Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012213.1 Corchorus olitorius cultivar O-4 contig12246, 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: 10571
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32


Found at i:5241 original size:52 final size:52

Alignment explanation


    Indices: 5180--5296  Score: 198
    Period size: 52  Copynumber: 2.2  Consensus size: 52

       5170 GTTTTCTTTC

                       *                                        
       5180 CGCAACAACTTTTGTCCCGAAGTTGAACAAATTCTGGGCCGAAGTTGTCCTG
          1 CGCAACAACTTCTGTCCCGAAGTTGAACAAATTCTGGGCCGAAGTTGTCCTG

                             *            *                 *   
       5232 CGCAACAACTTCTGTCCTGAAGTTGAACAAGTTCTGGGCCGAAGTTGTTCTG
          1 CGCAACAACTTCTGTCCCGAAGTTGAACAAATTCTGGGCCGAAGTTGTCCTG

                         
       5284 CGCAACAACTTCT
          1 CGCAACAACTTCT

       5297 CTTTTCGACA


Statistics
Matches: 61,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  52   61  1.00

ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27


Consensus pattern (52 bp):   
CGCAACAACTTCTGTCCCGAAGTTGAACAAATTCTGGGCCGAAGTTGTCCTG

Found at i:5245 original size:30 final size:29

Alignment explanation


    Indices: 5205--5296  Score: 74
    Period size: 30  Copynumber: 3.3  Consensus size: 29

       5195 CCCGAAGTTG

                 *                        
       5205 AACAAATTCTGGGCCGAAGTTGTCCTGCGC
          1 AACAACTTCTGGGCCGAAGTTGT-CTGCGC

                        *                 
       5235 AACAACTTCT-GTCCTGAA---GT-T--G-
          1 AACAACTTCTGGGCC-GAAGTTGTCTGCGC

                 *                        
       5257 AACAAGTTCTGGGCCGAAGTTGTTCTGCGC
          1 AACAACTTCTGGGCCGAAGTTG-TCTGCGC

                      
       5287 AACAACTTCT
          1 AACAACTTCT

       5297 CTTTTCGACA


Statistics
Matches: 47,  Mismatches: 5, Indels: 20
        0.65            0.07        0.28

Matches are distributed among these distances:
  22   12  0.26
  23    4  0.09
  25    2  0.04
  26    1  0.02
  27    3  0.06
  29    4  0.09
  30   21  0.45

ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27


Consensus pattern (29 bp):   
AACAACTTCTGGGCCGAAGTTGTCTGCGC

Found at i:5334 original size:21 final size:21

Alignment explanation


    Indices: 5310--5350  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5300 TTCGACAGGC

                *     *          
       5310 CAACTTCTGGGCAGAAGTTGA
          1 CAACATCTGGACAGAAGTTGA

                        *       
       5331 CAACATCTGGACTGAAGTTG
          1 CAACATCTGGACAGAAGTTG

       5351 TCCTGTATTT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

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


Consensus pattern (21 bp):   
CAACATCTGGACAGAAGTTGA

Found at i:6569 original size:21 final size:21

Alignment explanation


    Indices: 6543--6583  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6533 TTGAAGCCCT

                                  
       6543 ATTGGAGAC-AAGTGGTACTAA
          1 ATTGGA-ACTAAGTGGTACTAA

                  *             
       6564 ATTGGATCTAAGTGGTACTA
          1 ATTGGAACTAAGTGGTACTA

       6584 GGGTTTCTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    1  0.06
  21   17  0.94

ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29


Consensus pattern (21 bp):   
ATTGGAACTAAGTGGTACTAA
Done.