Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013680.1 Corchorus olitorius cultivar O-4 contig13713, 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: 2560
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32


Found at i:196 original size:35 final size:35

Alignment explanation


    Indices: 150--503  Score: 471
    Period size: 35  Copynumber: 10.0  Consensus size: 35

        140 ATCAATGTGA

                                               
        150 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                              **              * 
        185 AGATCAACTCTGATCATAAAAAAACTTCTTGAAAGG
          1 AGATCAACTCTGATCAT-CGAAAACTTCTTGAAATG

                         *      **                
        221 AGATCAACTCTGACCATATAAAAAAACTTCTTGAAATG
          1 AGATCAACTCTGATC--AT-CGAAAACTTCTTGAAATG

                            *                   
        259 AGATCAACTCTGATCAACGAAAAC-TCTTTGAAATG
          1 AGATCAACTCTGATCATCGAAAACTTC-TTGAAATG

                                               
        294 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                         *    *     * *         
        329 AGATCAACTCTGACCAT-AAAAACATGTTGAAAATG
          1 AGATCAACTCTGATCATCGAAAACTTCTTG-AAATG

                              *        *     * 
        364 AGATCAACTCTGATCAT-AAAAACTTCCTGAAAGG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                            *                * 
        398 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                                             * 
        433 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                                          *    
        468 AGATCAACTCTGATCATCGAAAACTTCTTGGAATG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

             
        503 A
          1 A

        504 CCGCACTGGA


Statistics
Matches: 286,  Mismatches: 26, Indels: 14
        0.88            0.08        0.04

Matches are distributed among these distances:
  34   31  0.11
  35  189  0.66
  36   32  0.11
  38   34  0.12

ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26


Consensus pattern (35 bp):   
AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

Found at i:503 original size:139 final size:140

Alignment explanation


    Indices: 150--503  Score: 516
    Period size: 139  Copynumber: 2.5  Consensus size: 140

        140 ATCAATGTGA

                                                                             
        150 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAACTTCTT
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCAT--AAAAACTTCTT

                *                               *     *                      
        215 GAAAGGAGATCAACTCTGACCATATAAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAA
         64 GAAATGAGATCAACTCTGACCA-AT-AAAAAACTTCCTGAAAGGAGATCAACTCTGATCAACGAA

                        * 
        280 AACTCTTTGAAATG
        127 AACTCTTTGAAACG

                                                            *         * *    
        294 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGACCATAAAAACATGTTGA
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAACTTCTTG-

                              *                                      *       
        359 AAATGAGATCAACTCTGATC-AT-AAAAACTTCCTGAAAGGAGATCAACTCTGATCACCGAAAAC
         65 AAATGAGATCAACTCTGACCAATAAAAAACTTCCTGAAAGGAGATCAACTCTGATCAACGAAAAC

                        
        422 T-TCTTGAAACG
        130 TCT-TTGAAACG

                                             *                   *           
        433 AGATCAACTCTGATCATCGAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCAT-AAAAACTTCTTG

            *     
        498 GAATGA
         65 AAATGA

        504 CCGCACTGGA


Statistics
Matches: 192,  Mismatches: 15, Indels: 11
        0.88            0.07        0.05

Matches are distributed among these distances:
 138    1  0.01
 139  101  0.53
 140    9  0.05
 141    2  0.01
 142   10  0.05
 143   18  0.09
 144   51  0.27

ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26


Consensus pattern (140 bp):   
AGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAACTTCTTGA
AATGAGATCAACTCTGACCAATAAAAAACTTCCTGAAAGGAGATCAACTCTGATCAACGAAAACT
CTTTGAAACG

Found at i:1446 original size:16 final size:16

Alignment explanation


    Indices: 1409--1445  Score: 60
    Period size: 14  Copynumber: 2.4  Consensus size: 16

       1399 TTTCCGACCC

                            
       1409 TTTTTTTCTTTTTCTT
          1 TTTTTTTCTTTTTCTT

                            
       1425 TTTTTTTC--TTTCTT
          1 TTTTTTTCTTTTTCTT

                   
       1439 TTTTTTT
          1 TTTTTTT

       1446 TGCGAAAATT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  14   13  0.62
  16    8  0.38

ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89


Consensus pattern (16 bp):   
TTTTTTTCTTTTTCTT
Done.