Locus 1446

Sequence ID	3R_DroMel_CAF1
Location	4,170,325 – 4,170,468
Length	143
Max. P	0.968446

overview

Window 8

Location	4,170,325 – 4,170,437
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.01
Mean single sequence MFE	-25.48
Consensus MFE	-14.93
Energy contribution	-14.46
Covariance contribution	-0.47
Combinations/Pair	1.33
Mean z-score	-1.99
Structure conservation index	0.59
SVM decision value	1.63
SVM RNA-class probability	0.968446
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4170325 112 + 27905053
UGGGCUCUGCCAGUUCUUCACGUUUUCGGGCUCCAUUUUAGCCAUAGUUUUGUUUUCUA--UA---UUCUUGUGGUAAAACGCCGCUUAACUGCCACAU---CUGCAGUUUAGCCGGCUU
..(((...))).........((....))((((.......))))........((((((((--((---....))))).)))))((((((.((((((.....---..)))))).)).)))).. ( -29.70)
>DroSim_CAF1 20726 112 + 1
UGGGCUCUGCCAGUUCUUCACGUUUUCGGGCUCCAUAUUAGCCAUAGUUUUGUUUUCUA--UA---UUCUUUUGGUAAAACGCCGCUUAACUGCCACAU---CUGCAGUUUAGCCGGCUU
..(((...))).........((....))((((.......))))........((((((((--..---......))).)))))((((((.((((((.....---..)))))).)).)))).. ( -27.30)
>DroEre_CAF1 10110 106 + 1
----AUCUGACGGUUCUUCACGUUUUCGGUCUCCAUUUUAGCCAUAGUUUUGUUUUCUA--UA---UUCUUAAG--ACAAUGCCGCUUAACUGCCACAU---CUGCAGUUUAGCCGGCUU
----....((((........))))...............((((...((.(((((((...--..---.....)))--)))).)).(((.((((((.....---..)))))).))).)))). ( -22.20)
>DroWil_CAF1 6628 100 + 1
---UAAUUACCCCUACUCCCCAUUUUUGGGG----------AGAAAUGUUUGUUUU-UAAGUUUUCUUCUUUUU------CUCCACAUUGCUGCCAUAUUGUCUUCAGCUCUGUUGGAAC
---............(((((((....)))))----------)).............-.................------.((((((..((((............))))..)).)))).. ( -22.80)
>DroYak_CAF1 20411 112 + 1
UGGUAUAUGACGGUCCUUUACGUUUUCGGGCUCCAUCUCAGCCAUAGUUUUGUUUUCUA--UA---UUCUUUUGGUAAAACGCCGCUUAACUGCCACAU---CUGCAGUUUAGCCGGUUU
((((..(((..(((((...........))))).)))....)))).......((((((((--..---......))).)))))((((((.((((((.....---..)))))).)).)))).. ( -25.40)
>consensus
UGGGAUCUGCCAGUUCUUCACGUUUUCGGGCUCCAUUUUAGCCAUAGUUUUGUUUUCUA__UA___UUCUUUUGGUAAAACGCCGCUUAACUGCCACAU___CUGCAGUUUAGCCGGCUU
....................((....))((((.......))))......................................((((((.((((((..........)))))).)).)))).. (-14.93 = -14.46 +  -0.47)

alignment

secondary structure

dotplot

Window 9

Location	4,170,325 – 4,170,437
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.01
Mean single sequence MFE	-25.29
Consensus MFE	-14.36
Energy contribution	-13.76
Covariance contribution	-0.60
Combinations/Pair	1.33
Mean z-score	-1.82
Structure conservation index	0.57
SVM decision value	0.99
SVM RNA-class probability	0.895430
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4170325 112 - 27905053
AAGCCGGCUAAACUGCAG---AUGUGGCAGUUAAGCGGCGUUUUACCACAAGAA---UA--UAGAAAACAAAACUAUGGCUAAAAUGGAGCCCGAAAACGUGAAGAACUGGCAGAGCCCA
..((((.((.((((((..---.....)))))).))))))(((((..(((.....---.(--(((.........))))((((.......)))).......))).))))).(((...))).. ( -28.10)
>DroSim_CAF1 20726 112 - 1
AAGCCGGCUAAACUGCAG---AUGUGGCAGUUAAGCGGCGUUUUACCAAAAGAA---UA--UAGAAAACAAAACUAUGGCUAAUAUGGAGCCCGAAAACGUGAAGAACUGGCAGAGCCCA
..(((((((.((((((..---.....)))))).))).(((((((..........---.(--(((.........))))((((.......))))..))))))).......))))........ ( -27.80)
>DroEre_CAF1 10110 106 - 1
AAGCCGGCUAAACUGCAG---AUGUGGCAGUUAAGCGGCAUUGU--CUUAAGAA---UA--UAGAAAACAAAACUAUGGCUAAAAUGGAGACCGAAAACGUGAAGAACCGUCAGAU----
..((((.((.((((((..---.....)))))).))))))...((--(((.....---((--(((.........))))).........)))))........................---- ( -22.14)
>DroWil_CAF1 6628 100 - 1
GUUCCAACAGAGCUGAAGACAAUAUGGCAGCAAUGUGGAG------AAAAAGAAGAAAACUUA-AAAACAAACAUUUCU----------CCCCAAAAAUGGGGAGUAGGGGUAAUUA---
.(((((.((..((((....(.....).))))..)))))))------.................-.......((....((----------(((((....))))))).....)).....--- ( -24.10)
>DroYak_CAF1 20411 112 - 1
AAACCGGCUAAACUGCAG---AUGUGGCAGUUAAGCGGCGUUUUACCAAAAGAA---UA--UAGAAAACAAAACUAUGGCUGAGAUGGAGCCCGAAAACGUAAAGGACCGUCAUAUACCA
...((.(((.((((((..---.....)))))).))).(((((((..........---.(--(((.........))))((((.......))))..)))))))...)).............. ( -24.30)
>consensus
AAGCCGGCUAAACUGCAG___AUGUGGCAGUUAAGCGGCGUUUUACCAAAAGAA___UA__UAGAAAACAAAACUAUGGCUAAAAUGGAGCCCGAAAACGUGAAGAACCGGCAGAUACCA
..((((.((.((((((..........)))))).))))))................................................................................. (-14.36 = -13.76 +  -0.60)

alignment

secondary structure

dotplot

Window 0

Location	4,170,365 – 4,170,468
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	70.39
Mean single sequence MFE	-23.10
Consensus MFE	-13.09
Energy contribution	-12.48
Covariance contribution	-0.60
Combinations/Pair	1.50
Mean z-score	-1.67
Structure conservation index	0.57
SVM decision value	1.01
SVM RNA-class probability	0.900504
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4170365 103 + 27905053
GCCAUAGUUUUGUUUUCUA--UA---UUCUUGUGGUAAAACGCCGCUUAACUGCCACAU---CUGCAGUUUAGCCGGCUUGC--UGGAGAUAAAAUUGCAUU---AUCAAGU----UUUC
.(((.......((((((((--((---....))))).)))))((((((.((((((.....---..)))))).)).))))....--))).(((((.......))---)))....----.... ( -26.60)
>DroSim_CAF1 20766 106 + 1
GCCAUAGUUUUGUUUUCUA--UA---UUCUUUUGGUAAAACGCCGCUUAACUGCCACAU---CUGCAGUUUAGCCGGCUUGC--UGGAGAUAAAAUUGCAUCAUCAUCAAGU----UUUC
((...((((((((((((..--..---.......(((((...((((((.((((((.....---..)))))).)).))))))))--))))))))))))))).............----.... ( -25.10)
>DroEre_CAF1 10146 104 + 1
GCCAUAGUUUUGUUUUCUA--UA---UUCUUAAG--ACAAUGCCGCUUAACUGCCACAU---CUGCAGUUUAGCCGGCUUGC--UAGAGAUAAAAUUGCAUUAUCAUCAAGU----UUUC
((...((((((((((.(((--..---.((....)--)(((.((((((.((((((.....---..)))))).)).))))))).--))))))))))))))).............----.... ( -23.50)
>DroWil_CAF1 6656 110 + 1
-AGAAAUGUUUGUUUU-UAAGUUUUCUUCUUUUU------CUCCACAUUGCUGCCAUAUUGUCUUCAGCUCUGUUGGAACAC--CUAAGAAAAAUAUGCAUAAUCAUCAUAUGUAUGUUC
-((((((....)))))-)...(((((((......------.((((((..((((............))))..)).))))....--..)))))))(((((((((.......))))))))).. ( -18.92)
>DroYak_CAF1 20451 106 + 1
GCCAUAGUUUUGUUUUCUA--UA---UUCUUUUGGUAAAACGCCGCUUAACUGCCACAU---CUGCAGUUUAGCCGGUUUGC--UAGAGAUAAAGUUGCAUUAUCAUCAGUU----UUCC
......((..(((...((.--((---((..((((((((...((((((.((((((.....---..)))))).)).))))))))--)))))))).))..)))..))........----.... ( -22.70)
>DroAna_CAF1 17242 102 + 1
-----AGUCUUGCACUCCAAUUA---UUCUUUUGGUUAUAACCCGCAUAUCUGCCACAU---CG---GAUUUGUCGGAUCACCCUGAGAAAGAAAGUGCAUCUUCAUCAAGU----UUUC
-----.....((((((....((.---(((((..(((.((...(((((.(((((......---))---))).)).))))).)))..))))).)).))))))............----.... ( -21.80)
>consensus
GCCAUAGUUUUGUUUUCUA__UA___UUCUUUUGGUAAAACGCCGCUUAACUGCCACAU___CUGCAGUUUAGCCGGCUUGC__UGGAGAUAAAAUUGCAUUAUCAUCAAGU____UUUC
.....(((((((((((............(....).......((((((.((((((..........)))))).)).))))........)))))))))))....................... (-13.09 = -12.48 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:49 2006