Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019452.1 Corchorus olitorius cultivar O-4 contig19485, 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: 10414
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:4214 original size:22 final size:23

Alignment explanation


    Indices: 4188--4245  Score: 66
    Period size: 22  Copynumber: 2.6  Consensus size: 23

       4178 GTCGATTTCA

                                   
       4188 AGAAGAAAATTTGTCGACTAAAG
          1 AGAAGAAAATTTGTCGACTAAAG

                 *    **           
       4211 -GAAGCAAA-CAGTCGACTAAAG
          1 AGAAGAAAATTTGTCGACTAAAG

                          
       4232 AGAAGAACAATTTG
          1 AGAAGAA-AATTTG

       4246 ACTAAGGAAT


Statistics
Matches: 26,  Mismatches: 6, Indels: 5
        0.70            0.16        0.14

Matches are distributed among these distances:
  21   11  0.42
  22   12  0.46
  23    2  0.08
  24    1  0.04

ACGTcount: A:0.48, C:0.12, G:0.22, T:0.17


Consensus pattern (23 bp):   
AGAAGAAAATTTGTCGACTAAAG

Found at i:6895 original size:19 final size:18

Alignment explanation


    Indices: 6871--6906  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6861 TGAAGACTTA

                               
       6871 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       6890 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       6907 ATTATTTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:9625 original size:8 final size:8

Alignment explanation


    Indices: 9612--9646  Score: 61
    Period size: 8  Copynumber: 4.4  Consensus size: 8

       9602 AAAAGTATCT

                    
       9612 TATCTTAC
          1 TATCTTAC

                    
       9620 TATCTTAC
          1 TATCTTAC

                    
       9628 TATCTTAC
          1 TATCTTAC

                *   
       9636 TATCATAC
          1 TATCTTAC

               
       9644 TAT
          1 TAT

       9647 TATATAAAAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   8   26  1.00

ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49


Consensus pattern (8 bp):   
TATCTTAC

Found at i:10003 original size:96 final size:96

Alignment explanation


    Indices: 9880--10073  Score: 327
    Period size: 96  Copynumber: 2.0  Consensus size: 96

       9870 TGTGCTAGTT

                                                   * *             *         
       9880 ATAATTTGAAAATTTTAACTATATTTTTTTAGTG-AAAACATTTTAACTAAATTTGCACACTATA
          1 ATAATTTGAAAATTTTAACTATA-TTTTTTAGTGAAAAAAAATTTAACTAAATTTACACACTATA

                                            
       9944 CAATAAACACCCGAAAATAACTTTCCATAAGC
         65 CAATAAACACCCGAAAATAACTTTCCATAAGC

                                  *      *                                   
       9976 ATAATTTGAAAATTTTAACTATCTTTTTTGGTGAAAAAAAATTTAACTAAATTTACACACTATAC
          1 ATAATTTGAAAATTTTAACTATATTTTTTAGTGAAAAAAAATTTAACTAAATTTACACACTATAC

                                           
      10041 AATAAACACCCGAAAATAACTTTCCATAAGC
         66 AATAAACACCCGAAAATAACTTTCCATAAGC

              
      10072 AT
          1 AT

      10074 GTTAAAATTT


Statistics
Matches: 92,  Mismatches: 5, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  95    9  0.10
  96   83  0.90

ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35


Consensus pattern (96 bp):   
ATAATTTGAAAATTTTAACTATATTTTTTAGTGAAAAAAAATTTAACTAAATTTACACACTATAC
AATAAACACCCGAAAATAACTTTCCATAAGC
Done.