Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014701.1 Corchorus olitorius cultivar O-4 contig14734, 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: 51877
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:9670 original size:2 final size:2

Alignment explanation


    Indices: 9663--9693  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       9653 ACGATGGATG

                                                          
       9663 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 T

       9694 TTTCCCTTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:28080 original size:2 final size:2

Alignment explanation


    Indices: 28075--28101  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      28065 TTTTCATTTT

                                                    
      28075 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 T

      28102 GTCTAGGTAC


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

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:37467 original size:3 final size:3

Alignment explanation


    Indices: 37459--37485  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

      37449 GGGTGATGCC

                                               
      37459 ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT

      37486 GTTTATGTGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Found at i:44222 original size:31 final size:30

Alignment explanation


    Indices: 44187--44263  Score: 93
    Period size: 29  Copynumber: 2.6  Consensus size: 30

      44177 ATACCGTACA

                                           
      44187 GGTCCCTCTACTTACAAAAAAGGATCAATTT
          1 GGTCCCTCTACTTACAAAAAAGG-TCAATTT

                   *      *     **        
      44218 GGTCCCTTTAC-TATAAAAACTGTCAATTT
          1 GGTCCCTCTACTTACAAAAAAGGTCAATTT

             *               
      44247 GATCCCTCTACTTACAA
          1 GGTCCCTCTACTTACAA

      44264 TTTGGTGTCA


Statistics
Matches: 38,  Mismatches: 7, Indels: 3
        0.79            0.15        0.06

Matches are distributed among these distances:
  29   16  0.42
  30   12  0.32
  31   10  0.26

ACGTcount: A:0.32, C:0.25, G:0.10, T:0.32


Consensus pattern (30 bp):   
GGTCCCTCTACTTACAAAAAAGGTCAATTT

Found at i:44304 original size:31 final size:29

Alignment explanation


    Indices: 44189--44310  Score: 95
    Period size: 31  Copynumber: 4.0  Consensus size: 29

      44179 ACCGTACAGG

                             ***          *
      44189 TCCCTCTACTTACAAAAAAGGATCAATTTGG
          1 TCCCTCTACTTACAAAATCTG-TCAA-TTGA

                 *                         
      44220 TCCCTTTACTATA-AAAA-CTGTCAATTTGA
          1 TCCCTCTACT-TACAAAATCTGTCAA-TTGA

                           **  *          
      44249 TCCCTCTACTTACAATTTGGTGTCAATTGA
          1 TCCCTCTACTTACAAAAT-CTGTCAATTGA

                                           
      44279 GTCCCTCTACTTAACAAAATCTGTCAATTGA
          1 -TCCCTCTACTT-ACAAAATCTGTCAATTGA

             
      44310 T
          1 T

      44311 TATATATTTG


Statistics
Matches: 74,  Mismatches: 11, Indels: 13
        0.76            0.11        0.13

Matches are distributed among these distances:
  28    2  0.03
  29   19  0.26
  30    6  0.08
  31   40  0.54
  32    7  0.09

ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35


Consensus pattern (29 bp):   
TCCCTCTACTTACAAAATCTGTCAATTGA

Found at i:51296 original size:7 final size:7

Alignment explanation


    Indices: 51265--51295  Score: 53
    Period size: 7  Copynumber: 4.3  Consensus size: 7

      51255 TGCAACTTGC

                   
      51265 TTTTATT
          1 TTTTATT

                   
      51272 TTTTATT
          1 TTTTATT

                   
      51279 TTTTATT
          1 TTTTATT

                    
      51286 TTTATATT
          1 TTT-TATT

              
      51294 TT
          1 TT

      51296 AAAAGAATCA


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

Matches are distributed among these distances:
   7   17  0.74
   8    6  0.26

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (7 bp):   
TTTTATT
Done.