Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012768.1 Corchorus capsularis cultivar CVL-1 contig12789, 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: 9190
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:506 original size:13 final size:13

Alignment explanation


    Indices: 488--521  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

        478 TAATTATTGT

                         
        488 TTGCTTTATTAAA
          1 TTGCTTTATTAAA

                        *
        501 TTGCTTTATTAAT
          1 TTGCTTTATTAAA

                    
        514 TTGCTTTA
          1 TTGCTTTA

        522 GATTTAGATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59


Consensus pattern (13 bp):   
TTGCTTTATTAAA

Found at i:529 original size:6 final size:6

Alignment explanation


    Indices: 518--550  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

        508 ATTAATTTGC

                                                  
        518 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT

        551 GCTTTGCTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55


Consensus pattern (6 bp):   
TTTAGA

Found at i:4795 original size:17 final size:16

Alignment explanation


    Indices: 4769--4803  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 16

       4759 CAATCTTGAC

                            
       4769 TTACCCATCTCCAACT
          1 TTACCCATCTCCAACT

                             
       4785 TTACTCCATCTCCAACT
          1 TTAC-CCATCTCCAACT

              
       4802 TT
          1 TT

       4804 CAAGTTTCAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  16    4  0.22
  17   14  0.78

ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37


Consensus pattern (16 bp):   
TTACCCATCTCCAACT

Found at i:6377 original size:101 final size:102

Alignment explanation


    Indices: 6224--6474  Score: 311
    Period size: 101  Copynumber: 2.5  Consensus size: 102

       6214 CTCCCGAGTA

                *               *                                      * *   
       6224 TTTTGGCTCTGTTTTTTGTTGATTTATTGAAGGCCACCAGCA-TCTATATGGAGTTGAAGACCAT
          1 TTTTTGCTCTGTTTTTTGTTCATTTATTGAAGGCCACCAGCATTCTATATGGAGTT-AAAAAC-T

                *                                  
       6288 T-TGGAATGATGAATGAAGATTTTGGAAGCTCCTAAAAT
         64 TCTGCAATGATGAATGAAGATTTTGGAAGCTCCTAAAAT

                                                                             
       6326 TTTTTGCT-TCG-TTTTTGTTCATTTATTGAAGGCCACCAGCATTCCT-T-TGGAGTTAAAAACT
          1 TTTTTGCTCT-GTTTTTTGTTCATTTATTGAAGGCCACCAGCATT-CTATATGGAGTTAAAAACT

                                *      *       *    
       6387 TGCTGCAATGATGAATGAAGGTTTTGGGAGCTCCTGAAAT
         64 T-CTGCAATGATGAATGAAGATTTTGGAAGCTCCTAAAAT

                                 *                            
       6427 TTTTTGCTCTGTTTTTTGTTCCTTT-TGTGAAGGCCACCAGCATT-TATA
          1 TTTTTGCTCTGTTTTTTGTTCATTTAT-TGAAGGCCACCAGCATTCTATA

       6475 GCTGTCTTTT


Statistics
Matches: 130,  Mismatches: 9, Indels: 20
        0.82            0.06        0.13

Matches are distributed among these distances:
  99    2  0.02
 100    5  0.04
 101   81  0.62
 102   40  0.31
 103    2  0.02

ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40


Consensus pattern (102 bp):   
TTTTTGCTCTGTTTTTTGTTCATTTATTGAAGGCCACCAGCATTCTATATGGAGTTAAAAACTTC
TGCAATGATGAATGAAGATTTTGGAAGCTCCTAAAAT

Found at i:7519 original size:10 final size:10

Alignment explanation


    Indices: 7504--7529  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       7494 AGTTGCTGCT

                      
       7504 AAATTCCAGA
          1 AAATTCCAGA

                      
       7514 AAATTCCAGA
          1 AAATTCCAGA

                  
       7524 AAATTC
          1 AAATTC

       7530 TAGAGTCCTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23


Consensus pattern (10 bp):   
AAATTCCAGA
Done.