Locus 798

Sequence ID	3R_DroMel_CAF1
Location	2,717,859 – 2,718,053
Length	194
Max. P	0.999967

overview

Window 9

Location	2,717,859 – 2,717,979
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	98.06
Mean single sequence MFE	-30.17
Consensus MFE	-27.72
Energy contribution	-28.08
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.85
Structure conservation index	0.92
SVM decision value	2.13
SVM RNA-class probability	0.988589
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2717859 120 + 27905053
AAUGACACGUGAUUUUAUUUGAUUUACUUACAUCUGCAGCUCAAUUUUCAGUUCGGCUUCUGGAGAGUCGAGUAUCUCGUUCUCCCGCUUUUUGUCGCUGGCCUUUCUUAUGGCCAACAG
...((((.((((.((.....)).))))........((((((.(((.....))).))))...((((((.((((...)))))))))).))....))))(.(((((........))))).).. ( -31.30)
>DroSec_CAF1 28133 120 + 1
AAUGACACGUGAUUUUAUUUGAUUUACUUACAUCUGCAGCUCAAUUUUCAGUUUGGCUUCUGGAGAGUCGAGUAUCUCGUUCUCCCGCUUUUUGUCGCUGGCCUUUCUUAUGGCCAACAG
...((((.((((.((.....)).))))........(((((.(((........))))))...((((((.((((...)))))))))).))....))))(.(((((........))))).).. ( -31.60)
>DroSim_CAF1 29321 120 + 1
AAUGACACGUGAUUUUAUUUGAUUUACUUACAUCUGCAGCUCAAUUUUCAGUUUGGCUUCUGGAGAGUCGAGUAUCUCGUUCUCCCGCUUUUUGUCGCUGGCCUUUCUUAUGGCCAACAG
...((((.((((.((.....)).))))........(((((.(((........))))))...((((((.((((...)))))))))).))....))))(.(((((........))))).).. ( -31.60)
>DroEre_CAF1 29211 120 + 1
AAUGACACGUGAUUUUAUUUGAUUUACUUACAUCUGCAGCUCAAUUUUCAGUUUGGCUUCUGGAGAGUCGAGUAUCUCGUUCUACCGCUUUUCGUCGCUGGCCUUUCUUAUGGCCAACAG
...(((..((((.((.....)).))))........(((((.(((........))))))...((((((.((((...)))))))).)))).....)))(.(((((........))))).).. ( -28.40)
>DroYak_CAF1 28930 120 + 1
AAUGACACGUGAUUUUAUUUGAUUUACUUACAUCUGCAGCUCAAUUUUCAGUUUGGCUUCUGGAGAGUCGAGUAUCUCGUUCUCCCGCUUUUUGUCGCUGGCCUUUCUUAUGGCCAACAG
...((((.((((.((.....)).))))........(((((.(((........))))))...((((((.((((...)))))))))).))....))))(.(((((........))))).).. ( -31.60)
>DroAna_CAF1 28034 120 + 1
AAUGACACGUGAUUUUAUUUGAUUUACUUACAUCUGCAGCUCAAUUUUCAGUUUGACUUCUGGUGAGUCGAGUAUCUCGUUUUCCAGCUUUUUGUCGCUGGCCUUUCUUAUGGCCAACAG
...((((...((...(((((((((((((....((...((((........)))).)).....)))))))))))))..))((......))....))))(.(((((........))))).).. ( -26.50)
>consensus
AAUGACACGUGAUUUUAUUUGAUUUACUUACAUCUGCAGCUCAAUUUUCAGUUUGGCUUCUGGAGAGUCGAGUAUCUCGUUCUCCCGCUUUUUGUCGCUGGCCUUUCUUAUGGCCAACAG
...(((..((((.((.....)).))))........((((((.(((.....))).))))...((((((.((((...)))))))))).)).....)))(.(((((........))))).).. (-27.72 = -28.08 +   0.36)

alignment

secondary structure

dotplot

Window 0

Location	2,717,859 – 2,717,979
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	98.06
Mean single sequence MFE	-32.58
Consensus MFE	-31.42
Energy contribution	-31.50
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-3.03
Structure conservation index	0.96
SVM decision value	4.99
SVM RNA-class probability	0.999967
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2717859 120 - 27905053
CUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCGAACUGAAAAUUGAGCUGCAGAUGUAAGUAAAUCAAAUAAAAUCACGUGUCAUU
..(((((((........)))))))((((....((.(((((.((((...))))..)))))...((((((........))).))))).(((........))).............))))... ( -34.00)
>DroSec_CAF1 28133 120 - 1
CUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGAGCUGCAGAUGUAAGUAAAUCAAAUAAAAUCACGUGUCAUU
..(((((((........)))))))((((....((.(((((.((((...))))..)))))...((((((........))).))))).(((........))).............))))... ( -34.30)
>DroSim_CAF1 29321 120 - 1
CUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGAGCUGCAGAUGUAAGUAAAUCAAAUAAAAUCACGUGUCAUU
..(((((((........)))))))((((....((.(((((.((((...))))..)))))...((((((........))).))))).(((........))).............))))... ( -34.30)
>DroEre_CAF1 29211 120 - 1
CUGUUGGCCAUAAGAAAGGCCAGCGACGAAAAGCGGUAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGAGCUGCAGAUGUAAGUAAAUCAAAUAAAAUCACGUGUCAUU
..(((((((........)))))))((((....((((.(((.((((...))))..)))))...((((((........))).))))).(((........))).............))))... ( -30.10)
>DroYak_CAF1 28930 120 - 1
CUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGAGCUGCAGAUGUAAGUAAAUCAAAUAAAAUCACGUGUCAUU
..(((((((........)))))))((((....((.(((((.((((...))))..)))))...((((((........))).))))).(((........))).............))))... ( -34.30)
>DroAna_CAF1 28034 120 - 1
CUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCUGGAAAACGAGAUACUCGACUCACCAGAAGUCAAACUGAAAAUUGAGCUGCAGAUGUAAGUAAAUCAAAUAAAAUCACGUGUCAUU
..(((((((........)))))))((((.....((((....((((...)))).....))))...............((((..(((........)))..))))...........))))... ( -28.50)
>consensus
CUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGAGCUGCAGAUGUAAGUAAAUCAAAUAAAAUCACGUGUCAUU
..(((((((........)))))))((((....((.(((((.((((...))))..)))))...((((((........))).))))).(((........))).............))))... (-31.42 = -31.50 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	2,717,899 – 2,718,013
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.11
Mean single sequence MFE	-31.95
Consensus MFE	-26.29
Energy contribution	-27.15
Covariance contribution	0.86
Combinations/Pair	1.03
Mean z-score	-2.27
Structure conservation index	0.82
SVM decision value	0.56
SVM RNA-class probability	0.783380
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2717899 114 - 27905053
AAGCAGGGAACUGUAUCUGUAACUGUAUCUGG------AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCGAACUGAAAAUUGA
..((((....)))).((.((....((.(((((------(..((((((((........))))))))...........(((..((((...)))).))))))))).))...)).))....... ( -33.20)
>DroSec_CAF1 28173 114 - 1
AAGCAGGGAACGGUAUCUGUAACUGUAUCUGG------AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGA
...(((((((((((.......))))).)))((------..(((((((((........)))))))...........(((((.((((...))))..)))))))...))...)))........ ( -32.10)
>DroSim_CAF1 29361 114 - 1
AAGCAGGGAACUGUAUCUGUAACUGUAUCUGG------AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGA
..((((....)))).((.((....((.(((((------(..((((((((........))))))))...........(((..((((...)))).))))))))).))...)).))....... ( -33.20)
>DroEre_CAF1 29251 114 - 1
AAGCAGGGAACUGUAUCUGUAACUGUAUCUGG------AACUGUUGGCCAUAAGAAAGGCCAGCGACGAAAAGCGGUAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGA
..((((....)))).((.((....((.(((((------(..((((((((........))))))))................((((...))))....)))))).))...)).))....... ( -31.50)
>DroYak_CAF1 28970 120 - 1
AAGCAGGGAACUGUAUCUGUAACUGUAUCUGGAACUGGAACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGA
..((((....))))...............(((..(((((..((((((((........))))))))...........(((..((((...)))).))))))))...)))............. ( -33.20)
>DroAna_CAF1 28074 114 - 1
ACGCAGGGAAGUGUAUCUGUAACUGUAUCUGU------AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCUGGAAAACGAGAUACUCGACUCACCAGAAGUCAAACUGAAAAUUGA
..(((((..(((.........)))...)))))------....(((((((........)))))))(((......((((....((((...)))).....))))..))).............. ( -28.50)
>consensus
AAGCAGGGAACUGUAUCUGUAACUGUAUCUGG______AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGAACGAGAUACUCGACUCUCCAGAAGCCAAACUGAAAAUUGA
..((((....)))).((.((....((.((((..........((((((((........)))))))).........(((((..((((...)))).))))))))).))...)).))....... (-26.29 = -27.15 +   0.86)

alignment

secondary structure

dotplot

Window 2

Location	2,717,939 – 2,718,053
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	93.56
Mean single sequence MFE	-33.10
Consensus MFE	-28.24
Energy contribution	-28.30
Covariance contribution	0.06
Combinations/Pair	1.10
Mean z-score	-2.27
Structure conservation index	0.85
SVM decision value	1.32
SVM RNA-class probability	0.941391
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2717939 114 - 27905053
GCUAAUGAUCGAAUCAUUUCGGAUAAUGGCCCGAAUGAAGAAGCAGGGAACUGUAUCUGUAACUGUAUCUGG------AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGA
((((.((.(((((....))))).)).))))(((.....(((.((((....)))).)))..............------...((((((((........))))))))........))).... ( -32.80)
>DroSec_CAF1 28213 114 - 1
GCUAAUGAUCGAAUCAUUUCGGAUAAUGGCCCGAAUGAAGAAGCAGGGAACGGUAUCUGUAACUGUAUCUGG------AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGA
((((.((.(((((....))))).)).))))(((.....(((.((((...((((...))))..)))).)))..------...((((((((........))))))))........))).... ( -32.60)
>DroSim_CAF1 29401 114 - 1
GCUAAUGAUCGAAUCAUUUCGGAUAAUGGCCCGAAUGAAGAAGCAGGGAACUGUAUCUGUAACUGUAUCUGG------AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGA
((((.((.(((((....))))).)).))))(((.....(((.((((....)))).)))..............------...((((((((........))))))))........))).... ( -32.80)
>DroEre_CAF1 29291 114 - 1
GCUAAUGAUCGAAUCAUUUCGGAUAAUGGGCCAAAUGAAGAAGCAGGGAACUGUAUCUGUAACUGUAUCUGG------AACUGUUGGCCAUAAGAAAGGCCAGCGACGAAAAGCGGUAGA
(((.....(((.....(((((((((.(((.........(((.((((....)))).)))....))))))))))------)).((((((((........)))))))).)))..)))...... ( -32.52)
>DroYak_CAF1 29010 120 - 1
GCUAAUGAUCGAAUCAUUUCGGAUAAUGGGCUGAAUGAAGAAGCAGGGAACUGUAUCUGUAACUGUAUCUGGAACUGGAACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGA
(((..((.((...((((((((((((.(((..((.....(((.((((....)))).))).)).)))))))))))).)))....(((((((........)))))))))))...)))...... ( -33.70)
>DroAna_CAF1 28114 114 - 1
GCUAAUGAUCGAAUCAUUUCGGAUAAUGGCCGGGCCAAAGACGCAGGGAAGUGUAUCUGUAACUGUAUCUGU------AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCUGGAAA
((((.((.(((((....))))).)).))))..((((((((..(((((..(((.........)))...)))))------..)).))))))..........(((((........)))))... ( -34.20)
>consensus
GCUAAUGAUCGAAUCAUUUCGGAUAAUGGCCCGAAUGAAGAAGCAGGGAACUGUAUCUGUAACUGUAUCUGG______AACUGUUGGCCAUAAGAAAGGCCAGCGACAAAAAGCGGGAGA
.(((.((.(((((....))))).)).)))((((.....(((.((((....)))).))).......................((((((((........))))))))........))))... (-28.24 = -28.30 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:25 2006