Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017411.1 Corchorus olitorius cultivar O-4 contig17444, 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: 6854
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29


Found at i:2406 original size:28 final size:27

Alignment explanation


    Indices: 2375--2433  Score: 73
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       2365 CTAAATCGAC

                                        
       2375 ATTTTCAACAACTAAGGGTAAAATAGTA
          1 ATTTTC-ACAACTAAGGGTAAAATAGTA

                  * **             *   
       2403 ATTTTCCCCGCTAAGGGTAAAATGGTA
          1 ATTTTCACAACTAAGGGTAAAATAGTA

                
       2430 ATTT
          1 ATTT

       2434 CACTTATATT


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  27   21  0.78
  28    6  0.22

ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32


Consensus pattern (27 bp):   
ATTTTCACAACTAAGGGTAAAATAGTA

Found at i:4113 original size:43 final size:40

Alignment explanation


    Indices: 4061--4182  Score: 111
    Period size: 43  Copynumber: 2.9  Consensus size: 40

       4051 AGGAAGATTT

                           *   *        *              
       4061 ATTAAAATTTCATAGTTAGGGTATCAAAGTTTCATATGGAGTA
          1 ATTAAAATTTCATAGGTA-AGTATCAAAATTTCATA-GG-GTA

                *              *                    
       4104 ATTACAATTTCATAGGTAATTATCAAAATTTCATAGGGTA
          1 ATTAAAATTTCATAGGTAAGTATCAAAATTTCATAGGGTA

                         *                          
       4144 ATTATCAAAATTTAATAGGGT-AGTTATCAAAATTTCATA
          1 A-T-T-AAAATTTCATA-GGTAAG-TATCAAAATTTCATA

       4183 AAAATATTCA


Statistics
Matches: 66,  Mismatches: 8, Indels: 9
        0.80            0.10        0.11

Matches are distributed among these distances:
  40    4  0.06
  41    3  0.05
  42   15  0.23
  43   26  0.39
  44   18  0.27

ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38


Consensus pattern (40 bp):   
ATTAAAATTTCATAGGTAAGTATCAAAATTTCATAGGGTA

Found at i:4146 original size:22 final size:22

Alignment explanation


    Indices: 4082--4182  Score: 129
    Period size: 22  Copynumber: 4.7  Consensus size: 22

       4072 ATAGTTAGGG

                   *                
       4082 TATCAAAGTTTCATATGGAGTAAT
          1 TATCAAAATTTCATA-GG-GTAAT

                                  
       4106 TA-C--AATTTCATA-GGTAAT
          1 TATCAAAATTTCATAGGGTAAT

                                  
       4124 TATCAAAATTTCATAGGGTAAT
          1 TATCAAAATTTCATAGGGTAAT

                       *        * 
       4146 TATCAAAATTTAATAGGGTAGT
          1 TATCAAAATTTCATAGGGTAAT

                           
       4168 TATCAAAATTTCATA
          1 TATCAAAATTTCATA

       4183 AAAATATTCA


Statistics
Matches: 69,  Mismatches: 4, Indels: 10
        0.83            0.05        0.12

Matches are distributed among these distances:
  18    7  0.10
  19    2  0.03
  21   17  0.25
  22   40  0.58
  23    1  0.01
  24    2  0.03

ACGTcount: A:0.41, C:0.09, G:0.13, T:0.38


Consensus pattern (22 bp):   
TATCAAAATTTCATAGGGTAAT

Found at i:5255 original size:20 final size:21

Alignment explanation


    Indices: 5219--5260  Score: 68
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       5209 TAATATGCTG

                                 
       5219 ATGTGGCATCATGTCAGTGAC
          1 ATGTGGCATCATGTCAGTGAC

                      *          
       5240 ATGTGGCA-CGTGTCAGTGAC
          1 ATGTGGCATCATGTCAGTGAC

             
       5260 A
          1 A

       5261 AGTGTCATAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  20   12  0.60
  21    8  0.40

ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26


Consensus pattern (21 bp):   
ATGTGGCATCATGTCAGTGAC
Done.