Locus 1

Sequence ID	sy_aureus.rRNA
Location	575,860 – 576,072
Length	212
Max. P	0.996651

overview

Window 1

Location	575,860 – 575,970
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	63.06
Mean single sequence MFE	-35.30
Consensus MFE	-15.51
Energy contribution	-14.82
Covariance contribution	-0.69
Combinations/Pair	1.77
Mean z-score	-3.26
Structure conservation index	0.44
SVM decision value	2.73
SVM RNA-class probability	0.996651
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 575860 110 + 2809430
AUAUUACCGAAGCUGUGGAUUGUCCUUUGGACAAUGGUAG--GAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGU--------AAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGU
.....(((..........(((((((...)))))))((((.--....((.(((((((.((......(((((.((..--------..)).)))))...)).))))))))).....))))))) ( -36.30)
>sp_agal.rRNA 16542 112 + 2160275
-UCAUAGCGG------GGGAUAACUAUUGGA-AACGAUAGCUAAUACCGCAUAAGAGUAAUUAACACAUGUUAGUUAUUUAAAAGGAGCAAUUGCUUCACUGUGAGAUGGACCUG-CGUU
-.....((((------(......((((((..-..)))))).......((((...(((((((((((....)))))))))))....(((((....)))))..)))).......))))-)... ( -35.20)
>sp_mutans.rRNA 17016 112 + 2030929
-UAUUAGCGG------GGGAUAACUAUUGGA-AACGAUAGCUAAUACCGCAUAAUAUUAAUUAUUGCAUGAUAAUUGAUUGAAAGAUGCAAGCGCAUCACUAGUAGAUGGACCUG-CGUU
-(((((((((------....((.((((((..-..)))))).))...)))).)))))(((((((((....)))))))))......(((((....)))))....((((......)))-)... ( -31.80)
>sp_pneumo.rRNA 15287 112 + 2038623
-UGGUAGCGG------GGGAUAACUAUUGGA-AACGAUAGCUAAUACCGCAUAAGAGUGGAUGUUGCAUGACAUUUGCUUAAAAGGUGCACUUGCAUCACUACCAGAUGGACCUG-CGUU
-(((((((((------....((.((((((..-..)))))).))...))))....(((..((((((....))))))..)))....(((((....)))))..)))))..........-.... ( -37.90)
>consensus
_UAUUAGCGG______GGGAUAACUAUUGGA_AACGAUAGCUAAUACCGCAUAAGAGUAAUUAAUGCAUGAUAGUUG_UUAAAAGGUGCAAGUGCAUCACUAAGAGAUGGACCUG_CGUU
.((((((.(.......((.....((((((.....))))))......))((((..(((((((((((....))))))))))).....))))........).))))))............... (-15.51 = -14.82 +  -0.69)

alignment

secondary structure

dotplot

Window 2

Location	575,899 – 576,009
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	62.41
Mean single sequence MFE	-36.30
Consensus MFE	-16.60
Energy contribution	-17.22
Covariance contribution	0.62
Combinations/Pair	1.65
Mean z-score	-2.80
Structure conservation index	0.46
SVM decision value	2.56
SVM RNA-class probability	0.995280
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 575899 110 + 2809430
--GAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGU--------AAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGA-U
--....(((((((..(((((((...(((((.((..--------..)).)))))..))))))).......)))))))(((((.((....(....).((((.......))))))))))).-. ( -38.90)
>sp_agal.rRNA 16575 115 + 2160275
CUAAUACCGCAUAAGAGUAAUUAACACAUGUUAGUUAUUUAAAAGGAGCAAUUGCUUCACUGUGAGAUGGACCUG-CGUUGU-AUUAGCUA---GUUGGUGAGGUAAAGGCUCACCAAGG
(((((((((((...(((((((((((....)))))))))))....(((((....)))))...............))-))..))-)))))...---.((((((((.......)))))))).. ( -36.10)
>sp_mutans.rRNA 17049 115 + 2030929
CUAAUACCGCAUAAUAUUAAUUAUUGCAUGAUAAUUGAUUGAAAGAUGCAAGCGCAUCACUAGUAGAUGGACCUG-CGUUGU-AUUAGCUA---GUUGGUAAGGUAAGAGCUUACCAAGG
(((((((.((((...((((((((((....))))))))))......)))).((((((...(((.....)))...))-))))))-)))))...---.((((((((.......)))))))).. ( -31.90)
>sp_pneumo.rRNA 15320 115 + 2038623
CUAAUACCGCAUAAGAGUGGAUGUUGCAUGACAUUUGCUUAAAAGGUGCACUUGCAUCACUACCAGAUGGACCUG-CGUUGU-AUUAGCUA---GUUGGUGGGGUAACGGCUCACCAAGG
(((((((((((...(((..((((((....))))))..)))....(((((....)))))....((....))...))-))..))-)))))...---.((((((((.......)))))))).. ( -38.30)
>consensus
CUAAUACCGCAUAAGAGUAAUUAAUGCAUGAUAGUUG_UUAAAAGGUGCAAGUGCAUCACUAAGAGAUGGACCUG_CGUUGU_AUUAGCUA___GUUGGUGAGGUAACGGCUCACCAAGG
........((....(((((((((((....)))))))))))....(((((....))))).............................))......((((((((.......)))))))).. (-16.60 = -17.22 +   0.62)

alignment

secondary structure

dotplot

Window 3

Location	575,970 – 576,072
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	72.74
Mean single sequence MFE	-44.55
Consensus MFE	-24.91
Energy contribution	-29.97
Covariance contribution	5.06
Combinations/Pair	1.24
Mean z-score	-2.16
Structure conservation index	0.56
SVM decision value	1.65
SVM RNA-class probability	0.970205
Prediction	RNA

Download alignment: ClustalW | MAF

>sy_aureus.rRNA 575970 102 + 2809430
GUGAGUAGCGAAAGACGGGUGAGAAUCCCGUCCACCGA-UUGACUA-----AGGUUUCCAGAGGAAG-GCUCGUCCGCUCUGGG--UUAGUCGGGUCCUAAGCU-------GAGGC--CG
((...((((....((((((.......))))))..((((-(((((..-----......((((((...(-(.....)).)))))))--)))))))).......)))-------)..))--.. ( -35.00)
>sp_agal.rRNA 16654 116 + 2160275
GU-AUUAGCUA---GUUGGUGAGGUAAAGGCUCACCAAGGCGACGAUACAUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCA
((-(((.(((.---.((((((((.......)))))))))))...)))))...((((((((....)))...)))))....(((((.(((.....)))))))).((((....))))...... ( -48.80)
>sp_mutans.rRNA 17128 116 + 2030929
GU-AUUAGCUA---GUUGGUAAGGUAAGAGCUUACCAAGGCGACGAUACAUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCA
((-(((.(((.---.((((((((.......)))))))))))...)))))...((((((((....)))...)))))....(((((.(((.....)))))))).((((....))))...... ( -46.50)
>sp_pneumo.rRNA 15399 116 + 2038623
GU-AUUAGCUA---GUUGGUGGGGUAACGGCUCACCAAGGCGACGAUACAUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCA
((-(((.(((.---.((((((((.......)))))))))))...)))))...((((((((....)))...)))))....(((((.(((.....)))))))).((((....))))...... ( -47.90)
>consensus
GU_AUUAGCUA___GUUGGUGAGGUAACGGCUCACCAAGGCGACGAUACAUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCA
.......(((.....((((((((.......)))))))).((...........((((((((....)))...)))))....(((((.(((.....)))))))).((((....))))))))). (-24.91 = -29.97 +   5.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Fri Apr 7 15:50:26 2006