Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018027.1 Corchorus olitorius cultivar O-4 contig18060, 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: 26819
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:8305 original size:17 final size:17

Alignment explanation


    Indices: 8283--8317  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       8273 AAAATAAAAA

                    *    *   
       8283 TTTAAGGTTAAAGGAAT
          1 TTTAAGGTGAAAGAAAT

                             
       8300 TTTAAGGTGAAAGAAAT
          1 TTTAAGGTGAAAGAAAT

             
       8317 T
          1 T

       8318 ATTTTTTTAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34


Consensus pattern (17 bp):   
TTTAAGGTGAAAGAAAT

Found at i:10222 original size:68 final size:74

Alignment explanation


    Indices: 10148--10296  Score: 202
    Period size: 78  Copynumber: 2.0  Consensus size: 74

      10138 TTTCTTCCCC

                                          *                        *         
      10148 AATATATATAGTCTTAT-A-A-T-A-TTGGCAAAAG-TTCAACATTAATATTGAAGGAATTGTAC
          1 AATATATATAGTCTTATAATATTGATTTGGAAAAAGTTTCAACATTAATATTGAAAGAATTGTAC

                     
      10207 TCCAGGTTT
         66 TCCAGGTTT

                                                                             
      10216 AATATATATAGTCTTATAATATTGGAATTTGGAAAAAGTTATTCAACATTAATATTGAAAGAATT
          1 AATATATATAGTCTTATAATATT-G-ATTTGGAAAAAG-T-TTCAACATTAATATTGAAAGAATT

                         
      10281 GTACTCCAGGTTT
         62 GTACTCCAGGTTT

               
      10294 AAT
          1 AAT

      10297 TACTTTTATT


Statistics
Matches: 69,  Mismatches: 2, Indels: 10
        0.85            0.02        0.12

Matches are distributed among these distances:
  68   17  0.25
  69    1  0.01
  70    1  0.01
  71    1  0.01
  74    1  0.01
  75    9  0.13
  78   39  0.57

ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38


Consensus pattern (74 bp):   
AATATATATAGTCTTATAATATTGATTTGGAAAAAGTTTCAACATTAATATTGAAAGAATTGTAC
TCCAGGTTT

Found at i:10372 original size:2 final size:2

Alignment explanation


    Indices: 10365--10399  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      10355 AATCAAGTAC

                                                                
      10365 TA TA TA 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

      10400 GCTTGAATAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:11899 original size:44 final size:43

Alignment explanation


    Indices: 11817--11899  Score: 123
    Period size: 43  Copynumber: 1.9  Consensus size: 43

      11807 TGATATAAAT

                                        * *            
      11817 AAGATTTCTTTGGTTAATTAATTATTCATGCAAAAATTAAAAA
          1 AAGATTTCTTTGGTTAATTAATTATTCAGGAAAAAATTAAAAA

                                                     
      11860 AAGATTTCTTTGGTTTAATTAATTATT-AGGAAAATAATTA
          1 AAGATTTCTTTGG-TTAATTAATTATTCAGGAAAA-AATTA

      11900 CTTGTGACAG


Statistics
Matches: 36,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  43   18  0.50
  44   18  0.50

ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42


Consensus pattern (43 bp):   
AAGATTTCTTTGGTTAATTAATTATTCAGGAAAAAATTAAAAA

Found at i:25625 original size:14 final size:14

Alignment explanation


    Indices: 25606--25633  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      25596 ACCATTGTAC

                          
      25606 GGTACAAAATTACT
          1 GGTACAAAATTACT

                          
      25620 GGTACAAAATTACT
          1 GGTACAAAATTACT

      25634 CAACAAATTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29


Consensus pattern (14 bp):   
GGTACAAAATTACT

Found at i:25772 original size:10 final size:10

Alignment explanation


    Indices: 25757--25789  Score: 59
    Period size: 10  Copynumber: 3.4  Consensus size: 10

      25747 TTACTCAACA

                      
      25757 AATTTGACCT
          1 AATTTGACCT

                      
      25767 AATTTGACCT
          1 AATTTGACCT

                      
      25777 AATTTGACC-
          1 AATTTGACCT

                
      25786 AATT
          1 AATT

      25790 AGGTCAACAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   9    4  0.17
  10   19  0.83

ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39


Consensus pattern (10 bp):   
AATTTGACCT
Done.