Locus 682

Sequence ID	3L_DroMel_CAF1
Location	2,021,042 – 2,021,182
Length	140
Max. P	0.921891

overview

Window 0

Location	2,021,042 – 2,021,143
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	71.68
Mean single sequence MFE	-21.47
Consensus MFE	-10.75
Energy contribution	-10.78
Covariance contribution	0.03
Combinations/Pair	1.50
Mean z-score	-1.74
Structure conservation index	0.50
SVM decision value	0.61
SVM RNA-class probability	0.800264
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2021042 101 + 23771897
-----------AUUUAGGC-------AUAUACUUACCGCCGUGCGAAAUUUGUUUUUCUGAGCUUUAGAUAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUA-
-----------...(((((-------..............((((((((((......(((((...))))).)))))))..))).....((((((.....))))))..........)))))- ( -22.30)
>DroSec_CAF1 71476 101 + 1
-----------CUUUAGGC-------AUACACUUACCGCCGUGCGAAAUUUGUUUUUCUGAGCUUUAGAUAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUC-
-----------....((((-------...(((........))).((((..(((...((.(((((......))))).))..)))....((((((.....)))))).)))).....)))).- ( -21.70)
>DroSim_CAF1 86615 101 + 1
-----------CUUUAGGU-------AUACACUUACCGCCGUGCGAAAUUUGUUUUUCUGAGCUUUAGAUAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUC-
-----------.....(((-------(......))))(.((((.((((..(((...((.(((((......))))).))..)))....((((((.....)))))).))))..)))).)..- ( -24.00)
>DroEre_CAF1 77976 101 + 1
-----------AUUUAAAC-------ACGCACUUACCAUCAUUCGAAAUUUGCUUUUUUGAGCUUCCGUGAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUA-
-----------........-------....((((((.....(((((((.......))))))).....))))))...(((........((((((.....))))))..........)))..- ( -21.27)
>DroYak_CAF1 74573 101 + 1
-----------AUUUAAGA-------ACACACUUACCACCUUCCGAAACAUAUUUUUCUGAGUUUUCGAGAGUUUUGACCACAUUCUGGCUGCUCUUUGCAGCCUUUUCUUAACGUCUA-
-----------..((((((-------(............((..(((((...((((....)))))))))..))...............((((((.....))))))..)))))))......- ( -21.10)
>DroAna_CAF1 69261 118 + 1
UUUCAGAUACGUUUUAGGAGAACAAAAUAACCUUACCUCUUUACGGUAUCGAUCUUGAUCGUCCUUUGAUAGUUUAACCCAUUCUUUGGUACCUUUUUGGAGUGAAA--GCAGCGUCCCC
.....(((((((...(((((................))))).)).)))))(((.(((....(((((..(.........(((.....))).......)..))).))..--.))).)))... ( -18.48)
>consensus
___________AUUUAGGC_______AUACACUUACCGCCGUGCGAAAUUUGUUUUUCUGAGCUUUAGAUAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUA_
..........................................(((...........((.(((((......))))).)).........((((((.....)))))).........))).... (-10.75 = -10.78 +   0.03)

alignment

secondary structure

dotplot

Window 1

Location	2,021,064 – 2,021,182
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.79
Mean single sequence MFE	-29.92
Consensus MFE	-14.08
Energy contribution	-14.12
Covariance contribution	0.03
Combinations/Pair	1.45
Mean z-score	-2.28
Structure conservation index	0.47
SVM decision value	1.14
SVM RNA-class probability	0.921891
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2021064 118 + 23771897
GUGCGAAAUUUGUUUUUCUGAGCUUUAGAUAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUA--CGAUGGUGUUCCUCCUUUGGUACUCGCGCAAAAAUCCAA
((((((...........(.(((((......))))).)((((......((((((.....)))))).........((....--)).))))((.((......)).)))))))).......... ( -29.50)
>DroSec_CAF1 71498 118 + 1
GUGCGAAAUUUGUUUUUCUGAGCUUUAGAUAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUC--CGGUGGCGUUCCUCCUUUGGAACUCUCGCAAAAAUCUUA
.(((((..........((.(((((......))))).))((((.....((((((.....)))))).........((....--)))))).(((((......)))))..)))))......... ( -33.60)
>DroSim_CAF1 86637 118 + 1
GUGCGAAAUUUGUUUUUCUGAGCUUUAGAUAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUC--CGGUGGCGUUCCUCCUUUGGAACUCUCGCAAAAAUCUUA
.(((((..........((.(((((......))))).))((((.....((((((.....)))))).........((....--)))))).(((((......)))))..)))))......... ( -33.60)
>DroEre_CAF1 77998 118 + 1
AUUCGAAAUUUGCUUUUUUGAGCUUCCGUGAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUA--AGCUGGCGUUUCUUCUAUGGUACUCGCGCAGAAAUCCUA
.(((.......((((....))))...(((((((....((((......((((((.....))))))........(((((..--....)))))........)))))))))))..)))...... ( -33.70)
>DroYak_CAF1 74595 118 + 1
UUCCGAAACAUAUUUUUCUGAGUUUUCGAGAGUUUUGACCACAUUCUGGCUGCUCUUUGCAGCCUUUUCUUAACGUCUA--GGUUGGCGUUUCUUCUAUGGUACUCACGCAAAAAUCCUA
(((.((((......)))).)))((((((.((((....((((......((((((.....)))))).......((((((..--....)))))).......)))))))).)).))))...... ( -28.70)
>DroAna_CAF1 69301 118 + 1
UUACGGUAUCGAUCUUGAUCGUCCUUUGAUAGUUUAACCCAUUCUUUGGUACCUUUUUGGAGUGAAA--GCAGCGUCCCCAUAUUUGAAUUAUUUCUUCGGAACUCACGCAUGAAACCAA
....(((((((((....)))(((....))).................))))))...((((.((....--)).((((...((....))......(((....)))...))))......)))) ( -20.40)
>consensus
GUGCGAAAUUUGUUUUUCUGAGCUUUAGAUAGUUUUGACCACAUCUUGGCUGCUCUUUGCAGCCUUUUCUUUACGUCUA__CGGUGGCGUUCCUCCUUUGGAACUCACGCAAAAAUCCUA
................((.(((((......))))).))((.......((((((.....))))))........(((((........))))).........))................... (-14.08 = -14.12 +   0.03)

alignment

secondary structure

dotplot

Window 2

Location	2,021,064 – 2,021,182
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.79
Mean single sequence MFE	-29.91
Consensus MFE	-11.81
Energy contribution	-11.78
Covariance contribution	-0.03
Combinations/Pair	1.25
Mean z-score	-2.29
Structure conservation index	0.39
SVM decision value	0.60
SVM RNA-class probability	0.794354
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2021064 118 - 23771897
UUGGAUUUUUGCGCGAGUACCAAAGGAGGAACACCAUCG--UAGACGUAAAGAAAAGGCUGCAAAGAGCAGCCAAGAUGUGGUCAAAACUAUCUAAAGCUCAGAAAAACAAAUUUCGCAC
(((..((((((.((..((.((......)).))(((((((--....)).........((((((.....)))))).....)))))..............)).))))))..)))......... ( -27.70)
>DroSec_CAF1 71498 118 - 1
UAAGAUUUUUGCGAGAGUUCCAAAGGAGGAACGCCACCG--GAGACGUAAAGAAAAGGCUGCAAAGAGCAGCCAAGAUGUGGUCAAAACUAUCUAAAGCUCAGAAAAACAAAUUUCGCAC
.........((((((((((((......)))))(((((((--....)).........((((((.....)))))).....))))).............................))))))). ( -36.60)
>DroSim_CAF1 86637 118 - 1
UAAGAUUUUUGCGAGAGUUCCAAAGGAGGAACGCCACCG--GAGACGUAAAGAAAAGGCUGCAAAGAGCAGCCAAGAUGUGGUCAAAACUAUCUAAAGCUCAGAAAAACAAAUUUCGCAC
.........((((((((((((......)))))(((((((--....)).........((((((.....)))))).....))))).............................))))))). ( -36.60)
>DroEre_CAF1 77998 118 - 1
UAGGAUUUCUGCGCGAGUACCAUAGAAGAAACGCCAGCU--UAGACGUAAAGAAAAGGCUGCAAAGAGCAGCCAAGAUGUGGUCAAAACUCACGGAAGCUCAAAAAAGCAAAUUUCGAAU
..(..((((((...((((((((((......(((.(....--..).)))........((((((.....))))))....))))))....)))).))))))..)................... ( -28.50)
>DroYak_CAF1 74595 118 - 1
UAGGAUUUUUGCGUGAGUACCAUAGAAGAAACGCCAACC--UAGACGUUAAGAAAAGGCUGCAAAGAGCAGCCAGAAUGUGGUCAAAACUCUCGAAAACUCAGAAAAAUAUGUUUCGGAA
...((.((((.((.((((((((((.....((((.(....--..).)))).......((((((.....))))))....))))))....)))).)))))).)).((((......)))).... ( -29.30)
>DroAna_CAF1 69301 118 - 1
UUGGUUUCAUGCGUGAGUUCCGAAGAAAUAAUUCAAAUAUGGGGACGCUGC--UUUCACUCCAAAAAGGUACCAAAGAAUGGGUUAAACUAUCAAAGGACGAUCAAGAUCGAUACCGUAA
((((......(((.(.(((((....................))))).))))--.......))))...((((((...((.(((......)))))...)).((((....)))).)))).... ( -20.77)
>consensus
UAGGAUUUUUGCGAGAGUACCAAAGAAGGAACGCCAACG__GAGACGUAAAGAAAAGGCUGCAAAGAGCAGCCAAGAUGUGGUCAAAACUAUCUAAAGCUCAGAAAAACAAAUUUCGCAC
...((((...((....))......................................((((((.....)))))).......)))).................................... (-11.81 = -11.78 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:24 2006