Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018183.1 Corchorus olitorius cultivar O-4 contig18216, 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: 53312
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34


Found at i:901 original size:54 final size:52

Alignment explanation


    Indices: 836--941  Score: 167
    Period size: 54  Copynumber: 2.0  Consensus size: 52

        826 TATAGCTAAA

                                        *                 *       
        836 TAAAACGAATCTAACATAGTTGTTTTATTATGGTGAAAAATAAGTATTTCCCAT
          1 TAAAACGAATCTAACATAGTTG-TTTATCATGGTG-AAAATAAGTAATTCCCAT

                 *                                              
        890 TAAAATGAATCTAACATAGTTGTTTATCATGGTGAAAATAAGTAATTCCCAT
          1 TAAAACGAATCTAACATAGTTGTTTATCATGGTGAAAATAAGTAATTCCCAT

        942 GCATGTTTAT


Statistics
Matches: 49,  Mismatches: 3, Indels: 2
        0.91            0.06        0.04

Matches are distributed among these distances:
  52   17  0.35
  53   11  0.22
  54   21  0.43

ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36


Consensus pattern (52 bp):   
TAAAACGAATCTAACATAGTTGTTTATCATGGTGAAAATAAGTAATTCCCAT

Found at i:2998 original size:15 final size:15

Alignment explanation


    Indices: 2980--3014  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       2970 TGAGGACGAC

                *          
       2980 GAAGGAGAAGAAGCA
          1 GAAGAAGAAGAAGCA

                          *
       2995 GAAGAAGAAGAAGCG
          1 GAAGAAGAAGAAGCA

                 
       3010 GAAGA
          1 GAAGA

       3015 GCTATTCATT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.54, C:0.06, G:0.40, T:0.00


Consensus pattern (15 bp):   
GAAGAAGAAGAAGCA

Found at i:6762 original size:7 final size:7

Alignment explanation


    Indices: 6752--6779  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

       6742 AAAAATATAA

                   
       6752 AATAGAT
          1 AATAGAT

                   
       6759 AATAGAT
          1 AATAGAT

                   
       6766 AATAGAT
          1 AATAGAT

                   
       6773 AATAGAT
          1 AATAGAT

       6780 TACTGGACTG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29


Consensus pattern (7 bp):   
AATAGAT

Found at i:12484 original size:34 final size:34

Alignment explanation


    Indices: 12414--12505  Score: 139
    Period size: 34  Copynumber: 2.7  Consensus size: 34

      12404 TACACGCATT

                         *         *    *      
      12414 TTGGGTTTGTTTTATGTTTTGGGTCATTGCTCATA
          1 TTGGGTTTG-TTTCTGTTTTGGGCCATTACTCATA

                                          *   
      12449 TTGGGTTTGTTTCTGTTTTGGGCCATTACTTATA
          1 TTGGGTTTGTTTCTGTTTTGGGCCATTACTCATA

                                   
      12483 TTGGGTTTGTTTCTGTTTTGGGC
          1 TTGGGTTTGTTTCTGTTTTGGGC

      12506 ATAGTGGGCC


Statistics
Matches: 53,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  34   44  0.83
  35    9  0.17

ACGTcount: A:0.09, C:0.10, G:0.27, T:0.54


Consensus pattern (34 bp):   
TTGGGTTTGTTTCTGTTTTGGGCCATTACTCATA

Found at i:32805 original size:46 final size:47

Alignment explanation


    Indices: 32738--32834  Score: 180
    Period size: 46  Copynumber: 2.1  Consensus size: 47

      32728 TCCATGCCTT

                                                           
      32738 TCTTTTTTTTCCAGAGGATTTAGATTATAATAAATGAGAG-TTGCAA
          1 TCTTTTTTTTCCAGAGGATTTAGATTATAATAAATGAGAGTTTGCAA

                                                           
      32784 TCTTTTTTTTCCAGAGGATTTAGATTATAATAAATGAGAGTTTGCAA
          1 TCTTTTTTTTCCAGAGGATTTAGATTATAATAAATGAGAGTTTGCAA

                 
      32831 -CTTT
          1 TCTTT

      32835 AATTTTTAGT


Statistics
Matches: 50,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  46   44  0.88
  47    6  0.12

ACGTcount: A:0.31, C:0.09, G:0.16, T:0.43


Consensus pattern (47 bp):   
TCTTTTTTTTCCAGAGGATTTAGATTATAATAAATGAGAGTTTGCAA

Found at i:35759 original size:16 final size:17

Alignment explanation


    Indices: 35733--35765  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

      35723 TCTCTCCTCC

                       *     
      35733 TGCCTTATTTTGGTAAT
          1 TGCCTTATTTTAGTAAT

                             
      35750 TGCC-TATTTTAGTAAT
          1 TGCCTTATTTTAGTAAT

      35766 AAATAGTGTC


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52


Consensus pattern (17 bp):   
TGCCTTATTTTAGTAAT

Found at i:49895 original size:40 final size:40

Alignment explanation


    Indices: 49840--49923  Score: 150
    Period size: 40  Copynumber: 2.1  Consensus size: 40

      49830 AATAATACAA

                                            *       
      49840 TTCTTAATTCCTTAATTGCTCATTGATAATCAGCTATACT
          1 TTCTTAATTCCTTAATTGCTCATTGATAATCAACTATACT

                                             *      
      49880 TTCTTAATTCCTTAATTGCTCATTGATAATCAATTATACT
          1 TTCTTAATTCCTTAATTGCTCATTGATAATCAACTATACT

                
      49920 TTCT
          1 TTCT

      49924 CCAGTTCAGT


Statistics
Matches: 42,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  40   42  1.00

ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48


Consensus pattern (40 bp):   
TTCTTAATTCCTTAATTGCTCATTGATAATCAACTATACT
Done.