Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014858.1 Corchorus olitorius cultivar O-4 contig14891, 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: 29139
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:6741 original size:7 final size:7

Alignment explanation


    Indices: 6729--6763  Score: 70
    Period size: 7  Copynumber: 5.0  Consensus size: 7

       6719 AGAATATATA

                   
       6729 TGCAAAG
          1 TGCAAAG

                   
       6736 TGCAAAG
          1 TGCAAAG

                   
       6743 TGCAAAG
          1 TGCAAAG

                   
       6750 TGCAAAG
          1 TGCAAAG

                   
       6757 TGCAAAG
          1 TGCAAAG

       6764 GGGGTTAGTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   28  1.00

ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14


Consensus pattern (7 bp):   
TGCAAAG

Found at i:11495 original size:69 final size:68

Alignment explanation


    Indices: 11384--11726  Score: 515
    Period size: 69  Copynumber: 5.0  Consensus size: 68

      11374 TAATTTATTT

                  *                 *                     *    *             
      11384 TTTTAAATAGTTCATCGCTCTTTGCATTCATAACGAAAATTTGTACATATCCGGGCGGTTAGCTT
          1 TTTTAAGTAGTTCATCGCTCTTTGTATTCATAACGAAAATTTGTACGTAT-GGGGCGGTTAGCTT

                
      11449 GATA
         65 GATA

                                                         *                   
      11453 TTTTAAGTAGTTCATCGCTCTTTGTATTCATAACGAAAATTTGTATGTATGGGTGCGGTTAGCTT
          1 TTTTAAGTAGTTCATCGCTCTTTGTATTCATAACGAAAATTTGTACGTATGGG-GCGGTTAGCTT

                
      11518 GATA
         65 GATA

                        *  *     *           *                     *         
      11522 TTTTAAGTAGTTGATTGCTCTCTGTATTCATAATGAAAATTTGTACGTATCGGGGAGGTTAGCTT
          1 TTTTAAGTAGTTCATCGCTCTTTGTATTCATAACGAAAATTTGTACGTAT-GGGGCGGTTAGCTT

                
      11587 GATA
         65 GATA

                                                                    *        
      11591 TTTTAAGTAGTTCATCGCTCTTTGTATTCATAACGAAAATTTGTACGTATTGGGGCCGTTAGCTT
          1 TTTTAAGTAGTTCATCGCTCTTTGTATTCATAACGAAAATTTGTACGTA-TGGGGCGGTTAGCTT

                
      11656 GATA
         65 GATA

                           *                 *                **             
      11660 TTTTAAGTAGTTCATTGCTCTTTGTATTCATAATGAAAATTTGTACGTATTAGGCGGTTAGCTTG
          1 TTTTAAGTAGTTCATCGCTCTTTGTATTCATAACGAAAATTTGTACGTATGGGGCGGTTAGCTTG

              
      11725 AT
         66 AT

      11727 TGTTCTGGGT


Statistics
Matches: 249,  Mismatches: 22, Indels: 7
        0.90            0.08        0.03

Matches are distributed among these distances:
  68   17  0.07
  69  228  0.92
  70    4  0.02

ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41


Consensus pattern (68 bp):   
TTTTAAGTAGTTCATCGCTCTTTGTATTCATAACGAAAATTTGTACGTATGGGGCGGTTAGCTTG
ATA

Found at i:20731 original size:11 final size:11

Alignment explanation


    Indices: 20715--20749  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      20705 TAGGGTTTGC

                       
      20715 TTTCTTTACTT
          1 TTTCTTTACTT

                   *   
      20726 TTTCTTTTCTT
          1 TTTCTTTACTT

               *       
      20737 TTTATTTACTT
          1 TTTCTTTACTT

              
      20748 TT
          1 TT

      20750 CTAGTTATAC


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

Matches are distributed among these distances:
  11   21  1.00

ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77


Consensus pattern (11 bp):   
TTTCTTTACTT

Found at i:21703 original size:15 final size:16

Alignment explanation


    Indices: 21679--21718  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      21669 AGAGATTGAA

                 *          
      21679 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                            
      21694 AGAAAACAATTAAACT
          1 AGAAAACAATTAAACT

                     
      21710 AGAAAACAA
          1 AGAAAACAA

      21719 AGCAAAGTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:28166 original size:24 final size:24

Alignment explanation


    Indices: 28137--28182  Score: 76
    Period size: 24  Copynumber: 1.9  Consensus size: 24

      28127 CAAAAAATTT

                                     
      28137 TCTTTTTTTTTAT-GACGCAAAAAC
          1 TCTTTTTTTTT-TCGACGCAAAAAC

                                  
      28161 TCTTTTTTTTTTCGACGCAAAA
          1 TCTTTTTTTTTTCGACGCAAAA

      28183 CACAAAACAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  23    1  0.05
  24   20  0.95

ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48


Consensus pattern (24 bp):   
TCTTTTTTTTTTCGACGCAAAAAC

Found at i:28639 original size:16 final size:15

Alignment explanation


    Indices: 28601--28642  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      28591 ACAGAGATTG

                   *       
      28601 ACAGAAATCAATTAA
          1 ACAGAAAACAATTAA

                           
      28616 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      28631 ACTAGAAAACAA
          1 AC-AGAAAACAA

      28643 AACAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.