Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012714.1 Corchorus olitorius cultivar O-4 contig12747, 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: 8206
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:2077 original size:21 final size:21

Alignment explanation


    Indices: 2053--2107  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       2043 CCGCCCAAAA

                           *     
       2053 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCTAAGC

                              *  
       2074 CCGTGCCACCACCGGCTATGC
          1 CCGTGCCACCACCGGCTAAGC

            *       *    
       2095 TCGTGCCATCACC
          1 CCGTGCCACCACC

       2108 ATTCCAAGCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.45, G:0.22, T:0.16


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCTAAGC

Found at i:5392 original size:15 final size:15

Alignment explanation


    Indices: 5359--5401  Score: 68
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       5349 TTACTTTGCT

                        *   
       5359 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTCTAA

                           
       5375 TTGTTTTCTGTCTAA
          1 TTGTTTTCTGTCTAA

                        
       5390 TTGTTTTCTGTC
          1 TTGTTTTCTGTC

       5402 AACCTCTGTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.12, G:0.14, T:0.63


Consensus pattern (15 bp):   
TTGTTTTCTGTCTAA

Found at i:6086 original size:27 final size:26

Alignment explanation


    Indices: 6031--6092  Score: 65
    Period size: 27  Copynumber: 2.3  Consensus size: 26

       6021 TCTAAATTTC

                           *            
       6031 TATTATTTTAATAATTGAATAATTAAAA
          1 TATTA-TTTAATAATGGAAT-ATTAAAA

                                        
       6059 TATTATTTAATAATGGCAAT-TTAGAAA
          1 TATTATTTAATAATGG-AATATTA-AAA

                    
       6086 TA-TATTT
          1 TATTATTT

       6093 GAAATAAAAG


Statistics
Matches: 31,  Mismatches: 1, Indels: 6
        0.82            0.03        0.16

Matches are distributed among these distances:
  26    8  0.26
  27   15  0.48
  28    8  0.26

ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47


Consensus pattern (26 bp):   
TATTATTTAATAATGGAATATTAAAA

Found at i:7119 original size:8 final size:9

Alignment explanation


    Indices: 7083--7120  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       7073 CCCAAATTAC

                     
       7083 TTATGGAAA
          1 TTATGGAAA

               *     
       7092 TTAAGGAAA
          1 TTATGGAAA

                     
       7101 TTATGGAAA
          1 TTATGGAAA

                     
       7110 TTAT-GAAA
          1 TTATGGAAA

               
       7118 TTA
          1 TTA

       7121 AATGAACTAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   8    7  0.26
   9   20  0.74

ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34


Consensus pattern (9 bp):   
TTATGGAAA
Done.