Locus 8252

Sequence ID	3R_DroMel_CAF1
Location	22,084,872 – 22,085,030
Length	158
Max. P	0.938242

overview

Window 6

Location	22,084,872 – 22,084,963
Length	91
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	85.85
Mean single sequence MFE	-37.28
Consensus MFE	-30.59
Energy contribution	-30.07
Covariance contribution	-0.52
Combinations/Pair	1.24
Mean z-score	-2.48
Structure conservation index	0.82
SVM decision value	0.87
SVM RNA-class probability	0.869930
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22084872 91 + 27905053
CGCUGCUGCUG-CGCUGUUCCUGCAGGCAGCGACGCCAACGCAGGGCGCAUGAAUUUUCGCUUGACAUUGAACAAGGUCAAGCAACAAGC---CU
.((((((((((-(.((((....))))))))))..(((.......)))))..........(((((((.((....)).)))))))....)))---.. ( -33.40)
>DroSec_CAF1 7641 91 + 1
CGCUUCUGCUG-CGCUGCCCCUGCAGGCAGCGACGCUAACGCAGGGCGCAUGAAUUUUCGCUUGACAUUGAACAAGGUCAAGCAACAAGC---CU
.((....((..-(((((((......)))))))..))....)).((((....((....))(((((((.((....)).))))))).....))---)) ( -34.20)
>DroSim_CAF1 8081 91 + 1
CGCUGCUGCUG-CGCUGCCCCUGCAGGCAGCGACGCCAACGCAGGGCGCAUGAAUUUUCGCUUGACAUUGAACAAGGUCAAGCAACAAGC---CU
..((((.((..-(((((((......)))))))..))....))))(((....((....))(((((((.((....)).))))))).....))---). ( -35.50)
>DroEre_CAF1 7738 91 + 1
CGCUGCUGCUG-CGCUGCCCCUGCAGGCAGCGACGGCAACGCAGGGCGCAUGAAUUUUCGCCUGACAUUGAACAAGGUCAAGCAACAAGC---CU
..(((((((((-(((((((......))))))).)))))..))))(((....((....))((.((((.((....)).)))).)).....))---). ( -37.10)
>DroYak_CAF1 6596 91 + 1
CGCUGCUGCUG-CUCUGCCGCUGCAGGCAGCGACGGCAACGCAGGGCGCAUGUAUUUUCGCUUGACAUUGAACAAGGUCAAGCAACAAGC---CU
.((((((((.(-(((((((((((....)))))..(....))))))))))).))......(((((((.((....)).)))))))....)))---.. ( -38.90)
>DroAna_CAF1 3705 95 + 1
CGCUGCCAACGUUGCUGCCGACGACGGCAGAGAUGCGGGCGUGGGGCGCAUGUGUUGGGGCCUGACAUUGAACAAGGUCAGGCAACAAUGUUGCC
(((.(((..(((..((((((....))))))..)))..)))))).((((...(..(((..(((((((.((....)).)))))))..)))..))))) ( -44.60)
>consensus
CGCUGCUGCUG_CGCUGCCCCUGCAGGCAGCGACGCCAACGCAGGGCGCAUGAAUUUUCGCUUGACAUUGAACAAGGUCAAGCAACAAGC___CU
((((.((((...(((((((......)))))))..(....)))))))))...........(((((((.((....)).)))))))............ (-30.59 = -30.07 +  -0.52)

alignment

secondary structure

dotplot

Window 7

Location	22,084,872 – 22,084,963
Length	91
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	85.85
Mean single sequence MFE	-37.15
Consensus MFE	-27.85
Energy contribution	-28.22
Covariance contribution	0.36
Combinations/Pair	1.20
Mean z-score	-2.12
Structure conservation index	0.75
SVM decision value	-0.04
SVM RNA-class probability	0.513599
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22084872 91 - 27905053
AG---GCUUGUUGCUUGACCUUGUUCAAUGUCAAGCGAAAAUUCAUGCGCCCUGCGUUGGCGUCGCUGCCUGCAGGAACAGCG-CAGCAGCAGCG
..---((...(((((((((.((....)).))))))))).......(((...((((((((...((.(((....))))).)))))-)))..))))). ( -35.40)
>DroSec_CAF1 7641 91 - 1
AG---GCUUGUUGCUUGACCUUGUUCAAUGUCAAGCGAAAAUUCAUGCGCCCUGCGUUAGCGUCGCUGCCUGCAGGGGCAGCG-CAGCAGAAGCG
..---((((.(((((((((.((....)).))))))))).......(((.....((....))(.((((((((....))))))))-).))).)))). ( -36.00)
>DroSim_CAF1 8081 91 - 1
AG---GCUUGUUGCUUGACCUUGUUCAAUGUCAAGCGAAAAUUCAUGCGCCCUGCGUUGGCGUCGCUGCCUGCAGGGGCAGCG-CAGCAGCAGCG
..---(((.((((((((((.((....)).)))))(((........(((.(((((((..((((....)))))))))))))).))-).)))))))). ( -38.20)
>DroEre_CAF1 7738 91 - 1
AG---GCUUGUUGCUUGACCUUGUUCAAUGUCAGGCGAAAAUUCAUGCGCCCUGCGUUGCCGUCGCUGCCUGCAGGGGCAGCG-CAGCAGCAGCG
..---((...(((((((((.((....)).))))))))).......(((...((((((((((.(.((.....)).).)))))))-)))..))))). ( -39.80)
>DroYak_CAF1 6596 91 - 1
AG---GCUUGUUGCUUGACCUUGUUCAAUGUCAAGCGAAAAUACAUGCGCCCUGCGUUGCCGUCGCUGCCUGCAGCGGCAGAG-CAGCAGCAGCG
.(---((.(((((((((((.((....)).)))))))).....)))...)))(((((((((((((((((....))))))).).)-)))).)))).. ( -38.60)
>DroAna_CAF1 3705 95 - 1
GGCAACAUUGUUGCCUGACCUUGUUCAAUGUCAGGCCCCAACACAUGCGCCCCACGCCCGCAUCUCUGCCGUCGUCGGCAGCAACGUUGGCAGCG
(((..((((((((((((((.((....)).)))))))...)))).))).)))....(((.((....((((((....))))))....)).))).... ( -34.90)
>consensus
AG___GCUUGUUGCUUGACCUUGUUCAAUGUCAAGCGAAAAUUCAUGCGCCCUGCGUUGGCGUCGCUGCCUGCAGGGGCAGCG_CAGCAGCAGCG
..........(((((((((.((....)).)))))))))........((...((((........((((((((....))))))))...))))..)). (-27.85 = -28.22 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	22,084,930 – 22,085,030
Length	100
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	92.57
Mean single sequence MFE	-26.23
Consensus MFE	-21.81
Energy contribution	-21.97
Covariance contribution	0.17
Combinations/Pair	1.12
Mean z-score	-2.65
Structure conservation index	0.83
SVM decision value	1.29
SVM RNA-class probability	0.938242
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22084930 100 + 27905053
GCUUGACAUUGAACAAGGUCAAGCAACAAGC---CUUAGCAACAAAUGUUGCCAGCGAAAU-UUGUUGCUUACGAAAUGCGAAUAGAAAUUGUUGAAAACCGAA
(((((((.((....)).)))))))(((((..---...((((((((((.(((....))).))-))))))))..((.....))........))))).......... ( -25.80)
>DroSec_CAF1 7699 100 + 1
GCUUGACAUUGAACAAGGUCAAGCAACAAGC---CUUAGCAACAAAUGUUGCCAGCGAAAU-UUGUUGCUUACGAAAUGCGAAUAGAAAUUGUUGAAAACCGAA
(((((((.((....)).)))))))(((((..---...((((((((((.(((....))).))-))))))))..((.....))........))))).......... ( -25.80)
>DroSim_CAF1 8139 100 + 1
GCUUGACAUUGAACAAGGUCAAGCAACAAGC---CUUAGCAACAAAUGUUGCCAGCGAAAU-UUGUUGCUUACGAAAUGCGAAUAGAAAUUGUUGAAAACCGAA
(((((((.((....)).)))))))(((((..---...((((((((((.(((....))).))-))))))))..((.....))........))))).......... ( -25.80)
>DroEre_CAF1 7796 100 + 1
GCCUGACAUUGAACAAGGUCAAGCAACAAGC---CUUAGCAACAAAUGUUGCCAGCGAAAU-UUGUUGCUUACGAAAUGCGAAUAGAAAUUGUUGAAAACCGAA
........((.(((((..(((((((((((((---....(((((....)))))..)).....-))))))))).((.....))....))..))))).))....... ( -22.90)
>DroYak_CAF1 6654 100 + 1
GCUUGACAUUGAACAAGGUCAAGCAACAAGC---CUUAGCAACAAAUGUUGCCAGCGAAAU-UUGUUGCUUACGAAAUGCGAAUAGAAAUUGUUGAAAACCGAA
(((((((.((....)).)))))))(((((..---...((((((((((.(((....))).))-))))))))..((.....))........))))).......... ( -25.80)
>DroAna_CAF1 3764 102 + 1
GCCUGACAUUGAACAAGGUCAGGCAACAAUGUUGCCUGGCAAC--AUGUUGCCAGCAAGACAAUGUUGCGUACGAAACCCACAUAGAAAUUGUCGAAAACCGAA
(((((((.((....)).)))))))((((.((((..(((((((.--...)))))))...)))).)))).........................(((.....))). ( -31.30)
>consensus
GCUUGACAUUGAACAAGGUCAAGCAACAAGC___CUUAGCAACAAAUGUUGCCAGCGAAAU_UUGUUGCUUACGAAAUGCGAAUAGAAAUUGUUGAAAACCGAA
(((((((.((....)).)))))))..............(((((....)))))((((((.......((((.........)))).......))))))......... (-21.81 = -21.97 +   0.17)

alignment

secondary structure

dotplot

Window 9

Location	22,084,930 – 22,085,030
Length	100
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	92.57
Mean single sequence MFE	-24.07
Consensus MFE	-20.92
Energy contribution	-20.89
Covariance contribution	-0.03
Combinations/Pair	1.10
Mean z-score	-1.65
Structure conservation index	0.87
SVM decision value	0.60
SVM RNA-class probability	0.794174
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22084930 100 - 27905053
UUCGGUUUUCAACAAUUUCUAUUCGCAUUUCGUAAGCAACAA-AUUUCGCUGGCAACAUUUGUUGCUAAG---GCUUGUUGCUUGACCUUGUUCAAUGUCAAGC
...((..((.(((((..((.....((.....))(((((((((-.....(((((((((....))))))..)---)))))))))))))..))))).))..)).... ( -22.50)
>DroSec_CAF1 7699 100 - 1
UUCGGUUUUCAACAAUUUCUAUUCGCAUUUCGUAAGCAACAA-AUUUCGCUGGCAACAUUUGUUGCUAAG---GCUUGUUGCUUGACCUUGUUCAAUGUCAAGC
...((..((.(((((..((.....((.....))(((((((((-.....(((((((((....))))))..)---)))))))))))))..))))).))..)).... ( -22.50)
>DroSim_CAF1 8139 100 - 1
UUCGGUUUUCAACAAUUUCUAUUCGCAUUUCGUAAGCAACAA-AUUUCGCUGGCAACAUUUGUUGCUAAG---GCUUGUUGCUUGACCUUGUUCAAUGUCAAGC
...((..((.(((((..((.....((.....))(((((((((-.....(((((((((....))))))..)---)))))))))))))..))))).))..)).... ( -22.50)
>DroEre_CAF1 7796 100 - 1
UUCGGUUUUCAACAAUUUCUAUUCGCAUUUCGUAAGCAACAA-AUUUCGCUGGCAACAUUUGUUGCUAAG---GCUUGUUGCUUGACCUUGUUCAAUGUCAGGC
...((..((.(((((..((.....((.....))(((((((((-.....(((((((((....))))))..)---)))))))))))))..))))).))..)).... ( -22.50)
>DroYak_CAF1 6654 100 - 1
UUCGGUUUUCAACAAUUUCUAUUCGCAUUUCGUAAGCAACAA-AUUUCGCUGGCAACAUUUGUUGCUAAG---GCUUGUUGCUUGACCUUGUUCAAUGUCAAGC
...((..((.(((((..((.....((.....))(((((((((-.....(((((((((....))))))..)---)))))))))))))..))))).))..)).... ( -22.50)
>DroAna_CAF1 3764 102 - 1
UUCGGUUUUCGACAAUUUCUAUGUGGGUUUCGUACGCAACAUUGUCUUGCUGGCAACAU--GUUGCCAGGCAACAUUGUUGCCUGACCUUGUUCAAUGUCAGGC
..(((...((.(((.......))).))..)))...((((((.(((..(((((((((...--.)))))).)))))).))))))(((((.((....)).))))).. ( -31.90)
>consensus
UUCGGUUUUCAACAAUUUCUAUUCGCAUUUCGUAAGCAACAA_AUUUCGCUGGCAACAUUUGUUGCUAAG___GCUUGUUGCUUGACCUUGUUCAAUGUCAAGC
................................((((((((((........(((((((....))))))).......))))))))))..((((........)))). (-20.92 = -20.89 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:06:55 2006