Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000462.1 Corchorus olitorius cultivar O-4 contig00462, 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, 697

Length: 1163
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45


Found at i:178 original size:14 final size:13

Alignment explanation


    Indices: 159--192  Score: 52
    Period size: 14  Copynumber: 2.6  Consensus size: 13

        149 ATTTCTATGT

                          
        159 TATCATATATATCA
          1 TATCATATATAT-A

                         
        173 TATCATATATATA
          1 TATCATATATATA

                    
        186 TAT-ATAT
          1 TATCATAT

        193 TAAAACTATA


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

Matches are distributed among these distances:
  12    4  0.20
  13    4  0.20
  14   12  0.60

ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47


Consensus pattern (13 bp):   
TATCATATATATA

Found at i:376 original size:4 final size:4

Alignment explanation


    Indices: 367--397  Score: 62
    Period size: 4  Copynumber: 7.8  Consensus size: 4

        357 ATCATATTAA

                                                  
        367 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
          1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT

        398 TGAATATCTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   27  1.00

ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52


Consensus pattern (4 bp):   
ATTG

Found at i:393 original size:77 final size:76

Alignment explanation


    Indices: 302--458  Score: 237
    Period size: 77  Copynumber: 2.0  Consensus size: 76

        292 TATATATTAA

                                      *                                      
        302 ATTGATTGATTGATTTGA-AT-ATATTTTGATCCAATTAGAATCAATTAGTACTAAAATCATATT
          1 ATTGATTGATTGA-TTGATATAATATCTTGATCCAATTAGAATCAATTAGTACT--AATCATATT

                          
        365 AAATTGATTGATTG
         63 AAATTGATTGATTG

                              *                                      *       
        379 ATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAA
          1 ATTGATTGATTGATTGATAT-AATATCTTGATCCAATTAGAATCAATTAGTACTAATCATATTAA

                        
        444 ATTGATTGATTG
         65 ATTGATTGATTG

               
        456 ATT
          1 ATT

        459 TGAATATTGA


Statistics
Matches: 74,  Mismatches: 3, Indels: 6
        0.89            0.04        0.07

Matches are distributed among these distances:
  76    4  0.05
  77   39  0.53
  79   31  0.42

ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43


Consensus pattern (76 bp):   
ATTGATTGATTGATTGATATAATATCTTGATCCAATTAGAATCAATTAGTACTAATCATATTAAA
TTGATTGATTG

Found at i:448 original size:61 final size:59

Alignment explanation


    Indices: 383--495  Score: 181
    Period size: 59  Copynumber: 1.9  Consensus size: 59

        373 TGATTGATTG

                                         *     *                         
        383 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAA
          1 ATTGATTGATTGATTTGAATA--TTGATCAAATTAAAATCAATTAGTACTAATGATATTAA

                                                          *     
        444 ATTGATTGATTGATTTGAATATTGATCAAATTAAAATCAATTAGTATTAATG
          1 ATTGATTGATTGATTTGAATATTGATCAAATTAAAATCAATTAGTACTAATG

        496 TCATTTAATT


Statistics
Matches: 49,  Mismatches: 3, Indels: 2
        0.91            0.06        0.04

Matches are distributed among these distances:
  59   28  0.57
  61   21  0.43

ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42


Consensus pattern (59 bp):   
ATTGATTGATTGATTTGAATATTGATCAAATTAAAATCAATTAGTACTAATGATATTAA

Found at i:468 original size:77 final size:80

Alignment explanation


    Indices: 304--469  Score: 259
    Period size: 79  Copynumber: 2.1  Consensus size: 80

        294 TATATTAAAT

                                  *                                          
        304 TGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATCATATTAAAT
          1 TGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACT-AAATCATATTAAAT

                           *
        369 TGATTGATTGATTGAT
         65 TGATTGATTGATTGAA

                                                                  *          
        385 TGATTGATTGATTTG-A-ATATCTTGATCCAATTAGAATCAATTAGTACT-AATGATATTAAATT
          1 TGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATCATATTAAATT

                            
        447 GATTGATTGATTTGAA
         66 GATTGATTGA-TTGAA

                    
        463 T-ATTGAT
          1 TGATTGAT

        470 CAAATTAAAA


Statistics
Matches: 81,  Mismatches: 3, Indels: 6
        0.90            0.03        0.07

Matches are distributed among these distances:
  77   29  0.36
  78    5  0.06
  79   31  0.38
  80    1  0.01
  81   15  0.19

ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43


Consensus pattern (80 bp):   
TGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATCATATTAAATT
GATTGATTGATTGAA
Done.