Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010599.1 Corchorus olitorius cultivar O-4 contig10631, 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: 9070
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33


Found at i:366 original size:18 final size:18

Alignment explanation


    Indices: 313--368  Score: 51
    Period size: 18  Copynumber: 3.1  Consensus size: 18

        303 TATATATATG

                  *            
        313 AATAAACTAAATAATAAAT
          1 AATAAATTAAA-AATAAAT

                **     * *    
        332 -ATATTTTAAATACAAAT
          1 AATAAATTAAAAATAAAT

                              
        349 AATAAATTAAAAATAAAT
          1 AATAAATTAAAAATAAAT

              
        367 AA
          1 AA

        369 ATATTATATA


Statistics
Matches: 27,  Mismatches: 9, Indels: 3
        0.69            0.23        0.08

Matches are distributed among these distances:
  17    5  0.19
  18   22  0.81

ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30


Consensus pattern (18 bp):   
AATAAATTAAAAATAAAT

Found at i:1914 original size:16 final size:15

Alignment explanation


    Indices: 1866--1924  Score: 75
    Period size: 16  Copynumber: 3.8  Consensus size: 15

       1856 GCAATTGGGT

                   *       
       1866 GGGTTCGGGTTTTTC
          1 GGGTTCGAGTTTTTC

                             
       1881 GGGTTCCGA-TTTTGTC
          1 GGGTT-CGAGTTTT-TC

                            
       1897 GGGTTCGAGTATTTTC
          1 GGGTTCGAGT-TTTTC

                        
       1913 GGGTTCGAGTTT
          1 GGGTTCGAGTTT

       1925 AATTTCGATT


Statistics
Matches: 39,  Mismatches: 1, Indels: 8
        0.81            0.02        0.17

Matches are distributed among these distances:
  15   14  0.36
  16   22  0.56
  17    3  0.08

ACGTcount: A:0.07, C:0.14, G:0.36, T:0.44


Consensus pattern (15 bp):   
GGGTTCGAGTTTTTC

Found at i:2070 original size:13 final size:14

Alignment explanation


    Indices: 2045--2075  Score: 55
    Period size: 13  Copynumber: 2.3  Consensus size: 14

       2035 AAGTTTATTG

                          
       2045 ATAATATATATAAT
          1 ATAATATATATAAT

                          
       2059 ATAATA-ATATAAT
          1 ATAATATATATAAT

                
       2072 ATAA
          1 ATAA

       2076 CATGATTATC


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.65
  14    6  0.35

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (14 bp):   
ATAATATATATAAT

Found at i:6358 original size:21 final size:21

Alignment explanation


    Indices: 6332--6402  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       6322 TGGTAGGAGT

                                  
       6332 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
       6353 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       6374 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       6395 TCATTGGA
          1 TCATTGGA

       6403 ATTGGCTAAG


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:6678 original size:65 final size:65

Alignment explanation


    Indices: 6596--6725  Score: 233
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       6586 GCTTGCTATT

                 *                   *                                  *    
       6596 GATTCCAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
          1 GATTCAAACTTTCTGCACTAGCCCAAGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC

                                                                             
       6661 GATTCAAACTTTCTGCACTAGCCCAAGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
          1 GATTCAAACTTTCTGCACTAGCCCAAGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC

       6726 CAATTTTTCC


Statistics
Matches: 62,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  65   62  1.00

ACGTcount: A:0.22, C:0.27, G:0.30, T:0.21


Consensus pattern (65 bp):   
GATTCAAACTTTCTGCACTAGCCCAAGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC

Found at i:7905 original size:21 final size:21

Alignment explanation


    Indices: 7879--7919  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7869 TTTAAACCCT

                                  
       7879 ATTGGAGAC-AAGTGGTACTAA
          1 ATTGGA-ACTAAGTGGTACTAA

                  *             
       7900 ATTGGATCTAAGTGGTACTA
          1 ATTGGAACTAAGTGGTACTA

       7920 GGGTTTATAA


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

Found at i:8397 original size:15 final size:15

Alignment explanation


    Indices: 8377--8405  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       8367 TGGAGGTTCG

                           
       8377 AAATCAACAAGCTCA
          1 AAATCAACAAGCTCA

                          
       8392 AAATCAACAAGCTC
          1 AAATCAACAAGCTC

       8406 CACTTAGTTT


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14


Consensus pattern (15 bp):   
AAATCAACAAGCTCA
Done.