Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018727.1 Corchorus olitorius cultivar O-4 contig18760, 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: 2856
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27


Found at i:95 original size:15 final size:15

Alignment explanation


    Indices: 75--106  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

         65 TATTAATTAG

                           
         75 AAGAAATTAAAATAC
          1 AAGAAATTAAAATAC

                           
         90 AAGAAATTAAAATAC
          1 AAGAAATTAAAATAC

              
        105 AA
          1 AA

        107 ATCATTCGGC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19


Consensus pattern (15 bp):   
AAGAAATTAAAATAC

Found at i:2495 original size:16 final size:15

Alignment explanation


    Indices: 2468--2497  Score: 51
    Period size: 16  Copynumber: 1.9  Consensus size: 15

       2458 ATTATTGATT

                           
       2468 AATTAATAATTAATG
          1 AATTAATAATTAATG

                           
       2483 AATTAACTAATTAAT
          1 AATTAA-TAATTAAT

       2498 TTAATAATGA


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:0.53, C:0.03, G:0.03, T:0.40


Consensus pattern (15 bp):   
AATTAATAATTAATG

Found at i:2552 original size:15 final size:15

Alignment explanation


    Indices: 2528--2567  Score: 57
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       2518 TAATAACTTT

                 *         
       2528 TCATATTTAATAAAA
          1 TCATAATTAATAAAA

                           
       2543 TCATAATTAATAAAA
          1 TCATAATTAATAAAA

                        
       2558 -CAT-ATTAATA
          1 TCATAATTAATA

       2568 CTTAATAATC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  13    7  0.29
  14    3  0.12
  15   14  0.58

ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38


Consensus pattern (15 bp):   
TCATAATTAATAAAA

Found at i:2726 original size:31 final size:33

Alignment explanation


    Indices: 2655--2726  Score: 85
    Period size: 34  Copynumber: 2.2  Consensus size: 33

       2645 CTATTTTCAT

                      *                     *  
       2655 AATAATTTAATTAATAATAATAATAACATTACTTA
          1 AATAA-TTAAATAATAATAATAATAACA-TACCTA

            *                                
       2690 CATAATTAAATAATAATAATAATAA-A-ACCTA
          1 AATAATTAAATAATAATAATAATAACATACCTA

                  
       2721 AATAAT
          1 AATAAT

       2727 CATTAATTAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  31    9  0.27
  33    1  0.03
  34   19  0.58
  35    4  0.12

ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35


Consensus pattern (33 bp):   
AATAATTAAATAATAATAATAATAACATACCTA

Found at i:2765 original size:21 final size:21

Alignment explanation


    Indices: 2731--2771  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2721 AATAATCATT

                           *     
       2731 AATTAATTCAATAATTTAAAC
          1 AATTAATTCAATAATCTAAAC

                                 
       2752 AATTAATT-AGATAATCTAAA
          1 AATTAATTCA-ATAATCTAAA

       2772 AATAATAATA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    1  0.06
  21   17  0.94

ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37


Consensus pattern (21 bp):   
AATTAATTCAATAATCTAAAC
Done.