Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015555.1 Corchorus capsularis cultivar CVL-1 contig15576, 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: 9327
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30


Found at i:34 original size:1 final size:1

Alignment explanation


    Indices: 30--56  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

         20 ATAAAAAGGG

                                       
         30 AAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAA

         57 GAAAGCTCAT


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

Matches are distributed among these distances:
   1   26  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:4588 original size:24 final size:25

Alignment explanation


    Indices: 4554--4600  Score: 87
    Period size: 24  Copynumber: 1.9  Consensus size: 25

       4544 AGCCATTGCT

                                     
       4554 TCTTTCTAATTAAATGCATGTTTGA
          1 TCTTTCTAATTAAATGCATGTTTGA

                                   
       4579 TCTTT-TAATTAAATGCATGTTT
          1 TCTTTCTAATTAAATGCATGTTT

       4601 CAAGAAGGGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24   17  0.77
  25    5  0.23

ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51


Consensus pattern (25 bp):   
TCTTTCTAATTAAATGCATGTTTGA

Found at i:8599 original size:34 final size:34

Alignment explanation


    Indices: 8561--8672  Score: 127
    Period size: 34  Copynumber: 3.2  Consensus size: 34

       8551 TACCTTAACT

                     *                   *    
       8561 CTGATTAATTTCCTTTTACTTAATTACTGGTTTA
          1 CTGATTAATCTCCTTTTACTTAATTACTGATTTA

                   * *       *              *     
       8595 CTGATTACTGTCACTTTGACTCTGAATTA-TCAATTTA
          1 CTGATTAATCTC-CTTTTACT-T-AATTACT-GATTTA

                                              
       8632 CTGATTAATCTCCTTTTACTTAATTACTGATTTA
          1 CTGATTAATCTCCTTTTACTTAATTACTGATTTA

                   
       8666 CTGATTA
          1 CTGATTA

       8673 CTATTACCTT


Statistics
Matches: 64,  Mismatches: 9, Indels: 10
        0.77            0.11        0.12

Matches are distributed among these distances:
  34   27  0.42
  35    9  0.14
  36    9  0.14
  37   19  0.30

ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48


Consensus pattern (34 bp):   
CTGATTAATCTCCTTTTACTTAATTACTGATTTA

Found at i:8632 original size:37 final size:36

Alignment explanation


    Indices: 8591--8709  Score: 127
    Period size: 37  Copynumber: 3.3  Consensus size: 36

       8581 TAATTACTGG

                         *                       
       8591 TTTACTGATTACTGTCACTTTGACTCTGAATTATCAA
          1 TTTACTGATTACTATCACTTTGACTCT-AATTATCAA

                       * *       *             * 
       8628 TTTACTGATTAATCTC-CTTTTACT-TAATTA-CTGA
          1 TTTACTGATTACTATCACTTTGACTCTAATTATC-AA

                           *  *                  
       8662 TTTACTGATTACTATTACCTTGACTCTTAATTATCAA
          1 TTTACTGATTACTATCACTTTGACTC-TAATTATCAA

                       
       8699 TTTACTGATTA
          1 TTTACTGATTA

       8710 ATCCTTCTAC


Statistics
Matches: 67,  Mismatches: 10, Indels: 10
        0.77            0.11        0.11

Matches are distributed among these distances:
  33    1  0.01
  34   19  0.28
  35    7  0.10
  36    7  0.10
  37   32  0.48
  38    1  0.01

ACGTcount: A:0.28, C:0.18, G:0.08, T:0.47


Consensus pattern (36 bp):   
TTTACTGATTACTATCACTTTGACTCTAATTATCAA

Found at i:8646 original size:71 final size:71

Alignment explanation


    Indices: 8561--8712  Score: 250
    Period size: 71  Copynumber: 2.1  Consensus size: 71

       8551 TACCTTAACT

                     *                   *             *    *                
       8561 CTGATTAATTTCCTTTTACTTAATTACTGGTTTACTGATTACTGTCACTTTGACTCTGAATTATC
          1 CTGATTAATCTCCTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTGAATTATC

                  
       8626 AATTTA
         66 AATTTA

                                                         *           *       
       8632 CTGATTAATCTCCTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTTAATTATC
          1 CTGATTAATCTCCTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTGAATTATC

                  
       8697 AATTTA
         66 AATTTA

                      
       8703 CTGATTAATC
          1 CTGATTAATC

       8713 CTTCTACTTC


Statistics
Matches: 75,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  71   75  1.00

ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47


Consensus pattern (71 bp):   
CTGATTAATCTCCTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTGAATTATC
AATTTA
Done.