ok, i apologize it may be just something very obvious but despite reading manual several times, i can not understand the following behavior. A sequence searched against build in e_coli index:
bowtie e_coli -c TTCTTTTTTACCTTCCCC -n 3 -e 90 -a
0 + gi|110640213|ref|NC_008253.1| 2745489 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0
0 - gi|110640213|ref|NC_008253.1| 3948415 GGGGAAGGTAAAAAAGAA IIIIIIIIIIIIIIIIII 0 9:C>T,10:T>G,12:G>A
0 + gi|110640213|ref|NC_008253.1| 2345717 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 13:G>T,16:T>C,17:G>C
0 + gi|110640213|ref|NC_008253.1| 1032847 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 11:G>C,13:A>T,16:G>C
0 + gi|110640213|ref|NC_008253.1| 2899814 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 11:T>C,15:A>C
0 + gi|110640213|ref|NC_008253.1| 2939803 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 9:C>A,10:A>C,15:G>C
0 + gi|110640213|ref|NC_008253.1| 550112 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 0:G>T,1:C>T
0 + gi|110640213|ref|NC_008253.1| 4879006 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 8:C>T,13:G>T,15:T>C
0 + gi|110640213|ref|NC_008253.1| 4630520 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 8:G>T,12:A>T,14:G>C
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 9 alignments to 1 output stream(s)
=========================================================
bowtie e_coli -c TTCTTTTTTACCTTCCCC -n 3 -e 90 -a --best
0 + gi|110640213|ref|NC_008253.1| 2745489 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0
0 + gi|110640213|ref|NC_008253.1| 550112 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 0:G>T,1:C>T
0 + gi|110640213|ref|NC_008253.1| 2899814 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 11:T>C,15:A>C
0 + gi|110640213|ref|NC_008253.1| 4760194 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 0:A>T,2:A>C,14:A>C
0 + gi|110640213|ref|NC_008253.1| 2345717 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 13:G>T,16:T>C,17:G>C
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 5 alignments to 1 output stream(s)
=========================================================
Q.1 what happened to other 4 alignments with best (no quality is considered as you see)
Q.2 Where is the alignment 4760194 coming from when --best is used
Thanks for your response
bowtie e_coli -c TTCTTTTTTACCTTCCCC -n 3 -e 90 -a
0 + gi|110640213|ref|NC_008253.1| 2745489 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0
0 - gi|110640213|ref|NC_008253.1| 3948415 GGGGAAGGTAAAAAAGAA IIIIIIIIIIIIIIIIII 0 9:C>T,10:T>G,12:G>A
0 + gi|110640213|ref|NC_008253.1| 2345717 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 13:G>T,16:T>C,17:G>C
0 + gi|110640213|ref|NC_008253.1| 1032847 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 11:G>C,13:A>T,16:G>C
0 + gi|110640213|ref|NC_008253.1| 2899814 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 11:T>C,15:A>C
0 + gi|110640213|ref|NC_008253.1| 2939803 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 9:C>A,10:A>C,15:G>C
0 + gi|110640213|ref|NC_008253.1| 550112 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 0:G>T,1:C>T
0 + gi|110640213|ref|NC_008253.1| 4879006 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 8:C>T,13:G>T,15:T>C
0 + gi|110640213|ref|NC_008253.1| 4630520 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 8:G>T,12:A>T,14:G>C
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 9 alignments to 1 output stream(s)
=========================================================
bowtie e_coli -c TTCTTTTTTACCTTCCCC -n 3 -e 90 -a --best
0 + gi|110640213|ref|NC_008253.1| 2745489 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0
0 + gi|110640213|ref|NC_008253.1| 550112 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 0:G>T,1:C>T
0 + gi|110640213|ref|NC_008253.1| 2899814 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 11:T>C,15:A>C
0 + gi|110640213|ref|NC_008253.1| 4760194 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 0:A>T,2:A>C,14:A>C
0 + gi|110640213|ref|NC_008253.1| 2345717 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 13:G>T,16:T>C,17:G>C
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 5 alignments to 1 output stream(s)
=========================================================
Q.1 what happened to other 4 alignments with best (no quality is considered as you see)
Q.2 Where is the alignment 4760194 coming from when --best is used
Thanks for your response