Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018816.1 Corchorus olitorius cultivar O-4 contig18849, 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: 22380
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:6158 original size:33 final size:33

Alignment explanation


    Indices: 6093--6165  Score: 85
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       6083 CTTCTTCTTC

                             *    *  *       
       6093 TCATGATCAAACTCAAACAAGTTCTTCTCATGA
          1 TCATGATCAAACTCAAAAAAGTGCTGCTCATGA

                     *                        
       6126 TCATGATCATACTCAAAAAAAGTGCTGC-CATGA
          1 TCATGATCAAACTC-AAAAAAGTGCTGCTCATGA

             *     
       6159 TGATGAT
          1 TCATGAT

       6166 ACTGATGATC


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  33   24  0.71
  34   10  0.29

ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29


Consensus pattern (33 bp):   
TCATGATCAAACTCAAAAAAGTGCTGCTCATGA

Found at i:6421 original size:21 final size:21

Alignment explanation


    Indices: 6397--6442  Score: 92
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       6387 TGAGACGATC

                                 
       6397 GTTAATTGGAATGAGCTTCCA
          1 GTTAATTGGAATGAGCTTCCA

                                 
       6418 GTTAATTGGAATGAGCTTCCA
          1 GTTAATTGGAATGAGCTTCCA

                
       6439 GTTA
          1 GTTA

       6443 TTGAAGCAGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35


Consensus pattern (21 bp):   
GTTAATTGGAATGAGCTTCCA

Found at i:9936 original size:19 final size:19

Alignment explanation


    Indices: 9912--9950  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       9902 CAATTTGATG

                               
       9912 AGGAAATTGGTTTTGTACT
          1 AGGAAATTGGTTTTGTACT

                               
       9931 AGGAAATTGGTTTTGTACT
          1 AGGAAATTGGTTTTGTACT

             
       9950 A
          1 A

       9951 CTACAAAAAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41


Consensus pattern (19 bp):   
AGGAAATTGGTTTTGTACT

Found at i:12172 original size:45 final size:45

Alignment explanation


    Indices: 12108--12197  Score: 153
    Period size: 45  Copynumber: 2.0  Consensus size: 45

      12098 AGCGATTTCC

                   *     *            *                  
      12108 AATATTTGTTACCTTTCTTGCTGGTTTTCAGGACCTCAAAAGGGT
          1 AATATTTCTTACCATTCTTGCTGGTTCTCAGGACCTCAAAAGGGT

                                                         
      12153 AATATTTCTTACCATTCTTGCTGGTTCTCAGGACCTCAAAAGGGT
          1 AATATTTCTTACCATTCTTGCTGGTTCTCAGGACCTCAAAAGGGT

      12198 CACAACACTT


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38


Consensus pattern (45 bp):   
AATATTTCTTACCATTCTTGCTGGTTCTCAGGACCTCAAAAGGGT

Found at i:20364 original size:29 final size:28

Alignment explanation


    Indices: 20330--20404  Score: 71
    Period size: 29  Copynumber: 2.6  Consensus size: 28

      20320 ACTTGTAGGG

                                          
      20330 TTTGGACGTTTTGTCCCATGAACT-ACAAT
          1 TTTGGACGTTTTGTCCCA--AACTCACAAT

                   *    **          *    
      20359 TTTGGACATTTTACCTCCAAACTCTCAAT
          1 TTTGGACGTTTTGTC-CCAAACTCACAAT

               *             
      20388 TTTAGACGTTTTGTCCC
          1 TTTGGACGTTTTGTCCC

      20405 CTATCAAACA


Statistics
Matches: 36,  Mismatches: 8, Indels: 5
        0.73            0.16        0.10

Matches are distributed among these distances:
  28    6  0.17
  29   27  0.75
  30    3  0.08

ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40


Consensus pattern (28 bp):   
TTTGGACGTTTTGTCCCAAACTCACAAT

Found at i:20650 original size:29 final size:31

Alignment explanation


    Indices: 20595--20666  Score: 96
    Period size: 29  Copynumber: 2.4  Consensus size: 31

      20585 TGAGTGGGGG

                *    *                     
      20595 AAAATTGTCCAAAATTGATAGTTTATGG-GC
          1 AAAAATGTCTAAAATTGATAGTTTATGGAGC

                                           
      20625 AAAAATGTCTAAAATTGA-AGTTTATGGAGC
          1 AAAAATGTCTAAAATTGATAGTTTATGGAGC

                 *       
      20655 -AAAACGTCTAAA
          1 AAAAATGTCTAAA

      20667 CACTACAAGC


Statistics
Matches: 38,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  29   20  0.53
  30   18  0.47

ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29


Consensus pattern (31 bp):   
AAAAATGTCTAAAATTGATAGTTTATGGAGC
Done.