Locus 7312

Sequence ID	2L_DroMel_CAF1
Location	20,463,816 – 20,464,014
Length	198
Max. P	0.998777

overview

Window 0

Location	20,463,816 – 20,463,934
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.26
Mean single sequence MFE	-40.60
Consensus MFE	-29.84
Energy contribution	-31.04
Covariance contribution	1.20
Combinations/Pair	1.06
Mean z-score	-2.96
Structure conservation index	0.73
SVM decision value	1.18
SVM RNA-class probability	0.927463
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20463816 118 + 22407834
UUUAGUUGC--CGUUGCGAGCGGACUUCGCUGGGCGCAUUGUUAAUGGUCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCGAGCCAAGCGAGGGGAAAUGGCAAAACAAACUUUCAA
.....((((--(((((....)...(((((((.(((.(((.....))).(((.(((((((((((........))))))))))))))))).)))))))...))))))))............. ( -41.30)
>DroSec_CAF1 16749 117 + 1
UUUAGUUGC--CGCUGCGAGUGGACUCUGCUGGGCGCAUUGUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCC-AGCCAAGCGGGGGGAAAUGGCAAAACAAACUUUCAA
.....((.(--(.(((((((....))).(((((((.(((.....))))))..(((((((((((........))))))))))))-)))...)))).)).)).................... ( -37.00)
>DroSim_CAF1 18671 120 + 1
UUUAGUUGCCCCGUUGCGAGUGGACUCUGCUGGGCGCAUUGUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCGAGCCAAGCGGGGGGAAAUGGCAAAACAAACUUUCAA
.....((.((((((((((..(((......)))..)))........((((((.(((((((((((........))))))))))))).))))))))))).))..................... ( -41.20)
>DroEre_CAF1 19214 116 + 1
UUUAGUGUC--CG-UGCGAGUGGACUCUGCUGGGCGCAUUGUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCUGGCCGAGCUGGAGGAAAUGGCAA-ACAAACUCUCAA
....(((((--((-.(((((....))).))))))))).(((((..((((((.(((((((((((........))))))))))).)))))).((((.......)))).)-))))........ ( -43.70)
>DroYak_CAF1 16359 118 + 1
UUUAGUUGC--CGUUGAGAGUGGACUCUGCUUGGCGCAUUGUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCAGGCCAAGCUGGAGGAAAUGGCAAAACAAACUCUCAA
.........--..((((((((...(((((((((((.(((.....)))...(.(((((((((((........))))))))))))..))))))).))))....((......)).)))))))) ( -39.80)
>consensus
UUUAGUUGC__CGUUGCGAGUGGACUCUGCUGGGCGCAUUGUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCGAGCCAAGCGGGGGGAAAUGGCAAAACAAACUUUCAA
...((((......((((.(.....(((((((.(((.(((.....)))...(.(((((((((((........))))))))))))..))).))))))).....).))))....))))..... (-29.84 = -31.04 +   1.20)

alignment

secondary structure

dotplot

Window 1

Location	20,463,854 – 20,463,974
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.50
Mean single sequence MFE	-38.66
Consensus MFE	-32.02
Energy contribution	-32.94
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-3.44
Structure conservation index	0.83
SVM decision value	3.22
SVM RNA-class probability	0.998777
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20463854 120 + 22407834
GUUAAUGGUCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCGAGCCAAGCGAGGGGAAAUGGCAAAACAAACUUUCAAGUCGUUUUGAUUUCUCUUUGCUGCUGCGAGCAACUUUCAG
.....((((((.(((((((((((........)))))))))))))).)))(((((((((((((..((((((..(((....))).)))))))))))))))))))((.....))......... ( -40.90)
>DroSec_CAF1 16787 119 + 1
GUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCC-AGCCAAGCGGGGGGAAAUGGCAAAACAAACUUUCAAGUCGUUUUGAUUUCUCUUUGCUGCUGCGAGCAACUUUCAG
.....((((.(.(((((((((((........))))))))))))-.))))(((((((((((((..((((((..(((....))).)))))))))))))))))))((.....))......... ( -39.80)
>DroSim_CAF1 18711 120 + 1
GUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCGAGCCAAGCGGGGGGAAAUGGCAAAACAAACUUUCAAGUCAUUUUGAUUUCUCUUUGCUGCUGCGAGCAACUUUCAG
.....((((((.(((((((((((........))))))))))))).))))(((((((((((((..(((((...(((....)))..))))))))))))))))))((.....))......... ( -39.30)
>DroEre_CAF1 19251 118 + 1
GUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCUGGCCGAGCUGGAGGAAAUGGCAA-ACAAACUCUCAAGUCUUUUUGAUUUCUCUUUGCUGCUGCGAA-AACUUUCAG
.....((((((.(((((((((((........))))))))))).))))))..(((((((.........-........(((((....)))))......(((((....)))))-..))))))) ( -35.80)
>DroYak_CAF1 16397 120 + 1
GUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCAGGCCAAGCUGGAGGAAAUGGCAAAACAAACUCUCAAGUCGUUUUGAUUUCUCUUUGCUGCUGCGAACAACUUUCAG
(((..(((((..(((((((((((........)))))))))))..)))))(((.(((((((....((((((..(((....))).)))))).)))))))..)))......)))......... ( -37.50)
>consensus
GUUAAUGGCCGUGCCAUUUUAUUUCAAAAUUAAUAAAGUGGCCGAGCCAAGCGGGGGGAAAUGGCAAAACAAACUUUCAAGUCGUUUUGAUUUCUCUUUGCUGCUGCGAGCAACUUUCAG
(((..((((...(((((((((((........)))))))))))...))))(((((((((((((..((((((..(((....))).))))))))))))))))))).........)))...... (-32.02 = -32.94 +   0.92)

alignment

secondary structure

dotplot

Window 2

Location	20,463,854 – 20,463,974
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.50
Mean single sequence MFE	-31.08
Consensus MFE	-26.26
Energy contribution	-26.46
Covariance contribution	0.20
Combinations/Pair	1.09
Mean z-score	-2.08
Structure conservation index	0.84
SVM decision value	1.98
SVM RNA-class probability	0.984747
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20463854 120 - 22407834
CUGAAAGUUGCUCGCAGCAGCAAAGAGAAAUCAAAACGACUUGAAAGUUUGUUUUGCCAUUUCCCCUCGCUUGGCUCGGCCACUUUAUUAAUUUUGAAAUAAAAUGGCACGACCAUUAAC
......(((((.....))))).....(((((((((((((((....)).))))))))..)))))........(((.(((((((.((((((........)))))).)))).))))))..... ( -30.00)
>DroSec_CAF1 16787 119 - 1
CUGAAAGUUGCUCGCAGCAGCAAAGAGAAAUCAAAACGACUUGAAAGUUUGUUUUGCCAUUUCCCCCCGCUUGGCU-GGCCACUUUAUUAAUUUUGAAAUAAAAUGGCACGGCCAUUAAC
......(((((.....))))).....(((((((((((((((....)).))))))))..)))))........(((((-(((((.((((((........)))))).)))).))))))..... ( -33.70)
>DroSim_CAF1 18711 120 - 1
CUGAAAGUUGCUCGCAGCAGCAAAGAGAAAUCAAAAUGACUUGAAAGUUUGUUUUGCCAUUUCCCCCCGCUUGGCUCGGCCACUUUAUUAAUUUUGAAAUAAAAUGGCACGGCCAUUAAC
......(((((.....))))).....((((((((((..(((....)).)..)))))..)))))........((((.((((((.((((((........)))))).)))).))))))..... ( -29.70)
>DroEre_CAF1 19251 118 - 1
CUGAAAGUU-UUCGCAGCAGCAAAGAGAAAUCAAAAAGACUUGAGAGUUUGU-UUGCCAUUUCCUCCAGCUCGGCCAGGCCACUUUAUUAAUUUUGAAAUAAAAUGGCACGGCCAUUAAC
(((...(((-.....))).(((((.(((..((((......))))...))).)-)))).........)))...((((..((((.((((((........)))))).))))..))))...... ( -29.00)
>DroYak_CAF1 16397 120 - 1
CUGAAAGUUGUUCGCAGCAGCAAAGAGAAAUCAAAACGACUUGAGAGUUUGUUUUGCCAUUUCCUCCAGCUUGGCCUGGCCACUUUAUUAAUUUUGAAAUAAAAUGGCACGGCCAUUAAC
(((...(((((.....)))))...(((((((((((((((((....)).))))))))..)))).))))))..(((((..((((.((((((........)))))).))))..)))))..... ( -33.00)
>consensus
CUGAAAGUUGCUCGCAGCAGCAAAGAGAAAUCAAAACGACUUGAAAGUUUGUUUUGCCAUUUCCCCCCGCUUGGCUCGGCCACUUUAUUAAUUUUGAAAUAAAAUGGCACGGCCAUUAAC
......(((((.....))))).....(((((((((((((((....)).))))))))..))))).........((((..((((.((((((........)))))).))))..))))...... (-26.26 = -26.46 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	20,463,894 – 20,464,014
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-31.29
Consensus MFE	-25.76
Energy contribution	-26.80
Covariance contribution	1.04
Combinations/Pair	1.07
Mean z-score	-2.01
Structure conservation index	0.82
SVM decision value	1.52
SVM RNA-class probability	0.960868
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20463894 120 + 22407834
GCCGAGCCAAGCGAGGGGAAAUGGCAAAACAAACUUUCAAGUCGUUUUGAUUUCUCUUUGCUGCUGCGAGCAACUUUCAGCAAACUGCUCAAGUUACAAAUGCAUUUUUAAUAAAUGCUC
(((((((..(((((((((((((..((((((..(((....))).)))))))))))))))))))))).)).))(((((..(((.....))).)))))......((((((.....)))))).. ( -36.90)
>DroSec_CAF1 16827 119 + 1
GCC-AGCCAAGCGGGGGGAAAUGGCAAAACAAACUUUCAAGUCGUUUUGAUUUCUCUUUGCUGCUGCGAGCAACUUUCAGCAAACUGCUCAAGUUACAAAUGCAUUUUUAAUAAAUGCUC
((.-(((..(((((((((((((..((((((..(((....))).))))))))))))))))))))))))(((((.............)))))...........((((((.....)))))).. ( -34.62)
>DroSim_CAF1 18751 120 + 1
GCCGAGCCAAGCGGGGGGAAAUGGCAAAACAAACUUUCAAGUCAUUUUGAUUUCUCUUUGCUGCUGCGAGCAACUUUCAGCAAACUGCUCAAGUUACAAAUGCAUUUUUAAUAAAUGCUC
(((((((..(((((((((((((..(((((...(((....)))..))))))))))))))))))))).)).))(((((..(((.....))).)))))......((((((.....)))))).. ( -33.20)
>DroEre_CAF1 19291 117 + 1
GCCUGGCCGAGCUGGAGGAAAUGGCAA-ACAAACUCUCAAGUCUUUUUGAUUUCUCUUUGCUGCUGCGAA-AACUUUCAGCA-ACUGCUCAAGUUACAAAUGCAUUUUUAAUAAAUGCUC
((..(((..(((.(((((((.((....-.)).....(((((....))))))))))))..))))))))...-(((((..(((.-...))).)))))......((((((.....)))))).. ( -24.70)
>DroYak_CAF1 16437 120 + 1
GCCAGGCCAAGCUGGAGGAAAUGGCAAAACAAACUCUCAAGUCGUUUUGAUUUCUCUUUGCUGCUGCGAACAACUUUCAGCAAACUGUUCCAGUUACAAAUGCAUUUUUAAUAAAUGCUC
.((((......)))).((((((..((((((..(((....))).)))))))))))).((((..((((.(((((.............)))))))))..)))).((((((.....)))))).. ( -27.02)
>consensus
GCCGAGCCAAGCGGGGGGAAAUGGCAAAACAAACUUUCAAGUCGUUUUGAUUUCUCUUUGCUGCUGCGAGCAACUUUCAGCAAACUGCUCAAGUUACAAAUGCAUUUUUAAUAAAUGCUC
((..(((..(((((((((((((..((((((..(((....))).))))))))))))))))))))))))....(((((..(((.....))).)))))......((((((.....)))))).. (-25.76 = -26.80 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:09 2006