Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001331.1 Corchorus capsularis cultivar CVL-1 contig01331, 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: 8040
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:404 original size:2 final size:2

Alignment explanation


    Indices: 397--425  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

        387 TCGGAGGGGG

                                                       
        397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        426 GCAATTATGC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:492 original size:2 final size:2

Alignment explanation


    Indices: 485--513  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

        475 CGGAGGAGTG

                                                       
        485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        514 GCAATTATGC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:745 original size:101 final size:101

Alignment explanation


    Indices: 570--772  Score: 397
    Period size: 101  Copynumber: 2.0  Consensus size: 101

        560 ACTGGCACTG

                                             *                               
        570 CTATTTGGGAGCACGACCCCCTTATTTTTTGGGTTGCCTACACGATTGATCACAATTTGATGTGA
          1 CTATTTGGGAGCACGACCCCCTTATTTTTTGGGATGCCTACACGATTGATCACAATTTGATGTGA

                                                
        635 CTGAGCCAGCAAGTATGTAACAAATGTCCACAAAAT
         66 CTGAGCCAGCAAGTATGTAACAAATGTCCACAAAAT

                                                                             
        671 CTATTTGGGAGCACGACCCCCTTATTTTTTGGGATGCCTACACGATTGATCACAATTTGATGTGA
          1 CTATTTGGGAGCACGACCCCCTTATTTTTTGGGATGCCTACACGATTGATCACAATTTGATGTGA

                                                
        736 CTGAGCCAGCAAGTATGTAACAAATGTCCACAAAAT
         66 CTGAGCCAGCAAGTATGTAACAAATGTCCACAAAAT

             
        772 C
          1 C

        773 AATGCTGACA


Statistics
Matches: 101,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 101  101  1.00

ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29


Consensus pattern (101 bp):   
CTATTTGGGAGCACGACCCCCTTATTTTTTGGGATGCCTACACGATTGATCACAATTTGATGTGA
CTGAGCCAGCAAGTATGTAACAAATGTCCACAAAAT

Found at i:6040 original size:34 final size:34

Alignment explanation


    Indices: 5986--6076  Score: 155
    Period size: 34  Copynumber: 2.7  Consensus size: 34

       5976 TTAAGTCCCA

                  *        *                  
       5986 AACGTTGCAAAATCGACTCAAATCAGTACCTAAT
          1 AACGTTACAAAATCGGCTCAAATCAGTACCTAAT

              *                               
       6020 AATGTTACAAAATCGGCTCAAATCAGTACCTAAT
          1 AACGTTACAAAATCGGCTCAAATCAGTACCTAAT

                                   
       6054 AACGTTACAAAATCGGCTCAAAT
          1 AACGTTACAAAATCGGCTCAAAT

       6077 AAGTCCCCAT


Statistics
Matches: 53,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  34   53  1.00

ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24


Consensus pattern (34 bp):   
AACGTTACAAAATCGGCTCAAATCAGTACCTAAT

Found at i:7481 original size:20 final size:20

Alignment explanation


    Indices: 7456--7494  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       7446 TAATATCCTA

                                
       7456 ATTCAATCAGTTAATCAAGT
          1 ATTCAATCAGTTAATCAAGT

                               
       7476 ATTCAATCAGTTAATCAAG
          1 ATTCAATCAGTTAATCAAG

       7495 CACCACTCTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33


Consensus pattern (20 bp):   
ATTCAATCAGTTAATCAAGT
Done.