Locus 1811

Sequence ID	X_DroMel_CAF1
Location	5,017,666 – 5,017,783
Length	117
Max. P	0.996850

overview

Window 0

Location	5,017,666 – 5,017,757
Length	91
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	75.21
Mean single sequence MFE	-32.03
Consensus MFE	-18.02
Energy contribution	-18.85
Covariance contribution	0.83
Combinations/Pair	1.00
Mean z-score	-3.04
Structure conservation index	0.56
SVM decision value	2.76
SVM RNA-class probability	0.996850
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5017666 91 + 22224390
-----------UAUGGGCCAUGUAAAGUUGAACGUGGGCAUAACAAUGUGCCCUUAACUUGGCCCACAGACUGCACUUUUGUGCCUCGUCUCUGUCUUACCA------
-----------..(((((((.....((((((....(((((((....)))))))))))))))))))).((((.((((....))))...))))...........------ ( -33.40)
>DroPse_CAF1 112375 94 + 1
GAAGGCUGGGACGAGUUCCAUGUAAACUUUAACGUGGGCAUAACAAUGUGCCCUUAACUUGGCCCAGACACUGCU-------GCUGCAGUUCUUUCCUCCC-------
((((((((((.((((((..((((........))))(((((((....)))))))..)))))).)))))..(((((.-------...))))).))))).....------- ( -34.40)
>DroSec_CAF1 83597 97 + 1
-----------UAUGGGCCAUGUAAAGUUGAACGUGGGCAUAACAAUGUGCCCUUAACUUGGCCCACAGACUGCACUUUUGUGCCUCGUCUCUGUCUUACCCUUGUAC
-----------..(((((((.....((((((....(((((((....)))))))))))))))))))).((((.((((....))))...))))................. ( -33.40)
>DroEre_CAF1 87997 96 + 1
-----------UAUGGGCCAUGUAAAGUUGAACGUGGGCAUAACAAUGUGCCGUUAACUUGGCCCAUAGACUGCAGUUUUGUACCUCGUCUCUGUCUUACCCUU-CAC
-----------(((((((((.....((((((.....((((((....)))))).)))))))))))))))....((((...((.....))...)))).........-... ( -27.50)
>DroYak_CAF1 85062 96 + 1
-----------UACGGGCCAUGUAAAGUUGAACGUGGGCAUAACAAUGUGCCCUUAACUUGGCCCAUAGACUGCAGUUUUGUGCCCCGUCUCUGUCUUACCCAU-CAC
-----------...((((((.....((((((....(((((((....)))))))))))))))))))..((((.(((......)))...)))).............-... ( -29.10)
>DroPer_CAF1 104062 94 + 1
GAAGGCUGGGACGAGUUCCAUGUAAACUUUAACGUGGGCAUAACAAUGUGCCCUUAACUUGGCCCAGACACUGCU-------GCUGCAGUUCUUUCCUCCC-------
((((((((((.((((((..((((........))))(((((((....)))))))..)))))).)))))..(((((.-------...))))).))))).....------- ( -34.40)
>consensus
___________UAUGGGCCAUGUAAAGUUGAACGUGGGCAUAACAAUGUGCCCUUAACUUGGCCCACAGACUGCA_UUUUGUGCCUCGUCUCUGUCUUACCC______
..............(((((((((........))))(((((((....))))))).......)))))........................................... (-18.02 = -18.85 +   0.83)

alignment

secondary structure

dotplot

Window 1

Location	5,017,666 – 5,017,757
Length	91
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	75.21
Mean single sequence MFE	-30.43
Consensus MFE	-18.74
Energy contribution	-20.68
Covariance contribution	1.95
Combinations/Pair	1.18
Mean z-score	-2.00
Structure conservation index	0.62
SVM decision value	1.54
SVM RNA-class probability	0.962597
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5017666 91 - 22224390
------UGGUAAGACAGAGACGAGGCACAAAAGUGCAGUCUGUGGGCCAAGUUAAGGGCACAUUGUUAUGCCCACGUUCAACUUUACAUGGCCCAUA-----------
------...........((((...((((....)))).))))((((((((......(((((........)))))..((........)).)))))))).----------- ( -33.60)
>DroPse_CAF1 112375 94 - 1
-------GGGAGGAAAGAACUGCAGC-------AGCAGUGUCUGGGCCAAGUUAAGGGCACAUUGUUAUGCCCACGUUAAAGUUUACAUGGAACUCGUCCCAGCCUUC
-------((((.((.((((((((...-------.))))).)))(..(((......(((((........)))))..((........)).)))..))).))))....... ( -30.10)
>DroSec_CAF1 83597 97 - 1
GUACAAGGGUAAGACAGAGACGAGGCACAAAAGUGCAGUCUGUGGGCCAAGUUAAGGGCACAUUGUUAUGCCCACGUUCAACUUUACAUGGCCCAUA-----------
.................((((...((((....)))).))))((((((((......(((((........)))))..((........)).)))))))).----------- ( -33.60)
>DroEre_CAF1 87997 96 - 1
GUG-AAGGGUAAGACAGAGACGAGGUACAAAACUGCAGUCUAUGGGCCAAGUUAACGGCACAUUGUUAUGCCCACGUUCAACUUUACAUGGCCCAUA-----------
...-.............((((..(((.....)))...))))(((((((((((((((((((........))))...))).)))).....)))))))).----------- ( -25.60)
>DroYak_CAF1 85062 96 - 1
GUG-AUGGGUAAGACAGAGACGGGGCACAAAACUGCAGUCUAUGGGCCAAGUUAAGGGCACAUUGUUAUGCCCACGUUCAACUUUACAUGGCCCGUA-----------
...-.............((((...(((......))).))))((((((((......(((((........)))))..((........)).)))))))).----------- ( -29.60)
>DroPer_CAF1 104062 94 - 1
-------GGGAGGAAAGAACUGCAGC-------AGCAGUGUCUGGGCCAAGUUAAGGGCACAUUGUUAUGCCCACGUUAAAGUUUACAUGGAACUCGUCCCAGCCUUC
-------((((.((.((((((((...-------.))))).)))(..(((......(((((........)))))..((........)).)))..))).))))....... ( -30.10)
>consensus
______GGGUAAGACAGAGACGAGGCACAAAA_UGCAGUCUAUGGGCCAAGUUAAGGGCACAUUGUUAUGCCCACGUUCAACUUUACAUGGCCCAUA___________
.................((((...(((......))).))))((((((((......(((((........)))))..((........)).))))))))............ (-18.74 = -20.68 +   1.95)

alignment

secondary structure

dotplot

Window 2

Location	5,017,686 – 5,017,783
Length	97
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	65.67
Mean single sequence MFE	-20.87
Consensus MFE	-4.91
Energy contribution	-5.13
Covariance contribution	0.22
Combinations/Pair	1.27
Mean z-score	-2.05
Structure conservation index	0.24
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5017686 97 + 22224390
ACGUGGGCAUAACAAUG---UGCCCUUAACUUGGCCCACAGACUGCACUUUUGUGCCUCGUCUCUGUCUUACCA------------CUCCGUCCCACUCUUUACGACUCUCU
.((((((((((....))---)))))......(((..((.((((.((((....))))...)))).)).....)))------------................)))....... ( -22.80)
>DroPse_CAF1 112406 79 + 1
ACGUGGGCAUAACAAUG---UGCCCUUAACUUGGCCCAGACACUGCU-------GCUGCAGUUCUUUCCUCCC-------------CUCUCUCCCCC----------UCUCC
....(((((((....))---))))).......((...(((.(((((.-------...))))))))..))....-------------...........----------..... ( -19.70)
>DroSec_CAF1 83617 109 + 1
ACGUGGGCAUAACAAUG---UGCCCUUAACUUGGCCCACAGACUGCACUUUUGUGCCUCGUCUCUGUCUUACCCUUGUACAGCCGUCUCCGUCCCACUCUUCUCGACUCUCU
.((.(((((((....))---)))))......(((..(..((((.((((....)))).......(((((........).))))..))))..)..))).......))....... ( -24.10)
>DroEre_CAF1 88017 108 + 1
ACGUGGGCAUAACAAUG---UGCCGUUAACUUGGCCCAUAGACUGCAGUUUUGUACCUCGUCUCUGUCUUACCCUU-CACAGCCGUCUGCGUUCCACUCUCCCAGACUCUUU
.....(((......(((---.((((......)))).))).....((((...((.....))...)))).........-....)))(((((.(.........).)))))..... ( -20.10)
>DroWil_CAF1 88743 97 + 1
ACGUGAGCAUAACAAUGUUGUGCCCUUAAGUUGGCCCU--GGCUGCAGCUUCGCCAUUCCUUUCUACCUUCACCUU-------CGUC----UUCUACUUCCUCUG--UCUUC
..(((((((((((...)))))))........((((...--(((....)))..)))).............))))...-------....----..............--..... ( -18.40)
>DroPer_CAF1 104093 79 + 1
ACGUGGGCAUAACAAUG---UGCCCUUAACUUGGCCCAGACACUGCU-------GCUGCAGUUCUUUCCUCCC-------------CUCUCUGCCCU----------UCUCC
....(((((......((---.(((........))).))((.(((((.-------...))))))).........-------------.....))))).----------..... ( -20.10)
>consensus
ACGUGGGCAUAACAAUG___UGCCCUUAACUUGGCCCACAGACUGCA_UUUUGUGCCUCGUCUCUGUCUUACCC____________CUCCGUCCCACUCU____G__UCUCC
..((((((((....)))....(((........))).........................................................)))))............... ( -4.91 =  -5.13 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:21 2006