Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018415.1 Corchorus olitorius cultivar O-4 contig18448, 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: 24904
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:10459 original size:33 final size:34

Alignment explanation


    Indices: 10422--10548  Score: 118
    Period size: 33  Copynumber: 3.7  Consensus size: 34

      10412 AAAGAAAAAA

                                              
      10422 GAAACAACAACACCAA-AAGATAAAAGCACAAAT
          1 GAAACAACAACACCAACAAGATAAAAGCACAAAT

                  *       *   *     *        *   *
      10455 GAAACATCAACCTAACAAGAGAGACATAAAG-AAAAAA
          1 GAAACAACAA-C-ACCAACA-AGATA-AAAGCACAAAT

                                              
      10492 GAAACAACAACACCAA-AAGATAAAAGCACAAAT
          1 GAAACAACAACACCAACAAGATAAAAGCACAAAT

                  *      *           
      10525 GAAACATCAAC-CTAACAAGATAAA
          1 GAAACAACAACACCAACAAGATAAA

      10549 CCTGATGTAA


Statistics
Matches: 75,  Mismatches: 12, Indels: 14
        0.74            0.12        0.14

Matches are distributed among these distances:
  32    7  0.09
  33   35  0.47
  34    2  0.03
  35    8  0.11
  36    2  0.03
  37   17  0.23
  38    4  0.05

ACGTcount: A:0.62, C:0.20, G:0.10, T:0.08


Consensus pattern (34 bp):   
GAAACAACAACACCAACAAGATAAAAGCACAAAT

Found at i:10481 original size:70 final size:70

Alignment explanation


    Indices: 10403--10544  Score: 284
    Period size: 70  Copynumber: 2.0  Consensus size: 70

      10393 AATCGGACTC

                                                                             
      10403 GAGAGACATAAAGAAAAAAGAAACAACAACACCAAAAGATAAAAGCACAAATGAAACATCAACCT
          1 GAGAGACATAAAGAAAAAAGAAACAACAACACCAAAAGATAAAAGCACAAATGAAACATCAACCT

                 
      10468 AACAA
         66 AACAA

                                                                             
      10473 GAGAGACATAAAGAAAAAAGAAACAACAACACCAAAAGATAAAAGCACAAATGAAACATCAACCT
          1 GAGAGACATAAAGAAAAAAGAAACAACAACACCAAAAGATAAAAGCACAAATGAAACATCAACCT

                 
      10538 AACAA
         66 AACAA

              
      10543 GA
          1 GA

      10545 TAAACCTGAT


Statistics
Matches: 72,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  70   72  1.00

ACGTcount: A:0.63, C:0.18, G:0.12, T:0.07


Consensus pattern (70 bp):   
GAGAGACATAAAGAAAAAAGAAACAACAACACCAAAAGATAAAAGCACAAATGAAACATCAACCT
AACAA

Found at i:13677 original size:23 final size:23

Alignment explanation


    Indices: 13651--13703  Score: 54
    Period size: 26  Copynumber: 2.2  Consensus size: 23

      13641 TAATTTATCT

                      *            
      13651 TTTTTAT-CTGTTTCTTCTTTCA
          1 TTTTTATGCTCTTTCTTCTTTCA

                    *                 
      13673 CTTTTCCTCTGCTCTTTCTTCTTTCA
          1 -TTTT--TATGCTCTTTCTTCTTTCA

                 
      13699 TTTTT
          1 TTTTT

      13704 CTTCTGCTCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 6
        0.76            0.06        0.18

Matches are distributed among these distances:
  23    5  0.20
  25    6  0.24
  26   14  0.56

ACGTcount: A:0.06, C:0.25, G:0.04, T:0.66


Consensus pattern (23 bp):   
TTTTTATGCTCTTTCTTCTTTCA

Found at i:13697 original size:26 final size:26

Alignment explanation


    Indices: 13661--13714  Score: 90
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      13651 TTTTTATCTG

                                      
      13661 TTTCTTCTTTCACTTTTCCTCTGCTC
          1 TTTCTTCTTTCACTTTTCCTCTGCTC

                        *     *       
      13687 TTTCTTCTTTCATTTTTCTTCTGCTC
          1 TTTCTTCTTTCACTTTTCCTCTGCTC

              
      13713 TT
          1 TT

      13715 GTCGATGGAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.04, C:0.30, G:0.04, T:0.63


Consensus pattern (26 bp):   
TTTCTTCTTTCACTTTTCCTCTGCTC

Found at i:24342 original size:17 final size:16

Alignment explanation


    Indices: 24316--24359  Score: 52
    Period size: 17  Copynumber: 2.7  Consensus size: 16

      24306 AGAAATAGGG

                 *          
      24316 AGGAAAGGAAATAACA
          1 AGGAAGGGAAATAACA

                          ** 
      24332 AGGGAAGGGAAATAGGA
          1 A-GGAAGGGAAATAACA

                       
      24349 AGGAAGGGAAA
          1 AGGAAGGGAAA

      24360 GGAAGTCATA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  16   11  0.46
  17   13  0.54

ACGTcount: A:0.55, C:0.02, G:0.39, T:0.05


Consensus pattern (16 bp):   
AGGAAGGGAAATAACA

Found at i:24353 original size:16 final size:16

Alignment explanation


    Indices: 24307--24359  Score: 61
    Period size: 16  Copynumber: 3.2  Consensus size: 16

      24297 TGAGAGGAAA

                    *     * 
      24307 GAAATAGGGAGGAAAG
          1 GAAATAGGAAGGAAGG

                  **         
      24323 GAAATAACAAGGGAAGG
          1 GAAATAGGAA-GGAAGG

                            
      24340 GAAATAGGAAGGAAGG
          1 GAAATAGGAAGGAAGG

                
      24356 GAAA
          1 GAAA

      24360 GGAAGTCATA


Statistics
Matches: 30,  Mismatches: 6, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  16   17  0.57
  17   13  0.43

ACGTcount: A:0.53, C:0.02, G:0.40, T:0.06


Consensus pattern (16 bp):   
GAAATAGGAAGGAAGG
Done.