Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011252.1 Corchorus olitorius cultivar O-4 contig11285, 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, 768

Length: 1280
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36


Found at i:282 original size:154 final size:154

Alignment explanation


    Indices: 1--729  Score: 1115
    Period size: 154  Copynumber: 4.7  Consensus size: 154

                                                  * *                        
          1 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCATTTGGA
          1 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA

                                      **     *                 *     *       
         66 ACACTTGTTATTTTGGGCCTATCGGGTACCATTCGTTCCGTTTTGAATCGTTTTCGATTTGGCAA
         66 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAATTGGCAA

                               *    
        131 ACCTAAATGCTTTTCTTTCTATTG
        131 ACCTAAATGCTTTTCTTTCCATTG

                                     *            * *                        
        155 TTTATGGCCTAACTATAATCATTTTTGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCATTTGGA
          1 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA

                                                                             
        220 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAATTGGCAA
         66 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAATTGGCAA

                *                   
        285 ACCTCAATGCTTTTCTTTCCATTG
        131 ACCTAAATGCTTTTCTTTCCATTG

                                   *                                         
        309 TTTATGGCCTAACTATAATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
          1 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA

                                       *                 *  *       *        
        374 ACACTTGTTATTTTGGGCCTATCGGGGGCCATTAGTTCCGTTTTGCATTGTCTTC-CATTAGGCA
         66 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAATT-GGCA

                       *             
        438 AACCTAAATGCATTTCTTTCCATTG
        130 AACCTAAATGCTTTTCTTTCCATTG

                                          *                       *          
        463 TTTATGGCCTAACTATAATCATTTTGGTGACATTAGTCCACTGTGAAGTTTTTAACTCATTTGGA
          1 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA

                                                  *          *       *       
        528 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCTGTTTTGAATCATCTTCGATTTGG-AA
         66 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAATTGGCAA

               *  *              *     
        592 ATCATCGAA-GCTTTTCTTT-AAGTTG
        131 A-CCT-AAATGCTTTTCTTTCCA-TTG

                                                 *                   *       
        617 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTACACTGTGAAGTTTTTAGCTAATTTGGA
          1 TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA

              *                     **                      
        682 ACTCTTGTTATTTTGGGCCTATCGAAGCCCATTAGTTCCGTTTTGAAT
         66 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAAT

        730 TGATGCGCCA


Statistics
Matches: 530,  Mismatches: 40, Indels: 10
        0.91            0.07        0.02

Matches are distributed among these distances:
 153    7  0.01
 154  519  0.98
 155    4  0.01

ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42


Consensus pattern (154 bp):   
TTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAATTGGCAA
ACCTAAATGCTTTTCTTTCCATTG

Found at i:862 original size:21 final size:21

Alignment explanation


    Indices: 836--948  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        826 TGCTAGAAGT

                                 
        836 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
        857 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
        878 TCATTGGAGCAGGTTCCAAGT
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
        899 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
        920 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
        941 TCATTGGA
          1 TCATTGGA

        949 AATGCCTAAG


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   84  0.99

ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Done.