Locus 3570

Sequence ID	2R_DroMel_CAF1
Location	11,891,100 – 11,891,290
Length	190
Max. P	0.997619

overview

Window 5

Location	11,891,100 – 11,891,211
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.51
Mean single sequence MFE	-24.06
Consensus MFE	-18.68
Energy contribution	-20.12
Covariance contribution	1.44
Combinations/Pair	1.03
Mean z-score	-2.45
Structure conservation index	0.78
SVM decision value	1.66
SVM RNA-class probability	0.970368
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11891100 111 - 20766785
GCAGCCCCAAAUAAGGCUACAGUCAAAAUAGUGAAUAAACUACUUUAUUCAAGCUGCAAAAAUAAAUGUGAAAAAUAUUUAAUCAGAUCAGCA-AGCUGAUUACAGUC--------AAGC
(((((.........(((....))).......((((((((....)))))))).))))).....(((((((.....)))))))....((((((..-..))))))......--------.... ( -25.10)
>DroSec_CAF1 31610 116 - 1
GCAGCCCCAAAUAUG-CUACAGUCAAAAUAGUGAU--AACUACAUAAUUCAAGCUGCACAAGUAAAUGUGCAA-AUAUUUAAUCAGAUCAGCGGAGCUGAUUACAGUACUAUAUAAAAGC
(((((......((((-.....((((......))))--.....))))......))))).....(((((((....-)))))))....(((((((...))))))).................. ( -21.50)
>DroSim_CAF1 31761 119 - 1
GCAGCCCCAAAUAUGGCUACAGUCAAAAUAGUGAAUAAACUACAUUAUUCAAGCUGCACAAGUAAAUGUGCAAAAUAUUUAAUCAGAUCAGCA-AGCUGAUUACAGUCCUAUAUAAAAGC
(((((........((((....))))......(((((((......))))))).))))).....(((((((.....)))))))....((((((..-..)))))).................. ( -25.20)
>DroEre_CAF1 33552 119 - 1
GCAGCCCCAAACAUGGCCACAGUCAAAAUGGUGAAUAAAAUACUUUAUUCAUGCUGCAGCAGUAAAUGUACAAAAUAUUUAAUCAGAUCAGCA-AGCCGAUUACAAUCCUGUUUUACAGC
(((((........((((....)))).....(((((((((....))))))))))))))((((((((((((.....)))))))....((((.(..-..).))))......)))))....... ( -24.70)
>DroYak_CAF1 32050 119 - 1
GCAGCCCCAAAUAUGGCCACAGUCAAAAUAGUGAAUAAAAUACUUUAUUCAUGUUGCAGAAGUAAAUGUACAAAAAAUUUAAUCAGAUCAGCA-AGCCGAUUACAAUCCGGUUGCAAAGC
((((((........(((.............(((((((((....)))))))))((((......(((((.........))))).......)))).-.)))(((....))).))))))..... ( -23.82)
>consensus
GCAGCCCCAAAUAUGGCUACAGUCAAAAUAGUGAAUAAACUACUUUAUUCAAGCUGCACAAGUAAAUGUGCAAAAUAUUUAAUCAGAUCAGCA_AGCUGAUUACAGUCCUAUAUAAAAGC
(((((........((((....))))......(((((((......))))))).))))).....(((((((.....)))))))....(((((((...))))))).................. (-18.68 = -20.12 +   1.44)

alignment

secondary structure

dotplot

Window 6

Location	11,891,131 – 11,891,251
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.17
Mean single sequence MFE	-34.60
Consensus MFE	-26.92
Energy contribution	-27.48
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-3.59
Structure conservation index	0.78
SVM decision value	2.56
SVM RNA-class probability	0.995246
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11891131 120 + 20766785
AAAUAUUUUUCACAUUUAUUUUUGCAGCUUGAAUAAAGUAGUUUAUUCACUAUUUUGACUGUAGCCUUAUUUGGGGCUGCAGCAAGCGAAUUAGAUGUUGAAGAAAAUUGUCUUCCUGUA
.(((.(((((((((((((..(((((....((((((((....)))))))).....(((.((((((((((....)))))))))))))))))).)))))).))))))).)))........... ( -36.90)
>DroSec_CAF1 31650 116 + 1
AAAUAU-UUGCACAUUUACUUGUGCAGCUUGAAUUAUGUAGUU--AUCACUAUUUUGACUGUAG-CAUAUUUGGGGCUGCAGCAAGCGAAUUAGAUGUUGAAGAAAAUUGUCUUCCUGUA
.(((((-(((...(((..((((((((((((.((.(((((((((--(.........)))))...)-)))).)).)))))))).))))..)))))))))))(((((......)))))..... ( -33.40)
>DroSim_CAF1 31800 120 + 1
AAAUAUUUUGCACAUUUACUUGUGCAGCUUGAAUAAUGUAGUUUAUUCACUAUUUUGACUGUAGCCAUAUUUGGGGCUGCAGCAAGCGAAUUAGAUGUUGAAGAAAAUUGUCUUCCUGUA
.(((((((((((((......))))))(((((..(((.(((((......))))).))).((((((((........))))))))))))).....)))))))(((((......)))))..... ( -36.40)
>DroEre_CAF1 33591 120 + 1
AAAUAUUUUGUACAUUUACUGCUGCAGCAUGAAUAAAGUAUUUUAUUCACCAUUUUGACUGUGGCCAUGUUUGGGGCUGCAGCAAGCGAAUUAGAUGUUGAAGAAAAUUGUCUUCCUGUA
.(((((((.....(((..((((((((((.((((((((....))))))))((((.......))))(((....))).)))))))).))..))).)))))))(((((......)))))..... ( -33.30)
>DroYak_CAF1 32089 120 + 1
AAAUUUUUUGUACAUUUACUUCUGCAACAUGAAUAAAGUAUUUUAUUCACUAUUUUGACUGUGGCCAUAUUUGGGGCUGCAGCAAGCGAAUUAGAUGUUGAAGAAAAUUGUCUUCCUGUA
.((((((((..(((((((.(((.((....((((((((....)))))))).....(((.(((..(((........)))..))))))))))).)))))))...))))))))........... ( -33.00)
>consensus
AAAUAUUUUGCACAUUUACUUCUGCAGCUUGAAUAAAGUAGUUUAUUCACUAUUUUGACUGUAGCCAUAUUUGGGGCUGCAGCAAGCGAAUUAGAUGUUGAAGAAAAUUGUCUUCCUGUA
...........(((((((....(((....(((((((......))))))).....(((.((((((((........))))))))))))))...))))))).(((((......)))))..... (-26.92 = -27.48 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	11,891,131 – 11,891,251
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.17
Mean single sequence MFE	-27.36
Consensus MFE	-18.68
Energy contribution	-19.48
Covariance contribution	0.80
Combinations/Pair	1.07
Mean z-score	-3.52
Structure conservation index	0.68
SVM decision value	0.52
SVM RNA-class probability	0.766577
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11891131 120 - 20766785
UACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAAGGCUACAGUCAAAAUAGUGAAUAAACUACUUUAUUCAAGCUGCAAAAAUAAAUGUGAAAAAUAUUU
.....(((((......))))).........(((((((((((.((((........)))).))).))).....((((((((....))))))))................)))))........ ( -23.70)
>DroSec_CAF1 31650 116 - 1
UACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAUG-CUACAGUCAAAAUAGUGAU--AACUACAUAAUUCAAGCUGCACAAGUAAAUGUGCAA-AUAUUU
((((.(((((......)))))............(((((.((((((......((((-.....((((......))))--.....))))......)))))))))))...))))...-...... ( -23.90)
>DroSim_CAF1 31800 120 - 1
UACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAUGGCUACAGUCAAAAUAGUGAAUAAACUACAUUAUUCAAGCUGCACAAGUAAAUGUGCAAAAUAUUU
((((.(((((......)))))............(((((.((((((........((((....))))......(((((((......))))))).)))))))))))...)))).......... ( -28.50)
>DroEre_CAF1 33591 120 - 1
UACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAACAUGGCCACAGUCAAAAUGGUGAAUAAAAUACUUUAUUCAUGCUGCAGCAGUAAAUGUACAAAAUAUUU
((((.(((((......)))))............(((.((((((((........((((....)))).....(((((((((....))))))))))))))))))))...)))).......... ( -32.70)
>DroYak_CAF1 32089 120 - 1
UACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAUGGCCACAGUCAAAAUAGUGAAUAAAAUACUUUAUUCAUGUUGCAGAAGUAAAUGUACAAAAAAUUU
((((.(((((......)))))............((((.(((((((........((((....)))).....(((((((((....))))))))))))))))))))...)))).......... ( -28.00)
>consensus
UACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAUGGCUACAGUCAAAAUAGUGAAUAAACUACUUUAUUCAAGCUGCACAAGUAAAUGUGCAAAAUAUUU
((((.(((((......)))))..............((((((((((........((((....))))......(((((((......))))))).))))))...)))).)))).......... (-18.68 = -19.48 +   0.80)

alignment

secondary structure

dotplot

Window 8

Location	11,891,171 – 11,891,290
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.98
Mean single sequence MFE	-24.04
Consensus MFE	-21.80
Energy contribution	-22.84
Covariance contribution	1.04
Combinations/Pair	1.03
Mean z-score	-2.11
Structure conservation index	0.91
SVM decision value	2.90
SVM RNA-class probability	0.997619
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11891171 119 - 20766785
GCCUUUCCUAACUAAAACUUGAGGAAAUUAUGAAAU-UCAUACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAAGGCUACAGUCAAAAUAGUGAAUAAAC
...((((((............)))))).((((....-.))))...(((((......)))))........((((((((((((.((((........)))).))).))....))))))).... ( -24.50)
>DroSec_CAF1 31689 117 - 1
GCCUUUCCUAACUAAAACUUGGGGAAAUUAUGAAAUAUCAUACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAUG-CUACAGUCAAAAUAGUGAU--AAC
...((((((((.......)))))))).........((((((....(((((......)))))..............((((((.(((.........)-)).))).)))....)))))--).. ( -20.80)
>DroSim_CAF1 31840 119 - 1
GCCUUUCCUAACUAAAACUUGGGGAAAUUAUGAAAU-UCAUACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAUGGCUACAGUCAAAAUAGUGAAUAAAC
...((((((((.......))))))))..((((....-.))))...(((((......)))))........((((((((((((.((((........)))).))).))....))))))).... ( -26.30)
>DroEre_CAF1 33631 119 - 1
GCCUUUCCUAACUAAAACUUGGGGAAAUUAUGAAAU-UCAUACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAACAUGGCCACAGUCAAAAUGGUGAAUAAAA
...((((((((.......))))))))..((((....-.))))...(((((......)))))........((((((((((((..(((........)))..))).))....))))))).... ( -24.30)
>DroYak_CAF1 32129 119 - 1
GCCUUUCCUAACUAAAACUUGGGGAAAUUAUGAAAU-UCAUACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAUGGCCACAGUCAAAAUAGUGAAUAAAA
...((((((((.......))))))))..((((....-.))))...(((((......)))))........((((((((((((..(((........)))..))).))....))))))).... ( -24.30)
>consensus
GCCUUUCCUAACUAAAACUUGGGGAAAUUAUGAAAU_UCAUACAGGAAGACAAUUUUCUUCAACAUCUAAUUCGCUUGCUGCAGCCCCAAAUAUGGCUACAGUCAAAAUAGUGAAUAAAC
...((((((((.......))))))))..(((((....)))))...(((((......)))))........((((((((((((.((((........)))).))).))....))))))).... (-21.80 = -22.84 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:51 2006