Locus 919

Sequence ID	X_DroMel_CAF1
Location	2,560,345 – 2,560,475
Length	130
Max. P	0.952981

overview

Window 9

Location	2,560,345 – 2,560,435
Length	90
Sequences	3
Columns	111
Reading direction	reverse
Mean pairwise identity	68.10
Mean single sequence MFE	-22.57
Consensus MFE	-9.65
Energy contribution	-10.00
Covariance contribution	0.35
Combinations/Pair	1.43
Mean z-score	-2.73
Structure conservation index	0.43
SVM decision value	1.21
SVM RNA-class probability	0.930494
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2560345 90 - 22224390
UUCGCUGGGCUUAAAAAUUUAACAUACAUGUGCAUGUAGAACAAGCAUGCACAAUAUGUAUUUAUG-----------------UAUUUCGUCCAUGAGUUU----UCUUGU
((((.(((((..(((.((.(((.((((((((((((((.......)))))))))...)))))))).)-----------------).))).)))))))))...----...... ( -22.30)
>DroSec_CAF1 2366 104 - 1
UCCGCUGAGCUAAAACAUUUAACAUACAUGUGUAUGUAAAACAAUCAUACACAAUAUGUAUUUACGCUCAUAGA------UGUUAGUUCGUCUAUUAGUUU-UUCUCUAGU
...((((((..(((((.....(((((..((((((((.........)))))))).)))))..........(((((------((......)))))))..))))-).))).))) ( -24.80)
>DroYak_CAF1 3964 110 - 1
UCCGCUGAAUUAAAAAAUGUAACAUACAAAUGCAUGUAGAACAAACAUGUGCA-CAUGCAUGCAUAUUCUUACAUCUACCUGUUAGUUCGCCAAUAAAUUUUUUCUCUAGU
...((.(((((((...((((((.(((...((((((((...(((....)))..)-)))))))...)))..)))))).......))))))))).................... ( -20.60)
>consensus
UCCGCUGAGCUAAAAAAUUUAACAUACAUGUGCAUGUAGAACAAACAUGCACAAUAUGUAUUUAUG_UC_UA_A______UGUUAGUUCGUCAAUAAGUUU_UUCUCUAGU
...((.(((((((...............(((((((((.......)))))))))..(((....))).................))))))))).................... ( -9.65 = -10.00 +   0.35)

alignment

secondary structure

dotplot

Window 0

Location	2,560,369 – 2,560,475
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	66.84
Mean single sequence MFE	-24.60
Consensus MFE	-5.58
Energy contribution	-6.76
Covariance contribution	1.18
Combinations/Pair	1.20
Mean z-score	-2.02
Structure conservation index	0.23
SVM decision value	-0.03
SVM RNA-class probability	0.519136
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2560369 106 + 22224390
--------CAUAAAUACAUAUUGUGCAUGCUUGUUCUACAUGCACAUGUAUGUUAAAUUUU------UAAGCCCAGCGAAAUUUAUUUUUGCCGCACUAGGUUGGCUAUUUACUCAGCUG
--------.......((((((((((((((.........)))))))).))))))........------...((...((((((.....)))))).))....((((((........)))))). ( -24.40)
>DroSec_CAF1 2396 114 + 1
UCUAUGAGCGUAAAUACAUAUUGUGUAUGAUUGUUUUACAUACACAUGUAUGUUAAAUGUU------UUAGCUCAGCGGAAUUUAUUUAUGCCGCACUAGGUUGGAUAUUUACUCAACUG
....(((((..((((((((((((((((((.........)))))))).)))))).....)))------)..)))))((((.((......)).))))....((((((........)))))). ( -30.10)
>DroSim_CAF1 4451 86 + 1
-----AAGCGUAAAUAAAUAUUGUGC-----------------------AUGUUAAAUGUU------UUAGCUCAGCGGAAUUUAUUUAUGCCGCACUAGGUUGGAUAUUUACUCAGCUG
-----..((((((((((((.((((..-----------------------..(((((.....------)))))...)))).)))))))))))).......((((((........)))))). ( -20.90)
>DroEre_CAF1 2569 105 + 1
UGUAUGAACAUGCA-------------UGUUUGUUCU--AUGCAUUUGUAUGAUAAAUGUUUUUGCUUUAGCUCAGCGGAACUUAUUUAUAUCGCACUAAGUUGGCUAUUUAUUCAGCUG
((((((((((....-------------....))))).--)))))..(((...(((((((.(((((((.......)))))))..)))))))...)))...((((((........)))))). ( -21.90)
>DroYak_CAF1 4001 112 + 1
UGUAAGAAUAUGCAUGCAUG-UGCACAUGUUUGUUCUACAUGCAUUUGUAUGUUACAUUUU------UUAAUUCAGCGGAACAUAUUUAUAGC-CAUUGAGUUUGCUAUUUAUUCAGCUG
(((((..(((((.(((((((-((.(((....)))..))))))))).))))).)))))....------......((((.((..(((...(((((-.(......).))))).))))).)))) ( -25.70)
>consensus
U_UA_GAACAUAAAUACAUAUUGUGCAUGUUUGUUCUACAUGCACAUGUAUGUUAAAUGUU______UUAGCUCAGCGGAAUUUAUUUAUGCCGCACUAGGUUGGCUAUUUACUCAGCUG
.....................................((((((....))))))......................(((..............)))....((((((........)))))). ( -5.58 =  -6.76 +   1.18)

alignment

secondary structure

dotplot

Window 1

Location	2,560,369 – 2,560,475
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	66.84
Mean single sequence MFE	-21.25
Consensus MFE	-5.83
Energy contribution	-5.03
Covariance contribution	-0.80
Combinations/Pair	1.50
Mean z-score	-2.48
Structure conservation index	0.27
SVM decision value	1.43
SVM RNA-class probability	0.952981
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2560369 106 - 22224390
CAGCUGAGUAAAUAGCCAACCUAGUGCGGCAAAAAUAAAUUUCGCUGGGCUUA------AAAAUUUAACAUACAUGUGCAUGUAGAACAAGCAUGCACAAUAUGUAUUUAUG--------
..((((......))))......(((.((((.(((.....))).)))).)))..------........(((((..(((((((((.......))))))))).))))).......-------- ( -25.40)
>DroSec_CAF1 2396 114 - 1
CAGUUGAGUAAAUAUCCAACCUAGUGCGGCAUAAAUAAAUUCCGCUGAGCUAA------AACAUUUAACAUACAUGUGUAUGUAAAACAAUCAUACACAAUAUGUAUUUACGCUCAUAGA
..((((..(....)..))))(((..((((.((......)).))))((((((((------(.......(((((..((((((((.........)))))))).))))).)))).)))))))). ( -24.10)
>DroSim_CAF1 4451 86 - 1
CAGCUGAGUAAAUAUCCAACCUAGUGCGGCAUAAAUAAAUUCCGCUGAGCUAA------AACAUUUAACAU-----------------------GCACAAUAUUUAUUUACGCUU-----
.((((((((((((((..........((((.((......)).))))((.((...------............-----------------------)).))))))))))))).))).----- ( -15.86)
>DroEre_CAF1 2569 105 - 1
CAGCUGAAUAAAUAGCCAACUUAGUGCGAUAUAAAUAAGUUCCGCUGAGCUAAAGCAAAAACAUUUAUCAUACAAAUGCAU--AGAACAAACA-------------UGCAUGUUCAUACA
....((((((....((...(((((((.(((........))).))))))).....))....................(((((--.(......))-------------)))))))))).... ( -16.00)
>DroYak_CAF1 4001 112 - 1
CAGCUGAAUAAAUAGCAAACUCAAUG-GCUAUAAAUAUGUUCCGCUGAAUUAA------AAAAUGUAACAUACAAAUGCAUGUAGAACAAACAUGUGCA-CAUGCAUGCAUAUUCUUACA
((((.(((((.(((((..........-))))).....))))).))))......------....(((((.(((...((((((((...(((....)))..)-)))))))...)))..))))) ( -24.90)
>consensus
CAGCUGAGUAAAUAGCCAACCUAGUGCGGCAUAAAUAAAUUCCGCUGAGCUAA______AACAUUUAACAUACAAAUGCAUGUAGAACAAACAUGCACAAUAUGUAUUUAUGCUC_UA_A
((((.((((.............................)))).))))......................................................................... ( -5.83 =  -5.03 +  -0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:15 2006