Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013602.1 Corchorus capsularis cultivar CVL-1 contig13623, 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: 17868
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:2037 original size:24 final size:27

Alignment explanation


    Indices: 2010--2062  Score: 76
    Period size: 26  Copynumber: 2.1  Consensus size: 27

       2000 TTCTAGTGAT

                                       
       2010 GAGAAT-AAG-GAAGGAAAAT-AGGAG
          1 GAGAATCAAGAGAAGGAAAATAAGGAG

                   *                   
       2034 GAGAATCGAGAGAAGGAAAATAAGGAG
          1 GAGAATCAAGAGAAGGAAAATAAGGAG

              
       2061 GA
          1 GA

       2063 ATTTCATCTC


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  24    6  0.24
  25    2  0.08
  26   10  0.40
  27    7  0.28

ACGTcount: A:0.53, C:0.02, G:0.38, T:0.08


Consensus pattern (27 bp):   
GAGAATCAAGAGAAGGAAAATAAGGAG

Found at i:2862 original size:19 final size:18

Alignment explanation


    Indices: 2838--2873  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2828 TGAAGATTTC

                               
       2838 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       2857 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       2874 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:7798 original size:5 final size:5

Alignment explanation


    Indices: 7788--7812  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

       7778 AAATTTTAAA

                                         
       7788 AAAAT AAAAT AAAAT AAAAT AAAAT
          1 AAAAT AAAAT AAAAT AAAAT AAAAT

       7813 TTCAACCAGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (5 bp):   
AAAAT

Found at i:13339 original size:42 final size:42

Alignment explanation


    Indices: 13279--13367  Score: 142
    Period size: 42  Copynumber: 2.1  Consensus size: 42

      13269 GTGCCCGGAT

                                 *                    
      13279 TGTGCCCGGTCATATGCGATTGCCCCATGCAATGGCCGGTCA
          1 TGTGCCCGGTCATATGCGATTACCCCATGCAATGGCCGGTCA

                       * *         *                  
      13321 TGTGCCCGGTCTTGTGCGATTACTCCATGCAATGGCCGGTCA
          1 TGTGCCCGGTCATATGCGATTACCCCATGCAATGGCCGGTCA

                 
      13363 TGTGC
          1 TGTGC

      13368 GATCCCTTCA


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  42   43  1.00

ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27


Consensus pattern (42 bp):   
TGTGCCCGGTCATATGCGATTACCCCATGCAATGGCCGGTCA
Done.