Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014291.1 Corchorus olitorius cultivar O-4 contig14324, 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: 23735
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:931 original size:42 final size:44

Alignment explanation


    Indices: 880--973  Score: 149
    Period size: 45  Copynumber: 2.2  Consensus size: 44

        870 AGTGCATTAC

                                     *                  
        880 CTAA-ATTCTACT-C-CATCTCTAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCGCATCTCTAGATAATTCATCAAAATAAAG

                                                         
        921 CTAATATTCTACTCCTGCATCTCTAGATAATTCATCAAAATAAAG
          1 CTAATATTCTACTCC-GCATCTCTAGATAATTCATCAAAATAAAG

                    
        966 CTAATATT
          1 CTAATATT

        974 AATTGTTCTT


Statistics
Matches: 48,  Mismatches: 1, Indels: 4
        0.91            0.02        0.08

Matches are distributed among these distances:
  41    4  0.08
  42    8  0.17
  43    1  0.02
  45   35  0.73

ACGTcount: A:0.38, C:0.21, G:0.06, T:0.34


Consensus pattern (44 bp):   
CTAATATTCTACTCCGCATCTCTAGATAATTCATCAAAATAAAG

Found at i:3771 original size:25 final size:24

Alignment explanation


    Indices: 3734--3780  Score: 69
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       3724 AATGAAGGAG

                                      
       3734 AAGGAAAAAGAAGGAAAAGAAAATAT
          1 AAGGAAAAAGAA-GAAAA-AAAATAT

                                  
       3760 AAGG-AAAAGAAGAAAAAAAAT
          1 AAGGAAAAAGAAGAAAAAAAAT

       3781 GGAAAAAAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    5  0.24
  25    7  0.33
  26    4  0.19

ACGTcount: A:0.72, C:0.00, G:0.21, T:0.06


Consensus pattern (24 bp):   
AAGGAAAAAGAAGAAAAAAAATAT

Found at i:5655 original size:21 final size:21

Alignment explanation


    Indices: 5631--5675  Score: 81
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       5621 GCTTTAGACT

                          *      
       5631 TTTATGGTTAGGATTCTTTTG
          1 TTTATGGTTAGGATCCTTTTG

                                 
       5652 TTTATGGTTAGGATCCTTTTG
          1 TTTATGGTTAGGATCCTTTTG

               
       5673 TTT
          1 TTT

       5676 TTTTTTTTCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.13, C:0.07, G:0.22, T:0.58


Consensus pattern (21 bp):   
TTTATGGTTAGGATCCTTTTG

Found at i:20262 original size:3 final size:3

Alignment explanation


    Indices: 20256--20281  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

      20246 AAAAAAAAAA

                                              
      20256 AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AA

      20282 AGCAACAATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Found at i:20431 original size:22 final size:22

Alignment explanation


    Indices: 20403--20453  Score: 86
    Period size: 22  Copynumber: 2.4  Consensus size: 22

      20393 CATATTAGTC

                     *            
      20403 ATAATAATTTGTTAAAACGGAT
          1 ATAATAATTCGTTAAAACGGAT

                                  
      20425 ATAATAATTCGTTAAAACGGAT
          1 ATAATAATTCGTTAAAACGGAT

                    
      20447 AT-ATAAT
          1 ATAATAAT

      20454 GTGTGTAAGG


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  21    5  0.18
  22   23  0.82

ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35


Consensus pattern (22 bp):   
ATAATAATTCGTTAAAACGGAT

Found at i:23513 original size:2 final size:2

Alignment explanation


    Indices: 23506--23549  Score: 79
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      23496 AGTACTACTC

                                       *                                  
      23506 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

              
      23548 TA
          1 TA

      23550 CTAGTTAAAG


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Done.