Locus 935

Sequence ID	X_DroMel_CAF1
Location	2,607,271 – 2,607,365
Length	94
Max. P	0.961444

overview

Window 4

Location	2,607,271 – 2,607,365
Length	94
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	78.11
Mean single sequence MFE	-37.00
Consensus MFE	-17.74
Energy contribution	-19.46
Covariance contribution	1.72
Combinations/Pair	1.15
Mean z-score	-2.42
Structure conservation index	0.48
SVM decision value	1.53
SVM RNA-class probability	0.961444
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2607271 94 + 22224390
UAAAGCUGAUUAGGAGGGGGUCGAGAAGGUAUCAAUUGAGU-----UUUGGCACCCUCUAU-------------------CUGAGGCUCCGUGGCCCACUGGCCAGCCUCAUUCCUCA
.......(((..((((((.(((((((.....((....)).)-----)))))).))))))))-------------------)(((((((....((((....)))))))))))....... ( -34.40)
>DroSec_CAF1 15235 110 + 1
UAAAGCUGAUUAG---GGAAUCGAGAAGGUAUCAAUUGAAU-----UUUGGCACCCUCUAUGAGCCACGUUGCUUUAAACCGGAGGCUACGUGGCCCACUGGCCAGCCUCAUCCCUCA
....((((..(((---((..((((((.(((..(((......-----.)))..))).))).)))(((((((.(((((......))))).))))))))).)))..))))........... ( -38.60)
>DroSim_CAF1 14913 110 + 1
UAAAGCUGAUUAG---GGAAUCGAGAAGGUAUCAAUUGAAU-----UUUGGCACCCUCUAUGAGCCACGUUGCUUUAAACCGGAGGCUACGUGGCCCACUGGCCAGCCUCAUCCCUCA
....((((..(((---((..((((((.(((..(((......-----.)))..))).))).)))(((((((.(((((......))))).))))))))).)))..))))........... ( -38.60)
>DroEre_CAF1 16227 115 + 1
UAAAGCUGAUUAGGAG-GGUGAGAGAAGGUAUCAAUUGAUACGAGUAUUGGUACCGUUUAUGAGGUACGUUGCC-UAAAUCUGAGGCUACGUGGC-UACUGGCCAGACUCAUUCCUCA
.............(((-((((((....(((((((((..........)))))))))(((....((.(((((.(((-(.......)))).))))).)-)...)))....)))).))))). ( -37.30)
>DroYak_CAF1 16580 110 + 1
UAAAGCUGAUUAGGAG-GGGACUAGAAGGUAUUAAUUGAUA-----AUUGGUACCCUUUAUGGGCUACGUUGCU-UAAAUCUGAGGCUCCGUGGC-UACUGGGCCGCCUCAUCCCUCA
.............(((-(((..((((.(((((((((.....-----))))))))).))))(((((......)))-))....((((((.....(((-(....)))))))))))))))). ( -36.10)
>consensus
UAAAGCUGAUUAGGAGGGGAUCGAGAAGGUAUCAAUUGAAU_____UUUGGCACCCUCUAUGAGCCACGUUGCU_UAAACCUGAGGCUACGUGGCCCACUGGCCAGCCUCAUCCCUCA
.............((((((....(((.(((.((((............)))).))).))).......................((((((....((((....)))))))))).)))))). (-17.74 = -19.46 +   1.72)

alignment

secondary structure

dotplot

Window 5

Location	2,607,271 – 2,607,365
Length	94
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	78.11
Mean single sequence MFE	-33.56
Consensus MFE	-17.48
Energy contribution	-19.04
Covariance contribution	1.56
Combinations/Pair	1.04
Mean z-score	-2.07
Structure conservation index	0.52
SVM decision value	0.73
SVM RNA-class probability	0.834279
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2607271 94 - 22224390
UGAGGAAUGAGGCUGGCCAGUGGGCCACGGAGCCUCAG-------------------AUAGAGGGUGCCAAA-----ACUCAAUUGAUACCUUCUCGACCCCCUCCUAAUCAGCUUUA
.((((..(((((((((((....))))....))))))).-------------------..((((((((.(((.-----......))).))))))))......))))............. ( -32.90)
>DroSec_CAF1 15235 110 - 1
UGAGGGAUGAGGCUGGCCAGUGGGCCACGUAGCCUCCGGUUUAAAGCAACGUGGCUCAUAGAGGGUGCCAAA-----AUUCAAUUGAUACCUUCUCGAUUCC---CUAAUCAGCUUUA
.......(((((((((...(((((((((((.((............)).)))))))))))((((((((.(((.-----......))).)))))))).......---....))))))))) ( -39.20)
>DroSim_CAF1 14913 110 - 1
UGAGGGAUGAGGCUGGCCAGUGGGCCACGUAGCCUCCGGUUUAAAGCAACGUGGCUCAUAGAGGGUGCCAAA-----AUUCAAUUGAUACCUUCUCGAUUCC---CUAAUCAGCUUUA
.......(((((((((...(((((((((((.((............)).)))))))))))((((((((.(((.-----......))).)))))))).......---....))))))))) ( -39.20)
>DroEre_CAF1 16227 115 - 1
UGAGGAAUGAGUCUGGCCAGUA-GCCACGUAGCCUCAGAUUUA-GGCAACGUACCUCAUAAACGGUACCAAUACUCGUAUCAAUUGAUACCUUCUCUCACC-CUCCUAAUCAGCUUUA
.((((...((((.((((.....-)))).((.((((.......)-))).))(((((........)))))....))))(((((....)))))..........)-)))............. ( -29.10)
>DroYak_CAF1 16580 110 - 1
UGAGGGAUGAGGCGGCCCAGUA-GCCACGGAGCCUCAGAUUUA-AGCAACGUAGCCCAUAAAGGGUACCAAU-----UAUCAAUUAAUACCUUCUAGUCCC-CUCCUAAUCAGCUUUA
.(((((.(((((((((......-))).....))))))((((.(-((.......((((.....))))....((-----((.....))))..)))..))))))-)))............. ( -27.40)
>consensus
UGAGGGAUGAGGCUGGCCAGUGGGCCACGUAGCCUCAGAUUUA_AGCAACGUAGCUCAUAGAGGGUGCCAAA_____AAUCAAUUGAUACCUUCUCGACCCCCUCCUAAUCAGCUUUA
(((((...((((((((((....))))....)))))).......................((((((((.(((............))).))))))))..................))))) (-17.48 = -19.04 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:37 2006