Locus 6742

Sequence ID	3R_DroMel_CAF1
Location	17,764,836 – 17,764,941
Length	105
Max. P	0.576881

overview

Window 0

Location	17,764,836 – 17,764,941
Length	105
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	83.39
Mean single sequence MFE	-16.58
Consensus MFE	-13.08
Energy contribution	-13.41
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.79
SVM decision value	0.01
SVM RNA-class probability	0.539878
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17764836 105 + 27905053
-UUAAUUUAUGCCCGCUUGCAAUUUCGGCAGACACUGCCAGGCUCGCUCACCAAAAAAAA------AAGAAAAUAAACGGAGGAAUAAAAUUGCAACAAAAAAGAUAU------AUAU
-.............(.(((((((((.(((((...)))))....((.(((...........------.............)))))...))))))))))...........------.... ( -15.96)
>DroSec_CAF1 53345 106 + 1
-UUAAUUUAUGCCCGCUUGCAAUUUCGGCAGACACCGCCAGGCUCGCUCACCAAAAAAAAA-----AAGAAAAUAAACGGAGGAAUAAAAUUGCAACAAAAAAGAUAU------AUAU
-.............(.(((((((((.(((.......)))....((.(((............-----.............)))))...))))))))))...........------.... ( -13.01)
>DroSim_CAF1 54209 112 + 1
GUUAAUUUAUGCCCGCUUGCAAUUUCGGCAGACACUGCCAGGCUCGCUCACCAAAAAAAAAAAAGAAAGAAAAUAAACGGAGGAAUAAAAUUGCAACAAAAAAGAUAU------AUAU
((...(((((.((((.(((...(((((((((...))))).((........))............)))).....))).))).)..)))))...))..............------.... ( -15.90)
>DroEre_CAF1 56006 103 + 1
-UUAAUUUAUGCCCGCUUGCAAUUUCGGCAGACACUGCCAGGCUCGCUCUCCAAAAAAUAC-----AAGAAA--AAACUGAGAAAUAAAAUUGCAACAAAA-AGAUGU------AUAU
-......(((((...((((((((((.(((((...)))))........((((..........-----......--.....))))....))))))))......-))..))------))). ( -16.40)
>DroYak_CAF1 57364 106 + 1
-UUAAUUUAUGCCCGCUUGCAAUUUCGGCAGACACUGCCAUCCUCGCUCUCCAAAAAA---------ACAAA--AAACGAAGGAAUAAAAUUGCAACAAAAAAGAUAUAUACAUAUAU
-.............(.(((((((((.(((((...))))).((((((............---------.....--...)).))))...))))))))))..................... ( -18.45)
>DroAna_CAF1 61792 86 + 1
-UUAAUUUAUGCCCGCUUGCAAUUUCGGCAGACACUGCCAGGCUCAC-------AAUAUA------CAAAAAAUAA---GAGGAAUGAAAUUGCAACAAAA---------------AU
-.............(.(((((((((((((((...)))))...(((..-------......------..........---)))....)))))))))))....---------------.. ( -19.77)
>consensus
_UUAAUUUAUGCCCGCUUGCAAUUUCGGCAGACACUGCCAGGCUCGCUCACCAAAAAAAA______AAGAAAAUAAACGGAGGAAUAAAAUUGCAACAAAAAAGAUAU______AUAU
..............(.(((((((((.(((((...)))))...(((..................................))).....))))))))))..................... (-13.08 = -13.41 +   0.33)

alignment

secondary structure

dotplot

Window 1

Location	17,764,836 – 17,764,941
Length	105
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	83.39
Mean single sequence MFE	-23.05
Consensus MFE	-17.06
Energy contribution	-17.31
Covariance contribution	0.25
Combinations/Pair	1.12
Mean z-score	-1.66
Structure conservation index	0.74
SVM decision value	0.09
SVM RNA-class probability	0.576881
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17764836 105 - 27905053
AUAU------AUAUCUUUUUUGUUGCAAUUUUAUUCCUCCGUUUAUUUUCUU------UUUUUUUUGGUGAGCGAGCCUGGCAGUGUCUGCCGAAAUUGCAAGCGGGCAUAAAUUAA-
....------........((((((((((((((.......((((((((.....------........)))))))).....(((((...))))))))))))).))))))..........- ( -22.52)
>DroSec_CAF1 53345 106 - 1
AUAU------AUAUCUUUUUUGUUGCAAUUUUAUUCCUCCGUUUAUUUUCUU-----UUUUUUUUUGGUGAGCGAGCCUGGCGGUGUCUGCCGAAAUUGCAAGCGGGCAUAAAUUAA-
....------........((((((((((((((.......((((((((.....-----.........)))))))).....(((((...))))))))))))).))))))..........- ( -21.74)
>DroSim_CAF1 54209 112 - 1
AUAU------AUAUCUUUUUUGUUGCAAUUUUAUUCCUCCGUUUAUUUUCUUUCUUUUUUUUUUUUGGUGAGCGAGCCUGGCAGUGUCUGCCGAAAUUGCAAGCGGGCAUAAAUUAAC
....------........((((((((((((((.......((((((((...................)))))))).....(((((...))))))))))))).))))))........... ( -22.11)
>DroEre_CAF1 56006 103 - 1
AUAU------ACAUCU-UUUUGUUGCAAUUUUAUUUCUCAGUUU--UUUCUU-----GUAUUUUUUGGAGAGCGAGCCUGGCAGUGUCUGCCGAAAUUGCAAGCGGGCAUAAAUUAA-
....------......-.((((((((((((((........((((--.(((((-----..........))))).))))..(((((...))))))))))))).))))))..........- ( -21.30)
>DroYak_CAF1 57364 106 - 1
AUAUAUGUAUAUAUCUUUUUUGUUGCAAUUUUAUUCCUUCGUUU--UUUGU---------UUUUUUGGAGAGCGAGGAUGGCAGUGUCUGCCGAAAUUGCAAGCGGGCAUAAAUUAA-
...(((((...........(((((((((((((..((((.(((((--(..(.---------.....)..)))))))))).(((((...))))))))))))).))))))))))......- ( -29.70)
>DroAna_CAF1 61792 86 - 1
AU---------------UUUUGUUGCAAUUUCAUUCCUC---UUAUUUUUUG------UAUAUU-------GUGAGCCUGGCAGUGUCUGCCGAAAUUGCAAGCGGGCAUAAAUUAA-
..---------------.((((((((((((((......(---((((..(...------...)..-------)))))...(((((...))))))))))))).))))))..........- ( -20.90)
>consensus
AUAU______AUAUCUUUUUUGUUGCAAUUUUAUUCCUCCGUUUAUUUUCUU______UUUUUUUUGGUGAGCGAGCCUGGCAGUGUCUGCCGAAAUUGCAAGCGGGCAUAAAUUAA_
..................((((((((((((((....(((.((((.........................)))))))...(((((...))))))))))))).))))))........... (-17.06 = -17.31 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:51 2006