment explanation


    Indices: 30--113  Score: 77
    Period size: 25  Copynumber: 3.4  Consensus size: 25

         20 TAGAATTTCA

                                     
         30 TCATTATTGATTATTATATGATAAT
          1 TCATTATTGATTATTATATGATAAT

                 *     *            * 
         55 TCATTTTTGA-AATT-TA-GA-ATTT
          1 TCATTATTGATTATTATATGATA-AT

                                       
         77 CATCATTATTGATTATTATATGATAAT
          1 --TCATTATTGATTATTATATGATAAT

                 *    
        104 TCATTTTTGA
          1 TCATTATTGA

        114 ATGATGATTT


Statistics
Matches: 45,  Mismatches: 7, Indels: 14
        0.68            0.11        0.21

Matches are distributed among these distances:
  21    1  0.02
  22    3  0.07
  23    2  0.04
  24   12  0.27
  25   21  0.47
  26    2  0.04
  27    3  0.07
  28    1  0.02

ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52


Consensus pattern (25 bp):   
TCATTATTGATTATTATATGATAAT

Found at i:73 original size:49 final size:49

Alignment explanation


    Indices: 1--114  Score: 228
    Period size: 49  Copynumber: 2.3  Consensus size: 49

                                                             
          1 ATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTATATG
          1 ATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTATATG

                                                             
         50 ATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTATATG
          1 ATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTATATG

                            
         99 ATAATTCATTTTTGAA
          1 ATAATTCATTTTTGAA

        115 TGATGATTTT


Statistics
Matches: 65,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   65  1.00

ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51


Consensus pattern (49 bp):   
ATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTATATG

Found at i:993 original size:23 final size:23

Alignment explanation


    Indices: 963--1022  Score: 102
    Period size: 23  Copynumber: 2.5  Consensus size: 23

        953 ATATACGATA

                                   
        963 AAATATAAATAATCAATAAATAT
          1 AAATATAAATAATCAATAAATAT

                                   
        986 AAATATAAATAATCAATAAATAT
          1 AAATATAAATAATCAATAAATAT

                          
       1009 AAATAAATAAATAA
          1 AAAT--ATAAATAA

       1023 AAAGGCCACT


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  23   27  0.77
  25    8  0.23

ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28


Consensus pattern (23 bp):   
AAATATAAATAATCAATAAATAT
Done.