Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020480.1 Corchorus olitorius cultivar O-4 contig20513, 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: 8050
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:1293 original size:27 final size:28

Alignment explanation


    Indices: 1226--1300  Score: 107
    Period size: 29  Copynumber: 2.7  Consensus size: 28

       1216 CCTGGAGTAC

                         *         *     
       1226 AAATGACCAAAATACCCCTGAATGTGCAA
          1 AAATGACCAAAATGCCCCTGAATAT-CAA

                   *                    
       1255 AAATGACTAAAATGCCCCTGAATAT-AA
          1 AAATGACCAAAATGCCCCTGAATATCAA

                               
       1282 AAATGACCAAAATGCCCCT
          1 AAATGACCAAAATGCCCCT

       1301 AGATGACCCT


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  27   20  0.48
  29   22  0.52

ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19


Consensus pattern (28 bp):   
AAATGACCAAAATGCCCCTGAATATCAA

Found at i:5298 original size:16 final size:16

Alignment explanation


    Indices: 5267--5299  Score: 57
    Period size: 17  Copynumber: 2.0  Consensus size: 16

       5257 GTCAAAGTTG

                            
       5267 AAGAAAAAATGAAAAA
          1 AAGAAAAAATGAAAAA

                             
       5283 AAGAAGAAAATGAAAAA
          1 AAGAA-AAAATGAAAAA

       5300 GAATCAATAA


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

Matches are distributed among these distances:
  16    5  0.31
  17   11  0.69

ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06


Consensus pattern (16 bp):   
AAGAAAAAATGAAAAA

Found at i:5948 original size:15 final size:14

Alignment explanation


    Indices: 5928--5965  Score: 58
    Period size: 15  Copynumber: 2.6  Consensus size: 14

       5918 AAAAGGTTGC

                           
       5928 TTTGTTTTGTTTCGG
          1 TTTGTTTTGTTTC-G

                          
       5943 TTTGTTTTGTTTCG
          1 TTTGTTTTGTTTCG

                *    
       5957 TTTGCTTTG
          1 TTTGTTTTG

       5966 ATATTTTATT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14    9  0.41
  15   13  0.59

ACGTcount: A:0.00, C:0.08, G:0.24, T:0.68


Consensus pattern (14 bp):   
TTTGTTTTGTTTCG

Found at i:6005 original size:24 final size:24

Alignment explanation


    Indices: 5959--6005  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5949 TTGTTTCGTT

                           *        
       5959 TGCTTTGATATTTTATTACTCTTG
          1 TGCTTTGATATTTTACTACTCTTG

                                    
       5983 TGCTTTGATATTTCTACTA-TCTT
          1 TGCTTTGATATTT-TACTACTCTT

       6006 CACCCATATC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24   17  0.81
  25    4  0.19

ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57


Consensus pattern (24 bp):   
TGCTTTGATATTTTACTACTCTTG
Done.