Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001689.1 Corchorus olitorius cultivar O-4 contig01689, 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, 799

Length: 1332
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32


Found at i:831 original size:51 final size:51

Alignment explanation


    Indices: 704--1207  Score: 845
    Period size: 51  Copynumber: 10.0  Consensus size: 51

        694 CTAATATATT

                   * *                            *   *        
        704 AAAAGGATCATCTTCCGCTTATCCTTTGAACTGTCTACTAATCCAATCTT-
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                 *         *                   
        754 AAAAGGACCGTCTTCCGCTTACCCTTTGAACCGTCTACCAATTCAATCTTA
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                          *                    
        805 AAAAGGACCGTCTTCCGCTTATCCTTTGAATTGTCTACCAATTCAATCTTA
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                          *                            *       
        856 AAAAGGACCGTCTTTCGCTTATCCTTTGAACTGTCTACCAATTTAATCTTA
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                                               
        907 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                                               
        958 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                          * *   *              
       1009 AAAAGGACCGTCTTCCGCTTATCCTTTGAATTTTCTTCCAATTCAATCTT-
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                                                               
       1059 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT-
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

                *                                      *       
       1109 AAAATGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTAAATCTT-
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

             *                                               
       1159 AGAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
          1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT

       1208 CGAGAAAACC


Statistics
Matches: 428,  Mismatches: 25, Indels: 2
        0.94            0.05        0.00

Matches are distributed among these distances:
  50  185  0.43
  51  243  0.57

ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35


Consensus pattern (51 bp):   
AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTA

Found at i:1144 original size:23 final size:23

Alignment explanation


    Indices: 1118--1194  Score: 57
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       1108 TAAAATGACC

                                   
       1118 GTCTTCCGCTTATCCTTTGAACT
          1 GTCTTCCGCTTATCCTTTGAACT

                *  **          *       *
       1141 GTCTACCAATTAAAT-CTTAGAAGGACC
          1 GTCTTCCGCTT--ATCCTTTG-A--ACT

                                   
       1168 GTCTTCCGCTTATCCTTTGAACT
          1 GTCTTCCGCTTATCCTTTGAACT

                
       1191 GTCT
          1 GTCT

       1195 ACCAATTCAA


Statistics
Matches: 38,  Mismatches: 10, Indels: 12
        0.63            0.17        0.20

Matches are distributed among these distances:
  23   14  0.37
  24    4  0.11
  25    6  0.16
  26    4  0.11
  27   10  0.26

ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38


Consensus pattern (23 bp):   
GTCTTCCGCTTATCCTTTGAACT
Done.