Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001782.1 Corchorus capsularis cultivar CVL-1 contig01782, 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, 629

Length: 1049
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:227 original size:18 final size:18

Alignment explanation


    Indices: 204--238  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        194 ATCATTATTG

                              
        204 ATTATTATATGATAATTA
          1 ATTATTATATGATAATTA

                             
        222 ATTATTATATGATAATT
          1 ATTATTATATGATAATT

        239 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:261 original size:21 final size:21

Alignment explanation


    Indices: 237--311  Score: 69
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        227 TATATGATAA

                                 
        237 TTCATTTTTGAAATTTAGAAT
          1 TTCATTTTTGAAATTTAGAAT

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

                                 
        286 TTCATTTTTGAAATTTAGAAT
          1 TTCATTTTTGAAATTTAGAAT

                 
        307 TTCAT
          1 TTCAT

        312 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:266 original size:24 final size:24

Alignment explanation


    Indices: 238--320  Score: 82
    Period size: 24  Copynumber: 3.4  Consensus size: 24

        228 ATATGATAAT

                 *                  
        238 TCATTTTTGAAATTTAGAATTTCA
          1 TCATTATTGAAATTTAGAATTTCA

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

                                    
        290 T--TT-TTGAAATTTAGAATTTCA
          1 TCATTATTGAAATTTAGAATTTCA

                      
        311 TCATTATTGA
          1 TCATTATTGA

        321 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:280 original size:49 final size:49

Alignment explanation


    Indices: 222--346  Score: 250
    Period size: 49  Copynumber: 2.6  Consensus size: 49

        212 ATGATAATTA

                                                             
        222 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

                                                             
        271 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

                                       
        320 ATTATTATATGATAATTCATTTTTGAA
          1 ATTATTATATGATAATTCATTTTTGAA

        347 TGATGATTTT


Statistics
Matches: 76,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   76  1.00

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


Consensus pattern (49 bp):   
ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

Found at i:290 original size:25 final size:25

Alignment explanation


    Indices: 262--345  Score: 77
    Period size: 25  Copynumber: 3.4  Consensus size: 25

        252 TAGAATTTCA

                                     
        262 TCATTATTGATTATTATATGATAAT
          1 TCATTATTGATTATTATATGATAAT

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

                                       
        309 CATCATTATTGATTATTATATGATAAT
          1 --TCATTATTGATTATTATATGATAAT

                 *    
        336 TCATTTTTGA
          1 TCATTATTGA

        346 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
Done.