Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014811.1 Corchorus olitorius cultivar O-4 contig14844, 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: 13765
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:1716 original size:122 final size:127

Alignment explanation


    Indices: 1497--1740  Score: 390
    Period size: 122  Copynumber: 1.9  Consensus size: 127

       1487 ATTTAAGAAA

                                                         *                   
       1497 TATATTCAAAAATTCTAATATAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
          1 TATATTCAAAAATTCTAATATAATATAAGTTTTTTAATTAAAATAATAAAATGGTAAAAAT---A

                                                                             
       1562 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTGTAAAA
         63 TA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTGTAAAA

             
       1627 G
        127 G

                  *                                                          
       1628 TATATTTAAAAATTCTAATAT-ATATAAGTTTTTTAATTAAAATAATAAAATGGTAAAAAT-TA-
          1 TATATTCAAAAATTCTAATATAATATAAGTTTTTTAATTAAAATAATAAAATGGTAAAAATATAG

                         *                                       
       1690 TA-AA-GATATTATATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAA
         66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAA

       1741 TTATAAAAAG


Statistics
Matches: 110,  Mismatches: 3, Indels: 9
        0.90            0.02        0.07

Matches are distributed among these distances:
 122   46  0.42
 123    2  0.02
 124    2  0.02
 126    2  0.02
 130   38  0.35
 131   20  0.18

ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38


Consensus pattern (127 bp):   
TATATTCAAAAATTCTAATATAATATAAGTTTTTTAATTAAAATAATAAAATGGTAAAAATATAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTGTAAAAG

Found at i:9997 original size:13 final size:13

Alignment explanation


    Indices: 9979--10003  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       9969 CCGTTTATAA

                         
       9979 TATTATTATTTAT
          1 TATTATTATTTAT

                        
       9992 TATTATTATTTA
          1 TATTATTATTTA

      10004 AAAAATGAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (13 bp):   
TATTATTATTTAT

Found at i:12287 original size:34 final size:32

Alignment explanation


    Indices: 12222--12288  Score: 82
    Period size: 34  Copynumber: 2.0  Consensus size: 32

      12212 AATACATTCT

                                   *  *     
      12222 ATTATATATATGTGAATTGAATGGTATTTGTG
          1 ATTATATATATGTGAATTGAATGCTAATTGTG

                                               
      12254 ATTATATAGTCATGTGAA-TGATATGCTAATTGTG
          1 ATTATATA-T-ATGTGAATTGA-ATGCTAATTGTG

             
      12288 A
          1 A

      12289 GCAATGATAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  32    8  0.27
  33    4  0.13
  34   18  0.60

ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43


Consensus pattern (32 bp):   
ATTATATATATGTGAATTGAATGCTAATTGTG
Done.