Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007544.1 Corchorus capsularis cultivar CVL-1 contig07565, 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: 7740
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31


Found at i:836 original size:22 final size:22

Alignment explanation


    Indices: 811--853  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        801 AAGTCCTATT

                                  
        811 AAAACCACTAATAAAAAGTGCG
          1 AAAACCACTAATAAAAAGTGCG

                 **              
        833 AAAACTGCTAATAAAAAGTGC
          1 AAAACCACTAATAAAAAGTGC

        854 AAGAAGGGTA


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

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.53, C:0.16, G:0.14, T:0.16


Consensus pattern (22 bp):   
AAAACCACTAATAAAAAGTGCG

Found at i:1456 original size:12 final size:12

Alignment explanation


    Indices: 1439--1464  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1429 GTGGCTTGCA

                        
       1439 AGCATGAACCAT
          1 AGCATGAACCAT

                        
       1451 AGCATGAACCAT
          1 AGCATGAACCAT

              
       1463 AG
          1 AG

       1465 GAGATAGTGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.42, C:0.23, G:0.19, T:0.15


Consensus pattern (12 bp):   
AGCATGAACCAT

Found at i:1523 original size:24 final size:24

Alignment explanation


    Indices: 1496--1545  Score: 91
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       1486 CAAAGCGCCA

                                    
       1496 TTAACAAAACTACCAACTTGCTTT
          1 TTAACAAAACTACCAACTTGCTTT

                           *        
       1520 TTAACAAAACTACCAGCTTGCTTT
          1 TTAACAAAACTACCAACTTGCTTT

              
       1544 TT
          1 TT

       1546 TAAATTTGAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36


Consensus pattern (24 bp):   
TTAACAAAACTACCAACTTGCTTT

Found at i:1703 original size:12 final size:12

Alignment explanation


    Indices: 1688--1713  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1678 CAAAAAAAAA

                        
       1688 AAAAAAAAGAGG
          1 AAAAAAAAGAGG

                        
       1700 AAAAAAAAGAGG
          1 AAAAAAAAGAGG

              
       1712 AA
          1 AA

       1714 TAAGCTTTAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (12 bp):   
AAAAAAAAGAGG

Found at i:1875 original size:18 final size:18

Alignment explanation


    Indices: 1852--1889  Score: 76
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       1842 GCTATCTGTC

                              
       1852 CAGGATCAATCACTAGTT
          1 CAGGATCAATCACTAGTT

                              
       1870 CAGGATCAATCACTAGTT
          1 CAGGATCAATCACTAGTT

              
       1888 CA
          1 CA

       1890 CCTCGTCCAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26


Consensus pattern (18 bp):   
CAGGATCAATCACTAGTT

Found at i:5144 original size:20 final size:20

Alignment explanation


    Indices: 5104--5145  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       5094 TCTCACAAGA

                       *    *   
       5104 TTCTAGCCGTTGGAACTCTT
          1 TTCTAGCCGTTAGAACACTT

                        *       
       5124 TTCTAGCCGTTATAACACTT
          1 TTCTAGCCGTTAGAACACTT

              
       5144 TT
          1 TT

       5146 TCAACAATTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43


Consensus pattern (20 bp):   
TTCTAGCCGTTAGAACACTT
Done.