Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016396.1 Corchorus olitorius cultivar O-4 contig16429, 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: 81258
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:19541 original size:21 final size:22

Alignment explanation


    Indices: 19491--19541  Score: 54
    Period size: 20  Copynumber: 2.4  Consensus size: 22

      19481 GTAAAAAACA

                              *   
      19491 AAAGAAAAAATTAAAAATTTTC
          1 AAAGAAAAAATTAAAAATCTTC

                                   
      19513 AACA-AAAAAA-T-AAAATCTTC
          1 AA-AGAAAAAATTAAAAATCTTC

                     
      19533 ACAAGAAAA
          1 A-AAGAAAA

      19542 GAGATTAGAG


Statistics
Matches: 25,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  20   10  0.40
  21    6  0.24
  22    8  0.32
  23    1  0.04

ACGTcount: A:0.67, C:0.10, G:0.04, T:0.20


Consensus pattern (22 bp):   
AAAGAAAAAATTAAAAATCTTC

Found at i:29556 original size:30 final size:30

Alignment explanation


    Indices: 29520--29577  Score: 107
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      29510 TTAATTGCTG

                                          
      29520 TTTTTTTACAGTAATTTCGTTAATTAGTGT
          1 TTTTTTTACAGTAATTTCGTTAATTAGTGT

                             *          
      29550 TTTTTTTACAGTAATTTGGTTAATTAGT
          1 TTTTTTTACAGTAATTTCGTTAATTAGT

      29578 TTAAGTTGGT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.24, C:0.05, G:0.14, T:0.57


Consensus pattern (30 bp):   
TTTTTTTACAGTAATTTCGTTAATTAGTGT

Found at i:43550 original size:24 final size:25

Alignment explanation


    Indices: 43517--43567  Score: 77
    Period size: 24  Copynumber: 2.1  Consensus size: 25

      43507 TCCTATATGA

                          *          
      43517 TGATCCAAAATTAGTTTATTTTCAT
          1 TGATCCAAAATTAGCTTATTTTCAT

                        *            
      43542 TGAT-CAAAATTGGCTTATTTTCAT
          1 TGATCCAAAATTAGCTTATTTTCAT

              
      43566 TG
          1 TG

      43568 GTGGGTTGAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  24   20  0.83
  25    4  0.17

ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47


Consensus pattern (25 bp):   
TGATCCAAAATTAGCTTATTTTCAT

Found at i:54397 original size:13 final size:13

Alignment explanation


    Indices: 54379--54413  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      54369 CTTCCTCTTC

                         
      54379 TCTTCTGTTCTCT
          1 TCTTCTGTTCTCT

                       * 
      54392 TCTTCTGTTCTTT
          1 TCTTCTGTTCTCT

                *    
      54405 TCTTTTGTT
          1 TCTTCTGTT

      54414 TATAGCCGAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.00, C:0.23, G:0.09, T:0.69


Consensus pattern (13 bp):   
TCTTCTGTTCTCT

Found at i:60943 original size:14 final size:14

Alignment explanation


    Indices: 60926--60955  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      60916 TTGAGAATCA

                          
      60926 TTCTTTGCTTTTTT
          1 TTCTTTGCTTTTTT

                  *       
      60940 TTCTTTTCTTTTTT
          1 TTCTTTGCTTTTTT

              
      60954 TT
          1 TT

      60956 TTAAATGAGT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83


Consensus pattern (14 bp):   
TTCTTTGCTTTTTT

Found at i:65181 original size:19 final size:20

Alignment explanation


    Indices: 65136--65193  Score: 73
    Period size: 21  Copynumber: 2.9  Consensus size: 20

      65126 GCTGCTCTAA

                                 
      65136 TAATCTCATATGTACAGTACC
          1 TAATCTCATATGTACAGTA-C

                  *            *
      65157 TAATCTAATATGTACAGT-G
          1 TAATCTCATATGTACAGTAC

                     *        
      65176 TAATCTCATCTGTACAGT
          1 TAATCTCATATGTACAGT

      65194 TGATAAACAG


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   16  0.48
  21   17  0.52

ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36


Consensus pattern (20 bp):   
TAATCTCATATGTACAGTAC

Found at i:68439 original size:24 final size:24

Alignment explanation


    Indices: 68407--68478  Score: 135
    Period size: 24  Copynumber: 3.0  Consensus size: 24

      68397 ACGTGGTCGT

                                    
      68407 GGTCAAGGTTACAGACCTGATGGC
          1 GGTCAAGGTTACAGACCTGATGGC

                                    
      68431 GGTCAAGGTTACAGACCTGATGGC
          1 GGTCAAGGTTACAGACCTGATGGC

                           *        
      68455 GGTCAAGGTTACAGATCTGATGGC
          1 GGTCAAGGTTACAGACCTGATGGC

      68479 CCAATCCAGA


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  24   47  1.00

ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22


Consensus pattern (24 bp):   
GGTCAAGGTTACAGACCTGATGGC
Done.