Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010540.1 Corchorus capsularis cultivar CVL-1 contig10561, 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: 23339
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34


Found at i:2393 original size:29 final size:29

Alignment explanation


    Indices: 2361--2422  Score: 79
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       2351 ACTTGTAGCA

                  *  *            *  *   
       2361 TTTGGATATTTTGTCCCCTGAATTTTAAT
          1 TTTGGACATCTTGTCCCCTGAACTTCAAT

                            *            
       2390 TTTGGACATCTTGTCCTCTGAACTTCAAT
          1 TTTGGACATCTTGTCCCCTGAACTTCAAT

                
       2419 TTTG
          1 TTTG

       2423 AGATGTGTTG


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48


Consensus pattern (29 bp):   
TTTGGACATCTTGTCCCCTGAACTTCAAT

Found at i:2627 original size:29 final size:28

Alignment explanation


    Indices: 2546--2630  Score: 91
    Period size: 29  Copynumber: 2.9  Consensus size: 28

       2536 AAAACATTCC

                     *    *             *
       2546 AAAATTAAAATTCAGGGGATAAAATGTTT
          1 AAAATTAAAGTTCATGGGA-AAAATGTTG

                                         
       2575 AAAATTAAAGTTCATGGGACAAAATGTTG
          1 AAAATTAAAGTTCATGGGA-AAAATGTTG

                                        
       2604 AAACATTACAAGTTCAAT-GGAAAAATG
          1 AAA-ATTA-AAGTTC-ATGGGAAAAATG

       2631 GTACTTTAAT


Statistics
Matches: 49,  Mismatches: 4, Indels: 5
        0.84            0.07        0.09

Matches are distributed among these distances:
  29   28  0.57
  30   10  0.20
  31    9  0.18
  32    2  0.04

ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27


Consensus pattern (28 bp):   
AAAATTAAAGTTCATGGGAAAAATGTTG

Found at i:14345 original size:36 final size:37

Alignment explanation


    Indices: 14298--14372  Score: 143
    Period size: 37  Copynumber: 2.1  Consensus size: 37

      14288 TCAAACTCAA

                                                 
      14298 ACCCACTGATTAAATT-ACAATTAGCTCCTGCTTCAC
          1 ACCCACTGATTAAATTAACAATTAGCTCCTGCTTCAC

                                                 
      14334 ACCCACTGATTAAATTAACAATTAGCTCCTGCTTCAC
          1 ACCCACTGATTAAATTAACAATTAGCTCCTGCTTCAC

              
      14371 AC
          1 AC

      14373 ATACAATAAC


Statistics
Matches: 38,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  36   16  0.42
  37   22  0.58

ACGTcount: A:0.32, C:0.31, G:0.08, T:0.29


Consensus pattern (37 bp):   
ACCCACTGATTAAATTAACAATTAGCTCCTGCTTCAC

Found at i:18664 original size:3 final size:3

Alignment explanation


    Indices: 18656--18689  Score: 68
    Period size: 3  Copynumber: 11.3  Consensus size: 3

      18646 ATTTCGAATC

                                                         
      18656 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T

      18690 GCACCCAAAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:19211 original size:2 final size:2

Alignment explanation


    Indices: 19204--19232  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      19194 TTGATGTAAA

                                                       
      19204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      19233 ACATCGAAAT


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


Consensus pattern (2 bp):   
AT

Found at i:22097 original size:6 final size:6

Alignment explanation


    Indices: 22087--22116  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      22077 CAACGGGAAG

                 *                            
      22087 AAATTG AAATTA AAATTA AAATTA AAATTA
          1 AAATTA AAATTA AAATTA AAATTA AAATTA

      22117 TACTATGTGC


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33


Consensus pattern (6 bp):   
AAATTA

Done.