Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018285.1 Corchorus olitorius cultivar O-4 contig18318, 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: 2878
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35


Found at i:287 original size:170 final size:171

Alignment explanation


    Indices: 7--386  Score: 610
    Period size: 170  Copynumber: 2.2  Consensus size: 171

          1 TAATTA

                               *                                             
          7 ATTTTTTTGGTAACATAATCACTAATTG---ATTTATTTATTTATGGTAATTTTTTTGGTAGCGA
          1 ATTTTTTTGGTAACATAATTACTAATTGATTATTTATTTATTTATGGTAATTTTTTTGGTAGCGA

                                 *                                           
         69 TTTATGGTAAAATTAAATAATTATCAATCAATTAAAACTTTGATTGACAAAATTAACTAACGACT
         66 TTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGACAAAATTAACTAACGACT

                          *                           
        134 AACTTGGATTCATTTATTTATTTACCATGTTCAAT-AA-TTT
        131 AACTT-GATTCATTCATTTATTTACCATGTTCAATCAATTTT

                                                           *                 
        174 A-TTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATTTATGTTAATTTTTTTGGTAGCG
          1 ATTTTTTTGGTAACATAATTACTAATTGA-TTATTTATTTATTTATGGTAATTTTTTTGGTAGCG

                                               *                             
        238 ATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGAC
         65 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGACAAAATTAACTAACGAC

                                    *                 
        303 TAACTTGATTCATTCATTTATTTAGCATGTTCAATCAATTTT
        130 TAACTTGATTCATTCATTTATTTACCATGTTCAATCAATTTT

                     *    *                 *         
        345 ATTTTTTTGCTAACGTAATTACTAATTGATTCGTTTATTTAT
          1 ATTTTTTTGGTAACATAATTACTAATTGATT-ATTTATTTAT

        387 GGCAAAATTA


Statistics
Matches: 196,  Mismatches: 9, Indels: 11
        0.91            0.04        0.05

Matches are distributed among these distances:
 166   25  0.13
 167    1  0.01
 169   27  0.14
 170  103  0.53
 171    6  0.03
 172   34  0.17

ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46


Consensus pattern (171 bp):   
ATTTTTTTGGTAACATAATTACTAATTGATTATTTATTTATTTATGGTAATTTTTTTGGTAGCGA
TTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGACAAAATTAACTAACGACT
AACTTGATTCATTCATTTATTTACCATGTTCAATCAATTTT

Found at i:798 original size:30 final size:30

Alignment explanation


    Indices: 764--941  Score: 320
    Period size: 30  Copynumber: 5.9  Consensus size: 30

        754 AAAGTTTGTC

                                          
        764 TAATTGAATAATATACAAAGTAAAAATATA
          1 TAATTGAATAATATACAAAGTAAAAATATA

                                            
        794 TAATTGAATAATATACAAAGTAAAAAAATATA
          1 TAATTGAATAATATACAAAGT--AAAAATATA

                                          
        826 TAATTGAATAATATACAAAGTAAAAATATA
          1 TAATTGAATAATATACAAAGTAAAAATATA

             *                            
        856 TGATTGAATAATATACAAAGTAAAAATATA
          1 TAATTGAATAATATACAAAGTAAAAATATA

                           *              
        886 TAATTGAATAATATATAAAGTAAAAATATA
          1 TAATTGAATAATATACAAAGTAAAAATATA

                                      
        916 TAATTGAATAATATACAAAGTAAAAA
          1 TAATTGAATAATATACAAAGTAAAAA

        942 AAAACACAAT


Statistics
Matches: 142,  Mismatches: 4, Indels: 4
        0.95            0.03        0.03

Matches are distributed among these distances:
  30  112  0.79
  32   30  0.21

ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30


Consensus pattern (30 bp):   
TAATTGAATAATATACAAAGTAAAAATATA

Found at i:1840 original size:2 final size:2

Alignment explanation


    Indices: 1833--1860  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       1823 TACAGTTTTA

                                                     
       1833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1861 GATTAGTTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Done.