Locus 5011

Sequence ID	X_DroMel_CAF1
Location	13,117,842 – 13,117,992
Length	150
Max. P	0.992299

overview

Window 1

Location	13,117,842 – 13,117,952
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.46
Mean single sequence MFE	-32.73
Consensus MFE	-24.26
Energy contribution	-26.02
Covariance contribution	1.76
Combinations/Pair	1.29
Mean z-score	-2.38
Structure conservation index	0.74
SVM decision value	2.32
SVM RNA-class probability	0.992299
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13117842 110 + 22224390
------GCAGCCUCUAUUUAUCGUGGCC----AGUCAUAUUAAAUUAAUUAUAGUCAUCAGUGGGUUGCAUUGUGAGCUAGAAAUGCGUGUUUCCCACUGAGACGACAGAGGCACUUAAA
------...(((((((((((..((((..----..))))..)))))........(((.((((((((..((((.....((.......))))))..)))))))))))...))))))....... ( -37.30)
>DroSec_CAF1 19084 110 + 1
------GCAGCCUCUAUUUAUCGUGGCC----AGUCAUAUUAAAUUAAUUAUAGUCAUCAGUGGGUUGCAUUGUGAGCUAGAAAUGCGUGUUUCCCACUGAGACGACAGAGGCACUUAAA
------...(((((((((((..((((..----..))))..)))))........(((.((((((((..((((.....((.......))))))..)))))))))))...))))))....... ( -37.30)
>DroSim_CAF1 29481 110 + 1
------GCAGCCUCUAUUUAUCGUGGCC----AGUCAUAUUAAAUUAAUUAUAGUCAUCAGUGGGUUGCAUUGUGAGCUAGAAAUGCGUGUUUCCCACUGAGACGACAGAGGCACUUAAA
------...(((((((((((..((((..----..))))..)))))........(((.((((((((..((((.....((.......))))))..)))))))))))...))))))....... ( -37.30)
>DroYak_CAF1 19329 110 + 1
------GCAGCCUCUAUUUAACGUGGUC----GGUCAUAUUAAAUUAAUUAUAGUCAUCAGUGGGAUGCAUUGUGGGCUAGAAAUGCUUGUUUUCCACUGAGACGACCACAGCACUCAAA
------................((((((----.....((......))......(((.(((((((((.(((.....(((.......)))))).)))))))))))))))))).......... ( -30.50)
>DroAna_CAF1 25376 100 + 1
AUAUGUGUCGAGUACAGAUAUCGUGGCCCCCGAGUCGC-----AUUAAUUAUAGUCAUCAGUGGCUCGUAUUGUGAGCUUCAUCCGCGUGCUUUCCCUUUGGA---------------AA
.........((((((.(....)((((....((((((((-----.................))))))))....(((.....)))))))))))))(((....)))---------------.. ( -21.23)
>consensus
______GCAGCCUCUAUUUAUCGUGGCC____AGUCAUAUUAAAUUAAUUAUAGUCAUCAGUGGGUUGCAUUGUGAGCUAGAAAUGCGUGUUUCCCACUGAGACGACAGAGGCACUUAAA
.........((((((.......(((((......)))))...............(((.((((((((..((((.....((.......))))))..)))))))))))...))))))....... (-24.26 = -26.02 +   1.76)

alignment

secondary structure

dotplot

Window 2

Location	13,117,872 – 13,117,992
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.86
Mean single sequence MFE	-26.04
Consensus MFE	-22.09
Energy contribution	-22.53
Covariance contribution	0.44
Combinations/Pair	1.20
Mean z-score	-1.59
Structure conservation index	0.85
SVM decision value	0.35
SVM RNA-class probability	0.700976
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13117872 120 + 22224390
UAAAUUAAUUAUAGUCAUCAGUGGGUUGCAUUGUGAGCUAGAAAUGCGUGUUUCCCACUGAGACGACAGAGGCACUUAAAUCAUAAAGAAAUACAAAUUCUGUGGGUAAAUUUUCCUGAA
.............(((.((((((((..((((.....((.......))))))..))))))))))).((((((.........((.....))........))))))(((........)))... ( -29.13)
>DroSec_CAF1 19114 119 + 1
UAAAUUAAUUAUAGUCAUCAGUGGGUUGCAUUGUGAGCUAGAAAUGCGUGUUUCCCACUGAGACGACAGAGGCACUUAAAUCAUAAAGAAAAACAAAUGCUGUG-GUAAAAUUUCGUGAA
........((((.(((.((((((((..((((.....((.......))))))..))))))))))).((...((((......((.....))........))))...-))........)))). ( -26.14)
>DroSim_CAF1 29511 120 + 1
UAAAUUAAUUAUAGUCAUCAGUGGGUUGCAUUGUGAGCUAGAAAUGCGUGUUUCCCACUGAGACGACAGAGGCACUUAAAUCAUAAAGAAAAACAAAUGCUGUGAGUAAAAUUUCGUUAA
.............(((.((((((((..((((.....((.......))))))..)))))))))))(((..((..(((((...(((............)))...)))))....))..))).. ( -26.70)
>DroYak_CAF1 19359 104 + 1
UAAAUUAAUUAUAGUCAUCAGUGGGAUGCAUUGUGGGCUAGAAAUGCUUGUUUUCCACUGAGACGACCACAGCACUCAAAAUAUAAAGAAA-ACUAAUGUU-UAAA--------------
.............(((.(((((((((.(((.....(((.......)))))).)))))))))))).........................((-((....)))-)...-------------- ( -22.20)
>consensus
UAAAUUAAUUAUAGUCAUCAGUGGGUUGCAUUGUGAGCUAGAAAUGCGUGUUUCCCACUGAGACGACAGAGGCACUUAAAUCAUAAAGAAAAACAAAUGCUGUGAGUAAAAUUUCGUGAA
.............(((.((((((((..((((.....((.......))))))..))))))))))).((((((.........((.....))........))))))................. (-22.09 = -22.53 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	13,117,872 – 13,117,992
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.86
Mean single sequence MFE	-23.43
Consensus MFE	-18.41
Energy contribution	-19.48
Covariance contribution	1.06
Combinations/Pair	1.04
Mean z-score	-1.80
Structure conservation index	0.79
SVM decision value	0.61
SVM RNA-class probability	0.798302
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13117872 120 - 22224390
UUCAGGAAAAUUUACCCACAGAAUUUGUAUUUCUUUAUGAUUUAAGUGCCUCUGUCGUCUCAGUGGGAAACACGCAUUUCUAGCUCACAAUGCAACCCACUGAUGACUAUAAUUAAUUUA
....((.........))(((((.....((..((.....))..))......))))).(((((((((((......(((((..........)))))..)))))))).)))............. ( -23.80)
>DroSec_CAF1 19114 119 - 1
UUCACGAAAUUUUAC-CACAGCAUUUGUUUUUCUUUAUGAUUUAAGUGCCUCUGUCGUCUCAGUGGGAAACACGCAUUUCUAGCUCACAAUGCAACCCACUGAUGACUAUAAUUAAUUUA
...............-....(((((((....((.....))..)))))))...(((.(((((((((((......(((((..........)))))..)))))))).))).)))......... ( -25.10)
>DroSim_CAF1 29511 120 - 1
UUAACGAAAUUUUACUCACAGCAUUUGUUUUUCUUUAUGAUUUAAGUGCCUCUGUCGUCUCAGUGGGAAACACGCAUUUCUAGCUCACAAUGCAACCCACUGAUGACUAUAAUUAAUUUA
....................(((((((....((.....))..)))))))...(((.(((((((((((......(((((..........)))))..)))))))).))).)))......... ( -25.10)
>DroYak_CAF1 19359 104 - 1
--------------UUUA-AACAUUAGU-UUUCUUUAUAUUUUGAGUGCUGUGGUCGUCUCAGUGGAAAACAAGCAUUUCUAGCCCACAAUGCAUCCCACUGAUGACUAUAAUUAAUUUA
--------------....-......(((-.(((..........))).)))(((((((..(((((((.......(((((..........)))))...)))))))))))))).......... ( -19.70)
>consensus
UUCACGAAAUUUUACUCACAGCAUUUGUUUUUCUUUAUGAUUUAAGUGCCUCUGUCGUCUCAGUGGGAAACACGCAUUUCUAGCUCACAAUGCAACCCACUGAUGACUAUAAUUAAUUUA
....................(((((((..((.......))..))))))).......(((((((((((......(((((..........)))))..)))))))).)))............. (-18.41 = -19.48 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:08 2006