Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008675.1 Corchorus olitorius cultivar O-4 contig08702, 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: 12879
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29


Found at i:1209 original size:263 final size:263

Alignment explanation


    Indices: 742--1242  Score: 1002
    Period size: 263  Copynumber: 1.9  Consensus size: 263

        732 AAATTTGCAA

                                                                             
        742 TCCCCAAATACCATGTTATATTTGCCAATAAACAAGTGACTTCCCTAGCTTTCAACTTGGATAGG
          1 TCCCCAAATACCATGTTATATTTGCCAATAAACAAGTGACTTCCCTAGCTTTCAACTTGGATAGG

                                                                             
        807 ATTATTAAGATGATGTTATGTTTGGTAGGAAAGTAAGGGAAAATAGCATTTTCTTGCTTATTTTC
         66 ATTATTAAGATGATGTTATGTTTGGTAGGAAAGTAAGGGAAAATAGCATTTTCTTGCTTATTTTC

                                                                             
        872 CTTTGATAAGAGTGAAATAGTGTTGCCTGAATTTGCTGTCATATGAGGCTTCACTTGATGCTTGA
        131 CTTTGATAAGAGTGAAATAGTGTTGCCTGAATTTGCTGTCATATGAGGCTTCACTTGATGCTTGA

                                                                             
        937 AAAGGTTGCTAAATGGATAATATAAACATACTAGTAAAAGTACTAGTATGTTTATATTTCCCTTA
        196 AAAGGTTGCTAAATGGATAATATAAACATACTAGTAAAAGTACTAGTATGTTTATATTTCCCTTA

               
       1002 CTT
        261 CTT

                                                                             
       1005 TCCCCAAATACCATGTTATATTTGCCAATAAACAAGTGACTTCCCTAGCTTTCAACTTGGATAGG
          1 TCCCCAAATACCATGTTATATTTGCCAATAAACAAGTGACTTCCCTAGCTTTCAACTTGGATAGG

                                                                             
       1070 ATTATTAAGATGATGTTATGTTTGGTAGGAAAGTAAGGGAAAATAGCATTTTCTTGCTTATTTTC
         66 ATTATTAAGATGATGTTATGTTTGGTAGGAAAGTAAGGGAAAATAGCATTTTCTTGCTTATTTTC

                                                                             
       1135 CTTTGATAAGAGTGAAATAGTGTTGCCTGAATTTGCTGTCATATGAGGCTTCACTTGATGCTTGA
        131 CTTTGATAAGAGTGAAATAGTGTTGCCTGAATTTGCTGTCATATGAGGCTTCACTTGATGCTTGA

                                                       
       1200 AAAGGTTGCTAAATGGATAATATAAACATACTAGTAAAAGTAC
        196 AAAGGTTGCTAAATGGATAATATAAACATACTAGTAAAAGTAC

       1243 AAAGATGAAC


Statistics
Matches: 238,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 263  238  1.00

ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36


Consensus pattern (263 bp):   
TCCCCAAATACCATGTTATATTTGCCAATAAACAAGTGACTTCCCTAGCTTTCAACTTGGATAGG
ATTATTAAGATGATGTTATGTTTGGTAGGAAAGTAAGGGAAAATAGCATTTTCTTGCTTATTTTC
CTTTGATAAGAGTGAAATAGTGTTGCCTGAATTTGCTGTCATATGAGGCTTCACTTGATGCTTGA
AAAGGTTGCTAAATGGATAATATAAACATACTAGTAAAAGTACTAGTATGTTTATATTTCCCTTA
CTT

Found at i:2953 original size:16 final size:16

Alignment explanation


    Indices: 2932--2965  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2922 ATTCTAATTC

                            
       2932 TTTTTCAGATTTCAAA
          1 TTTTTCAGATTTCAAA

                   *     *  
       2948 TTTTTCATATTTCTAA
          1 TTTTTCAGATTTCAAA

              
       2964 TT
          1 TT

       2966 GCTTATTTTC


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.26, C:0.12, G:0.03, T:0.59


Consensus pattern (16 bp):   
TTTTTCAGATTTCAAA

Found at i:6041 original size:21 final size:18

Alignment explanation


    Indices: 6016--6058  Score: 59
    Period size: 21  Copynumber: 2.2  Consensus size: 18

       6006 AGCCAAAGAC

                                 
       6016 ATTATCATATCAATAAAAATT
          1 ATTATCATAT--ATAAAAA-T

                              
       6037 ATTATCATATATAAAAAT
          1 ATTATCATATATAAAAAT

                
       6055 ATTA
          1 ATTA

       6059 ATATAAAAAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  18    5  0.23
  19    7  0.32
  21   10  0.45

ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40


Consensus pattern (18 bp):   
ATTATCATATATAAAAAT

Found at i:10099 original size:31 final size:31

Alignment explanation


    Indices: 10061--10120  Score: 102
    Period size: 31  Copynumber: 1.9  Consensus size: 31

      10051 TCAGTTAAAC

                            *              
      10061 GACAATCAATTGAACCGAAAGAAAGACAGAT
          1 GACAATCAATTGAACCAAAAGAAAGACAGAT

                           *             
      10092 GACAATCAATTGAACTAAAAGAAAGACAG
          1 GACAATCAATTGAACCAAAAGAAAGACAG

      10121 CACAAACAAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.53, C:0.15, G:0.18, T:0.13


Consensus pattern (31 bp):   
GACAATCAATTGAACCAAAAGAAAGACAGAT

Found at i:11361 original size:60 final size:59

Alignment explanation


    Indices: 11286--11397  Score: 143
    Period size: 59  Copynumber: 1.9  Consensus size: 59

      11276 ACATAACACA

                    * *      *        *       *                         
      11286 AAAATTGTTCTGATTTTGATAATTTAGGGGGTAATAGTTCCAAATTAAAAGTTCAATGGG
          1 AAAATTGTCCCGA-TTTAATAATTTAAGGGGTAACAGTTCCAAATTAAAAGTTCAATGGG

                               *           *       *            
      11346 AAAATTGTCCCGATTTAATGATTTAAGGGGTGACAGTTCTAAATTAAAAGTT
          1 AAAATTGTCCCGATTTAATAATTTAAGGGGTAACAGTTCCAAATTAAAAGTT

      11398 TAGGGAGAAA


Statistics
Matches: 44,  Mismatches: 8, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  59   33  0.75
  60   11  0.25

ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36


Consensus pattern (59 bp):   
AAAATTGTCCCGATTTAATAATTTAAGGGGTAACAGTTCCAAATTAAAAGTTCAATGGG
Done.