Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023368.1 Corchorus olitorius cultivar O-4 contig23401, 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: 17149
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31


Found at i:1318 original size:21 final size:21

Alignment explanation


    Indices: 1292--1381  Score: 130
    Period size: 21  Copynumber: 4.3  Consensus size: 21

       1282 TGTTAGGAGA

                                  
       1292 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
       1313 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                 *               
       1334 TCATTAGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       1355 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                  
       1376 TCATTG
          1 TCATTG

       1382 AAATTGCCTA


Statistics
Matches: 65,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   63  0.97

ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:3383 original size:33 final size:33

Alignment explanation


    Indices: 3339--3416  Score: 86
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       3329 GTGTTTTAGA

                  *     *                   * 
       3339 TGTTTGCGATGATACTAAACCTAATTTGA-GTGT
          1 TGTTTGTGATGACACTAAACCT-ATTTGAGGTAT

                               *  *   *      
       3372 TGTTTGTGATGACACTAAATCTGTTTTAGGTAT
          1 TGTTTGTGATGACACTAAACCTATTTGAGGTAT

                        
       3405 TGTTTGTGATGA
          1 TGTTTGTGATGA

       3417 AACAAATTCT


Statistics
Matches: 38,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  32    4  0.11
  33   34  0.89

ACGTcount: A:0.24, C:0.09, G:0.23, T:0.44


Consensus pattern (33 bp):   
TGTTTGTGATGACACTAAACCTATTTGAGGTAT

Found at i:3428 original size:33 final size:34

Alignment explanation


    Indices: 3371--3466  Score: 110
    Period size: 33  Copynumber: 2.9  Consensus size: 34

       3361 AATTTGAGTG

                         *                     
       3371 TTGTTTGTGATGACACTAAA-TCTGTTTTAGG-TA
          1 TTGTTTGTGATGAAAC-AAATTCTGTTTTAGGATA

                                              
       3404 TTGTTTGTGATGAAACAAATTCTGTTTT-GGATA
          1 TTGTTTGTGATGAAACAAATTCTGTTTTAGGATA

            * **                           
       3437 CTAATTGTGATGAAA-ACAATTCTGTTTTAG
          1 TTGTTTGTGATGAAACA-AATTCTGTTTTAG

       3467 TTGATCATAG


Statistics
Matches: 55,  Mismatches: 4, Indels: 7
        0.83            0.06        0.11

Matches are distributed among these distances:
  32    6  0.11
  33   48  0.87
  34    1  0.02

ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44


Consensus pattern (34 bp):   
TTGTTTGTGATGAAACAAATTCTGTTTTAGGATA

Found at i:7777 original size:21 final size:21

Alignment explanation


    Indices: 7751--7821  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       7741 TACTAGGAGA

                                  
       7751 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
       7772 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       7793 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       7814 TCATTGGA
          1 TCATTGGA

       7822 ATTGCCTAAG


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    2  0.04
  21   46  0.96

ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:16339 original size:21 final size:21

Alignment explanation


    Indices: 16315--16385  Score: 97
    Period size: 21  Copynumber: 3.4  Consensus size: 21

      16305 CTTAGGCAAT

                         *       
      16315 TCCAATGAGCTTGAAACATAC
          1 TCCAATGAGCTTGGAACATAC

                             * * 
      16336 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACATAC

                             * * 
      16357 TCCAATGAGCTTGGAACTTGC
          1 TCCAATGAGCTTGGAACATAC

                    
      16378 TCCAATGA
          1 TCCAATGA

      16386 TCTCCTAGCA


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   45  1.00

ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACATAC
Done.