Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010045.1 Corchorus capsularis cultivar CVL-1 contig10066, 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: 27516
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:7861 original size:108 final size:108

Alignment explanation


    Indices: 7672--7906  Score: 287
    Period size: 108  Copynumber: 2.1  Consensus size: 108

       7662 TTGTGCTCGC

                             *                    *     *                    
       7672 GAAAATGATTAGTCTCTGAAAAGAAATTGAGTAATGATTTACTTTTCATATCATATATGATACAG
          1 GAAAATGATTAGTCTCTAAAAAGAAATTGAGTAATGATATACTTCTCATAT-ATATATGATACAG

                *                *    *                 
       7737 GAAGGAATTTGGTTAAAC-ATTAGCGTTCATTTCATCCCGACCT
         65 GAAGAAATTTGGTTAAACAATCAGCGCTCATTTCATCCCGACCT

                                                                          ** 
       7780 GAAAATGATTAGTCTCTAAAAAGAAATTG-GATAATGATATACTTCTCATAT-TATATGATATGG
          1 GAAAATGATTAGTCTCTAAAAAGAAATTGAG-TAATGATATACTTCTCATATATATATGATACAG

                                                      *  ** 
       7843 GAAGAAAATTTTGGTTAAACAAGATCAGCGCTCATTTCATCCTGATGT
         65 GAAG-AAA-TTTGGTTAAAC-A-ATCAGCGCTCATTTCATCCCGACCT

                 *          
       7891 GAAAAGGATTAGTCTC
          1 GAAAATGATTAGTCTC

       7907 GCACTAAATT


Statistics
Matches: 109,  Mismatches: 12, Indels: 9
        0.84            0.09        0.07

Matches are distributed among these distances:
 106   14  0.13
 107    3  0.03
 108   57  0.52
 111   35  0.32

ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33


Consensus pattern (108 bp):   
GAAAATGATTAGTCTCTAAAAAGAAATTGAGTAATGATATACTTCTCATATATATATGATACAGG
AAGAAATTTGGTTAAACAATCAGCGCTCATTTCATCCCGACCT

Found at i:11690 original size:18 final size:18

Alignment explanation


    Indices: 11664--11698  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      11654 CTGAAGTTGA

                        *     
      11664 CTTTCATGGTTATGATGG
          1 CTTTCATGGTTACGATGG

                *            
      11682 CTTTGATGGTTACGATG
          1 CTTTCATGGTTACGATG

      11699 ATGATCTGAA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.17, C:0.11, G:0.29, T:0.43


Consensus pattern (18 bp):   
CTTTCATGGTTACGATGG

Found at i:14440 original size:29 final size:30

Alignment explanation


    Indices: 14389--14458  Score: 81
    Period size: 29  Copynumber: 2.3  Consensus size: 30

      14379 TCATAAGGGT

                                   *        
      14389 AAAATGTCATGATTTTGGAAGTTTA-GGGGAC
          1 AAAATGTCATGATTTT-GAAGTTCATGGGG-C

                    *                     
      14420 AAAATGTCCTGATTTT-AAGTTCATGGGGC
          1 AAAATGTCATGATTTTGAAGTTCATGGGGC

                 *    
      14449 AAAATATCAT
          1 AAAATGTCAT

      14459 TGACGCAATA


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  29   15  0.44
  30    4  0.12
  31   15  0.44

ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33


Consensus pattern (30 bp):   
AAAATGTCATGATTTTGAAGTTCATGGGGC

Found at i:20117 original size:13 final size:13

Alignment explanation


    Indices: 20099--20123  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      20089 TTCAATATTC

                         
      20099 TAAATATTATTTA
          1 TAAATATTATTTA

                        
      20112 TAAATATTATTT
          1 TAAATATTATTT

      20124 GGAATTGTAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA

Found at i:26597 original size:46 final size:46

Alignment explanation


    Indices: 26530--26622  Score: 186
    Period size: 46  Copynumber: 2.0  Consensus size: 46

      26520 AGGTTTTAAT

                                                          
      26530 GACCGAAACTAATCCTTTTCGGATCAAGAACATAACAAAAAACAAA
          1 GACCGAAACTAATCCTTTTCGGATCAAGAACATAACAAAAAACAAA

                                                          
      26576 GACCGAAACTAATCCTTTTCGGATCAAGAACATAACAAAAAACAAA
          1 GACCGAAACTAATCCTTTTCGGATCAAGAACATAACAAAAAACAAA

             
      26622 G
          1 G

      26623 GAGAGACTTT


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  46   47  1.00

ACGTcount: A:0.49, C:0.22, G:0.12, T:0.17


Consensus pattern (46 bp):   
GACCGAAACTAATCCTTTTCGGATCAAGAACATAACAAAAAACAAA
Done.