Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021738.1 Corchorus olitorius cultivar O-4 contig21771, 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: 25451
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:421 original size:31 final size:31

Alignment explanation


    Indices: 358--431  Score: 98
    Period size: 31  Copynumber: 2.4  Consensus size: 31

        348 TAACCACTAT

                                     *     
        358 TTTGAGTCTAAACCTCTCAAAAGTTTCTCAA
          1 TTTGAGTCTAAACCTCTCAAAAGTTACTCAA

                            *                
        389 TTTGAG-CATAAACCTTTCAAAAGTTGAC-CAA
          1 TTTGAGTC-TAAACCTCTCAAAAGTT-ACTCAA

                        
        420 TTTGAGTCTAAA
          1 TTTGAGTCTAAA

        432 AACGGAAAAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
  30    1  0.03
  31   35  0.92
  32    2  0.05

ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34


Consensus pattern (31 bp):   
TTTGAGTCTAAACCTCTCAAAAGTTACTCAA

Found at i:5364 original size:33 final size:33

Alignment explanation


    Indices: 5327--5416  Score: 117
    Period size: 33  Copynumber: 2.7  Consensus size: 33

       5317 AGAATTTGTT

                                            *
       5327 TCATCACAAACAACACCTAAAACAGATTTAGTG
          1 TCATCACAAACAACACCTAAAACAGATTTAGTA

                            *    **  *       
       5360 TCATCACAAACAACACTTAAATTAGGTTTAGTA
          1 TCATCACAAACAACACCTAAAACAGATTTAGTA

                   *       *        
       5393 TCATCACTAACAACATCTAAAACA
          1 TCATCACAAACAACACCTAAAACA

       5417 CTCTTTGCAA


Statistics
Matches: 47,  Mismatches: 10, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  33   47  1.00

ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24


Consensus pattern (33 bp):   
TCATCACAAACAACACCTAAAACAGATTTAGTA

Found at i:8646 original size:21 final size:21

Alignment explanation


    Indices: 8622--8671  Score: 75
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       8612 CTTAGGCAAT

                     *            
       8622 TCCAATGAGTTTGGAACCTT-C
          1 TCCAATGAGCTTGGAA-CTTGC

                                 
       8643 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACTTGC

                    
       8664 TCCAATGA
          1 TCCAATGA

       8672 ACTCCTAGCA


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  20    3  0.11
  21   24  0.89

ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACTTGC

Found at i:9532 original size:19 final size:19

Alignment explanation


    Indices: 9508--9545  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       9498 ACTATTAATA

                   *      *    
       9508 CCCATTATTTTCTACAAAG
          1 CCCATTACTTTCTAAAAAG

                               
       9527 CCCATTACTTTCTAAAAAG
          1 CCCATTACTTTCTAAAAAG

       9546 GGCATCTGCT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34


Consensus pattern (19 bp):   
CCCATTACTTTCTAAAAAG

Found at i:12177 original size:2 final size:2

Alignment explanation


    Indices: 12160--12193  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      12150 TATACAAATT

                  *         *                                 
      12160 TA TA AA TA TA TC TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      12194 ATAAATCAAG


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:21334 original size:76 final size:76

Alignment explanation


    Indices: 21182--21334  Score: 173
    Period size: 76  Copynumber: 2.0  Consensus size: 76

      21172 GGACAAGGGC

                     *                                     *       *  *      
      21182 CCCGACTCCTCCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTTAAGACCAAG
          1 CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCAAG

            * *        
      21247 TTGGGCAGTGT
         66 GTAGGCAGTGT

                            *   *          *      *                   *    * 
      21258 CCCGACTCCACCTGGGTGCCTACATGGTTTGTC-TGAGGACCCATGTGATTTGCCTGATCACCCA
          1 CCCGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAGCACCCATGTGATTTGCCTGAACACCAA

                   *    
      21322 GGTAGGCTGTGT
         65 GGTAGGCAGTGT

             
      21334 C
          1 C

      21335 ATGGCTCGGT


Statistics
Matches: 63,  Mismatches: 13, Indels: 2
        0.81            0.17        0.03

Matches are distributed among these distances:
  76   59  0.94
  77    4  0.06

ACGTcount: A:0.16, C:0.31, G:0.27, T:0.26


Consensus pattern (76 bp):   
CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCAAG
GTAGGCAGTGT

Found at i:23575 original size:60 final size:60

Alignment explanation


    Indices: 23506--23624  Score: 220
    Period size: 60  Copynumber: 2.0  Consensus size: 60

      23496 TTTGAAGAAA

                                                                        
      23506 CTAGGGATGCACACAAAGAAGTTTCAAGCTCATCGGAGTTACCTAAGATGCCATTTGATG
          1 CTAGGGATGCACACAAAGAAGTTTCAAGCTCATCGGAGTTACCTAAGATGCCATTTGATG

                      *                             *                  
      23566 CTAGGGATGCGCACAAAGAAGTTTCAAGCTCATCGGAGTTGCCTAAGATGCCATTTGAT
          1 CTAGGGATGCACACAAAGAAGTTTCAAGCTCATCGGAGTTACCTAAGATGCCATTTGAT

      23625 CCATTGAAGA


Statistics
Matches: 57,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  60   57  1.00

ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25


Consensus pattern (60 bp):   
CTAGGGATGCACACAAAGAAGTTTCAAGCTCATCGGAGTTACCTAAGATGCCATTTGATG
Done.