Locus 496

Sequence ID	X_DroMel_CAF1
Location	1,425,790 – 1,425,940
Length	150
Max. P	0.999773

overview

Window 3

Location	1,425,790 – 1,425,901
Length	111
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	78.12
Mean single sequence MFE	-35.37
Consensus MFE	-26.88
Energy contribution	-26.22
Covariance contribution	-0.66
Combinations/Pair	1.17
Mean z-score	-5.08
Structure conservation index	0.76
SVM decision value	3.28
SVM RNA-class probability	0.998917
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1425790 111 + 22224390
UUUUUAACAUUUUAAAAAUGGCUGCCUUUUUGCACCACACGCACACACACAUACAUAUAUAUGUACUGCCAGUUUUCCGAGAGUGUGUGUGUGUGUGUGUGCGCA-AUCAGA
(((((((....)))))))((..(((......(((((((((((((((((((.(((((....)))))((............)).))))))))))))))).)))))))-..)).. ( -38.90)
>DroSec_CAF1 30519 105 + 1
UUUUUAACAUUUUAAAAAUGGCUGCCUUUUUGCACCACACGGACACACACA------CAUAUGUACUGCCAGUUUUCCGAGUGUUUGUGUGUGUCUGUGUGUGCA-UUCAGA
.......((((.....)))).(((......(((((.(((((((((((((((------.((((..((.....)).......)))).))))))))))))))))))))-..))). ( -35.40)
>DroAna_CAF1 40293 97 + 1
UUUUUAACAUUUUAAAAAUGGCUGCCUUUUUGCAUCAAACACACAUACACU------CAUAC--ACU-------CUCUUCGUAUGUGUGUGUGUGUGUGUAUGCAAUUCCGA
.......((((.....)))).........((((((...((((((((((((.------(((((--...-------......))))).))))))))))))..))))))...... ( -31.80)
>consensus
UUUUUAACAUUUUAAAAAUGGCUGCCUUUUUGCACCACACGCACACACACA______CAUAUGUACUGCCAGUUUUCCGAGUGUGUGUGUGUGUGUGUGUGUGCA_UUCAGA
.......((((.....))))..........(((((.((((((((((((((....................................)))))))))))))))))))....... (-26.88 = -26.22 +  -0.66)

alignment

secondary structure

dotplot

Window 4

Location	1,425,790 – 1,425,901
Length	111
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	78.12
Mean single sequence MFE	-32.93
Consensus MFE	-23.06
Energy contribution	-22.62
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-4.29
Structure conservation index	0.70
SVM decision value	4.05
SVM RNA-class probability	0.999773
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1425790 111 - 22224390
UCUGAU-UGCGCACACACACACACACACACUCUCGGAAAACUGGCAGUACAUAUAUAUGUAUGUGUGUGUGCGUGUGGUGCAAAAAGGCAGCCAUUUUUAAAAUGUUAAAAA
(((..(-(((((.(((((.((((((((((((.((((....)))).))(((((....))))))))))))))).)))))))))))..)))......(((((((....))))))) ( -39.90)
>DroSec_CAF1 30519 105 - 1
UCUGAA-UGCACACACAGACACACACAAACACUCGGAAAACUGGCAGUACAUAUG------UGUGUGUGUCCGUGUGGUGCAAAAAGGCAGCCAUUUUUAAAAUGUUAAAAA
(((...-(((((((((.(((((((((.......(((....)))(((.......))------)))))))))).)))).)))))...)))......(((((((....))))))) ( -31.20)
>DroAna_CAF1 40293 97 - 1
UCGGAAUUGCAUACACACACACACACACAUACGAAGAG-------AGU--GUAUG------AGUGUAUGUGUGUUUGAUGCAAAAAGGCAGCCAUUUUUAAAAUGUUAAAAA
......((((((..(((((((.((((.((((((.....-------..)--)))))------.)))).)))))))...))))))...........(((((((....))))))) ( -27.70)
>consensus
UCUGAA_UGCACACACACACACACACACACACUCGGAAAACUGGCAGUACAUAUG______UGUGUGUGUGCGUGUGGUGCAAAAAGGCAGCCAUUUUUAAAAUGUUAAAAA
.......(((((((((.(((((((((....................................))))))))).)))).)))))............(((((((....))))))) (-23.06 = -22.62 +  -0.44)

alignment

secondary structure

dotplot

Window 5

Location	1,425,830 – 1,425,940
Length	110
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	76.22
Mean single sequence MFE	-29.01
Consensus MFE	-17.85
Energy contribution	-17.30
Covariance contribution	-0.55
Combinations/Pair	1.14
Mean z-score	-3.03
Structure conservation index	0.62
SVM decision value	3.51
SVM RNA-class probability	0.999316
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1425830 110 + 22224390
GCACACACACAUACAUAUAUAUGUACUGCCAGUUUUCCGAGAGUGUGUGUGUGUGUGUGUGCGCA-AUCAGACAAUUUAAGCACAUAAAUAUAUAUUGGAUUGGA-AAAUGC
((((((((((((((((((((......................))))))))))))))))))))(((-......((((((((...............))))))))..-...))) ( -35.51)
>DroSec_CAF1 30559 104 + 1
GGACACACACA------CAUAUGUACUGCCAGUUUUCCGAGUGUUUGUGUGUGUCUGUGUGUGCA-UUCAGACAAUUUAAGCACAUAAAUAUAUAUUGGAUUGGA-AAAUGC
((....(((..------....)))....)).((((((((((((((((((((((((((.((....)-).))))).......))))))))))))........)))))-)))).. ( -25.91)
>DroAna_CAF1 40333 97 + 1
ACACAUACACU------CAUAC--ACU-------CUCUUCGUAUGUGUGUGUGUGUGUGUAUGCAAUUCCGACAAUAUAAGCCCAUAAAUAUAUAUUGAAUUGAAAAAAUGC
((((((((((.------(((((--(..-------(.....)..)))))).))))))))))...((((((....((((((............))))))))))))......... ( -25.60)
>consensus
GCACACACACA______CAUAUGUACUGCCAGUUUUCCGAGUGUGUGUGUGUGUGUGUGUGUGCA_UUCAGACAAUUUAAGCACAUAAAUAUAUAUUGGAUUGGA_AAAUGC
((((((((((....................................))))))))))......(((.......((((((((...............))))))))......))) (-17.85 = -17.30 +  -0.55)

alignment

secondary structure

dotplot

Window 6

Location	1,425,830 – 1,425,940
Length	110
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	76.22
Mean single sequence MFE	-25.60
Consensus MFE	-14.52
Energy contribution	-14.74
Covariance contribution	0.22
Combinations/Pair	1.05
Mean z-score	-2.65
Structure conservation index	0.57
SVM decision value	2.01
SVM RNA-class probability	0.985645
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1425830 110 - 22224390
GCAUUU-UCCAAUCCAAUAUAUAUUUAUGUGCUUAAAUUGUCUGAU-UGCGCACACACACACACACACACUCUCGGAAAACUGGCAGUACAUAUAUAUGUAUGUGUGUGUGC
(((.((-..((((...(((((....)))))......))))...)).-)))(((((((((((.......(((.((((....)))).)))((((....)))).))))))))))) ( -28.20)
>DroSec_CAF1 30559 104 - 1
GCAUUU-UCCAAUCCAAUAUAUAUUUAUGUGCUUAAAUUGUCUGAA-UGCACACACAGACACACACAAACACUCGGAAAACUGGCAGUACAUAUG------UGUGUGUGUCC
((((((-..((((...(((((....)))))......))))...)))-))).......(((((((((.......(((....)))(((.......))------)))))))))). ( -24.80)
>DroAna_CAF1 40333 97 - 1
GCAUUUUUUCAAUUCAAUAUAUAUUUAUGGGCUUAUAUUGUCGGAAUUGCAUACACACACACACACACAUACGAAGAG-------AGU--GUAUG------AGUGUAUGUGU
(((....(((....(((((((............)))))))...))).)))......(((((.((((.((((((.....-------..)--)))))------.)))).))))) ( -23.80)
>consensus
GCAUUU_UCCAAUCCAAUAUAUAUUUAUGUGCUUAAAUUGUCUGAA_UGCACACACACACACACACACACACUCGGAAAACUGGCAGUACAUAUG______UGUGUGUGUGC
(((......((((...(((((....)))))......)))).......))).......(((((((((....................................))))))))). (-14.52 = -14.74 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:00 2006