Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014143.1 Corchorus olitorius cultivar O-4 contig14176, 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: 10439
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:5097 original size:2 final size:2

Alignment explanation


    Indices: 5086--5119  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       5076 AATTGATTGG

                                                                
       5086 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5120 TTTGTTTCCC


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:7374 original size:14 final size:13

Alignment explanation


    Indices: 7355--7393  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

       7345 AAATTGTAAA

                         
       7355 ATTTAAAAAATTT
          1 ATTTAAAAAATTT

                   *    * 
       7368 CATTTAAGAAATAT
          1 -ATTTAAAAAATTT

                        
       7382 ATTTAAAAAATT
          1 ATTTAAAAAATT

       7394 CTAATATATA


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41


Consensus pattern (13 bp):   
ATTTAAAAAATTT

Found at i:7631 original size:123 final size:127

Alignment explanation


    Indices: 7379--7633  Score: 392
    Period size: 131  Copynumber: 2.0  Consensus size: 127

       7369 ATTTAAGAAA

                                                                             
       7379 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAA
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT---A

            *                                                          *     
       7444 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
         63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA

             
       7509 G
        127 G

                                              *  *                           
       7510 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA-
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAG

                                          *    *                          
       7573 TA-AA-GATATTAGATTTAATTAAATAAAATTAGATTTTTTAGTTGAGTAAAACTATAAAAG
         66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG

             
       7633 T
          1 T

       7634 TTAAATAATG


Statistics
Matches: 118,  Mismatches: 6, Indels: 8
        0.89            0.05        0.06

Matches are distributed among these distances:
 123   54  0.46
 124    2  0.02
 125    2  0.02
 127    1  0.01
 131   59  0.50

ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37


Consensus pattern (127 bp):   
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG

Found at i:7659 original size:123 final size:127

Alignment explanation


    Indices: 7385--7641  Score: 333
    Period size: 123  Copynumber: 2.0  Consensus size: 127

       7375 GAAATATATT

                         * *                                           *     
       7385 TAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAATAGGTA
          1 TAAAAAATTCTAAGAAATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT---ACA-GTA

                                                                 *          *
       7450 TAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATAT
         62 TAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAA

            *
       7515 T
        127 A

                         * *            *  *                                 
       7516 TAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA-TA-AA-
          1 TAAAAAATTCTAAGAAATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAGTATAAG

                                    *    *                           *    
       7577 GATATTAGATTTAATTAAATAAAATTAGATTTTTTAGTTGAGTAAAACTATAAAAGTTTAAA
         66 GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAA

               
       7639 TAA
          1 TAA

       7642 TGGCATTTAA


Statistics
Matches: 117,  Mismatches: 9, Indels: 8
        0.87            0.07        0.06

Matches are distributed among these distances:
 123   59  0.50
 124    2  0.02
 125    2  0.02
 127    1  0.01
 131   53  0.45

ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37


Consensus pattern (127 bp):   
TAAAAAATTCTAAGAAATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAGTATAAG
GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAA
Done.