Locus 8489

Sequence ID	3R_DroMel_CAF1
Location	22,653,390 – 22,653,487
Length	97
Max. P	0.799952

overview

Window 8

Location	22,653,390 – 22,653,487
Length	97
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	75.66
Mean single sequence MFE	-22.12
Consensus MFE	-6.48
Energy contribution	-5.64
Covariance contribution	-0.84
Combinations/Pair	1.35
Mean z-score	-1.72
Structure conservation index	0.29
SVM decision value	0.07
SVM RNA-class probability	0.566446
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22653390 97 + 27905053
AGCCAUCUCGAAUAUAUUUUGCAGCUUAGCUUGCUGCAAAAGCCAUGUUUUUU-----GUACCACAUGUACUACAGUAGCUCUUCGAGUUGGUAGACAAAUU
.((((.((((((....(((((((((.......)))))))))((..(((.....-----((((.....)))).)))...))..)))))).))))......... ( -30.50)
>DroSec_CAF1 101406 80 + 1
AGUCAUCUGAAAUAUAU-----------------UGCAACAGCCAUGUUUUUU-----GUACCACAUGUACUACCGUAGCUCUUCGAGUUGGUAGACAAAUU
.(((....((((.((((-----------------.((....)).)))).))))-----((((.....))))(((((..((((...))))))))))))..... ( -15.30)
>DroSim_CAF1 103229 80 + 1
AGUCAUCUGAACUAUAU-----------------UGCAACAGCCAUGUUUUUU-----GUAGCACAUGUACUACAGUAGCUCUUCGAGUUGGUAGACAAAUU
.(((..(((...(((((-----------------(((.((((.........))-----)).))).)))))...)))((((((...))))))...)))..... ( -14.40)
>DroEre_CAF1 109490 93 + 1
AGCCAUCUGAAAUAAAUUUUGCAGCUUAG----CUGCAACAGCCCUGUUUUUU-----CUGCCACAUGUAGUGCAGCAGCACUUCGAGUUGGUGAACGAAUU
.((((.(((((.......(((((((...)----))))))..((.((((.....-----((((.....)))).))))..))..))).)).))))......... ( -22.70)
>DroYak_CAF1 105447 98 + 1
AGCUAUCUCAGAUAUAUUUUGCAGCUUAG----CUGCAAAAGCACUGUUUUUUUUUAUCAGCCACUUGUAGUGCAGUAGCUCCACGAGUUGGUGGACAAAUU
.(((((..........(((((((((...)----))))))))((((((.....................)))))).)))))(((((......)))))...... ( -27.70)
>consensus
AGCCAUCUGAAAUAUAUUUUGCAGCUUAG____CUGCAACAGCCAUGUUUUUU_____GUACCACAUGUACUACAGUAGCUCUUCGAGUUGGUAGACAAAUU
...................................((....))..(((((........((((.....)))).....((((((...))))))..))))).... ( -6.48 =  -5.64 +  -0.84)

alignment

secondary structure

dotplot

Window 9

Location	22,653,390 – 22,653,487
Length	97
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	75.66
Mean single sequence MFE	-22.46
Consensus MFE	-7.26
Energy contribution	-6.54
Covariance contribution	-0.72
Combinations/Pair	1.43
Mean z-score	-1.93
Structure conservation index	0.32
SVM decision value	0.61
SVM RNA-class probability	0.799952
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22653390 97 - 27905053
AAUUUGUCUACCAACUCGAAGAGCUACUGUAGUACAUGUGGUAC-----AAAAAACAUGGCUUUUGCAGCAAGCUAAGCUGCAAAAUAUAUUCGAGAUGGCU
..........(((.((((((((((((.(((.((((.....))))-----.....)))))))))(((((((.......)))))))......)))))).))).. ( -29.70)
>DroSec_CAF1 101406 80 - 1
AAUUUGUCUACCAACUCGAAGAGCUACGGUAGUACAUGUGGUAC-----AAAAAACAUGGCUGUUGCA-----------------AUAUAUUUCAGAUGACU
.(((((.(((((..(((...)))....)))))..(((((.....-----.....)))))((....)).-----------------........))))).... ( -12.40)
>DroSim_CAF1 103229 80 - 1
AAUUUGUCUACCAACUCGAAGAGCUACUGUAGUACAUGUGCUAC-----AAAAAACAUGGCUGUUGCA-----------------AUAUAGUUCAGAUGACU
...(..(((..(.....)..((((((.(((((((....))))))-----).........((....)).-----------------...)))))))))..).. ( -15.90)
>DroEre_CAF1 109490 93 - 1
AAUUCGUUCACCAACUCGAAGUGCUGCUGCACUACAUGUGGCAG-----AAAAAACAGGGCUGUUGCAG----CUAAGCUGCAAAAUUUAUUUCAGAUGGCU
..........(((.((.((((((((((..((.....))..))))-----..............((((((----(...)))))))....)))))))).))).. ( -26.20)
>DroYak_CAF1 105447 98 - 1
AAUUUGUCCACCAACUCGUGGAGCUACUGCACUACAAGUGGCUGAUAAAAAAAAACAGUGCUUUUGCAG----CUAAGCUGCAAAAUAUAUCUGAGAUAGCU
..((((((..(((.((.((((.((....)).)))).)))))..))))))......(((...((((((((----(...))))))))).....)))........ ( -28.10)
>consensus
AAUUUGUCUACCAACUCGAAGAGCUACUGUAGUACAUGUGGUAC_____AAAAAACAUGGCUGUUGCAG____CUAAGCUGCAAAAUAUAUUUCAGAUGGCU
...(((((..............(((((((.....)).))))).................((....))............................))))).. ( -7.26 =  -6.54 +  -0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:12:36 2006