Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012600.1 Corchorus olitorius cultivar O-4 contig12633, 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: 9068
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34


Found at i:6343 original size:57 final size:57

Alignment explanation


    Indices: 6255--6362  Score: 180
    Period size: 57  Copynumber: 1.9  Consensus size: 57

       6245 TCAAATATCA

                                                    *                
       6255 AGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTCGGACCAAGGCTTATTG
          1 AGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCTTATTG

                       *            *                     *    
       6312 AGTGACATGTTTTTTATTAGATGCCTAAAAAAGACGTTTTAGGACCGAGGC
          1 AGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGC

       6363 ATGATGCTAT


Statistics
Matches: 47,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  57   47  1.00

ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32


Consensus pattern (57 bp):   
AGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCTTATTG

Found at i:7677 original size:36 final size:36

Alignment explanation


    Indices: 7630--7699  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       7620 TTCAATAACC

                         *      *               
       7630 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
       7666 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

       7700 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:8593 original size:205 final size:201

Alignment explanation


    Indices: 8212--8624  Score: 718
    Period size: 205  Copynumber: 2.0  Consensus size: 201

       8202 GCTTAATAAC

                 *                                                          *
       8212 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAC
          1 TTTATTAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

              *           *                                                  
       8277 GATACAACACATTATTACTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTG
         66 GAAACAACACATTACTACTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTG

                                                                *            
       8342 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
        131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAAATATT-AAGATC

                   
       8407 CGATTTA
        195 CGATTTA

                                                                             
       8414 TTTATTAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATTAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                             *          *                  *                 
       8479 GAAACAACACATTACTATTATATATATTGAACTATACCAAAAAAAAATTAGTTGAACATTAGTGG
         66 GAAACAACACATTACTACTATATATA--AAACTATA-CAAAAAAAAAGTAGTTGAACATTAGTGG

                                                                             
       8544 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAAATATTAAGA
        128 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAAATATTAAGA

                     
       8609 TCCGATTTA
        193 TCCGATTTA

                   
       8618 TTTATTA
          1 TTTATTA

       8625 TTAAGGAAAC


Statistics
Matches: 200,  Mismatches: 8, Indels: 4
        0.94            0.04        0.02

Matches are distributed among these distances:
 202   86  0.43
 204   27  0.14
 205   87  0.44

ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36


Consensus pattern (201 bp):   
TTTATTAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GAAACAACACATTACTACTATATATAAAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAAATATTAAGATCC
GATTTA

Found at i:9041 original size:2 final size:2

Alignment explanation


    Indices: 9029--9064  Score: 63
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       9019 AGTTTAGACT

                                                                 
       9029 TA TA GTA 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 TA TA T

       9065 TTAC


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   31  0.94
   3    2  0.06

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
TA

Done.