Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011941.1 Corchorus olitorius cultivar O-4 contig11974, 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: 20909
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:1216 original size:13 final size:13

Alignment explanation


    Indices: 1198--1231  Score: 68
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       1188 CTTGTCCCGG

                         
       1198 TTCACTACCTCAT
          1 TTCACTACCTCAT

                         
       1211 TTCACTACCTCAT
          1 TTCACTACCTCAT

                    
       1224 TTCACTAC
          1 TTCACTAC

       1232 GTCACTTTAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38


Consensus pattern (13 bp):   
TTCACTACCTCAT

Found at i:2383 original size:80 final size:80

Alignment explanation


    Indices: 2250--2400  Score: 284
    Period size: 80  Copynumber: 1.9  Consensus size: 80

       2240 CGAATAACAG

                                *                                         *  
       2250 TCATGCCAATCATGAACACAGTACTATGATAATTTAGTTTCATATTTCTAATGCAGGGTCTTTAG
          1 TCATGCCAATCATGAACACAATACTATGATAATTTAGTTTCATATTTCTAATGCAGGGTCTTCAG

                           
       2315 TTATCTAAAGAGAGT
         66 TTATCTAAAGAGAGT

                                                                             
       2330 TCATGCCAATCATGAACACAATACTATGATAATTTAGTTTCATATTTCTAATGCAGGGTCTTCAG
          1 TCATGCCAATCATGAACACAATACTATGATAATTTAGTTTCATATTTCTAATGCAGGGTCTTCAG

                  
       2395 TTATCT
         66 TTATCT

       2401 GATTCTCTTT


Statistics
Matches: 69,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  80   69  1.00

ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37


Consensus pattern (80 bp):   
TCATGCCAATCATGAACACAATACTATGATAATTTAGTTTCATATTTCTAATGCAGGGTCTTCAG
TTATCTAAAGAGAGT

Found at i:9290 original size:14 final size:13

Alignment explanation


    Indices: 9266--9302  Score: 58
    Period size: 14  Copynumber: 2.8  Consensus size: 13

       9256 TTTAGCTTAA

                         
       9266 ATTAT-TATTATT
          1 ATTATATATTATT

                          
       9278 ATTATAATATTATT
          1 ATTAT-ATATTATT

                       
       9292 ATTATATATTA
          1 ATTATATATTA

       9303 GGACAATAAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  12    5  0.22
  13    6  0.26
  14   12  0.52

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (13 bp):   
ATTATATATTATT
Done.