Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002518.1 Corchorus capsularis cultivar CVL-1 contig02525, 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, 772

Length: 1288
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36


Found at i:315 original size:18 final size:18

Alignment explanation


    Indices: 292--326  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        282 ATCATTATTG

                              
        292 ATTATTATATGATAATTA
          1 ATTATTATATGATAATTA

                             
        310 ATTATTATATGATAATT
          1 ATTATTATATGATAATT

        327 CATTTTGAAA


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:377 original size:25 final size:25

Alignment explanation


    Indices: 349--432  Score: 77
    Period size: 25  Copynumber: 3.4  Consensus size: 25

        339 TAGAATTTCA

                                     
        349 TCATTATTGATTATTATATGATAAT
          1 TCATTATTGATTATTATATGATAAT

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

                                       
        396 CATCATTATTGATTATTATATGATAAT
          1 --TCATTATTGATTATTATATGATAAT

                 *    
        423 TCATTTTTGA
          1 TCATTATTGA

        433 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:400 original size:49 final size:49

Alignment explanation


    Indices: 310--433  Score: 241
    Period size: 49  Copynumber: 2.6  Consensus size: 49

        300 ATGATAATTA

                                                             
        310 ATTATTATATGATAATTCA-TTTTGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

                                                             
        358 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

                                       
        407 ATTATTATATGATAATTCATTTTTGAA
          1 ATTATTATATGATAATTCATTTTTGAA

        434 TGATGATTTT


Statistics
Matches: 75,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  48   19  0.25
  49   56  0.75

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


Consensus pattern (49 bp):   
ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

Found at i:407 original size:24 final size:23

Alignment explanation


    Indices: 326--407  Score: 78
    Period size: 24  Copynumber: 3.4  Consensus size: 23

        316 ATATGATAAT

                                   
        326 TCATTTTGAAATTTAGAATTTCA
          1 TCATTTTGAAATTTAGAATTTCA

                       *           *    
        349 TCATTATTGATTATTATATGATAATTCA
          1 TCATT-TTGA-AATT-TA-GA-ATTTCA

                                   
        377 T--TTTTGAAATTTAGAATTTCA
          1 TCATTTTGAAATTTAGAATTTCA

                      
        398 TCATTATTGA
          1 TCATT-TTGA

        408 TTATTATATG


Statistics
Matches: 47,  Mismatches: 4, Indels: 15
        0.71            0.06        0.23

Matches are distributed among these distances:
  21    6  0.13
  22    2  0.04
  23    9  0.19
  24   11  0.23
  25    7  0.15
  26    4  0.09
  27    2  0.04
  28    6  0.13

ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50


Consensus pattern (23 bp):   
TCATTTTGAAATTTAGAATTTCA
Done.