Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016981.1 Corchorus olitorius cultivar O-4 contig17014, 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: 27680
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30


Found at i:5256 original size:9 final size:9

Alignment explanation


    Indices: 5244--5273  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

       5234 GAAATACCGT

                     
       5244 ACCGGTTTG
          1 ACCGGTTTG

                     
       5253 ACCGGTTTG
          1 ACCGGTTTG

               *     
       5262 ACCAGTTTG
          1 ACCGGTTTG

               
       5271 ACC
          1 ACC

       5274 ATAGTCAACT


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

Matches are distributed among these distances:
   9   20  1.00

ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30


Consensus pattern (9 bp):   
ACCGGTTTG

Found at i:6079 original size:21 final size:19

Alignment explanation


    Indices: 6054--6111  Score: 80
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       6044 GCTGCTCTAA

                                 
       6054 TAATCTCATCTGTACAGTACC
          1 TAATCTCATCTGTACAGT--C

                  *           *
       6075 TAATCTAATCTGTACAGTG
          1 TAATCTCATCTGTACAGTC

                              
       6094 TAATCTCATCTGTACAGT
          1 TAATCTCATCTGTACAGT

       6112 TGCTAAACAG


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  19   17  0.50
  21   17  0.50

ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36


Consensus pattern (19 bp):   
TAATCTCATCTGTACAGTC

Found at i:9230 original size:18 final size:18

Alignment explanation


    Indices: 9207--9245  Score: 69
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       9197 ACATGTTAGA

                              
       9207 AATGGCAACAGAAATGGC
          1 AATGGCAACAGAAATGGC

                   *          
       9225 AATGGCATCAGAAATGGC
          1 AATGGCAACAGAAATGGC

               
       9243 AAT
          1 AAT

       9246 CAACGCCATG


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

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15


Consensus pattern (18 bp):   
AATGGCAACAGAAATGGC

Found at i:15375 original size:14 final size:15

Alignment explanation


    Indices: 15356--15385  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      15346 CAATTAAAGC

                           
      15356 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
      15370 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
      15385 A
          1 A

      15386 TTAAAGAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:15769 original size:21 final size:21

Alignment explanation


    Indices: 15743--15792  Score: 73
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      15733 GGAATGGCGA

                        **       
      15743 TGGCACGGGCATGGCCGGTGG
          1 TGGCACGGGCATAACCGGTGG

                      *          
      15764 TGGCACGGGCTTAACCGGTGG
          1 TGGCACGGGCATAACCGGTGG

                    
      15785 TGGCACGG
          1 TGGCACGG

      15793 TGAATGGGCG


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16


Consensus pattern (21 bp):   
TGGCACGGGCATAACCGGTGG

Found at i:19516 original size:16 final size:15

Alignment explanation


    Indices: 19478--19519  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      19468 ACAGAGATTG

                           
      19478 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
      19493 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      19508 ACTAGAAAACAA
          1 AC-AGAAAACAA

      19520 AACAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.