Locus 3720

Sequence ID	X_DroMel_CAF1
Location	9,915,189 – 9,915,301
Length	112
Max. P	0.754861

overview

Window 7

Location	9,915,189 – 9,915,301
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.68
Mean single sequence MFE	-36.98
Consensus MFE	-22.30
Energy contribution	-23.02
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-2.14
Structure conservation index	0.60
SVM decision value	0.46
SVM RNA-class probability	0.744015
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9915189 112 + 22224390
UAAGCCGCAAUUUAUUAUGUCCUCUGGCGGUGAUAC---AUCCCCACUGGACUCCAAUUGGGUCAGCGGUGGUCCGG-----CUCCCCAAGCCCAUGCUGUCCAACUGGACACGCAUUAA
...(((((..........((((..(((.((((...)---))).)))..))))(((....)))...))))).....((-----((.....)))).(((((((((....))))).))))... ( -38.50)
>DroSec_CAF1 12503 112 + 1
UAAGCCGCAAUUUAUUAUGCCCUCUGGCGGCGAUAC---AUCCCCACUGGACUCCAAUUGGGUCAGCGGUGGUCCGG-----CUCCCCAAGCUCAUGCUGUCCAACUGGACACGCAUUAA
..(((((.....((((.((((....))))..)))).---....(((((((((.((....)))))..))))))..)))-----))..........(((((((((....))))).))))... ( -36.10)
>DroSim_CAF1 12691 112 + 1
UAAGCCGCAAUUUAUUAUGCCCUCUGGCGGCGAUAC---AUCCCCACUGGACUCCAAUUGGGUCAGCGGUGGUCCGG-----CUCCCCAAGCUCAUGCUGUCCAACUGGACACGCAUUAA
..(((((.....((((.((((....))))..)))).---....(((((((((.((....)))))..))))))..)))-----))..........(((((((((....))))).))))... ( -36.10)
>DroEre_CAF1 12791 95 + 1
UA--------------AUGCCCACUGGC---GACAC---AUCCCAACUGGACUCCAAUUGGGUCAGCGGACGUCCAG-----CUCCCCAGGCACAAGCUGUCCAACUGGACACGCAUUAA
((--------------((((((.(((((---((...---.))((((.(((...))).))))))))).))..((((((-----.......(((....)))......))))))..)))))). ( -32.52)
>DroYak_CAF1 12579 116 + 1
UAAGCCGCAAUUUGUUAUGCCCUCUGGC----ACACUGGAGCCCAACUGGAAUCCAAUUGGGUCAGCGGCCGUGCACAGGCUGUCCCCAGGCACUGGCUGUCCAACUGGACACGCAUUAA
..((((((.........((((....)))----)..((((.((((((.(((...))).))))))..((((((.......))))))..))))))...))))((((....))))......... ( -41.70)
>consensus
UAAGCCGCAAUUUAUUAUGCCCUCUGGCGG_GAUAC___AUCCCCACUGGACUCCAAUUGGGUCAGCGGUGGUCCGG_____CUCCCCAAGCACAUGCUGUCCAACUGGACACGCAUUAA
...(((((..........(((....))).............(((...(((...)))...)))...)))))..........................(((((((....))))).))..... (-22.30 = -23.02 +   0.72)

alignment

secondary structure

dotplot

Window 8

Location	9,915,189 – 9,915,301
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.68
Mean single sequence MFE	-43.54
Consensus MFE	-25.64
Energy contribution	-26.16
Covariance contribution	0.52
Combinations/Pair	1.08
Mean z-score	-2.20
Structure conservation index	0.59
SVM decision value	0.49
SVM RNA-class probability	0.754861
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9915189 112 - 22224390
UUAAUGCGUGUCCAGUUGGACAGCAUGGGCUUGGGGAG-----CCGGACCACCGCUGACCCAAUUGGAGUCCAGUGGGGAU---GUAUCACCGCCAGAGGACAUAAUAAAUUGCGGCUUA
....((((..(((((((((.((((.(((..((((....-----)))).)))..))))..)))))))))((((..(((((..---......)).)))..)))).........))))..... ( -40.70)
>DroSec_CAF1 12503 112 - 1
UUAAUGCGUGUCCAGUUGGACAGCAUGAGCUUGGGGAG-----CCGGACCACCGCUGACCCAAUUGGAGUCCAGUGGGGAU---GUAUCGCCGCCAGAGGGCAUAAUAAAUUGCGGCUUA
...((((.(((((....)))))))))(((((.((.((.-----.((..((.((((((((((....)).)).)))))))).)---)..)).))(((....)))............))))). ( -42.70)
>DroSim_CAF1 12691 112 - 1
UUAAUGCGUGUCCAGUUGGACAGCAUGAGCUUGGGGAG-----CCGGACCACCGCUGACCCAAUUGGAGUCCAGUGGGGAU---GUAUCGCCGCCAGAGGGCAUAAUAAAUUGCGGCUUA
...((((.(((((....)))))))))(((((.((.((.-----.((..((.((((((((((....)).)).)))))))).)---)..)).))(((....)))............))))). ( -42.70)
>DroEre_CAF1 12791 95 - 1
UUAAUGCGUGUCCAGUUGGACAGCUUGUGCCUGGGGAG-----CUGGACGUCCGCUGACCCAAUUGGAGUCCAGUUGGGAU---GUGUC---GCCAGUGGGCAU--------------UA
.((((((..((((((((...((((....).)))...))-----))))))..((((((.(((((((((...)))))))))..---(....---.)))))))))))--------------)) ( -41.00)
>DroYak_CAF1 12579 116 - 1
UUAAUGCGUGUCCAGUUGGACAGCCAGUGCCUGGGGACAGCCUGUGCACGGCCGCUGACCCAAUUGGAUUCCAGUUGGGCUCCAGUGU----GCCAGAGGGCAUAACAAAUUGCGGCUUA
......(((((((....)))).(((((.((.((....))))))).)))))(((((.(((((((((((...))))))))).))...(((----(((....)))))).......)))))... ( -50.60)
>consensus
UUAAUGCGUGUCCAGUUGGACAGCAUGAGCUUGGGGAG_____CCGGACCACCGCUGACCCAAUUGGAGUCCAGUGGGGAU___GUAUC_CCGCCAGAGGGCAUAAUAAAUUGCGGCUUA
...((((.(((((....)))))))))..((((..((........(((....)))....(((.(((((...))))).)))..............))...)))).................. (-25.64 = -26.16 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:34 2006