Locus 1105

Sequence ID	2R_DroMel_CAF1
Location	4,424,342 – 4,424,461
Length	119
Max. P	0.993354

overview

Window 4

Location	4,424,342 – 4,424,461
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	93.36
Mean single sequence MFE	-37.22
Consensus MFE	-33.00
Energy contribution	-32.76
Covariance contribution	-0.24
Combinations/Pair	1.14
Mean z-score	-1.89
Structure conservation index	0.89
SVM decision value	2.28
SVM RNA-class probability	0.991703
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4424342 119 + 20766785
GUAUUAGUUUGGUUAUCUUUGCUUAAAGCGCUAUCAAUGAAGGUCAUUUAAUGUUCGACCUUUCGCUGUACUUACCUCCUUGGAAUGCUCCAGGAGCCAGGUCUUGGCGGAGGUGGCGU
.....(((..((....))..)))....((((((((...(((((((...........)))))))(((((.((((..(((((.(((....))))))))..))))..)))))..)))))))) ( -37.60)
>DroSec_CAF1 527 119 + 1
GUAUUAGUUUGGUUAUCUUUGCUUAAAGCGCUAUCAAUGAAGGUCAAUUAAUCUUCGACCUUUCGCUGUACUUACCUCCUUGGAAUGCUCCAGGAGCCAGGUCUUGGCGGAGGUGGCGU
.....(((..((....))..)))....((((((((..(((((((......)))))))....(((((((.((((..(((((.(((....))))))))..))))..))))))))))))))) ( -37.70)
>DroSim_CAF1 320 119 + 1
GUAUUAGUUUGGUUAUCUUUGCUUAAAGCGCUAUCAAUGAAGGUCAAUUAAUGUUCGACCUUUCGCUGUACUUACCUCCUUGGAAUGCUCCAGGAGCCAGGUCUUGGCGGAGGUGGCGU
.....(((..((....))..)))....((((((((...((((((((((....))).)))))))(((((.((((..(((((.(((....))))))))..))))..)))))..)))))))) ( -38.50)
>DroEre_CAF1 577 119 + 1
AUAUUAGUUUAGUUAUCUUUGCUUAAGGCGUUAUCAAUGAAGGACAAUUAAUUUUCGACCUUUCGUUGUACUUACCUCCUUGGAAUGCUCCAGGAGCCAGGUCUUGGCGGAGGUGGCGU
...........((((((((((((.(((((((...(((((((((................))))))))).))....(((((.(((....))))))))....))))))))))))))))).. ( -38.39)
>DroYak_CAF1 537 119 + 1
ACAUUGGUUUAGUUAUCUUAGCUUCAAGAGUUAUCAAUGAAGGUCAAUCAAUGUUCGACCUUUCGUCGUACUUACCUCCUUGGAAUGCUCCAGGAGCCAUGUCUUGGCGGAAGUGGCGU
.(((((((.......((((......))))...)))))))(((((((((....))).)))))).((((..((((.((((((.(((....)))))))((((.....)))))))))))))). ( -33.90)
>consensus
GUAUUAGUUUGGUUAUCUUUGCUUAAAGCGCUAUCAAUGAAGGUCAAUUAAUGUUCGACCUUUCGCUGUACUUACCUCCUUGGAAUGCUCCAGGAGCCAGGUCUUGGCGGAGGUGGCGU
.....(((..((....))..)))....((((((((...(((((((...........)))))))(((((.((((..(((((.(((....))))))))..))))..)))))..)))))))) (-33.00 = -32.76 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	4,424,342 – 4,424,461
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	93.36
Mean single sequence MFE	-29.63
Consensus MFE	-28.70
Energy contribution	-28.54
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-1.63
Structure conservation index	0.97
SVM decision value	2.39
SVM RNA-class probability	0.993354
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4424342 119 - 20766785
ACGCCACCUCCGCCAAGACCUGGCUCCUGGAGCAUUCCAAGGAGGUAAGUACAGCGAAAGGUCGAACAUUAAAUGACCUUCAUUGAUAGCGCUUUAAGCAAAGAUAACCAAACUAAUAC
..((.((((((((((.....))))...(((......))).)))))).....(((.(((.(((((.........)))))))).)))...))((.....)).................... ( -29.60)
>DroSec_CAF1 527 119 - 1
ACGCCACCUCCGCCAAGACCUGGCUCCUGGAGCAUUCCAAGGAGGUAAGUACAGCGAAAGGUCGAAGAUUAAUUGACCUUCAUUGAUAGCGCUUUAAGCAAAGAUAACCAAACUAAUAC
..((.((((((((((.....))))...(((......))).)))))).....(((.(((.((((((.......))))))))).)))...))((.....)).................... ( -31.90)
>DroSim_CAF1 320 119 - 1
ACGCCACCUCCGCCAAGACCUGGCUCCUGGAGCAUUCCAAGGAGGUAAGUACAGCGAAAGGUCGAACAUUAAUUGACCUUCAUUGAUAGCGCUUUAAGCAAAGAUAACCAAACUAAUAC
..((.((((((((((.....))))...(((......))).)))))).....(((.(((.((((((.......))))))))).)))...))((.....)).................... ( -31.90)
>DroEre_CAF1 577 119 - 1
ACGCCACCUCCGCCAAGACCUGGCUCCUGGAGCAUUCCAAGGAGGUAAGUACAACGAAAGGUCGAAAAUUAAUUGUCCUUCAUUGAUAACGCCUUAAGCAAAGAUAACUAAACUAAUAU
..((.((((((((((.....))))...(((......))).)))))).....(((.(((.((.(((.......))).))))).)))............)).................... ( -26.80)
>DroYak_CAF1 537 119 - 1
ACGCCACUUCCGCCAAGACAUGGCUCCUGGAGCAUUCCAAGGAGGUAAGUACGACGAAAGGUCGAACAUUGAUUGACCUUCAUUGAUAACUCUUGAAGCUAAGAUAACUAAACCAAUGU
.((..((((((((((.....))))((((((......)).)))))).)))).))....((((((((.......))))))))(((((.....(((((....))))).........))))). ( -27.94)
>consensus
ACGCCACCUCCGCCAAGACCUGGCUCCUGGAGCAUUCCAAGGAGGUAAGUACAGCGAAAGGUCGAACAUUAAUUGACCUUCAUUGAUAGCGCUUUAAGCAAAGAUAACCAAACUAAUAC
..((.((((((((((.....))))...(((......))).)))))).....(((.(((.((((((.......))))))))).)))............)).................... (-28.70 = -28.54 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:40 2006