Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000869.1 Corchorus capsularis cultivar CVL-1 contig00869, 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: 12528
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:290 original size:18 final size:19

Alignment explanation


    Indices: 269--304  Score: 56
    Period size: 18  Copynumber: 1.9  Consensus size: 19

        259 ATATAATGAT

                   *           
        269 TATTAGTGTTA-TTATTAA
          1 TATTAGTATTATTTATTAA

                              
        287 TATTAGTATTATTTATTA
          1 TATTAGTATTATTTATTA

        305 TTAGTAATTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18   10  0.62
  19    6  0.38

ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58


Consensus pattern (19 bp):   
TATTAGTATTATTTATTAA

Found at i:4567 original size:21 final size:21

Alignment explanation


    Indices: 4541--4585  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4531 TAAAATGGGG

                   **            
       4541 TTTGCTATTTACCGCCCCCCT
          1 TTTGCTAAATACCGCCCCCCT

                             *   
       4562 TTTGCTAAATACCGCCCTCCT
          1 TTTGCTAAATACCGCCCCCCT

               
       4583 TTT
          1 TTT

       4586 TATAATTTTT


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.13, C:0.38, G:0.09, T:0.40


Consensus pattern (21 bp):   
TTTGCTAAATACCGCCCCCCT

Found at i:9426 original size:173 final size:175

Alignment explanation


    Indices: 9117--9463  Score: 531
    Period size: 173  Copynumber: 2.0  Consensus size: 175

       9107 AGTTGATGGG

                               *                     *       *               
       9117 TAATGTCTTATAGAAACGTGGATTGGTGTTTTTTGCTTGATGTGAGTTTGTATTGCCATGTGAAA
          1 TAATGTCTTATAGAAACGTAGATTGGTGTTTTTTGCTTGATATGAGTTTATATTGCCATGTGAAA

                                      *                 *       *  *         
       9182 ATTGATTTTATGTTGAATATATGAATTAGGGATGTGAATGCATAGATCTATAGATTAGGGGGATA
         66 ATTGATTTTATGTTGAATATATGAATGAGGGATGTGAATGCATAAATCTATAAATGAGGGGGATA

                                                          
       9247 GAATTGAAAA-T-GAGAAGTTTAGGGACCTAATTGCAAAAAAATTA
        131 GAATTGAAAATTCGA-AAGTTTAGGGACCTAATTGCAAAAAAATTA

                            *                            *                 * 
       9291 TAATGTCTTATAG-AATGTAGATTGGTGTTTGTTT-CTTGATATGGGTTTATATTGCCATGTGGA
          1 TAATGTCTTATAGAAACGTAGATTGGTGTTT-TTTGCTTGATATGAGTTTATATTGCCATGTGAA

                      *                                                      
       9354 AATTGATTTTGTGTTGAATATATGAATGAGGGATGTGAATGCATAAATCTATAAATGAGGGGGAT
         65 AATTGATTTTATGTTGAATATATGAATGAGGGATGTGAATGCATAAATCTATAAATGAGGGGGAT

                           *                             
       9419 AGAATTGAAAATTTCTAAAGTTTAGGGACCTAATTGCAAAAAAAT
        130 AGAATTGAAAA-TTCGAAAGTTTAGGGACCTAATTGCAAAAAAAT

       9464 ATACAGTAAG


Statistics
Matches: 157,  Mismatches: 12, Indels: 7
        0.89            0.07        0.04

Matches are distributed among these distances:
 173  111  0.71
 174   16  0.10
 175   29  0.18
 176    1  0.01

ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37


Consensus pattern (175 bp):   
TAATGTCTTATAGAAACGTAGATTGGTGTTTTTTGCTTGATATGAGTTTATATTGCCATGTGAAA
ATTGATTTTATGTTGAATATATGAATGAGGGATGTGAATGCATAAATCTATAAATGAGGGGGATA
GAATTGAAAATTCGAAAGTTTAGGGACCTAATTGCAAAAAAATTA

Found at i:12269 original size:24 final size:25

Alignment explanation


    Indices: 12221--12269  Score: 73
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      12211 TTATTTTCCA

                                *    
      12221 TCAAACTTCAAACTTTTCAATTCTC
          1 TCAAACTTCAAACTTTTCAAATCTC

                *                    
      12246 TCAACCTTCAAAC-TTTCAAATCTC
          1 TCAAACTTCAAACTTTTCAAATCTC

      12270 AATCATTCAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24   10  0.45
  25   12  0.55

ACGTcount: A:0.33, C:0.31, G:0.00, T:0.37


Consensus pattern (25 bp):   
TCAAACTTCAAACTTTTCAAATCTC
Done.