Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012906.1 Corchorus capsularis cultivar CVL-1 contig12927, 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: 13597
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30


Found at i:1045 original size:3 final size:3

Alignment explanation


    Indices: 1037--1081  Score: 83
    Period size: 3  Copynumber: 15.3  Consensus size: 3

       1027 TCATTTCCCC

                                                                         
       1037 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA- CAT C
          1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C

       1082 TTCCGTGAGC


Statistics
Matches: 41,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2    2  0.05
   3   39  0.95

ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31


Consensus pattern (3 bp):   
CAT

Found at i:2246 original size:60 final size:61

Alignment explanation


    Indices: 2153--2273  Score: 226
    Period size: 60  Copynumber: 2.0  Consensus size: 61

       2143 AACATACCCC

                                                                         
       2153 ATGTTAATTTGCGAAGATGATGAAGAATTTGGAAG-TTGGTGGTTGTGATTCTAGGTGTCA
          1 ATGTTAATTTGCGAAGATGATGAAGAATTTGGAAGATTGGTGGTTGTGATTCTAGGTGTCA

                                                                         
       2213 ATGTTAATTTGCGAAGATGATGAAGAATTTGGAAGAATTGGTGGTTGTGATTCTAGGTGTC
          1 ATGTTAATTTGCGAAGATGATGAAGAATTTGGAAG-ATTGGTGGTTGTGATTCTAGGTGTC

       2274 CTGATTACAA


Statistics
Matches: 59,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  60   35  0.59
  62   24  0.41

ACGTcount: A:0.27, C:0.05, G:0.31, T:0.36


Consensus pattern (61 bp):   
ATGTTAATTTGCGAAGATGATGAAGAATTTGGAAGATTGGTGGTTGTGATTCTAGGTGTCA

Found at i:5885 original size:1 final size:1

Alignment explanation


    Indices: 5835--5870  Score: 63
    Period size: 1  Copynumber: 36.0  Consensus size: 1

       5825 ACTTCTCTCC

                       *                        
       5835 TTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       5871 CTTCTCTTCA


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   1   33  1.00

ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97


Consensus pattern (1 bp):   
T

Found at i:7820 original size:27 final size:27

Alignment explanation


    Indices: 7782--7834  Score: 88
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       7772 ACGGCAGAGT

                  *        *           
       7782 TGGTATGCCAGCAGCGGGAATCATGGC
          1 TGGTATACCAGCAGCAGGAATCATGGC

                                      
       7809 TGGTATACCAGCAGCAGGAATCATGG
          1 TGGTATACCAGCAGCAGGAATCATGG

       7835 TGCGACCAAC


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.26, C:0.21, G:0.34, T:0.19


Consensus pattern (27 bp):   
TGGTATACCAGCAGCAGGAATCATGGC

Found at i:10267 original size:28 final size:29

Alignment explanation


    Indices: 10226--10309  Score: 82
    Period size: 28  Copynumber: 3.0  Consensus size: 29

      10216 TAGCCAAAGA

                   * *            **     
      10226 TGCCGCAGCAACCCAAAAATT-GTAAAAT
          1 TGCCGCAACTACCCAAAAATTCCAAAAAT

                    *                    
      10254 TGCCGCAAGTACCC-AAAATTCCAAAAAT
          1 TGCCGCAACTACCCAAAAATTCCAAAAAT

                       *      *  *      
      10282 TGCCGCAACTAGCCAAAATTTACAAAAA
          1 TGCCGCAACTACCCAAAAATTCCAAAAA

      10310 CCCCGTAACT


Statistics
Matches: 45,  Mismatches: 9, Indels: 3
        0.79            0.16        0.05

Matches are distributed among these distances:
  27    6  0.13
  28   28  0.62
  29   11  0.24

ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18


Consensus pattern (29 bp):   
TGCCGCAACTACCCAAAAATTCCAAAAAT

Found at i:10328 original size:47 final size:46

Alignment explanation


    Indices: 10277--10374  Score: 133
    Period size: 46  Copynumber: 2.1  Consensus size: 46

      10267 CAAAATTCCA

                                                  *   *  * 
      10277 AAAATTGCCGCAACTAGCCAAAATTTACAAAAACCCCGTAACTAGCC
          1 AAAATTGCCGCAACTAGCCAAAA-TTACAAAAACCCCGCAACAAGAC

                   *                 *   *                
      10324 AAAATTGTCGCAACTAGCCAAAATTGCAAGAACCCCGCAACAAGAC
          1 AAAATTGCCGCAACTAGCCAAAATTACAAAAACCCCGCAACAAGAC

                 
      10370 AAAAT
          1 AAAAT

      10375 CACCAAGGCA


Statistics
Matches: 45,  Mismatches: 6, Indels: 1
        0.87            0.12        0.02

Matches are distributed among these distances:
  46   23  0.51
  47   22  0.49

ACGTcount: A:0.45, C:0.28, G:0.12, T:0.15


Consensus pattern (46 bp):   
AAAATTGCCGCAACTAGCCAAAATTACAAAAACCCCGCAACAAGAC

Found at i:13441 original size:27 final size:27

Alignment explanation


    Indices: 13403--13455  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      13393 ACGGCAGAGT

                                       
      13403 TGGTATGCCAGCAGCGGGAATCATGGC
          1 TGGTATGCCAGCAGCGGGAATCATGGC

                                      
      13430 TGGTATGCCAGCAGCGGGAATCATGG
          1 TGGTATGCCAGCAGCGGGAATCATGG

      13456 TGCGACCAGC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.23, C:0.21, G:0.38, T:0.19


Consensus pattern (27 bp):   
TGGTATGCCAGCAGCGGGAATCATGGC

Done.