Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022551.1 Corchorus olitorius cultivar O-4 contig22584, 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: 6615
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:888 original size:29 final size:28

Alignment explanation


    Indices: 845--900  Score: 76
    Period size: 29  Copynumber: 2.0  Consensus size: 28

        835 GACGCAGAAA

                                        
        845 TTTTTTTTTTCGACGCAAAACACAAAAC
          1 TTTTTTTTTTCGACGCAAAACACAAAAC

                       *       *  *     
        873 TTTTTTTTCTTTGACGCAAGACTCAAAA
          1 TTTTTTTT-TTCGACGCAAAACACAAAA

        901 AAAATTAAAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  28    8  0.33
  29   16  0.67

ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39


Consensus pattern (28 bp):   
TTTTTTTTTTCGACGCAAAACACAAAAC

Found at i:1337 original size:16 final size:15

Alignment explanation


    Indices: 1299--1340  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1289 ACAGAGGTTG

                           
       1299 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       1314 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1329 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1341 AGCAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:6518 original size:42 final size:44

Alignment explanation


    Indices: 6415--6615  Score: 284
    Period size: 46  Copynumber: 4.6  Consensus size: 44

       6405 TCTTATCTCT

                                    *                     
       6415 TTCCAAAAATGCCCCTTCCTGGTTAGAAGGTCCCTGTTTTCTTCTA
          1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG-TTT-TTCTA

                             *                          
       6461 TTCCAAAAATGCCCCTTTCTGGTTGGAAGGTCCCTG-TTTT-TA
          1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTTCTA

                                              *          
       6503 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTA
          1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTT-TCTA

                               *              *          
       6548 TTTCCAAAAATGCCCCTTCTTGGTTGGAAGGTCCATG-TTTT-TA
          1 -TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTTCTA

                       *             
       6591 TTCCAAAAATGGCCCTTCCTGGTTG
          1 TTCCAAAAATGCCCCTTCCTGGTTG


Statistics
Matches: 142,  Mismatches: 9, Indels: 12
        0.87            0.06        0.07

Matches are distributed among these distances:
  42   59  0.42
  43    7  0.05
  44    4  0.03
  45    5  0.04
  46   67  0.47

ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36


Consensus pattern (44 bp):   
TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTTCTA

Found at i:6615 original size:88 final size:88

Alignment explanation


    Indices: 6415--6615  Score: 334
    Period size: 88  Copynumber: 2.3  Consensus size: 88

       6405 TCTTATCTCT

                                    *         *                              
       6415 TTCCAAAAATGCCCCTTCCTGGTTAGAAGGTCCCTGTTTTCTTCTATTCCAAAAATGCCCCTTTC
          1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTCTATTCCAAAAATGCCCCTTTC

                          *        
       6480 TGGTTGGAAGGTCCCTGTTTTTA
         66 TGGTTGGAAGGTCCATGTTTTTA

                                                                             
       6503 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTC-TCTATTTCCAAAAATGCCCC-TT
          1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTCTA-TTCCAAAAATGCCCCTTT

                                     
       6566 CTTGGTTGGAAGGTCCATGTTTTTA
         65 C-TGGTTGGAAGGTCCATGTTTTTA

                       *             
       6591 TTCCAAAAATGGCCCTTCCTGGTTG
          1 TTCCAAAAATGCCCCTTCCTGGTTG


Statistics
Matches: 107,  Mismatches: 4, Indels: 4
        0.93            0.03        0.03

Matches are distributed among these distances:
  87    7  0.07
  88  100  0.93

ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36


Consensus pattern (88 bp):   
TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTCTATTCCAAAAATGCCCCTTTC
TGGTTGGAAGGTCCATGTTTTTA
Done.