Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016553.1 Corchorus olitorius cultivar O-4 contig16586, 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: 3330
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38


Found at i:151 original size:24 final size:25

Alignment explanation


    Indices: 123--169  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

        113 AATATTTACA

                                     
        123 TTAATT-AAATTCTTAGGTATTTTT
          1 TTAATTCAAATTCTTAGGTATTTTT

                                   
        147 TTAATTCAAATTCTTAGGTATTT
          1 TTAATTCAAATTCTTAGGTATTT

        170 GTGCAAACGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (25 bp):   
TTAATTCAAATTCTTAGGTATTTTT

Found at i:483 original size:204 final size:204

Alignment explanation


    Indices: 239--653  Score: 733
    Period size: 204  Copynumber: 2.0  Consensus size: 204

        229 GTTTCCTTAA

                                                                             
        239 TAATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
          1 TAATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT

                                                                             
        304 TAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATACTTCTATATAT-ATAAT
         66 TAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATACTTCTATATATAATAAT

             *        *                                                      
        368 AGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
        131 AATAATGTGTGGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC

               *     
        433 ATTTACCAT
        196 ATTCACCAT

                                                                        *    
        442 TAATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATTTAAT
          1 TAATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAAT

                                              *              *  *            
        507 TTAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAA
         65 TTAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATACTTCTATATATAATAA

                                                                     *       
        572 TAATAATGTGTGGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAGTTAATAA
        130 TAATAATGTGTGGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAA

                      
        637 CATTCACCAT
        195 CATTCACCAT

             *     
        647 TGATAAA
          1 TAATAAA

        654 GTTATTAAGC


Statistics
Matches: 201,  Mismatches: 9, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
 203   18  0.09
 204  102  0.51
 205   81  0.40

ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44


Consensus pattern (204 bp):   
TAATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
TAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATACTTCTATATATAATAAT
AATAATGTGTGGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
ATTCACCAT

Found at i:1219 original size:36 final size:36

Alignment explanation


    Indices: 1172--1241  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1162 GAGATTTTGG

                         *      *               
       1172 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
       1208 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       1242 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:2601 original size:58 final size:57

Alignment explanation


    Indices: 2506--2619  Score: 156
    Period size: 58  Copynumber: 2.0  Consensus size: 57

       2496 ATAGCATCAT

                      *                   *                           
       2506 GCCTCGGTCCTAAAACGTCTGTTTTAGACATCTAATAAAAAAACATGTCACTCGATAA
          1 GCCTCGGTCCGAAAACGTCTGTTTTAGACACCTAAT-AAAAAACATGTCACTCGATAA

                *               *     *            *           *    
       2564 GCCTTGGTCCGAAAACGTCTTTTTTATACACCTAATAAAGAACATGTCACTTGATA
          1 GCCTCGGTCCGAAAACGTCTGTTTTAGACACCTAATAAAAAACATGTCACTCGATA

       2620 TTTGATTAAT


Statistics
Matches: 49,  Mismatches: 7, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  57   18  0.37
  58   31  0.63

ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30


Consensus pattern (57 bp):   
GCCTCGGTCCGAAAACGTCTGTTTTAGACACCTAATAAAAAACATGTCACTCGATAA
Done.