Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020928.1 Corchorus olitorius cultivar O-4 contig20961, 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: 2385
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40


Found at i:1451 original size:7 final size:7

Alignment explanation


    Indices: 1439--1486  Score: 57
    Period size: 7  Copynumber: 7.3  Consensus size: 7

       1429 TATTTATATA

                   
       1439 TATAATG
          1 TATAATG

                   
       1446 TATAATG
          1 TATAATG

               *   
       1453 TATTATG
          1 TATAATG

                   
       1460 --TAATG
          1 TATAATG

                   
       1465 TATAATG
          1 TATAATG

                   
       1472 TATAA-G
          1 TATAATG

               *   
       1478 TATTATG
          1 TATAATG

              
       1485 TA
          1 TA

       1487 CATATATATT


Statistics
Matches: 35,  Mismatches: 3, Indels: 6
        0.80            0.07        0.14

Matches are distributed among these distances:
   5    4  0.11
   6    5  0.14
   7   26  0.74

ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46


Consensus pattern (7 bp):   
TATAATG

Found at i:1465 original size:12 final size:12

Alignment explanation


    Indices: 1448--1486  Score: 51
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       1438 ATATAATGTA

                        
       1448 TAATGTATTATG
          1 TAATGTATTATG

                    *   
       1460 TAATGTATAATG
          1 TAATGTATTATG

                *        
       1472 TATAAGTATTATG
          1 TA-ATGTATTATG

              
       1485 TA
          1 TA

       1487 CATATATATT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  12   13  0.57
  13   10  0.43

ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46


Consensus pattern (12 bp):   
TAATGTATTATG

Found at i:1494 original size:26 final size:26

Alignment explanation


    Indices: 1436--1494  Score: 93
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       1426 TAGTATTTAT

                                      
       1436 ATATATAATGTATAATGTATTATGTA
          1 ATATATAATGTATAATGTATTATGTA

              *                       
       1462 ATGTATAATGTATAA-GTATTATGTA
          1 ATATATAATGTATAATGTATTATGTA

                    
       1487 CATATATA
          1 -ATATATA

       1495 TTAAAACTTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  25   10  0.33
  26   20  0.67

ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44


Consensus pattern (26 bp):   
ATATATAATGTATAATGTATTATGTA
Done.