Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015610.1 Corchorus capsularis cultivar CVL-1 contig15631, 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: 10599
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:3034 original size:27 final size:28

Alignment explanation


    Indices: 3004--3066  Score: 92
    Period size: 30  Copynumber: 2.2  Consensus size: 28

       2994 CGAAGATCCC

                                   *    
       3004 TTTGTTT-GTGAAGGAGAACAATTTGAT
          1 TTTGTTTGGTGAAGGAGAACAATCTGAT

                                          
       3031 TTTGTTCTTGGTGAAGGAGAACAATCTGAT
          1 TTTG-T-TTGGTGAAGGAGAACAATCTGAT

                  
       3061 TTTGTT
          1 TTTGTT

       3067 CTTGATGAAG


Statistics
Matches: 32,  Mismatches: 1, Indels: 5
        0.84            0.03        0.13

Matches are distributed among these distances:
  27    4  0.12
  28    2  0.06
  29    3  0.09
  30   23  0.72

ACGTcount: A:0.25, C:0.06, G:0.25, T:0.43


Consensus pattern (28 bp):   
TTTGTTTGGTGAAGGAGAACAATCTGAT

Found at i:3046 original size:30 final size:30

Alignment explanation


    Indices: 3011--3078  Score: 118
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       3001 CCCTTTGTTT

                           *              
       3011 GTGAAGGAGAACAATTTGATTTTGTTCTTG
          1 GTGAAGGAGAACAATCTGATTTTGTTCTTG

                                          
       3041 GTGAAGGAGAACAATCTGATTTTGTTCTTG
          1 GTGAAGGAGAACAATCTGATTTTGTTCTTG

            *       
       3071 ATGAAGGA
          1 GTGAAGGA

       3079 TTTGTTTGTG


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  30   36  1.00

ACGTcount: A:0.29, C:0.07, G:0.28, T:0.35


Consensus pattern (30 bp):   
GTGAAGGAGAACAATCTGATTTTGTTCTTG

Found at i:3374 original size:12 final size:12

Alignment explanation


    Indices: 3357--3382  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       3347 AGTATGCTAG

                        
       3357 GACTCGATGGAA
          1 GACTCGATGGAA

                        
       3369 GACTCGATGGAA
          1 GACTCGATGGAA

              
       3381 GA
          1 GA

       3383 GACGACAAGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.35, C:0.15, G:0.35, T:0.15


Consensus pattern (12 bp):   
GACTCGATGGAA

Found at i:5475 original size:1 final size:1

Alignment explanation


    Indices: 5469--5493  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

       5459 TTTAACTTTT

                                     
       5469 AAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAA

       5494 CCCTATAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:9467 original size:27 final size:28

Alignment explanation


    Indices: 9414--9492  Score: 88
    Period size: 28  Copynumber: 2.7  Consensus size: 28

       9404 TCTCGTTTTT

                *                       
       9414 AAAAGTTAAGGGACCAATTTATCCCCAA
          1 AAAAATTAAGGGACCAATTTATCCCCAA

                                      *  
       9442 AAAAATTAA-GGAGCCAATTTATCCCAAA
          1 AAAAATTAAGGGA-CCAATTTATCCCCAA

                             *     
       9470 ATAAATAGTTAAGGGACTAATTT
          1 A-AAA-A-TTAAGGGACCAATTT

       9493 GGGTATTAAA


Statistics
Matches: 43,  Mismatches: 3, Indels: 7
        0.81            0.06        0.13

Matches are distributed among these distances:
  27    3  0.07
  28   23  0.53
  29    3  0.07
  30    1  0.02
  31   10  0.23
  32    3  0.07

ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25


Consensus pattern (28 bp):   
AAAAATTAAGGGACCAATTTATCCCCAA
Done.