Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024609.1 Corchorus olitorius cultivar O-4 contig24642, 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: 5027
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36


Found at i:1706 original size:21 final size:21

Alignment explanation


    Indices: 1673--1714  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1663 CATATGTTTT

                    *      *     
       1673 AACACTAATTTAAACTAATTA
          1 AACACTAAATTAAACAAATTA

                *                
       1694 AACATTAAATTAAACAAATTA
          1 AACACTAAATTAAACAAATTA

       1715 TGAAAATGCA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31


Consensus pattern (21 bp):   
AACACTAAATTAAACAAATTA

Found at i:2308 original size:16 final size:16

Alignment explanation


    Indices: 2283--2352  Score: 70
    Period size: 16  Copynumber: 4.4  Consensus size: 16

       2273 CGGGTTGATC

                            
       2283 GGGTTCGGGTCATTTT
          1 GGGTTCGGGTCATTTT

                 *    *     
       2299 GGGTTTGGGTAATTTT
          1 GGGTTCGGGTCATTTT

                         *   
       2315 CGGGTTCGGGTC-GTTT
          1 -GGGTTCGGGTCATTTT

                 * *       *
       2331 GGGTTTGAGTCATTTC
          1 GGGTTCGGGTCATTTT

                  
       2347 GGGTTC
          1 GGGTTC

       2353 AGGTACCCAA


Statistics
Matches: 42,  Mismatches: 10, Indels: 4
        0.75            0.18        0.07

Matches are distributed among these distances:
  15    9  0.21
  16   24  0.57
  17    9  0.21

ACGTcount: A:0.07, C:0.11, G:0.39, T:0.43


Consensus pattern (16 bp):   
GGGTTCGGGTCATTTT

Found at i:2323 original size:33 final size:31

Alignment explanation


    Indices: 2281--2352  Score: 99
    Period size: 32  Copynumber: 2.3  Consensus size: 31

       2271 GTCGGGTTGA

                          *          *       
       2281 TCGGGTTCGGGTCATTTTGGGTTTGGGTAATTT
          1 TCGGGTTCGGGTC-GTTTGGGTTTGAGTAA-TT

                                       *   
       2314 TCGGGTTCGGGTCGTTTGGGTTTGAGTCATT
          1 TCGGGTTCGGGTCGTTTGGGTTTGAGTAATT

                    
       2345 TCGGGTTC
          1 TCGGGTTC

       2353 AGGTACCCAA


Statistics
Matches: 36,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  31   10  0.28
  32   13  0.36
  33   13  0.36

ACGTcount: A:0.07, C:0.12, G:0.38, T:0.43


Consensus pattern (31 bp):   
TCGGGTTCGGGTCGTTTGGGTTTGAGTAATT

Found at i:2405 original size:17 final size:17

Alignment explanation


    Indices: 2365--2405  Score: 50
    Period size: 16  Copynumber: 2.5  Consensus size: 17

       2355 GTACCCAAAA

                             
       2365 TTTCGGGTCATTTCTGG
          1 TTTCGGGTCATTTCTGG

            *                 
       2382 GTT-GGGTCAGTTTC-GG
          1 TTTCGGGTCA-TTTCTGG

                    
       2398 TTTCGGGT
          1 TTTCGGGT

       2406 TGGGCGGATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 4
        0.77            0.08        0.15

Matches are distributed among these distances:
  16   10  0.50
  17   10  0.50

ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44


Consensus pattern (17 bp):   
TTTCGGGTCATTTCTGG

Found at i:4524 original size:21 final size:21

Alignment explanation


    Indices: 4498--4610  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       4488 TGCTAGAAGT

                                 
       4498 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
       4519 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
       4540 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
       4561 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
       4582 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
       4603 TCATTGGA
          1 TCATTGGA

       4611 AATGCCTAAG


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   84  0.99

ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Done.