Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012996.1 Corchorus capsularis cultivar CVL-1 contig13017, 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: 12964
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:1054 original size:2 final size:2

Alignment explanation


    Indices: 1047--1085  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       1037 AGTAATGTAA

                                                                      
       1047 AT AT AT AT AT 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 AT AT AT AT AT A

       1086 AATGGGGGTA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:2358 original size:18 final size:16

Alignment explanation


    Indices: 2335--2380  Score: 60
    Period size: 14  Copynumber: 2.9  Consensus size: 16

       2325 CCTTAATTGT

                              
       2335 TTTTAATTAATGTTAGGC
          1 TTTTAATTAATGTTA--C

                            
       2353 TTTTAATTAA--TTAC
          1 TTTTAATTAATGTTAC

                          
       2367 TTTTAATTAATGTT
          1 TTTTAATTAATGTT

       2381 TCTCTCGCTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  14   11  0.42
  16    5  0.19
  18   10  0.38

ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57


Consensus pattern (16 bp):   
TTTTAATTAATGTTAC

Found at i:8283 original size:37 final size:37

Alignment explanation


    Indices: 8242--8336  Score: 120
    Period size: 37  Copynumber: 2.6  Consensus size: 37

       8232 ATCTAAGTCC

                           *                      
       8242 AAATAGGACGTTGCAGACAAAGACAAAAAG-CAAAATT
          1 AAATAGGACGTTGCAAACAAAGAC-AAAAGCCAAAATT

                 **      *                       
       8279 AAATACAACGTTGGAAACAAAGACAAAAGCCAAAATT
          1 AAATAGGACGTTGCAAACAAAGACAAAAGCCAAAATT

                     *   *       
       8316 AAATAGGACATTGGAAACAAA
          1 AAATAGGACGTTGCAAACAAA

       8337 AAGCAAAATT


Statistics
Matches: 50,  Mismatches: 7, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  36    5  0.10
  37   45  0.90

ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14


Consensus pattern (37 bp):   
AAATAGGACGTTGCAAACAAAGACAAAAGCCAAAATT

Found at i:8344 original size:31 final size:31

Alignment explanation


    Indices: 8264--8346  Score: 85
    Period size: 37  Copynumber: 2.5  Consensus size: 31

       8254 GCAGACAAAG

                                    *      
       8264 ACAAAAAGCAAAATTAAATACAACGTTGGAA
          1 ACAAAAAGCAAAATTAAATACAACATTGGAA

                                      **         
       8295 ACAAAGACAAAAGCCAAAATTAAATAGGACATTGGAA
          1 AC----A-AAAAG-CAAAATTAAATACAACATTGGAA

                           
       8332 ACAAAAAGCAAAATT
          1 ACAAAAAGCAAAATT

       8347 GACCTTCTTA


Statistics
Matches: 43,  Mismatches: 3, Indels: 12
        0.74            0.05        0.21

Matches are distributed among these distances:
  31    9  0.21
  32    5  0.12
  33    1  0.02
  35    1  0.02
  36    5  0.12
  37   22  0.51

ACGTcount: A:0.59, C:0.13, G:0.13, T:0.14


Consensus pattern (31 bp):   
ACAAAAAGCAAAATTAAATACAACATTGGAA

Found at i:8457 original size:27 final size:28

Alignment explanation


    Indices: 8391--8461  Score: 90
    Period size: 27  Copynumber: 2.5  Consensus size: 28

       8381 TCTAATAATT

                             *  *        
       8391 AATAATGGAATAATTTTTTCTTAGAAAAA
          1 AATAATGGAATAA-TTTATCGTAGAAAAA

                  *           *         
       8420 AATAATAGAATAATTTATGGTA-AAAAA
          1 AATAATGGAATAATTTATCGTAGAAAAA

                           
       8447 AATAATGGAATAATT
          1 AATAATGGAATAATT

       8462 AAAATATTAT


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  27   19  0.51
  28    6  0.16
  29   12  0.32

ACGTcount: A:0.54, C:0.01, G:0.11, T:0.34


Consensus pattern (28 bp):   
AATAATGGAATAATTTATCGTAGAAAAA

Found at i:8522 original size:29 final size:30

Alignment explanation


    Indices: 8488--8551  Score: 103
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       8478 ATGGCAATTT

                                     *    
       8488 AGAAATATGTTTT-AAAAAAGGGTATAATC
          1 AGAAATATGTTTTAAAAAAAGGGTACAATC

                                          
       8517 AGAAATATGTTTTAAAAAAAGGGTACAATC
          1 AGAAATATGTTTTAAAAAAAGGGTACAATC

            *    
       8547 GGAAA
          1 AGAAA

       8552 ACATAAAGTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  29   13  0.41
  30   19  0.59

ACGTcount: A:0.50, C:0.05, G:0.19, T:0.27


Consensus pattern (30 bp):   
AGAAATATGTTTTAAAAAAAGGGTACAATC

Found at i:12800 original size:2 final size:2

Alignment explanation


    Indices: 12793--12837  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

      12783 ATGCATGTGG

                                                                          
      12793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                
      12835 AT A
          1 AT A

      12838 GACTAGACCT


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.