Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005486.1 Corchorus capsularis cultivar CVL-1 contig05504, 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: 7885
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Found at i:1518 original size:2 final size:2

Alignment explanation


    Indices: 1511--1536  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1501 GCCAAATTAA

                                                  
       1511 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       1537 TATTCTATGG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2046 original size:2 final size:2

Alignment explanation


    Indices: 2039--2072  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       2029 AATGTGGGAC

                                                                
       2039 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2073 GACACACAGA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:2299 original size:69 final size:69

Alignment explanation


    Indices: 2188--2326  Score: 251
    Period size: 69  Copynumber: 2.0  Consensus size: 69

       2178 AATGAGATAT

                                                                             
       2188 AGACTGGAGTCCGTGGGAGTTACCACAGATTCGAGGCTAAATCACACATGTAATTACATATTTAA
          1 AGACTGGAGTCCGTGGGAGTTACCACAGATTCGAGGCTAAATCACACATGTAATTACATATTTAA

                
       2253 GTGA
         66 GTGA

                 *    *               *                                      
       2257 AGACTTGAGTTCGTGGGAGTTACCACGGATTCGAGGCTAAATCACACATGTAATTACATATTTAA
          1 AGACTGGAGTCCGTGGGAGTTACCACAGATTCGAGGCTAAATCACACATGTAATTACATATTTAA

                
       2322 GTGA
         66 GTGA

             
       2326 A
          1 A

       2327 TTTTTAGTTT


Statistics
Matches: 67,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  69   67  1.00

ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27


Consensus pattern (69 bp):   
AGACTGGAGTCCGTGGGAGTTACCACAGATTCGAGGCTAAATCACACATGTAATTACATATTTAA
GTGA

Found at i:5495 original size:24 final size:24

Alignment explanation


    Indices: 5474--5520  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5464 CACCATCCGT

                                    
       5474 AAAATTGACCCAAATTTTATCCCC
          1 AAAATTGACCCAAATTTTATCCCC

             **               *    
       5498 ATGATTGACCCAAATTTTGTCCC
          1 AAAATTGACCCAAATTTTATCCC

       5521 TCATGATGTG


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.32, C:0.28, G:0.09, T:0.32


Consensus pattern (24 bp):   
AAAATTGACCCAAATTTTATCCCC
Done.