Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007208.1 Corchorus olitorius cultivar O-4 contig07233, 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: 2104
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41


Found at i:604 original size:35 final size:35

Alignment explanation


    Indices: 553--635  Score: 157
    Period size: 35  Copynumber: 2.4  Consensus size: 35

        543 TACGAACTCA

                                               
        553 AAAATACCCTTAAAAATCTTAATTAGTCAATTACT
          1 AAAATACCCTTAAAAATCTTAATTAGTCAATTACT

                       *                       
        588 AAAATACCCTTGAAAATCTTAATTAGTCAATTACT
          1 AAAATACCCTTAAAAATCTTAATTAGTCAATTACT

                         
        623 AAAATACCCTTAA
          1 AAAATACCCTTAA

        636 TATTCTTTAA


Statistics
Matches: 46,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  35   46  1.00

ACGTcount: A:0.46, C:0.18, G:0.04, T:0.33


Consensus pattern (35 bp):   
AAAATACCCTTAAAAATCTTAATTAGTCAATTACT

Found at i:1363 original size:132 final size:131

Alignment explanation


    Indices: 1193--1458  Score: 380
    Period size: 132  Copynumber: 2.0  Consensus size: 131

       1183 ATTGTTTAAA

                    *                                                        
       1193 ACTTTTTATAGTTTTTACTCAACTAAAAACTCTATTTTTATTTAAATTAAATCTAATAT-CTT-T
          1 ACTTTTTACAGTTTTTACTCAACTAAAAACTCTATTTTTATTT-AATTAAATCTAATATCCTTAT

                                                               *             
       1256 -TATGAAT-TTTTTACCATTTTACTATTTTAATTTAAAAAAACTTATATTATATTAGAACTTTTT
         65 CTAT-AATATTTTTACCATTTTACTATTTT-ATTT-AAAAAACTTATA-TACATTAGAA-TTTTT

                   
       1319 TAAATAT
        125 TAAATAT

                                                                             
       1326 ACTTTTTACAG-TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA
          1 ACTTTTTACAGTTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-

                 **                           *                              
       1390 CCTATTTTATTTTTACCATTTTACTATTTTATTTTAAAAACTTATATACATTAGAATTTTTTAAA
         65 -CTATAATATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATACATTAGAATTTTTTAAA

               
       1455 TAT
        129 TAT

             
       1458 A
          1 A

       1459 TTTCTTAAAT


Statistics
Matches: 122,  Mismatches: 5, Indels: 13
        0.87            0.04        0.09

Matches are distributed among these distances:
 131   15  0.12
 132   47  0.39
 133   20  0.16
 134   11  0.09
 135    5  0.04
 136   24  0.20

ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51


Consensus pattern (131 bp):   
ACTTTTTACAGTTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATC
TATAATATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATACATTAGAATTTTTTAAATA
T
Done.