Locus 5437

Sequence ID	2L_DroMel_CAF1
Location	15,483,859 – 15,483,949
Length	90
Max. P	0.956969

overview

Window 2

Location	15,483,859 – 15,483,949
Length	90
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	76.65
Mean single sequence MFE	-21.83
Consensus MFE	-13.24
Energy contribution	-14.05
Covariance contribution	0.81
Combinations/Pair	1.25
Mean z-score	-1.34
Structure conservation index	0.61
SVM decision value	-0.01
SVM RNA-class probability	0.527205
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15483859 90 + 22407834
U--------U-UCAACCGCAUCGAUAAUCGCUU-UCAAUUUUCUACUGCCGCUUAGUAUGCAUGCGG-------UCC--------AUUUGCAUGUUUUCGGCUGAUGAAAUUGAU
.--------.-((((...((((((.........-))...........((((........((((((((-------...--------..))))))))...)))).))))...)))). ( -19.70)
>DroVir_CAF1 260193 99 + 1
--------------AUCGCAUCGAUAAUUGUUUCUCAAUUUUCGGCUACCGCUUCAUAUGCAUGCAAUGUGCGAUCCCAAAGCUAAUUUGCGU--UUUUGGCUGAUGAAACCGAU
--------------((((((((((.(((((.....))))).))(((((..((.......))((((((...((.........))....))))))--...)))))))))....)))) ( -20.80)
>DroEre_CAF1 232377 90 + 1
U--------U-UCAACCGCAUCGAUAAUCGCUU-UCAAUUUUCUACUGCCGCUUAGUAUGCAUGCGA-------UCC--------AUUUGCAUGUUUUCGGCUGAUGAAAUUGAU
.--------.-((((...((((((.........-))...........((((........((((((((-------...--------..))))))))...)))).))))...)))). ( -20.50)
>DroYak_CAF1 231438 90 + 1
U--------U-UCAACCGCAUCGAUAAUCGCUU-UCAAUUUUCUACUGCCGCUUAGUAUGCAUGCGA-------UCC--------AUUUGCAUGUUUUCGGCUGAUGAAAUUGAU
.--------.-((((...((((((.........-))...........((((........((((((((-------...--------..))))))))...)))).))))...)))). ( -20.50)
>DroMoj_CAF1 272700 114 + 1
CUGAUGUGAG-UCGAUCGCAUCGAUAAUCGUUUCUCAAUUUUCGACUGCCGCUUCAUAUGCAUGCAAUGUGCCAUCCGAAAGCUAAUUUGCGUAUUUUUGGCUGAUGAAAACAAU
.((((((((.-....))))))))...............((((((.(.((((....(((((((.((.....))....(....)......)))))))...)))).).)))))).... ( -25.60)
>DroAna_CAF1 238704 92 + 1
U--------UUUGAACCGCAUCGAUGAUCGCUU-UCAAUUUCCAACUGCCGCUUAGUAUGCAUGCGG------AACC--------AUUUGCAUAUUUUCGGCUGAUGAAAUUGAU
.--------........(((((...))).))..-((((((((.....((((...((((((((...(.------...)--------...))))))))..))))....)))))))). ( -23.90)
>consensus
U________U_UCAACCGCAUCGAUAAUCGCUU_UCAAUUUUCUACUGCCGCUUAGUAUGCAUGCGA_______UCC________AUUUGCAUGUUUUCGGCUGAUGAAAUUGAU
..................................((((((((.....((((...((((((((..........................))))))))..))))....)))))))). (-13.24 = -14.05 +   0.81)

alignment

secondary structure

dotplot

Window 3

Location	15,483,859 – 15,483,949
Length	90
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	76.65
Mean single sequence MFE	-23.49
Consensus MFE	-16.29
Energy contribution	-16.90
Covariance contribution	0.61
Combinations/Pair	1.28
Mean z-score	-1.89
Structure conservation index	0.69
SVM decision value	1.47
SVM RNA-class probability	0.956969
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15483859 90 - 22407834
AUCAAUUUCAUCAGCCGAAAACAUGCAAAU--------GGA-------CCGCAUGCAUACUAAGCGGCAGUAGAAAAUUGA-AAGCGAUUAUCGAUGCGGUUGA-A--------A
.(((((..((((.((((.....(((((..(--------(..-------...)))))))......))))....((.(((((.-...))))).))))))..)))))-.--------. ( -24.40)
>DroVir_CAF1 260193 99 - 1
AUCGGUUUCAUCAGCCAAAA--ACGCAAAUUAGCUUUGGGAUCGCACAUUGCAUGCAUAUGAAGCGGUAGCCGAAAAUUGAGAAACAAUUAUCGAUGCGAU--------------
...((((.....))))....--.((((.......(((((.(((((.(((((....)).)))..)))))..)))))(((((.....))))).....))))..-------------- ( -20.70)
>DroEre_CAF1 232377 90 - 1
AUCAAUUUCAUCAGCCGAAAACAUGCAAAU--------GGA-------UCGCAUGCAUACUAAGCGGCAGUAGAAAAUUGA-AAGCGAUUAUCGAUGCGGUUGA-A--------A
.(((((..((((.((((.....(((((..(--------(..-------...)))))))......))))....((.(((((.-...))))).))))))..)))))-.--------. ( -24.40)
>DroYak_CAF1 231438 90 - 1
AUCAAUUUCAUCAGCCGAAAACAUGCAAAU--------GGA-------UCGCAUGCAUACUAAGCGGCAGUAGAAAAUUGA-AAGCGAUUAUCGAUGCGGUUGA-A--------A
.(((((..((((.((((.....(((((..(--------(..-------...)))))))......))))....((.(((((.-...))))).))))))..)))))-.--------. ( -24.40)
>DroMoj_CAF1 272700 114 - 1
AUUGUUUUCAUCAGCCAAAAAUACGCAAAUUAGCUUUCGGAUGGCACAUUGCAUGCAUAUGAAGCGGCAGUCGAAAAUUGAGAAACGAUUAUCGAUGCGAUCGA-CUCACAUCAG
((((((((..(((((((.......((......)).......))))..(((((.(((.......)))))))).......)))))))))))....((((.((....-.)).)))).. ( -23.14)
>DroAna_CAF1 238704 92 - 1
AUCAAUUUCAUCAGCCGAAAAUAUGCAAAU--------GGUU------CCGCAUGCAUACUAAGCGGCAGUUGGAAAUUGA-AAGCGAUCAUCGAUGCGGUUCAAA--------A
.((((((((..(.((((....((((((..(--------(...------.))..)))))).....)))).)...))))))))-..((.(((...)))))........--------. ( -23.90)
>consensus
AUCAAUUUCAUCAGCCGAAAACAUGCAAAU________GGA_______UCGCAUGCAUACUAAGCGGCAGUAGAAAAUUGA_AAGCGAUUAUCGAUGCGGUUGA_A________A
.(((((..((((.((((.....(((((..........................)))))......))))....((.(((((.....))))).))))))..)))))........... (-16.29 = -16.90 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:10 2006