Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004488.1 Corchorus olitorius cultivar O-4 contig04504, 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, 710

Length: 1184
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:311 original size:153 final size:154

Alignment explanation


    Indices: 4--335  Score: 594
    Period size: 153  Copynumber: 2.2  Consensus size: 154

          1 CAA

                              *      *  *                        *           
          4 TTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAAAACTTGTTATTTTGGGCCTAT
          1 TTTGGTGAGATTAGTCCACTGTGAAATTATTAGCTCATTTGGAAAACTTGTTAGTTTGGGCCTAT

               *                                                             
         69 CGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGGTTTTCTTTCCAT
         66 CGGAGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGGTTTTCTTTCCAT

                                    
        134 TGTTTATGGACTAACTATAATCAT
        131 TGTTTATGGACTAACTATAATCAT

                                                        *                    
        158 TTTGGTGAGATTAGTCCACTGT-AAATTATTAGCTCATTTGGAACACTTGTTAGTTTGGGCCTAT
          1 TTTGGTGAGATTAGTCCACTGTGAAATTATTAGCTCATTTGGAAAACTTGTTAGTTTGGGCCTAT

                                                                             
        222 CGGAGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGGTTTTCTTTCCAT
         66 CGGAGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGGTTTTCTTTCCAT

                                    
        287 TGTTTATGGACTAACTATAATCAT
        131 TGTTTATGGACTAACTATAATCAT

                              *      
        311 TTTGGTGAGATTAGTCCAATGTGAA
          1 TTTGGTGAGATTAGTCCACTGTGAA

        336 GTGATACGAA


Statistics
Matches: 170,  Mismatches: 7, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
 153  147  0.86
 154   23  0.14

ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40


Consensus pattern (154 bp):   
TTTGGTGAGATTAGTCCACTGTGAAATTATTAGCTCATTTGGAAAACTTGTTAGTTTGGGCCTAT
CGGAGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGGTTTTCTTTCCAT
TGTTTATGGACTAACTATAATCAT

Found at i:1162 original size:21 final size:21

Alignment explanation


    Indices: 1138--1184  Score: 76
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       1128 CTTAGGCAAT

                                 
       1138 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGAAACCTTC

                    *    *       
       1159 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGAAACCTTC

                 
       1180 TCCAA
          1 TCCAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.28, C:0.30, G:0.13, T:0.30


Consensus pattern (21 bp):   
TCCAATGAGCTTGAAACCTTC
Done.