Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018776.1 Corchorus olitorius cultivar O-4 contig18809, 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: 15815
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:260 original size:21 final size:21

Alignment explanation


    Indices: 236--275  Score: 80
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        226 ACATCTTAGA

                                 
        236 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

                               
        257 CAACTCCGATGAGCTTGAA
          1 CAACTCCGATGAGCTTGAA

        276 GCTTCTTTGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20


Consensus pattern (21 bp):   
CAACTCCGATGAGCTTGAAAC

Found at i:2708 original size:14 final size:14

Alignment explanation


    Indices: 2689--2716  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       2679 ATGTTCAAGT

                          
       2689 TTCTCATGGATTTG
          1 TTCTCATGGATTTG

                          
       2703 TTCTCATGGATTTG
          1 TTCTCATGGATTTG

       2717 GAAAAATCCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50


Consensus pattern (14 bp):   
TTCTCATGGATTTG

Found at i:4513 original size:11 final size:10

Alignment explanation


    Indices: 4466--4513  Score: 55
    Period size: 11  Copynumber: 4.8  Consensus size: 10

       4456 TTGAAATAAT

                    * 
       4466 TCTTCAATGA
          1 TCTTCAATTA

                      
       4476 TCTTC-A-TA
          1 TCTTCAATTA

                       
       4484 TCTTCAAATTA
          1 TCTTC-AATTA

                       
       4495 TCTTCAATTAA
          1 TCTTCAATT-A

                    
       4506 TCTTCAAT
          1 TCTTCAAT

       4514 CACAAACTTC


Statistics
Matches: 33,  Mismatches: 1, Indels: 7
        0.80            0.02        0.17

Matches are distributed among these distances:
   8    6  0.18
   9    1  0.03
  10   10  0.30
  11   16  0.48

ACGTcount: A:0.31, C:0.21, G:0.02, T:0.46


Consensus pattern (10 bp):   
TCTTCAATTA

Found at i:9237 original size:15 final size:16

Alignment explanation


    Indices: 9213--9252  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       9203 AGAGGTTGAC

                 *    *     
       9213 AGAAATCAATTAAA-T
          1 AGAAAACAATGAAACT

                            
       9228 AGAAAACAATGAAACT
          1 AGAAAACAATGAAACT

                     
       9244 AGAAAACAA
          1 AGAAAACAA

       9253 AGCAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   12  0.55
  16   10  0.45

ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATGAAACT

Found at i:12556 original size:21 final size:22

Alignment explanation


    Indices: 12532--12572  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      12522 CACTGAATGA

                      *           
      12532 TGGCACGG-GCATGGCCGGTGG
          1 TGGCACGGTGAATGGCCGGTGG

                                
      12553 TGGCACGGTGAATGGCCGGT
          1 TGGCACGGTGAATGGCCGGT

      12573 TGTGACTTGG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    8  0.44
  22   10  0.56

ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17


Consensus pattern (22 bp):   
TGGCACGGTGAATGGCCGGTGG

Found at i:12910 original size:32 final size:32

Alignment explanation


    Indices: 12873--12945  Score: 146
    Period size: 32  Copynumber: 2.3  Consensus size: 32

      12863 GCCAGGTAGA

                                            
      12873 TGGCTCGGGTGGCCGGGCCATGGCCTGGCATG
          1 TGGCTCGGGTGGCCGGGCCATGGCCTGGCATG

                                            
      12905 TGGCTCGGGTGGCCGGGCCATGGCCTGGCATG
          1 TGGCTCGGGTGGCCGGGCCATGGCCTGGCATG

                     
      12937 TGGCTCGGG
          1 TGGCTCGGG

      12946 GCGGCTTGGG


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   41  1.00

ACGTcount: A:0.05, C:0.27, G:0.48, T:0.19


Consensus pattern (32 bp):   
TGGCTCGGGTGGCCGGGCCATGGCCTGGCATG
Done.