Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001141.1 Corchorus capsularis cultivar CVL-1 contig01141, 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: 15039
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29


Found at i:3524 original size:33 final size:33

Alignment explanation


    Indices: 3482--3577  Score: 192
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       3472 GGCTTAAACC

                                             
       3482 CTTAAACCCATACGTTTGGCCCCATCTCATATG
          1 CTTAAACCCATACGTTTGGCCCCATCTCATATG

                                             
       3515 CTTAAACCCATACGTTTGGCCCCATCTCATATG
          1 CTTAAACCCATACGTTTGGCCCCATCTCATATG

                                          
       3548 CTTAAACCCATACGTTTGGCCCCATCTCAT
          1 CTTAAACCCATACGTTTGGCCCCATCTCAT

       3578 GATTCAAACT


Statistics
Matches: 63,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   63  1.00

ACGTcount: A:0.24, C:0.34, G:0.11, T:0.30


Consensus pattern (33 bp):   
CTTAAACCCATACGTTTGGCCCCATCTCATATG

Found at i:4181 original size:11 final size:11

Alignment explanation


    Indices: 4165--4189  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       4155 TTAAAACAAC

                       
       4165 TAACCTATAAT
          1 TAACCTATAAT

                       
       4176 TAACCTATAAT
          1 TAACCTATAAT

               
       4187 TAA
          1 TAA

       4190 GACTTCCATA


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

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36


Consensus pattern (11 bp):   
TAACCTATAAT

Found at i:6245 original size:200 final size:199

Alignment explanation


    Indices: 5859--6246  Score: 541
    Period size: 203  Copynumber: 1.9  Consensus size: 199

       5849 AATACTTTAG

                *                            *         *                   * 
       5859 GCTCTTCATCTTCATTAATATGATCAAAGAGTTCATGATTTTGGTTCAGAAGAACTACTAAAAGA
          1 GCTCCTCATCTTCATTAATATGATCAAAGAGTTAATGATTTTGATTCAGAAGAACTACTAAAAAA

                                  *                    *                     
       5924 TTTAGACCTTCAAATTCACAATTTCTACAGTATTAGCTATAATTTGTTGCATCAAACAGATAACG
         66 TTTAGACCTTCAAATTCACAATGTCTACAGTATTAGCTATAATGTGTTGCATCAAACA-AT-ACG

              *    ** *      *                                               
       5989 CCTGCTATGGTATAGCCGAACCTAGAAATCAACAAAGTGGAATGGGCAAAACCAGCACCTTATGC
        129 CCAGCTACAGAATAGCCAAACCTAGAAATCAACAAAGTGGAATGGGCAAAACCAGCACCTTATGC

                  
       6054 AGTTAT
        194 AGTTAT

                                                                        *    
       6060 GCTCCTCATCTTCACTT-ATATGATCAAAGAGTTAAATGATTTTGATTCAGAAGCAACTATTAAA
          1 GCTCCTCATCTTCA-TTAATATGATCAAAGAGTT-AATGATTTTGATTCAGAAG-AACTACTAAA

                                                     *             *         
       6124 AAATTTAGACCTTCAAATTCACAATGTCTACAGTATTAGCTTTAATGTGTTCAGCTTCAAAC-AT
         63 AAATTTAGACCTTCAAATTCACAATGTCTACAGTATTAGCTATAATGTGTT--GCATCAAACAAT

               *                                                *        
       6188 -C-TCAGCTACAGAATAGCCAAACCTAGAAATCAACAAAGTGGAATGGGCAACACCAGCAC
        126 ACGCCAGCTACAGAATAGCCAAACCTAGAAATCAACAAAGTGGAATGGGCAAAACCAGCAC

       6247 TAGCAGTGGT


Statistics
Matches: 166,  Mismatches: 16, Indels: 11
        0.86            0.08        0.06

Matches are distributed among these distances:
 200   51  0.31
 201   30  0.18
 202   19  0.11
 203   58  0.35
 205    8  0.05

ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29


Consensus pattern (199 bp):   
GCTCCTCATCTTCATTAATATGATCAAAGAGTTAATGATTTTGATTCAGAAGAACTACTAAAAAA
TTTAGACCTTCAAATTCACAATGTCTACAGTATTAGCTATAATGTGTTGCATCAAACAATACGCC
AGCTACAGAATAGCCAAACCTAGAAATCAACAAAGTGGAATGGGCAAAACCAGCACCTTATGCAG
TTAT

Found at i:6440 original size:16 final size:16

Alignment explanation


    Indices: 6419--6449  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       6409 AGCTTCTTCA

                            
       6419 GAAATCATAACAATGG
          1 GAAATCATAACAATGG

                     *     
       6435 GAAATCATATCAATG
          1 GAAATCATAACAATG

       6450 AAAATAAATT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23


Consensus pattern (16 bp):   
GAAATCATAACAATGG
Done.