Locus 7847

Sequence ID	X_DroMel_CAF1
Location	19,550,191 – 19,550,492
Length	301
Max. P	0.606562

overview

Window 6

Location	19,550,191 – 19,550,311
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.70
Mean single sequence MFE	-37.40
Consensus MFE	-28.12
Energy contribution	-28.32
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.75
SVM decision value	0.04
SVM RNA-class probability	0.555586
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19550191 120 - 22224390
GCGGGGAGCGUUUAACAACGAACGUUGGCGUUUUUCGCCAAUGACGGCCAGCGACGAGAGUACAUAAGAUUUAUAGUUGCUAUUUUUAAAAGCGGCGUAUUAAGAACCGUAGGCCAGCGA
(((..((((((....((((....))))))))))..))).......((((.(((((....))..............((((((.........))))))...........))).))))..... ( -36.80)
>DroSec_CAF1 13736 116 - 1
GCGGGGAGCGUUUAA---CGAACGUUGGCGUUUUUCGCCAAUGACGGCCAGCGACGAGAGUACAUAAGAUUUAUAGUUGCUAUUUUUA-AAGCGGCGUAUUAAGAGCCGUAGGCCAGCGA
(((..(((((((.((---(....))))))))))..))).......((((((((((..((((.......))))...)))))).......-..(((((.........))))).))))..... ( -40.80)
>DroSim_CAF1 14675 116 - 1
GCGGGGAGCGUUUAA---CGAACGUUGGCGUUUUUCGCCAAUGACGGCCAGCGACGAGAGUACAUAAGAUUUAUAGUUGCUAUUUUUA-AAGCGGCGUAUUAAGAGCCGUAGGCCAGCGA
(((..(((((((.((---(....))))))))))..))).......((((((((((..((((.......))))...)))))).......-..(((((.........))))).))))..... ( -40.80)
>DroEre_CAF1 13692 110 - 1
GCGGGGAGCGUUUAA---CGAACG------UUUUUCGCCAAUGACGGCCAGCGACGAGAGUACAUAAGAUUUAUAGUAGCUAUUUUUA-AAGCGGCGUAUUAAGAACCGUAGGCCAGCGA
(((..((((((((..---.)))))------)))..))).......((((.(((((....))..............((.(((.......-.))).))...........))).))))..... ( -32.80)
>DroYak_CAF1 13402 110 - 1
GCGGGGAGCGUUUAA---CGAACG------UUUUUCGCCAAUGACGGCCAGCGACGAGAGUACAUAAGAUUUAUAGUUGCUAUUUUUA-AAGCGGCGUAUUAAGAACCGUAGGCCAGCGA
(((..((((((((..---.)))))------)))..))).......((((.(((((....))..............((((((.......-.))))))...........))).))))..... ( -35.80)
>consensus
GCGGGGAGCGUUUAA___CGAACGUUGGCGUUUUUCGCCAAUGACGGCCAGCGACGAGAGUACAUAAGAUUUAUAGUUGCUAUUUUUA_AAGCGGCGUAUUAAGAACCGUAGGCCAGCGA
(((..((((((((......)))))......)))..))).......((((.(((((....))..............((((((.........))))))...........))).))))..... (-28.12 = -28.32 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	19,550,311 – 19,550,415
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.84
Mean single sequence MFE	-36.78
Consensus MFE	-29.02
Energy contribution	-29.02
Covariance contribution	-0.00
Combinations/Pair	1.07
Mean z-score	-1.38
Structure conservation index	0.79
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19550311 104 + 22224390
UGA--------UCUCGAUAUAUUGG--------GAUCUUGGUGCCGCCGGUGCUGUGGCAGCGUGUAAAGUAAAGGCAUCGCAUCCCCGAGCCCAUGUAAAUCGGCCACAUGCACUCACU
.((--------((((((....))))--------))))..((((.....(((((((((((.(((((.........(((.(((......)))))))))))......)))))).))))))))) ( -34.30)
>DroSec_CAF1 13852 102 + 1
UGA--------UCUCGAGAUCUUGG--------GAUCUUGGUGCCGCCGGUGCUGUGGCAGCGUGUAAAGUAAGAGCAUCGCAUC--CGAGCCCAUGUAAAUCGGCCACAUGCACUCACU
.((--------((((((....))))--------))))..((((.....(((((((((((.((((((.........))).)))...--(((...........))))))))).))))))))) ( -34.60)
>DroSim_CAF1 14791 110 + 1
UGA--------UCUCGAGAUCUUGGGAUCUUGGGAUCUUGGUGCCGCCGGUGCUGUGGCAGCGUGUAAAGUAAGAGCAUCGCAUC--CGAGCCCAUGUAAAUCGGCCACAUGCACUCACU
.((--------((((((((((....))))))))))))..((((.....(((((((((((.((((((.........))).)))...--(((...........))))))))).))))))))) ( -43.20)
>DroEre_CAF1 13802 110 + 1
UGAUUUCGAGAUCUCGAGAUCUUGG--------GAUCUUGGUGCCGCCGGUGCUGUGGCAGUGUGUAAAGUAAGAGCAUCACAUC--CGAGCCCAUGUAAAUCGGCCACAUGCACUCACU
.(((..(((((((....))))))).--------.)))..((((.....(((((((((((.((((((.........))).)))...--(((...........))))))))).))))))))) ( -39.10)
>DroYak_CAF1 13512 102 + 1
UGA--------UCUCGAGAUCUUGG--------GAUCUUGGUGCCGCCGGUGCUGUGGCAGUGUGUAAAGUAAAAGCAUCGCAUC--CGAGCCCAUGUAAAUCGGCCACAUGCACUCACU
.((--------((((((....))))--------))))..((((.....(((((((((((.((((((.........))).)))...--(((...........))))))))).))))))))) ( -32.70)
>consensus
UGA________UCUCGAGAUCUUGG________GAUCUUGGUGCCGCCGGUGCUGUGGCAGCGUGUAAAGUAAGAGCAUCGCAUC__CGAGCCCAUGUAAAUCGGCCACAUGCACUCACU
..............(((((((............)))))))(((.....(((((((((((.((((((.........))).))).....(((...........))))))))).)))))))). (-29.02 = -29.02 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	19,550,375 – 19,550,492
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.75
Mean single sequence MFE	-24.62
Consensus MFE	-22.82
Energy contribution	-23.18
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.17
Structure conservation index	0.93
SVM decision value	0.15
SVM RNA-class probability	0.606562
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19550375 117 + 22224390
GCAUCCCCGAGCCCAUGUAAAUCGGCCACAUGCACUCACUCAGCCGAACAUCUGUCAGUCC---AUGGCACACACUUAACAAAAUCGACCUGCCACGUCCUCAAUCGAACAGGAUGUGAA
(((....(((.....(((...(((((....((....))....))))).....(((((....---.)))))........)))...)))...)))((((((((.........)))))))).. ( -24.20)
>DroSec_CAF1 13916 115 + 1
GCAUC--CGAGCCCAUGUAAAUCGGCCACAUGCACUCACUCAGCCGAACAUCUGUCAGUCC---AUGGCACACACUUAACAAAAUCGACCUGCCACGUCCUCAAUCGAACAGGAUGUGAA
(((..--(((.....(((...(((((....((....))....))))).....(((((....---.)))))........)))...)))...)))((((((((.........)))))))).. ( -24.60)
>DroSim_CAF1 14863 118 + 1
GCAUC--CGAGCCCAUGUAAAUCGGCCACAUGCACUCACUCAGCCGAACAUCUGUCAGUCCACCAUGGCACACACUUAACAAAAUCGACCUGCCACGUCCUCAAUCGAACAGGAUGUGAA
(((..--(((.....(((...(((((....((....))....))))).....(((((........)))))........)))...)))...)))((((((((.........)))))))).. ( -24.60)
>DroEre_CAF1 13874 115 + 1
ACAUC--CGAGCCCAUGUAAAUCGGCCACAUGCACUCACUCAGCCGAACAUCUGCCAGUCC---AUGGCACACACUUAACAAAAUCGACCUGCCACGUCCUCAAUCGAACAGGAUGUGAA
.....--(((.....(((...(((((....((....))....))))).....(((((....---.)))))........)))...)))......((((((((.........)))))))).. ( -25.40)
>DroYak_CAF1 13576 115 + 1
GCAUC--CGAGCCCAUGUAAAUCGGCCACAUGCACUCACUCAGCCGAACAUCUGCCUGUCC---AUGGCACACACUUAACAAAAACGACCUGCCACGUCCUCAAUCGAACAGGAUGUGAA
(((..--((.....((((...(((((....((....))....))))))))).((((.....---..))))...............))...)))((((((((.........)))))))).. ( -24.30)
>consensus
GCAUC__CGAGCCCAUGUAAAUCGGCCACAUGCACUCACUCAGCCGAACAUCUGUCAGUCC___AUGGCACACACUUAACAAAAUCGACCUGCCACGUCCUCAAUCGAACAGGAUGUGAA
(((....(((.....(((...(((((....((....))....))))).....(((((........)))))........)))...)))...)))((((((((.........)))))))).. (-22.82 = -23.18 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:56 2006