Locus 3808

Sequence ID	3R_DroMel_CAF1
Location	10,334,372 – 10,334,494
Length	122
Max. P	0.967731

overview

Window 3

Location	10,334,372 – 10,334,462
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	91.14
Mean single sequence MFE	-23.63
Consensus MFE	-20.46
Energy contribution	-19.43
Covariance contribution	-1.03
Combinations/Pair	1.20
Mean z-score	-2.36
Structure conservation index	0.87
SVM decision value	1.61
SVM RNA-class probability	0.967731
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10334372 90 + 27905053
CCGAGUGAAUAUUGGCAAAUUUAUGAACUUUAAGCUGCAUUUAUGCGUGCGGCUUAUAAGCAAUAAAGGUAACUUAGUGCCAACAAUGUC
........((((((.....(((((...(((((((((((((......)))))))))).)))..)))))((((......))))..)))))). ( -23.00)
>DroVir_CAF1 214436 85 + 1
-----CGAGUAUUGGCAAAUUUAUGAACAUAAAGCUGCAUUUAUGCGUGCGGCUUAUAUGCAAUAAAGGUAACUUAGUGCCAACAGUGUC
-----......((((((..(((((...(((((((((((((......))))))))).))))..)))))..........))))))....... ( -22.60)
>DroPse_CAF1 208216 88 + 1
--GGCCGAAUAUUGGCAAAUUUAUGAACUUUAAGCCGCAUUUAUGCGUGCGGCUUAUAAGCAAUAAAGGUAACUUAGUGCCAACAAUGUC
--.(((((...)))))...(((((...(((((((((((((......)))))))))).)))..)))))((((......))))......... ( -26.50)
>DroGri_CAF1 209349 85 + 1
-----CGAGUAUUGGUAAAUUUAUGAACAUAAAGCUGCACUUAUGCGUGCGGCUUAUAUGCAAUAAAGGUAACUUAGUGCCAACAGUGUC
-----....(((((.....(((((...(((((((((((((......))))))))).))))..)))))((((......))))..))))).. ( -24.30)
>DroMoj_CAF1 221177 85 + 1
-----CGAGUAUUGGCAAAUUUAUGAACAUAAAGCAGCGUUUAUGCGUGCGGCUUAUAUGCAAUAAAGGUAACUUAGUGCCAACAGUGUC
-----......((((((..(((((...((((((((.((((....))))...)))).))))..)))))..........))))))....... ( -18.90)
>DroPer_CAF1 212111 88 + 1
--GGCCGAAUAUUGGCAAAUUUAUGAACUUUAAGCCGCAUUUAUGCGUGCGGCUUAUAAGCAAUAAAGGUAACUUAGUGCCAACAAUGUC
--.(((((...)))))...(((((...(((((((((((((......)))))))))).)))..)))))((((......))))......... ( -26.50)
>consensus
_____CGAAUAUUGGCAAAUUUAUGAACAUAAAGCUGCAUUUAUGCGUGCGGCUUAUAAGCAAUAAAGGUAACUUAGUGCCAACAAUGUC
.........(((((.....(((((...(((..((((((((......))))))))...)))..)))))((((......))))..))))).. (-20.46 = -19.43 +  -1.03)

alignment

secondary structure

dotplot

Window 4

Location	10,334,386 – 10,334,494
Length	108
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	89.43
Mean single sequence MFE	-29.22
Consensus MFE	-24.52
Energy contribution	-24.00
Covariance contribution	-0.52
Combinations/Pair	1.19
Mean z-score	-2.86
Structure conservation index	0.84
SVM decision value	1.56
SVM RNA-class probability	0.963922
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10334386 108 + 27905053
GCAAAUUUAUGAACUUUAAGCUGCAUUUAUGCGUGCGGCUUAUAAGCAAUAAAGGUAACUUAGUGCCAACAAUGUCAUAAAGGCCGCUGUCACAUAAACAA-CAACGGC-
.....(((((((.(((((((((((((......)))))))))).))).......((((......)))).......))))))).((((.(((..........)-)).))))- ( -28.60)
>DroPse_CAF1 208228 108 + 1
GCAAAUUUAUGAACUUUAAGCCGCAUUUAUGCGUGCGGCUUAUAAGCAAUAAAGGUAACUUAGUGCCAACAAUGUCAUAAAGGCCGCUGUCGCAUAAACCA-CUCCAAC-
((...(((((((.(((((((((((((......)))))))))).))).......((((......)))).......))))))).)).((....))........-.......- ( -28.40)
>DroGri_CAF1 209358 109 + 1
GUAAAUUUAUGAACAUAAAGCUGCACUUAUGCGUGCGGCUUAUAUGCAAUAAAGGUAACUUAGUGCCAACAGUGUCAUAAAGGCCGAUGCCACAUAAACAG-CAAUAACA
((...(((((((.(((((((((((((......))))))))).)))).......((((......)))).......)))))))(((....))).........)-)....... ( -28.80)
>DroYak_CAF1 201815 109 + 1
GCAAAUUUAUGAACUUUAAGCUGCAUUUAUGCGUGCGGCUUAUAAGCUAUAAAGGUAACUUAGUGCCAACAAUGUCAUAAAGGCCGCUGUCACAUAAACAA-CCACGGCA
((...(((((((.(((((((((((((......)))))))))).))).......((((......)))).......))))))).)).(((((...........-..))))). ( -29.42)
>DroMoj_CAF1 221186 107 + 1
GCAAAUUUAUGAACAUAAAGCAGCGUUUAUGCGUGCGGCUUAUAUGCAAUAAAGGUAACUUAGUGCCAACAGUGUCAUAAAGGCCGAUGCGGCAUAAA---CCAACAGCA
((...(((((....)))))...))(((((((((((((((((.((((((.....((((......)))).....)).)))).)))))).))).)))))))---)........ ( -31.70)
>DroPer_CAF1 212123 108 + 1
GCAAAUUUAUGAACUUUAAGCCGCAUUUAUGCGUGCGGCUUAUAAGCAAUAAAGGUAACUUAGUGCCAACAAUGUCAUAAAGGCCGCUGUCGCAUAAACCA-CUCCAAC-
((...(((((((.(((((((((((((......)))))))))).))).......((((......)))).......))))))).)).((....))........-.......- ( -28.40)
>consensus
GCAAAUUUAUGAACUUUAAGCUGCAUUUAUGCGUGCGGCUUAUAAGCAAUAAAGGUAACUUAGUGCCAACAAUGUCAUAAAGGCCGCUGUCACAUAAACAA_CAACAAC_
((...(((((((.(((((((((((((......)))))))))).))).......((((......)))).......))))))).)).......................... (-24.52 = -24.00 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:35 2006