Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008446.1 Corchorus capsularis cultivar CVL-1 contig08467, 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: 19459
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31


Found at i:4862 original size:157 final size:157

Alignment explanation


    Indices: 4576--4889  Score: 574
    Period size: 157  Copynumber: 2.0  Consensus size: 157

       4566 AGTCCCTTCT

                                                                             
       4576 AATTAGCCAATCTATAATAACATGAATGCACAAGAAATTATACTCTAACATAGTCAAAAATTAAG
          1 AATTAGCCAATCTATAATAACATGAATGCACAAGAAATTATACTCTAACATAGTCAAAAATTAAG

                                                                    *        
       4641 ATTGCAAATGAACTGACAGGATATAAAAATACTGAAGACAAGCGAATATACGTTAATTTTGCAAA
         66 ATTGCAAATGAACTGACAGGATATAAAAATACTGAAGACAAGCGAATATACGTTAAGTTTGCAAA

                                  *    
       4706 ATTGTGAGTGCAAAGTTACTTTGATTA
        131 ATTGTGAGTGCAAAGTTACTTTCATTA

                                        *                 *  *               
       4733 AATTAGCCAATCTATAATAACATGAATGGACAAGAAATTATACTCTTACTTAGTCAAAAATTAAG
          1 AATTAGCCAATCTATAATAACATGAATGCACAAGAAATTATACTCTAACATAGTCAAAAATTAAG

                                                                             
       4798 ATTGCAAATGAACTGACAGGATATAAAAATACTGAAGACAAGCGAATATACGTTAAGTTTGCAAA
         66 ATTGCAAATGAACTGACAGGATATAAAAATACTGAAGACAAGCGAATATACGTTAAGTTTGCAAA

                              *        
       4863 ATTGTGAGTGCAAAGTTATTTTCATTA
        131 ATTGTGAGTGCAAAGTTACTTTCATTA

       4890 CTATGGTCCA


Statistics
Matches: 151,  Mismatches: 6, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 157  151  1.00

ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29


Consensus pattern (157 bp):   
AATTAGCCAATCTATAATAACATGAATGCACAAGAAATTATACTCTAACATAGTCAAAAATTAAG
ATTGCAAATGAACTGACAGGATATAAAAATACTGAAGACAAGCGAATATACGTTAAGTTTGCAAA
ATTGTGAGTGCAAAGTTACTTTCATTA

Found at i:9519 original size:26 final size:26

Alignment explanation


    Indices: 9483--9538  Score: 112
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       9473 GGTTTTGGTG

                                      
       9483 TCCCTTTTTACATGTCCACTTACAAT
          1 TCCCTTTTTACATGTCCACTTACAAT

                                      
       9509 TCCCTTTTTACATGTCCACTTACAAT
          1 TCCCTTTTTACATGTCCACTTACAAT

                
       9535 TCCC
          1 TCCC

       9539 ATAAAGCATT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   30  1.00

ACGTcount: A:0.21, C:0.34, G:0.04, T:0.41


Consensus pattern (26 bp):   
TCCCTTTTTACATGTCCACTTACAAT

Found at i:11926 original size:35 final size:35

Alignment explanation


    Indices: 11880--12026  Score: 244
    Period size: 35  Copynumber: 4.2  Consensus size: 35

      11870 AGCCGCACTT

                          *        *            
      11880 GATCAACTCTGATCATC-GAAAATTTCTTGAAATGA
          1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA

                                               
      11915 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
          1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA

                                                
      11950 GATCAACTCTGACCTCT-AAAAGCTTCTTGAAATGA
          1 GATCAACTCTGACCTCTGAAAA-CTTCTTGAAATGA

                                               
      11985 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
          1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA

                   
      12020 GATCAAC
          1 GATCAAC

      12027 ACTGTGATGC


Statistics
Matches: 107,  Mismatches: 2, Indels: 6
        0.93            0.02        0.05

Matches are distributed among these distances:
  34    7  0.07
  35   96  0.90
  36    4  0.04

ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29


Consensus pattern (35 bp):   
GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA

Found at i:14778 original size:33 final size:33

Alignment explanation


    Indices: 14680--14784  Score: 113
    Period size: 33  Copynumber: 3.2  Consensus size: 33

      14670 TTGCAAAGAG

                    *               *      * 
      14680 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

             **                 *    *        
      14713 TAATTT-GAGTGTTGTTTGCAATGACACTAAATC
          1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC

                              *        *     
      14746 TGTTTTAGGTGTTGTTTGTGATGAAACAAAATC
          1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

                  
      14779 TGTTTT
          1 TGTTTT

      14785 GGATGCTAAT


Statistics
Matches: 58,  Mismatches: 12, Indels: 4
        0.78            0.16        0.05

Matches are distributed among these distances:
  32    1  0.02
  33   56  0.97
  34    1  0.02

ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

Found at i:14886 original size:33 final size:33

Alignment explanation


    Indices: 14803--14874  Score: 108
    Period size: 33  Copynumber: 2.2  Consensus size: 33

      14793 ATTGTGATGA

                *      *                     
      14803 AAAAAAAATCTCTTTTGGTTGATCATAGCATTG
          1 AAAATAAATCTGTTTTGGTTGATCATAGCATTG

             *                  *            
      14836 AGAATAAATCTGTTTTGGTTTATCATAGCATTG
          1 AAAATAAATCTGTTTTGGTTGATCATAGCATTG

                  
      14869 AAAATA
          1 AAAATA

      14875 GGACTGTTTT


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38


Consensus pattern (33 bp):   
AAAATAAATCTGTTTTGGTTGATCATAGCATTG
Done.