Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009776.1 Corchorus capsularis cultivar CVL-1 contig09797, 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: 16573
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:759 original size:3 final size:3

Alignment explanation


    Indices: 751--783  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

        741 TTCTTCCTTT

                                                       
        751 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

        784 AATGCACTTA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
TAA

Found at i:1206 original size:3 final size:3

Alignment explanation


    Indices: 1198--1235  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       1188 TGTATATGTA

                                                              
       1198 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA

       1236 CCAGCGGTTC


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TAT

Found at i:2467 original size:2 final size:2

Alignment explanation


    Indices: 2462--2486  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       2452 ATGATGTGTG

                                                 
       2462 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       2487 GCACGATCAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:2941 original size:109 final size:109

Alignment explanation


    Indices: 2748--2949  Score: 291
    Period size: 109  Copynumber: 1.9  Consensus size: 109

       2738 TCGATAAAAA

                         *    *     *    *              *             *      
       2748 TACAATTAACTCTTCATTGAAATTTTAAAGTGACAAATATTTTGGAATACAAATTTTATTCTATA
          1 TACAATTAACTCTCCATTAAAATTCTAAAATGACAAATATTTTGAAATACAAATTTTACTCTATA

                          *                             
       2813 GTGACAAATAAATTGGAATGGGGGAGTAGTAAAAGCTAATAGAG
         66 GTGACAAATAAATTAGAATGGGGGAGTAGTAAAAGCTAATAGAG

                                                                             
       2857 TACAATTAA-TACTCCATTAAAATTCTAAAATGACAAATATTTTGAAATA-AAATTTTTACTCTA
          1 TACAATTAACT-CTCCATTAAAATTCTAAAATGACAAATATTTTGAAATACAAA-TTTTACTCTA

                   **                     
       2920 TAGTGACTGATAAATTAGAATGGGGGAGTA
         64 TAGTGACAAATAAATTAGAATGGGGGAGTA

       2950 ATTAAAAGAA


Statistics
Matches: 82,  Mismatches: 9, Indels: 4
        0.86            0.09        0.04

Matches are distributed among these distances:
 108    4  0.05
 109   78  0.95

ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34


Consensus pattern (109 bp):   
TACAATTAACTCTCCATTAAAATTCTAAAATGACAAATATTTTGAAATACAAATTTTACTCTATA
GTGACAAATAAATTAGAATGGGGGAGTAGTAAAAGCTAATAGAG

Found at i:4400 original size:15 final size:16

Alignment explanation


    Indices: 4371--4400  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       4361 ACTTACTCAA

                            
       4371 TTAAGTTTCTTCAATG
          1 TTAAGTTTCTTCAATG

                           
       4387 TTAAGTTT-TTCAAT
          1 TTAAGTTTCTTCAAT

       4401 AACTTAATAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53


Consensus pattern (16 bp):   
TTAAGTTTCTTCAATG
Done.