Locus 9353

Sequence ID	3R_DroMel_CAF1
Location	24,869,874 – 24,870,004
Length	130
Max. P	0.995303

overview

Window 8

Location	24,869,874 – 24,869,966
Length	92
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	71.11
Mean single sequence MFE	-24.98
Consensus MFE	-17.26
Energy contribution	-16.82
Covariance contribution	-0.44
Combinations/Pair	1.23
Mean z-score	-1.95
Structure conservation index	0.69
SVM decision value	2.23
SVM RNA-class probability	0.990679
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24869874 92 + 27905053
---------------------------AAUCAUUGCAUUUAUUGAGCUUUGUAUCUUUUGAUAGAAAAUGUAGAUGGUUCAUUUUGUGUAUCAUGGCGAUCUUCUUUCUGAGCUCAUCG
---------------------------...............(((((((..((((....))))((((....((((.((.(((..........))))).))))..)))).)))))))... ( -16.10)
>DroSec_CAF1 3138 118 + 1
UUCAUUUAUUGACUUUCAAAUGAAAAAGAGUAUUU-AUUUGUAGAGCUUUCUAUCUUUUGAUAGAAAAGAUAGAUGGCUCGUUUUGUGCAUCAUGGCGAUCUUCUUCCCGAGCUCAUAG
(((((((..........)))))))...((((....-.......(((((.((((((((((.....)))))))))).))))).............(((.((......))))).)))).... ( -29.50)
>DroSim_CAF1 3137 118 + 1
UUCAUUUAUUGACUUUCAAAUGAAAAAGAGUAUUG-AUUUGUAGAGCUUUCUAUCUUUUGAUAGAAAAGAUAGAUGGCUCGUUUUGUGCAUCAGGGCGAUCUUCUUUCCGAGCUCAUAG
(((((((..........)))))))...((((.(((-.......(((((.((((((((((.....)))))))))).)))))((((((.....))))))...........))))))).... ( -31.10)
>DroEre_CAF1 3196 101 + 1
----------AACUUU-ACAUUAACA----AAUUC-AUUAGAUGGGCUUUCUAUCUUUUAAUAGAAAAGAUAGAAAGUUCGU--AGUGUAACAUGGCGAUCUUCUUCCCGAGCUCAUAG
----------....((-((((((...----...((-....))(((((((((((((((((.....))))))))))))))))))--)))))))..(((.((......)))))......... ( -26.70)
>DroYak_CAF1 3311 90 + 1
----------AACU----------------AAUUG-AUUUUGAGAGCUGUGUAUCUUUUGAUAGAAAAGAUAGAUAGUUCAU--AGUGCAUCAUGGCGAUCUUCCUUCCGAGCUCAUAG
----------....----------------...((-(.((((.(((((((.((((((((.....)))))))).)))))))..--..(((......)))..........)))).)))... ( -21.50)
>consensus
__________AACUUU_A_AU_AA_A__A_AAUUG_AUUUGUAGAGCUUUCUAUCUUUUGAUAGAAAAGAUAGAUGGUUCGUUUUGUGCAUCAUGGCGAUCUUCUUUCCGAGCUCAUAG
...........................................(((((.((((((((((.....)))))))))).))))).......((......))((.(((......))).)).... (-17.26 = -16.82 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	24,869,874 – 24,869,966
Length	92
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	71.11
Mean single sequence MFE	-20.06
Consensus MFE	-11.37
Energy contribution	-12.17
Covariance contribution	0.80
Combinations/Pair	1.10
Mean z-score	-1.82
Structure conservation index	0.57
SVM decision value	1.08
SVM RNA-class probability	0.912126
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24869874 92 - 27905053
CGAUGAGCUCAGAAAGAAGAUCGCCAUGAUACACAAAAUGAACCAUCUACAUUUUCUAUCAAAAGAUACAAAGCUCAAUAAAUGCAAUGAUU---------------------------
...((((((.((((((.((((.(.(((..........)))..).))))...))))))(((....)))....))))))...............--------------------------- ( -11.40)
>DroSec_CAF1 3138 118 - 1
CUAUGAGCUCGGGAAGAAGAUCGCCAUGAUGCACAAAACGAGCCAUCUAUCUUUUCUAUCAAAAGAUAGAAAGCUCUACAAAU-AAAUACUCUUUUUCAUUUGAAAGUCAAUAAAUGAA
...(((..(((.((((((((..((......)).......((((..((((((((((.....))))))))))..)))).......-......))))))))...)))...)))......... ( -26.00)
>DroSim_CAF1 3137 118 - 1
CUAUGAGCUCGGAAAGAAGAUCGCCCUGAUGCACAAAACGAGCCAUCUAUCUUUUCUAUCAAAAGAUAGAAAGCUCUACAAAU-CAAUACUCUUUUUCAUUUGAAAGUCAAUAAAUGAA
...(((((((((...(.....)...)))).)).......((((..((((((((((.....))))))))))..))))......)-)).........((((((((........)))))))) ( -25.50)
>DroEre_CAF1 3196 101 - 1
CUAUGAGCUCGGGAAGAAGAUCGCCAUGUUACACU--ACGAACUUUCUAUCUUUUCUAUUAAAAGAUAGAAAGCCCAUCUAAU-GAAUU----UGUUAAUGU-AAAGUU----------
.((((.((((........))..))))))(((((..--((((((((((((((((((.....)))))))))))))....((....-)).))----)))...)))-))....---------- ( -21.20)
>DroYak_CAF1 3311 90 - 1
CUAUGAGCUCGGAAGGAAGAUCGCCAUGAUGCACU--AUGAACUAUCUAUCUUUUCUAUCAAAAGAUACACAGCUCUCAAAAU-CAAUU----------------AGUU----------
....(((((.(((((((((((.(.((((......)--)))..).)))).)))))))((((....))))...))))).......-.....----------------....---------- ( -16.20)
>consensus
CUAUGAGCUCGGAAAGAAGAUCGCCAUGAUGCACAAAACGAACCAUCUAUCUUUUCUAUCAAAAGAUAGAAAGCUCUACAAAU_CAAUA_U__U_UU_AU_U_AAAGUC__________
....(((((((........(((.....)))........)))....((((((((((.....))))))))))..))))........................................... (-11.37 = -12.17 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	24,869,887 – 24,870,004
Length	117
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	85.71
Mean single sequence MFE	-35.56
Consensus MFE	-28.42
Energy contribution	-28.02
Covariance contribution	-0.40
Combinations/Pair	1.25
Mean z-score	-2.91
Structure conservation index	0.80
SVM decision value	2.56
SVM RNA-class probability	0.995303
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24869887 117 + 27905053
AUUGAGCUUUGUAUCUUUUGAUAGAAAAUGUAGAUGGUUCAUUUUGUGUAUCAUGGCGAUCUUCUUUCUGAGCUCAUCGAUUUUCAUAGAGUCUUGGAUUCAUUGGC--CUGCACUCUG
..((((((.(.(((.((((.....)))).))).).))))))....(((((....(((.(.......((..(((((.............))).))..)).....).))--)))))).... ( -23.22)
>DroSec_CAF1 3177 117 + 1
GUAGAGCUUUCUAUCUUUUGAUAGAAAAGAUAGAUGGCUCGUUUUGUGCAUCAUGGCGAUCUUCUUCCCGAGCUCAUAGAUUUUCAUAGAGACUUGGAUUCACUGGC--CUGCACUCUG
...(((((.((((((((((.....)))))))))).))))).....(((((....(((((......))((((((((.((........))))).)))))........))--)))))).... ( -38.00)
>DroSim_CAF1 3176 117 + 1
GUAGAGCUUUCUAUCUUUUGAUAGAAAAGAUAGAUGGCUCGUUUUGUGCAUCAGGGCGAUCUUCUUUCCGAGCUCAUAGAUUUUCAUAGAGUCUUGGAUUCACUGGC--CUGCACUCUG
...(((((.((((((((((.....)))))))))).))))).....(((((....(((.(.......(((((((((.((........))))).)))))).....).))--)))))).... ( -39.30)
>DroEre_CAF1 3220 114 + 1
GAUGGGCUUUCUAUCUUUUAAUAGAAAAGAUAGAAAGUUCGU--AGUGUAACAUGGCGAUCUUCUUCCCGAGCUCAUAGAUA-UCAUUGAGUUUUGGAUUCUUUGGC--CUGCACUCUG
.((((((((((((((((((.....))))))))))))))))))--((((((....(((.(......(((.(((((((......-....))))))).))).....).))--)))))))... ( -41.30)
>DroYak_CAF1 3324 117 + 1
UGAGAGCUGUGUAUCUUUUGAUAGAAAAGAUAGAUAGUUCAU--AGUGCAUCAUGGCGAUCUUCCUUCCGAGCUCAUAGAUUUUCAUAGACUUUCGGAUUCUUUGGCCACUGCACUCUG
...(((((((.((((((((.....)))))))).)))))))..--((((((...((((.(.......((((((....((........))....)))))).....).)))).))))))... ( -36.00)
>consensus
GUAGAGCUUUCUAUCUUUUGAUAGAAAAGAUAGAUGGUUCGUUUUGUGCAUCAUGGCGAUCUUCUUUCCGAGCUCAUAGAUUUUCAUAGAGUCUUGGAUUCAUUGGC__CUGCACUCUG
...(((((.((((((((((.....)))))))))).))))).....(((((.....((.(.......(((((((((.............))).)))))).....).))...))))).... (-28.42 = -28.02 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:32:30 2006