Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013719.1 Corchorus capsularis cultivar CVL-1 contig13740, 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: 22533
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32


Found at i:3725 original size:4 final size:4

Alignment explanation


    Indices: 3716--3747  Score: 55
    Period size: 4  Copynumber: 8.0  Consensus size: 4

       3706 TTCGTCTCTA

                                             *     
       3716 TTTC TTTC TTTC TTTC TTTC TTTC TTTT TTTC
          1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC

       3748 CAACTTTTGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   4   26  1.00

ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78


Consensus pattern (4 bp):   
TTTC

Found at i:8753 original size:25 final size:27

Alignment explanation


    Indices: 8712--8778  Score: 70
    Period size: 25  Copynumber: 2.5  Consensus size: 27

       8702 TAAAATATAA

                                     * 
       8712 ATATA-TATAATATTTATAT-TG-ATT
          1 ATATATTATAATATTTATATCTGAAAT

                                        
       8736 ATATATTATAAT-TATTATATCTGAAAT
          1 ATATATTATAATAT-TTATATCTGAAAT

                            
       8763 ATATATATATATATAT
          1 ATATAT-TATA-ATAT

       8779 ATAGAAGTTT


Statistics
Matches: 35,  Mismatches: 1, Indels: 8
        0.80            0.02        0.18

Matches are distributed among these distances:
  24    6  0.17
  25   12  0.34
  26    2  0.06
  27    8  0.23
  28    4  0.11
  29    2  0.06
  30    1  0.03

ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51


Consensus pattern (27 bp):   
ATATATTATAATATTTATATCTGAAAT

Found at i:16618 original size:28 final size:29

Alignment explanation


    Indices: 16586--16653  Score: 75
    Period size: 28  Copynumber: 2.4  Consensus size: 29

      16576 CAAAAATGAC

                                         
      16586 ACGTGGCACGTGGCATTTTTG-ACACGTG
          1 ACGTGGCACGTGGCATTTTTGTACACGTG

                 *  *   * *              
      16614 ACGTGCCATGTGTCCTTTTTGTACACGTG
          1 ACGTGGCACGTGGCATTTTTGTACACGTG

            * *        
      16643 GCATGGCACGT
          1 ACGTGGCACGT

      16654 CGGATGCCCG


Statistics
Matches: 31,  Mismatches: 8, Indels: 1
        0.77            0.20        0.03

Matches are distributed among these distances:
  28   17  0.55
  29   14  0.45

ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31


Consensus pattern (29 bp):   
ACGTGGCACGTGGCATTTTTGTACACGTG

Found at i:18679 original size:25 final size:26

Alignment explanation


    Indices: 18651--18700  Score: 68
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      18641 GTAATTTTAT

                     *                 
      18651 TTTAATA-TGTTTT-ATATATAATGTA
          1 TTTAATAGTATTTTCATA-ATAATGTA

                                     
      18676 TTTAATAGTATTTTCATAATAATGT
          1 TTTAATAGTATTTTCATAATAATGT

      18701 CTAAAAATTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  25    7  0.32
  26   12  0.55
  27    3  0.14

ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54


Consensus pattern (26 bp):   
TTTAATAGTATTTTCATAATAATGTA

Found at i:18688 original size:36 final size:36

Alignment explanation


    Indices: 18616--18689  Score: 89
    Period size: 36  Copynumber: 2.1  Consensus size: 36

      18606 TAAATATTAA

                                          **    
      18616 TTAATAGTTATTATATATAAATATTGTAATTTTATT
          1 TTAATAGTTATTATATATAAATATTGTAATAGTATT

                                  *               
      18652 TTAATATGTT-TTATATATAATGTATT-TAATAGTATT
          1 TTAATA-GTTATTATATATAA-ATATTGTAATAGTATT

              
      18688 TT
          1 TT

      18690 CATAATAATG


Statistics
Matches: 33,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  36   26  0.79
  37    7  0.21

ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57


Consensus pattern (36 bp):   
TTAATAGTTATTATATATAAATATTGTAATAGTATT

Found at i:18768 original size:12 final size:13

Alignment explanation


    Indices: 18751--18783  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

      18741 GAAGTAAAAA

                         
      18751 TAAATAAAT-ATT
          1 TAAATAAATAATT

                         
      18763 TAAATAAATAATT
          1 TAAATAAATAATT

                    
      18776 TAAATAAA
          1 TAAATAAA

      18784 AGTGACCATG


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

Matches are distributed among these distances:
  12    9  0.45
  13   11  0.55

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (13 bp):   
TAAATAAATAATT

Done.