Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019895.1 Corchorus olitorius cultivar O-4 contig19928, 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: 5488
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36


Found at i:66 original size:18 final size:17

Alignment explanation


    Indices: 37--85  Score: 57
    Period size: 15  Copynumber: 2.9  Consensus size: 17

         27 GTAGTGATCA

                               
         37 TATAACTAATAATAATTGT
          1 TATAA-TAATAATAA-TGT

                             
         56 TATAATAATAATAA-GT
          1 TATAATAATAATAATGT

                     *     
         72 T-TAATAATTATAAT
          1 TATAATAATAATAAT

         86 AAGAAGATGT


Statistics
Matches: 28,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  15   11  0.39
  16    3  0.11
  18    9  0.32
  19    5  0.18

ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43


Consensus pattern (17 bp):   
TATAATAATAATAATGT

Found at i:221 original size:115 final size:115

Alignment explanation


    Indices: 56--279  Score: 353
    Period size: 115  Copynumber: 1.9  Consensus size: 115

         46 TAATAATTGT

                                                         *          *       *
         56 TATAATAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACGTAAAAAAA-TGTTAGTATT
          1 TATAATAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACATAAAAAAATTATTAGTATC

                     *                                         
        120 ATTTTAA-ATTTTTGTAATATGGAAAGAAAAACGTAATGACTAATGATATA
         66 A-TTTAAGACTTTTGTAATATGGAAAGAAAAACGTAATGACTAATGATATA

                           *                 *   *                           
        170 TATAACTAATAATAATTTTAATAATTATAATAATAAGTTGTTTAACATAAAAAAATTATTAGTAT
          1 TATAA-TAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACATAAAAAAATTATTAGTAT

                                                         
        235 CATTTAAGACTTTTGTAATATGGAAAGAAAAACGTAATGACTAAT
         65 CATTTAAGACTTTTGTAATATGGAAAGAAAAACGTAATGACTAAT

        280 TCCTCAAAAA


Statistics
Matches: 100,  Mismatches: 7, Indels: 4
        0.90            0.06        0.04

Matches are distributed among these distances:
 114    5  0.05
 115   50  0.50
 116   45  0.45

ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37


Consensus pattern (115 bp):   
TATAATAATAATAAGTTTAATAATTATAATAAGAAGATGTTTAACATAAAAAAATTATTAGTATC
ATTTAAGACTTTTGTAATATGGAAAGAAAAACGTAATGACTAATGATATA

Found at i:321 original size:144 final size:142

Alignment explanation


    Indices: 146--407  Score: 436
    Period size: 144  Copynumber: 1.8  Consensus size: 142

        136 ATATGGAAAG

                                                                             
        146 AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT
          1 AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT

                                                                             
        211 TTAACATAAAAA-AATTATTAGTATCATTTAAGACTTTTGTAATATGGAAAGAAAAACGTAATGA
         66 TTAACATAAAAATAATTATTA-T-T-ATTTAAGACTTTTGTAATATGGAAAGAAAAACGTAATGA

                           
        275 CTAATTCCTCAAAAA
        128 CTAATTCCTCAAAAA

                                                                             
        290 AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT
          1 AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT

                **           *         *        *           *    
        355 TTAATGTAAAAATAATTGTTATTATTTTAGACTTTTTTAATATGGAAATAAAA
         66 TTAACATAAAAATAATTATTATTATTTAAGACTTTTGTAATATGGAAAGAAAA

        408 TCCGATTGGA


Statistics
Matches: 111,  Mismatches: 6, Indels: 4
        0.92            0.05        0.03

Matches are distributed among these distances:
 142   27  0.24
 143    1  0.01
 144   76  0.68
 145    7  0.06

ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37


Consensus pattern (142 bp):   
AAAAACGTAATGACTAATGATATATATAACTAATAATAATTTTAATAATTATAATAATAAGTTGT
TTAACATAAAAATAATTATTATTATTTAAGACTTTTGTAATATGGAAAGAAAAACGTAATGACTA
ATTCCTCAAAAA

Found at i:862 original size:32 final size:32

Alignment explanation


    Indices: 826--889  Score: 101
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        816 AAAGAAAATT

                           *    *   *       
        826 ATATATTTTTTATGTTATATGCTATAAATTAA
          1 ATATATTTTTTATGTCATATACTACAAATTAA

                                            
        858 ATATATTTTTTATGTCATATACTACAAATTAA
          1 ATATATTTTTTATGTCATATACTACAAATTAA

        890 TGTAATTTAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  32   29  1.00

ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50


Consensus pattern (32 bp):   
ATATATTTTTTATGTCATATACTACAAATTAA

Found at i:1723 original size:20 final size:20

Alignment explanation


    Indices: 1698--1742  Score: 72
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       1688 ACAGCGGACA

                                
       1698 CTTAAGTCATTGCGTTAGAT
          1 CTTAAGTCATTGCGTTAGAT

                    *           
       1718 CTTAAGTCGTTGCGTTAGAT
          1 CTTAAGTCATTGCGTTAGAT

            *    
       1738 ATTAA
          1 CTTAA

       1743 ACAACGGAAC


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40


Consensus pattern (20 bp):   
CTTAAGTCATTGCGTTAGAT
Done.