Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010305.1 Corchorus olitorius cultivar O-4 contig10337, 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: 18301
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:2994 original size:12 final size:11

Alignment explanation


    Indices: 2961--2994  Score: 50
    Period size: 11  Copynumber: 3.0  Consensus size: 11

       2951 ACCAATATTG

                *      
       2961 AATATATTTTT
          1 AATAAATTTTT

                       
       2972 AATAAATTTTT
          1 AATAAATTTTT

                        
       2983 AATAAATATTTT
          1 AATAAAT-TTTT

       2995 TTAAGAGTTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  11   17  0.81
  12    4  0.19

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (11 bp):   
AATAAATTTTT

Found at i:6927 original size:104 final size:104

Alignment explanation


    Indices: 6747--6958  Score: 406
    Period size: 104  Copynumber: 2.0  Consensus size: 104

       6737 TACTCCAATG

                                                                             
       6747 TATTGTACACAAAATCGGTGTTAAAAATGATTTTACTTTATATTATCTATATAACTATTATTTAT
          1 TATTGTACACAAAATCGGTGTTAAAAATGATTTTACTTTATATTATCTATATAACTATTATTTAT

                                                   
       6812 TCATAAAACTTAATTTATAATTATTGGAAATAAAAATAT
         66 TCATAAAACTTAATTTATAATTATTGGAAATAAAAATAT

                      *                                                      
       6851 TATTGTACACTAAATCGGTGTTAAAAATGATTTTACTTTATATTATCTATATAACTATTATTTAT
          1 TATTGTACACAAAATCGGTGTTAAAAATGATTTTACTTTATATTATCTATATAACTATTATTTAT

                               *                   
       6916 TCATAAAACTTAATTTATAGTTATTGGAAATAAAAATAT
         66 TCATAAAACTTAATTTATAATTATTGGAAATAAAAATAT

                
       6955 TATT
          1 TATT

       6959 AGTAAATAAA


Statistics
Matches: 106,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 104  106  1.00

ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44


Consensus pattern (104 bp):   
TATTGTACACAAAATCGGTGTTAAAAATGATTTTACTTTATATTATCTATATAACTATTATTTAT
TCATAAAACTTAATTTATAATTATTGGAAATAAAAATAT

Found at i:10718 original size:94 final size:94

Alignment explanation


    Indices: 10557--10745  Score: 335
    Period size: 94  Copynumber: 2.0  Consensus size: 94

      10547 TAAATATAAT

                                                                *            
      10557 CCTATGTCACACAATTGATTTTGGACACCTAATTTATTCTCTACTTAAAGAAGTTCTTGGCCTTC
          1 CCTATGTCACACAATTGATTTTGGACACCTAATTTATTCTCTACTTAAAGAAATTCTTGGCCTTC

                              *          
      10622 AAGCAAAAATTAAACATATCACAAATTTG
         66 AAGCAAAAATTAAACATACCACAAATTTG

                                                            *                
      10651 CCTATGTCACACAATTGATTTTGGACACC-AAGTTTATTCTCTACTTACAGAAATTCTTGGCCTT
          1 CCTATGTCACACAATTGATTTTGGACACCTAA-TTTATTCTCTACTTAAAGAAATTCTTGGCCTT

                                          
      10715 CAAGCAAAAATTAAACATACCACAAATTTG
         65 CAAGCAAAAATTAAACATACCACAAATTTG

             
      10745 C
          1 C

      10746 TTATCTCGAG


Statistics
Matches: 91,  Mismatches: 3, Indels: 2
        0.95            0.03        0.02

Matches are distributed among these distances:
  93    2  0.02
  94   89  0.98

ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33


Consensus pattern (94 bp):   
CCTATGTCACACAATTGATTTTGGACACCTAATTTATTCTCTACTTAAAGAAATTCTTGGCCTTC
AAGCAAAAATTAAACATACCACAAATTTG
Done.