How is it possible python to be faster than pypy

I run a piece of code with python2.7 and the cProfile says 35s while cProfile on pypy says 73s ! How is that possible assuming pypy is faster interpreter. The code implements the BWT transformation on input a bitstream. I have two files: bwt.py which is called in fm.py. I called the function as:

pypy -m cProfle fm.py inputfile

and then

python -m cProfle fm.py inputfile

The code from bwt.py is the following:

def rotations(t):
    ''' Return list of rotations of input string t '''
    tt = t * 2
    return [ tt[i:i+len(t)] for i in xrange(0, len(t)) ]

def bwm(t):
    return sorted(rotations(t))

def bwtViaBwm(t):
    ''' Given T, returns BWT(T) by way of the BWM '''

    return ''.join(map(lambda x: x[-1], bwm(t)))

def rankBwt(bw):
    ''' Given BWT string bw, return parallel list of B-ranks.  Also
        returns tots: map from character to # times it appears. '''
    tots = dict()
    ranks = []
    for c in bw:
        if c not in tots: tots[c] = 0
        ranks.append(tots[c])

        tots[c] += 1
    return ranks, tots
def firstCol(tots):
    ''' Return map from character to the range of rows prefixed by
        the character. '''
    first = {}
    totc = 0
    for c, count in sorted(tots.iteritems()):
        first[c] = (totc, totc + count)
        totc += count

    return first

def reverseBwt(bw):
    ''' Make T from BWT(T) '''
    ranks, tots = rankBwt(bw)
    first = firstCol(tots)
    rowi = 0 # start in first row
    t = '$' # start with rightmost character
    while bw[rowi] != '$':
        c = bw[rowi]

        t = c + t # prepend to answer
        # jump to row that starts with c of same rank
        rowi = first[c][0] + ranks[rowi]
    return t



def suffixArray(s):
    satups = sorted([(s[i:], i) for i in xrange(0, len(s))])
    print satups

    return map(lambda x: x[1], satups)

def bwtViaSa(t):
    # Given T, returns BWT(T) by way of the suffix array
    bw = []
    for si in suffixArray(t):
        if si == 0:
            bw.append('$')
        else:
            bw.append(t[si-1])

    return ''.join(bw) # return string-ized version of list bw



def readfile(sd):
    s=""
    with open(sd,'r') as myfile:
        s =myfile.read()
    return s.rstrip('\n')
def writefile(sd,N):

    with open(sd, "wb") as sink:
        sink.write(''.join(random.choice(string.ascii_uppercase + string.digits) for _ in xrange(N)))
        sink.write('$')
    return



def main():
    data=readfile('inp')
    b=bwtViaBwm(data)

    ranks,tots = rankBwt(b)
    print "Input stream = "+ data
    print "BWT = " + bwtViaSa(data)
    print '\n'.join(bwm(data))
    print ("Lc ranking:")
    print zip(b,ranks) 

    fc=[x[0] for x in bwm(data)]
    fc= ''.join(fc)
    print ("First column="+ fc)

    ranks,tots = rankBwt(fc)
    print("Fc ranking:")
    print zip(fc,ranks) 

    print reverseBwt(bwtViaSa(data))

if __name__=='__main__':
    main()

And this is the code form the fm.py which i call it through pypy:

import bwt
import sys
from collections import Counter

def build_FM(fname):
    stream=bwt.readfile(fname)
    #print bwt.suffixArray(stream)
    b=bwt.bwtViaBwm(stream)

    ranks,tots = bwt.rankBwt(b)
    lc=zip(b,ranks)
    fc=[x[0] for x in bwt.bwm(stream)]
    fc= ''.join(fc)
    fc= zip(fc,ranks)
    #print lc,fc


def main():
    fname= sys.argv[1]

    build_FM(fname)
    return


if __name__=='__main__':
    main()