Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018306.1 Corchorus olitorius cultivar O-4 contig18339, 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: 17302
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31


Found at i:2207 original size:38 final size:37

Alignment explanation


    Indices: 2147--2220  Score: 94
    Period size: 38  Copynumber: 2.0  Consensus size: 37

       2137 ACTGATGCTA

                                                  
       2147 AAGAGTGAACCCATACCACAGGGGGTTAAACTGTTGGT
          1 AAGAGTGAACCCATACCACAGGGGGTT-AACTGTTGGT

                   *    * *  *          *       
       2185 AAGAGTGGACCCGTGCCTCAGGGGGTTAGCTGTTGG
          1 AAGAGTGAACCCATACCACAGGGGGTTAACTGTTGG

       2221 CTAGACTCGA


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  37    8  0.26
  38   23  0.74

ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22


Consensus pattern (37 bp):   
AAGAGTGAACCCATACCACAGGGGGTTAACTGTTGGT

Found at i:2261 original size:6 final size:6

Alignment explanation


    Indices: 2250--2287  Score: 76
    Period size: 6  Copynumber: 6.3  Consensus size: 6

       2240 CGTTAACGGA

                                                        
       2250 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG
          1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG

       2288 GTGCAGCCTG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   32  1.00

ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50


Consensus pattern (6 bp):   
TGATTG

Found at i:4614 original size:21 final size:21

Alignment explanation


    Indices: 4588--4628  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4578 TTGAAGCCCT

                                  
       4588 ATTGGAGAC-AAGTGGTACTAA
          1 ATTGGA-ACTAAGTGGTACTAA

                  *             
       4609 ATTGGATCTAAGTGGTACTA
          1 ATTGGAACTAAGTGGTACTA

       4629 GGGTTTCTAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    1  0.06
  21   17  0.94

ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29


Consensus pattern (21 bp):   
ATTGGAACTAAGTGGTACTAA

Found at i:12977 original size:76 final size:76

Alignment explanation


    Indices: 12827--12970  Score: 186
    Period size: 76  Copynumber: 1.9  Consensus size: 76

      12817 ACAAGGACCC

                                                               *           * 
      12827 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
      12892 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *                    *                            **     
      12903 CGACTCCAGCTGGGCGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                  
      12965 GATGGG
         63 GATGGG

      12971 TTGTGTCTTA


Statistics
Matches: 59,  Mismatches: 6, Indels: 6
        0.83            0.08        0.08

Matches are distributed among these distances:
  75    4  0.07
  76   49  0.83
  77    6  0.10

ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.