Locus 2113

Sequence ID	2L_DroMel_CAF1
Location	5,693,783 – 5,693,922
Length	139
Max. P	0.998795

overview

Window 0

Location	5,693,783 – 5,693,893
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	96.91
Mean single sequence MFE	-27.86
Consensus MFE	-27.10
Energy contribution	-27.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.97
SVM decision value	3.23
SVM RNA-class probability	0.998795
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5693783 110 + 22407834
CAUGUUUAUUAAUUUGCUACUAUUUCUGCGCAUUUUUCACAGCUUCUGUUUUCAGCACCUUGGGGGAUUCCCCAUGGCGCACAUCAAAGCAAAUGCCAAAGCGUUGCCAA
.((((((....(((((((........(((((..........(((.........)))..(.(((((....))))).))))))......)))))))....))))))...... ( -26.94)
>DroSec_CAF1 139012 110 + 1
CAUGUUUAUAAAUUUGCUACUAUUUCUGCGCAAUUUUCAUAGCUUCUGUUUUCAGCACCUUGGGGGAUUCCCCAUGGCGCACAUCAAAGCAAAUGCCAAAGCGUUGCCAA
.((((((....(((((((........(((((..........(((.........)))..(.(((((....))))).))))))......)))))))....))))))...... ( -26.94)
>DroSim_CAF1 138508 110 + 1
CAUGUUUAUAAAUUUGCUACUAUUUCUGCGCAUUUUUCAUAGCUUCUGUUUUCAGCACCUUGGGGGAUUCCCCACGGCGCACAUCAAAGCAAAUGCCAAAGCGUUGCCAA
.((((((....(((((((........(((((..........(((.........)))..(.(((((....))))).))))))......)))))))....))))))...... ( -26.94)
>DroEre_CAF1 141652 110 + 1
CAUGUUUAUUAAUUUGCUACUAUUUCUGCGCAUUUUUCACAGCUUCUGUUUUCAGCACCUUGGGGGAUUCCCCAUGGCGCACAUCAAAGCAAAUGCCGAAGCGUGGCCAA
(((((((....(((((((........(((((..........(((.........)))..(.(((((....))))).))))))......)))))))....)))))))..... ( -31.54)
>DroYak_CAF1 140633 110 + 1
CAUGUUUAUUAAUUUGCUACUAUUUCUGCGCAUUUUUCACAGCUUCUGUUUUCAGCACCUUGGGGGAUUCCCCACCGCGCACAUCAAAGCAAAUGCCAAAGCGUUGCCAA
.((((((....(((((((........(((((..........(((.........)))....(((((....)))))..)))))......)))))))....))))))...... ( -26.94)
>consensus
CAUGUUUAUUAAUUUGCUACUAUUUCUGCGCAUUUUUCACAGCUUCUGUUUUCAGCACCUUGGGGGAUUCCCCAUGGCGCACAUCAAAGCAAAUGCCAAAGCGUUGCCAA
.((((((....(((((((........(((((..........(((.........)))....(((((....)))))..)))))......)))))))....))))))...... (-27.10 = -27.10 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	5,693,783 – 5,693,893
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	96.91
Mean single sequence MFE	-32.29
Consensus MFE	-30.20
Energy contribution	-30.80
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.13
Structure conservation index	0.94
SVM decision value	3.13
SVM RNA-class probability	0.998530
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5693783 110 - 22407834
UUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCCAUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUGUGAAAAAUGCGCAGAAAUAGUAGCAAAUUAAUAAACAUG
...((.((..(((((((((((((((.....(((((.(((((....))))).)))))........)))))......)))))).))))....)).))............... ( -32.52)
>DroSec_CAF1 139012 110 - 1
UUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCCAUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUAUGAAAAUUGCGCAGAAAUAGUAGCAAAUUUAUAAACAUG
..(....)(((((.(((((......)))))(((((.(((((....))))).)))))........)))))((((((..(((((((....).)).)))).))))))...... ( -32.10)
>DroSim_CAF1 138508 110 - 1
UUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCCGUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUAUGAAAAAUGCGCAGAAAUAGUAGCAAAUUUAUAAACAUG
...((.((..(((((((((((((((.....(((((.(((((....))))).)))))........)))))......)))))).))))....)).))............... ( -32.52)
>DroEre_CAF1 141652 110 - 1
UUGGCCACGCUUCGGCAUUUGCUUUGAUGUGCGCCAUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUGUGAAAAAUGCGCAGAAAUAGUAGCAAAUUAAUAAACAUG
...((.(((((((.(((((......)))))(((((.(((((....))))).)))))........)))))((((.......))))......)).))............... ( -34.50)
>DroYak_CAF1 140633 110 - 1
UUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCGGUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUGUGAAAAAUGCGCAGAAAUAGUAGCAAAUUAAUAAACAUG
...((.((..(((((((((((((((.....((((..(((((....)))))..))))........)))))......)))))).))))....)).))............... ( -29.82)
>consensus
UUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCCAUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUGUGAAAAAUGCGCAGAAAUAGUAGCAAAUUAAUAAACAUG
...((.((..(((((((((((((((.....(((((.(((((....))))).)))))........)))))......)))))).))))....)).))............... (-30.20 = -30.80 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	5,693,815 – 5,693,922
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	95.89
Mean single sequence MFE	-34.91
Consensus MFE	-32.96
Energy contribution	-32.76
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-1.11
Structure conservation index	0.94
SVM decision value	0.17
SVM RNA-class probability	0.615536
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5693815 107 - 22407834
GGACCUGCGGAAAUGGGAACCCUGCGAUGUUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCCAUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUGUGAAAAA
.....(((.(((..((....)).(((.((....)).)))))).)))...(((((.....(((((.(((((....))))).)))))........)))))......... ( -34.22)
>DroSec_CAF1 139044 107 - 1
GGACCUGCAGAAAUGGGAACCCCGCGAUGUUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCCAUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUAUGAAAAU
.(.((.(((....((((...))))...))).)))...(((((.(((((......)))))(((((.(((((....))))).)))))........)))))......... ( -34.10)
>DroSim_CAF1 138540 107 - 1
GGACCUGCAGAAAUGGGAACCCCGCGAUGUUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCCGUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUAUGAAAAA
.(.((.(((....((((...))))...))).)))...(((((.(((((......)))))(((((.(((((....))))).)))))........)))))......... ( -34.10)
>DroEre_CAF1 141684 107 - 1
GGACCUGCAGAAAUGGGAACCCUGCGUUGUUGGCCACGCUUCGGCAUUUGCUUUGAUGUGCGCCAUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUGUGAAAAA
((.((.((((....((....))....)))).))))..(((((.(((((......)))))(((((.(((((....))))).)))))........)))))......... ( -40.60)
>DroYak_CAF1 140665 107 - 1
GGACCUGCGGAAAUGGGAACCCUGCGAUGUUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCGGUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUGUGAAAAA
.....(((.(((..((....)).(((.((....)).)))))).)))...(((((.....((((..(((((....)))))..))))........)))))......... ( -31.52)
>consensus
GGACCUGCAGAAAUGGGAACCCUGCGAUGUUGGCAACGCUUUGGCAUUUGCUUUGAUGUGCGCCAUGGGGAAUCCCCCAAGGUGCUGAAAACAGAAGCUGUGAAAAA
.(.((.(((.....((....)).....))).)))...(((((.(((((......)))))(((((.(((((....))))).)))))........)))))......... (-32.96 = -32.76 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:55 2006