Locus 2099

Sequence ID	2R_DroMel_CAF1
Location	7,858,491 – 7,858,581
Length	90
Max. P	0.990423

overview

Window 8

Location	7,858,491 – 7,858,581
Length	90
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	88.36
Mean single sequence MFE	-21.16
Consensus MFE	-15.42
Energy contribution	-15.54
Covariance contribution	0.12
Combinations/Pair	1.19
Mean z-score	-2.28
Structure conservation index	0.73
SVM decision value	0.85
SVM RNA-class probability	0.867142
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7858491 90 + 20766785
AAGGUUGUUUAAACAAAUGACUUUACUGUUCAACUCGUAAACAUUUCACUGUUUACAAAAA-CGAACAAUGGAAACUU-GUAUGGAAUUGGA
(((((..(((....)))..)))))....(((((.(((((((((......))))))).....-((.((((.(....)))-)).)))).))))) ( -19.60)
>DroSec_CAF1 1383 91 + 1
AAAGUUGUUUAAACAAACGACUUUACUGUUCAAGUCGUAAACAUUUCGCUGUUUACAAAAAGCGAACAAUGGAAACUU-UUAAGGCAUCGGA
((((((((((....)))))))))).(((.....(((.((((...((((((..........))))))....(....).)-))).)))..))). ( -18.70)
>DroSim_CAF1 1375 91 + 1
UAAGUUGUUUAAACAAACGACUUUACUGUUCAAGUCGUAAACAUUUCGCUGUUUACAAAAAGCGAACAAUGGAAACUU-UUAAGGCAUCGGA
.(((((((((....)))))))))..(((.....(((.((((...((((((..........))))))....(....).)-))).)))..))). ( -17.40)
>DroEre_CAF1 2567 91 + 1
AAGGCUGUUUAAACAAACGACUUUACUGUUCGAGUCGUAAACAUUUCGCUGUUUACAGCAA-CGAACAAUGGAAACUUUUUAAGGCAACGAA
...(((((((......(((((((........))))))).........((((....))))..-.))))...(....).......)))...... ( -19.60)
>DroYak_CAF1 1394 90 + 1
AAGGUUGUUUAAAUAAACGACUCUACUGUUCGAGCCGUAAACAAUUCGCUGUUUACGGCAA-CGAACAAUGGAAACUU-UUAAGGUACCGAA
...(((((((....)))))))((((.((((((.((((((((((......))))))))))..-)))))).)))).....-............. ( -30.50)
>consensus
AAGGUUGUUUAAACAAACGACUUUACUGUUCAAGUCGUAAACAUUUCGCUGUUUACAAAAA_CGAACAAUGGAAACUU_UUAAGGCAUCGGA
((((((((((....)))))))))).........((((((((((......)))))))..............(....).......)))...... (-15.42 = -15.54 +   0.12)

alignment

secondary structure

dotplot

Window 9

Location	7,858,491 – 7,858,581
Length	90
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	88.36
Mean single sequence MFE	-21.34
Consensus MFE	-18.58
Energy contribution	-18.42
Covariance contribution	-0.16
Combinations/Pair	1.21
Mean z-score	-2.16
Structure conservation index	0.87
SVM decision value	2.21
SVM RNA-class probability	0.990423
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7858491 90 - 20766785
UCCAAUUCCAUAC-AAGUUUCCAUUGUUCG-UUUUUGUAAACAGUGAAAUGUUUACGAGUUGAACAGUAAAGUCAUUUGUUUAAACAACCUU
...........((-((((..(.((((((((-..((((((((((......)))))))))).))))))))...)..))))))............ ( -19.40)
>DroSec_CAF1 1383 91 - 1
UCCGAUGCCUUAA-AAGUUUCCAUUGUUCGCUUUUUGUAAACAGCGAAAUGUUUACGACUUGAACAGUAAAGUCGUUUGUUUAAACAACUUU
.............-........((((((((....(((((((((......)))))))))..))))))))(((((.((((....)))).))))) ( -18.40)
>DroSim_CAF1 1375 91 - 1
UCCGAUGCCUUAA-AAGUUUCCAUUGUUCGCUUUUUGUAAACAGCGAAAUGUUUACGACUUGAACAGUAAAGUCGUUUGUUUAAACAACUUA
.............-........((((((((....(((((((((......)))))))))..)))))))).((((.((((....)))).)))). ( -18.30)
>DroEre_CAF1 2567 91 - 1
UUCGUUGCCUUAAAAAGUUUCCAUUGUUCG-UUGCUGUAAACAGCGAAAUGUUUACGACUCGAACAGUAAAGUCGUUUGUUUAAACAGCCUU
...((((..(((((..(.....((((((((-..(.((((((((......)))))))).).)))))))).....).....))))).))))... ( -19.50)
>DroYak_CAF1 1394 90 - 1
UUCGGUACCUUAA-AAGUUUCCAUUGUUCG-UUGCCGUAAACAGCGAAUUGUUUACGGCUCGAACAGUAGAGUCGUUUAUUUAAACAACCUU
...(((.......-..(.(((.((((((((-..(((((((((((....))))))))))).)))))))).))).)((((....)))).))).. ( -31.10)
>consensus
UCCGAUGCCUUAA_AAGUUUCCAUUGUUCG_UUUUUGUAAACAGCGAAAUGUUUACGACUUGAACAGUAAAGUCGUUUGUUUAAACAACCUU
......................((((((((...((((((((((......)))))))))).))))))))...((.((((....)))).))... (-18.58 = -18.42 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:15 2006