Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013102.1 Corchorus olitorius cultivar O-4 contig13135, 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: 13153
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:7380 original size:27 final size:27

Alignment explanation


    Indices: 7320--7393  Score: 94
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       7310 AGGGTCACAT

                       *        **      
       7320 AGGGGCATTTTAGTCATTTTTTACATTC
          1 AGGGGCATTTTGGTCA-TTTGCACATTC

                                       
       7348 AGGGGCATTTTGGTCATTTGCACATTC
          1 AGGGGCATTTTGGTCATTTGCACATTC

                  *       *    
       7375 AGGGGCGTTTTGGTAATTT
          1 AGGGGCATTTTGGTCATTT

       7394 ATAGTTCACT


Statistics
Matches: 41,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  27   26  0.63
  28   15  0.37

ACGTcount: A:0.19, C:0.14, G:0.26, T:0.42


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTGCACATTC

Found at i:9363 original size:15 final size:15

Alignment explanation


    Indices: 9328--9356  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       9318 CACTTATCCA

                           
       9328 CACACACAACAAAAG
          1 CACACACAACAAAAG

                           
       9343 CACACACAA-AAAAG
          1 CACACACAACAAAAG

       9357 GATCACATAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    5  0.36
  15    9  0.64

ACGTcount: A:0.62, C:0.31, G:0.07, T:0.00


Consensus pattern (15 bp):   
CACACACAACAAAAG

Found at i:12614 original size:42 final size:46

Alignment explanation


    Indices: 12561--12669  Score: 145
    Period size: 42  Copynumber: 2.4  Consensus size: 46

      12551 TCTATATTTA

                *                                         
      12561 AACTTAGAAAATATCATCAAACACT-T-TGTAAA-C-AGAAGAGAC
          1 AACTCAGAAAATATCATCAAACACTATATGTAAACCAAGAAGAGAC

                                         *                  
      12603 AACTCAGAAAATATCATCAAACACTATATTTAAACTCAAAGAAGAGAC
          1 AACTCAGAAAATATCATCAAACACTATATGTAAAC-C-AAGAAGAGAC

                               
      12651 AACTCAGAAAATATACATC
          1 AACTCAGAAAATAT-CATC

      12670 TTAGAAAAAA


Statistics
Matches: 58,  Mismatches: 2, Indels: 7
        0.87            0.03        0.10

Matches are distributed among these distances:
  42   24  0.41
  43    1  0.02
  44    5  0.09
  46    1  0.02
  48   23  0.40
  49    4  0.07

ACGTcount: A:0.51, C:0.18, G:0.09, T:0.21


Consensus pattern (46 bp):   
AACTCAGAAAATATCATCAAACACTATATGTAAACCAAGAAGAGAC

Found at i:13084 original size:2 final size:2

Alignment explanation


    Indices: 13077--13153  Score: 154
    Period size: 2  Copynumber: 38.5  Consensus size: 2

      13067 AACAAATAAA

                                                                          
      13077 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                                                
      13119 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A


Statistics
Matches: 75,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   75  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.