Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005789.1 Corchorus capsularis cultivar CVL-1 contig05807, 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: 5138
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34


Found at i:571 original size:22 final size:21

Alignment explanation


    Indices: 541--599  Score: 61
    Period size: 19  Copynumber: 2.9  Consensus size: 21

        531 AATTCTTGCT

                *                *
        541 TCTTGAAATAATTCTTCAATTG
          1 TCTTCAAATAA-TCTTCAATTA

                                  
        563 TCTTC--A-AATCTTCAAATTA
          1 TCTTCAAATAATCTTC-AATTA

                              
        582 TCTTCAAATAATCTTCAA
          1 TCTTCAAATAATCTTCAA

        600 ACACGAACTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 9
        0.74            0.05        0.21

Matches are distributed among these distances:
  18    5  0.16
  19   11  0.35
  20    1  0.03
  21    3  0.10
  22   11  0.35

ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42


Consensus pattern (21 bp):   
TCTTCAAATAATCTTCAATTA

Found at i:586 original size:11 final size:11

Alignment explanation


    Indices: 569--600  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

        559 ATTGTCTTCA

                       
        569 AATCTTCAAAT
          1 AATCTTCAAAT

            *          
        580 TATCTTCAAAT
          1 AATCTTCAAAT

                      
        591 AATCTTCAAA
          1 AATCTTCAAA

        601 CACGAACTTC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38


Consensus pattern (11 bp):   
AATCTTCAAAT

Found at i:600 original size:22 final size:22

Alignment explanation


    Indices: 541--600  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

        531 AATTCTTGCT

                *                 *
        541 TCTTGAAATAATTCTTC-AATTG
          1 TCTTCAAATAA-TCTTCAAATTA

                                  
        563 TCTTC--A-AATCTTCAAATTA
          1 TCTTCAAATAATCTTCAAATTA

                               
        582 TCTTCAAATAATCTTCAAA
          1 TCTTCAAATAATCTTCAAA

        601 CACGAACTTC


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  18    5  0.16
  19   11  0.34
  20    1  0.03
  21    1  0.03
  22   14  0.44

ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42


Consensus pattern (22 bp):   
TCTTCAAATAATCTTCAAATTA

Found at i:4880 original size:35 final size:34

Alignment explanation


    Indices: 4860--5100  Score: 340
    Period size: 35  Copynumber: 6.9  Consensus size: 34

       4850 TACTCATTGA

                                           *  
       4860 ACTACTTAATTACCCTGAATTAAGTTGATTATTG
          1 ACTACTTAATTACCCTGAATTAAGTTGATTACTG

              *            *                   
       4894 AATTACTTAATTACCTTGAATTAAGTTGATTACTG
          1 -ACTACTTAATTACCCTGAATTAAGTTGATTACTG

                                               
       4929 ACTCACTTAATTACCCTGAATTAAGTTGATTACTG
          1 ACT-ACTTAATTACCCTGAATTAAGTTGATTACTG

            *             *                    
       4964 GCTTACTTAATTACACTGAATTAAGTTGATTACTG
          1 AC-TACTTAATTACCCTGAATTAAGTTGATTACTG

            *                                  
       4999 GCTTACTTAATTACCCTGAATTAAGTTGATTACTG
          1 AC-TACTTAATTACCCTGAATTAAGTTGATTACTG

            *                                   
       5034 GCTTACTTAATTACCCTGAATTAAGTT-ATTTACTG
          1 AC-TACTTAATTACCCTGAATTAAGTTGA-TTACTG

                                       *    
       5069 ATCTACTTAATTACCCTGAATTAAGTTAATTA
          1 A-CTACTTAATTACCCTGAATTAAGTTGATTA

       5101 TTACTGATTC


Statistics
Matches: 192,  Mismatches: 9, Indels: 10
        0.91            0.04        0.05

Matches are distributed among these distances:
  34    3  0.02
  35  186  0.97
  36    3  0.02

ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41


Consensus pattern (34 bp):   
ACTACTTAATTACCCTGAATTAAGTTGATTACTG

Found at i:4971 original size:105 final size:105

Alignment explanation


    Indices: 4831--5102  Score: 377
    Period size: 105  Copynumber: 2.6  Consensus size: 105

       4821 TTACTAAACA

                 *   *           * * *   *                                   
       4831 TAATTTCCCCGAATTAAGTTACTCATTGAACTACTTAATTACCCTGAATTAAGTTGATTATTGAA
          1 TAATTACCCTGAATTAAGTTATTTACTGATCTACTTAATTACCCTGAATTAAGTTGATTATTGAA

                         *                          
       4896 TTACTTAATTACCTTGAATTAAGTTGATTACTGACTCACT
         66 TTACTTAATTACCCTGAATTAAGTTGATTACTGACTCACT

                                          *             *                 *  
       4936 TAATTACCCTGAATTAAGTTGA-TTACTG-GCTTACTTAATTACACTGAATTAAGTTGATTACTG
          1 TAATTACCCTGAATTAAGTT-ATTTACTGATC-TACTTAATTACCCTGAATTAAGTTGATTATTG

            **                                 *  *   
       4999 GCTTACTTAATTACCCTGAATTAAGTTGATTACTGGCTTACT
         64 AATTACTTAATTACCCTGAATTAAGTTGATTACTGACTCACT

                                                                   *      
       5041 TAATTACCCTGAATTAAGTTATTTACTGATCTACTTAATTACCCTGAATTAAGTTAATTATT
          1 TAATTACCCTGAATTAAGTTATTTACTGATCTACTTAATTACCCTGAATTAAGTTGATTATT

       5103 ACTGATTCAT


Statistics
Matches: 147,  Mismatches: 16, Indels: 8
        0.86            0.09        0.05

Matches are distributed among these distances:
 104    2  0.01
 105  143  0.97
 106    2  0.01

ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41


Consensus pattern (105 bp):   
TAATTACCCTGAATTAAGTTATTTACTGATCTACTTAATTACCCTGAATTAAGTTGATTATTGAA
TTACTTAATTACCCTGAATTAAGTTGATTACTGACTCACT
Done.