Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015680.1 Corchorus olitorius cultivar O-4 contig15713, 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: 24838
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:190 original size:13 final size:13

Alignment explanation


    Indices: 172--201  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

        162 AAATTTGATT

                         
        172 TTTTCTTCTTTTC
          1 TTTTCTTCTTTTC

                   *     
        185 TTTTCTTTTTTTC
          1 TTTTCTTCTTTTC

                
        198 TTTT
          1 TTTT

        202 TTTGTCCTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (13 bp):   
TTTTCTTCTTTTC

Found at i:198 original size:18 final size:18

Alignment explanation


    Indices: 171--223  Score: 63
    Period size: 18  Copynumber: 2.8  Consensus size: 18

        161 GAAATTTGAT

                                
        171 TTTTTCTTCTTTTCTTT-TC
          1 TTTTT-TTCTTTT-TTTGTC

                              
        190 TTTTTTTCTTTTTTTGTC
          1 TTTTTTTCTTTTTTTGTC

            *               
        208 CTTTTTTCTGTTTTTT
          1 TTTTTTTCT-TTTTTT

        224 CGAAGAAAAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  17    3  0.10
  18   17  0.55
  19   11  0.35

ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81


Consensus pattern (18 bp):   
TTTTTTTCTTTTTTTGTC

Found at i:3977 original size:36 final size:36

Alignment explanation


    Indices: 3922--4019  Score: 142
    Period size: 36  Copynumber: 2.7  Consensus size: 36

       3912 TGATGATGAT

                      *   *                      
       3922 GTGCAGTTTCCACTTACGCTTCTTGAAAGAGGGGAAG
          1 GTGCA-TTTCGACTGACGCTTCTTGAAAGAGGGGAAG

                                                
       3959 GTGCATTTCGACTGACGCTTCTTGAAAGAGGGGAAG
          1 GTGCATTTCGACTGACGCTTCTTGAAAGAGGGGAAG

               *      *         *    
       3995 GTGAATTTCGGCTGACGCTTTTTGA
          1 GTGCATTTCGACTGACGCTTCTTGA

       4020 CAAACTGGGG


Statistics
Matches: 56,  Mismatches: 5, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  36   51  0.91
  37    5  0.09

ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30


Consensus pattern (36 bp):   
GTGCATTTCGACTGACGCTTCTTGAAAGAGGGGAAG

Found at i:5294 original size:13 final size:13

Alignment explanation


    Indices: 5276--5300  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5266 GTTCTTAAGT

                         
       5276 AGAAAGAAAAAAA
          1 AGAAAGAAAAAAA

                        
       5289 AGAAAGAAAAAA
          1 AGAAAGAAAAAA

       5301 GAATGAAGGT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (13 bp):   
AGAAAGAAAAAAA

Found at i:22257 original size:16 final size:17

Alignment explanation


    Indices: 22224--22258  Score: 54
    Period size: 18  Copynumber: 2.1  Consensus size: 17

      22214 TTAAAAATTC

                              
      22224 AAAAACTACCCATCTTAA
          1 AAAAACTACCCA-CTTAA

                             
      22242 AAAAACTACCCA-TTAA
          1 AAAAACTACCCACTTAA

             
      22258 A
          1 A

      22259 GAATAAATAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    5  0.29
  18   12  0.71

ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20


Consensus pattern (17 bp):   
AAAAACTACCCACTTAA

Found at i:22482 original size:2 final size:2

Alignment explanation


    Indices: 22475--22499  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      22465 ATATAAAAGG

                                                 
      22475 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

      22500 CTTTAAACAA


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

Done.