Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012840.1 Corchorus olitorius cultivar O-4 contig12873, 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: 13557
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:3122 original size:4 final size:4

Alignment explanation


    Indices: 3113--3166  Score: 54
    Period size: 4  Copynumber: 13.5  Consensus size: 4

       3103 TTCAGGATGG

                                  **      * *        *              *  
       3113 AGCA AGCA AGCA AGCA AGTG AGCA CGAA AGCA AACA AGCA AGCA ACCA
          1 AGCA AGCA AGCA AGCA AGCA AGCA AGCA AGCA AGCA AGCA AGCA AGCA

                   
       3161 AGCA AG
          1 AGCA AG

       3167 GCCGCAGCGC


Statistics
Matches: 38,  Mismatches: 12, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
   4   38  1.00

ACGTcount: A:0.50, C:0.24, G:0.24, T:0.02


Consensus pattern (4 bp):   
AGCA

Found at i:3317 original size:18 final size:18

Alignment explanation


    Indices: 3294--3342  Score: 80
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       3284 GAACGCAACA

                       *      
       3294 AGCTTGCTTCCTCGAGGC
          1 AGCTTGCTTCCGCGAGGC

                              
       3312 AGCTTGCTTCCGCGAGGC
          1 AGCTTGCTTCCGCGAGGC

                    *    
       3330 AGCTTGCTGCCGC
          1 AGCTTGCTTCCGC

       3343 TGCTGCATAG


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   29  1.00

ACGTcount: A:0.10, C:0.35, G:0.31, T:0.24


Consensus pattern (18 bp):   
AGCTTGCTTCCGCGAGGC

Found at i:4762 original size:2 final size:2

Alignment explanation


    Indices: 4757--4781  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       4747 AAAAAAAACA

                                                 
       4757 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       4782 AAATCAATCC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:5933 original size:19 final size:18

Alignment explanation


    Indices: 5909--5944  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       5899 TGAAGACTTA

                               
       5909 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       5928 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       5945 ATTATTTCCA


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:7316 original size:22 final size:22

Alignment explanation


    Indices: 7274--7316  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       7264 TTTCTAATTA

                           **     
       7274 ATTGTTTTCTTTAATTTTCTTG
          1 ATTGTTTTCTTTAATAGTCTTG

                                  
       7296 ATTGTTTTC-TTAGATAGTCTT
          1 ATTGTTTTCTTTA-ATAGTCTT

       7317 AATTACTAGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    3  0.17
  22   15  0.83

ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63


Consensus pattern (22 bp):   
ATTGTTTTCTTTAATAGTCTTG
Done.