Locus 4108

Sequence ID	2R_DroMel_CAF1
Location	13,506,510 – 13,506,615
Length	105
Max. P	0.998195

overview

Window 7

Location	13,506,510 – 13,506,615
Length	105
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	80.17
Mean single sequence MFE	-25.51
Consensus MFE	-15.08
Energy contribution	-16.08
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-3.22
Structure conservation index	0.59
SVM decision value	2.78
SVM RNA-class probability	0.996986
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13506510 105 + 20766785
GCAAUUCAUACGUUUGUAUGAAUUU-UUUCAAACGAAAAAUUUCUCCAAGUGCAUUAGCUGGCAGGACUUCACGUCCUGCACGCACAAAACAAACAAAUAACAGCC
...........((((((..(((.((-((((....)))))).))).....((((........(((((((.....)))))))..))))...))))))........... ( -27.90)
>DroSec_CAF1 54978 99 + 1
GCAAUUCAUAUGUUUGUGCUCUUU--UUUCGAACCGAAAAUUUCUCGAAGUGCAUUAGCUGGCAGGA-----CGUCCUGCACGCACAAAACAAACAAAUAACAGCU
..........(((((((((.((((--(((((...))))).......)))).))....((..(((((.-----...)))))..)).....))))))).......... ( -23.31)
>DroSim_CAF1 55659 105 + 1
GCAAUUCAUAUGUUUGUUCUCUUUU-UUUCAAACCGAAAAUUUCUCCAAGUGCAUUAGCUGGCAGGACUUCACGUCCUGCACGGACAAAACAAACAAAUAACAGCU
..........((((((((......(-((((.....)))))....(((....((....))..(((((((.....)))))))..)))...)))))))).......... ( -25.20)
>DroEre_CAF1 56055 90 + 1
-------------UUGCUUCUACUUCUUUCAA-U--GAAAUUUCUCGAAGUGCAUUAGCUGGCAGGACUUCACGUCCUGCACGCACAAAACAAACAAAUAGGAGCU
-------------..(((((((((((......-.--..........)))))......((..(((((((.....)))))))..))...............)))))). ( -25.03)
>DroYak_CAF1 57600 103 + 1
CCAAUUCAUAUAUUUGUUCGUUUUUUCUUCAA-U--GAAAUUUCUCGAAGUGCAUUAGCUAGCAGGACUUCAUGUCCUGCACGCACAAAACAAACAAAUAAGAGCU
..........((((((((.((((((((.....-.--)))..........((((.(.....)(((((((.....)))))))..))))))))).))))))))...... ( -26.10)
>consensus
GCAAUUCAUAUGUUUGUUCGCUUUU_UUUCAAAC__AAAAUUUCUCGAAGUGCAUUAGCUGGCAGGACUUCACGUCCUGCACGCACAAAACAAACAAAUAACAGCU
...........((((((..................................((....))..(((((((.....))))))).........))))))........... (-15.08 = -16.08 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	13,506,510 – 13,506,615
Length	105
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	80.17
Mean single sequence MFE	-31.68
Consensus MFE	-21.22
Energy contribution	-22.70
Covariance contribution	1.48
Combinations/Pair	1.23
Mean z-score	-3.25
Structure conservation index	0.67
SVM decision value	3.03
SVM RNA-class probability	0.998195
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13506510 105 - 20766785
GGCUGUUAUUUGUUUGUUUUGUGCGUGCAGGACGUGAAGUCCUGCCAGCUAAUGCACUUGGAGAAAUUUUUCGUUUGAAA-AAAUUCAUACAAACGUAUGAAUUGC
.((..((((.(((((((...(((((((((((((.....)))))))......)))))).....(((.((((((....))))-)).)))..))))))).))))...)) ( -32.70)
>DroSec_CAF1 54978 99 - 1
AGCUGUUAUUUGUUUGUUUUGUGCGUGCAGGACG-----UCCUGCCAGCUAAUGCACUUCGAGAAAUUUUCGGUUCGAAA--AAAGAGCACAAACAUAUGAAUUGC
.((..((((.(((((((...(((((((((((...-----.)))))......))))))..(((((...)))))((((....--...))))))))))).))))...)) ( -29.20)
>DroSim_CAF1 55659 105 - 1
AGCUGUUAUUUGUUUGUUUUGUCCGUGCAGGACGUGAAGUCCUGCCAGCUAAUGCACUUGGAGAAAUUUUCGGUUUGAAA-AAAAGAGAACAAACAUAUGAAUUGC
.((..((((.((((((((((.((((.(((((((.....)))))))).((....))....)))....(((((.....))))-)....)))))))))).))))...)) ( -33.30)
>DroEre_CAF1 56055 90 - 1
AGCUCCUAUUUGUUUGUUUUGUGCGUGCAGGACGUGAAGUCCUGCCAGCUAAUGCACUUCGAGAAAUUUC--A-UUGAAAGAAGUAGAAGCAA-------------
.(((.((((((.(((.....(((((((((((((.....)))))))......))))))...(((....)))--.-...))).)))))).)))..------------- ( -29.40)
>DroYak_CAF1 57600 103 - 1
AGCUCUUAUUUGUUUGUUUUGUGCGUGCAGGACAUGAAGUCCUGCUAGCUAAUGCACUUCGAGAAAUUUC--A-UUGAAGAAAAAACGAACAAAUAUAUGAAUUGG
...((.((((((((((((((.((((((((((((.....)))))))......)))))((((((((....))--.-))))))..))))))))))))))...))..... ( -33.80)
>consensus
AGCUGUUAUUUGUUUGUUUUGUGCGUGCAGGACGUGAAGUCCUGCCAGCUAAUGCACUUCGAGAAAUUUU__GUUUGAAA_AAAAAAGAACAAACAUAUGAAUUGC
.....((((.(((((((((((((((((((((((.....)))))))......)))))).........((((......))))......)))))))))).))))..... (-21.22 = -22.70 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:01 2006