Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023755.1 Corchorus olitorius cultivar O-4 contig23788, 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: 16955
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32


Found at i:2917 original size:28 final size:26

Alignment explanation


    Indices: 2832--2928  Score: 104
    Period size: 28  Copynumber: 3.5  Consensus size: 26

       2822 GGTGTCCCTG

                    *             *     
       2832 AAATGACCGAAATGCCCCTAGCCTAGCA
          1 AAATGACCAAAATGCCCCT-GCAT-GCA

                                *       
       2860 AAATGACCAAAATGCCCCTGGATGTACA
          1 AAATGACCAAAATGCCCCTGCATG--CA

                             *          
       2888 AAATGACCAAAATGCCCTTGTTCATGCA
          1 AAATGACCAAAATGCCCCTG--CATGCA

                         
       2916 AAATGACCAAAAT
          1 AAATGACCAAAAT

       2929 AAAAGTAAAT


Statistics
Matches: 60,  Mismatches: 5, Indels: 8
        0.82            0.07        0.11

Matches are distributed among these distances:
  26    1  0.02
  27    2  0.03
  28   54  0.90
  30    3  0.05

ACGTcount: A:0.40, C:0.26, G:0.15, T:0.19


Consensus pattern (26 bp):   
AAATGACCAAAATGCCCCTGCATGCA

Found at i:3166 original size:24 final size:24

Alignment explanation


    Indices: 3139--3188  Score: 100
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       3129 GATCATCTCC

                                    
       3139 CGAACTGTCTTCCAATTCAATCTT
          1 CGAACTGTCTTCCAATTCAATCTT

                                    
       3163 CGAACTGTCTTCCAATTCAATCTT
          1 CGAACTGTCTTCCAATTCAATCTT

              
       3187 CG
          1 CG

       3189 GGGAATCGTC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.24, C:0.30, G:0.10, T:0.36


Consensus pattern (24 bp):   
CGAACTGTCTTCCAATTCAATCTT

Found at i:3281 original size:50 final size:50

Alignment explanation


    Indices: 3214--3539  Score: 393
    Period size: 50  Copynumber: 6.5  Consensus size: 50

       3204 AACCAACTTA

                               *  *                *           
       3214 TTTGAACTGTCTTCCAATTTAACCTTAAAAGGA-CAGTCCTCCGCTTATCC
          1 TTTGAACTGTCTTCCAATTCAATCTTAAAAGGATC-GTCTTCCGCTTATCC

                 **           *  *  *        *                
       3264 TTTGATTTGTCTTCCAATCCACTCATAAAAGGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCC

                   *        *    *              *             
       3314 TTTGAACAGTCTTCCAGTTCATTCTTAAAAGGATCGCCTTCCGCTTATCC
          1 TTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCC

                        *    *        * *    *       *        
       3364 TTTGAACTGTCTACCAACTCAATCTTGATAGGACCGTCTTCTGCTTATCC
          1 TTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCC

              *    *                       *                  
       3414 TTCGAACGGTCTTCCAATTCAATCTTAAAAGCATCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCC

              *                                       *       
       3464 TTCGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCACTTATCC
          1 TTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCC

              **                 *    
       3514 TTCAAACTGTCTTCCAATTCACTCTT
          1 TTTGAACTGTCTTCCAATTCAATCTT

       3540 CTGTATATTT


Statistics
Matches: 234,  Mismatches: 41, Indels: 2
        0.84            0.15        0.01

Matches are distributed among these distances:
  50  233  1.00
  51    1  0.00

ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36


Consensus pattern (50 bp):   
TTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCC

Found at i:3525 original size:23 final size:23

Alignment explanation


    Indices: 3449--3529  Score: 65
    Period size: 23  Copynumber: 3.3  Consensus size: 23

       3439 TAAAAGCATC

                   *          *    
       3449 GTCTTCCGCTTATCCTTCGAACT
          1 GTCTTCCACTTATCCTTCAAACT

                    *          *     * 
       3472 GTCTTCCAATTCAAT-CTTAAAAGGAT
          1 GTCTTCCACTT--ATCCTTCAAA--CT

                                    
       3498 CGTCTTCCACTTATCCTTCAAACT
          1 -GTCTTCCACTTATCCTTCAAACT

                    
       3522 GTCTTCCA
          1 GTCTTCCA

       3530 ATTCACTCTT


Statistics
Matches: 44,  Mismatches: 8, Indels: 12
        0.69            0.12        0.19

Matches are distributed among these distances:
  23   17  0.39
  24    6  0.14
  25    4  0.09
  26    7  0.16
  27   10  0.23

ACGTcount: A:0.22, C:0.31, G:0.10, T:0.37


Consensus pattern (23 bp):   
GTCTTCCACTTATCCTTCAAACT

Found at i:4600 original size:1 final size:1

Alignment explanation


    Indices: 4596--4621  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       4586 TAGGCTGTAG

                                      
       4596 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

       4622 AAAGGTCCAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Done.