Locus 4562

Sequence ID	3L_DroMel_CAF1
Location	13,114,793 – 13,114,977
Length	184
Max. P	0.979069

overview

Window 5

Location	13,114,793 – 13,114,913
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.93
Mean single sequence MFE	-39.22
Consensus MFE	-34.37
Energy contribution	-35.52
Covariance contribution	1.15
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.88
SVM decision value	1.01
SVM RNA-class probability	0.899258
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13114793 120 + 23771897
UGGCGGAGUCCAGUUAACGCUUCAAUGGUGGCAAAUGGCUAAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCUGCCUUUUUUCUUGGCGCCGAGUU
.(((((((...(((...(((((......((((.....))))......(((((((((((.......))))))))))))))))....)))..)))))))(((.........)))........ ( -41.80)
>DroSec_CAF1 102465 120 + 1
UGGCGGAGUCCAGUUAACGCUUCAAUGGUGGCAAAUGGCUAAAUUCGGGGGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCUGCCUUUUUACUUGGCGCCGAGUU
.(((((((...(((...(((((......((((.....))))......((.((((((((.......)))))))).)))))))....)))..)))))))........(((((....))))). ( -37.80)
>DroSim_CAF1 100192 120 + 1
UUGCGGAGUCCAGUUAACGCUUCAAUGGUGGCAAAUGGCUAAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCUGCCUUUUUACUUGGCGCCGAGUU
..((((((...(((...(((((......((((.....))))......(((((((((((.......))))))))))))))))....)))..)))))).........(((((....))))). ( -40.60)
>DroEre_CAF1 99088 96 + 1
UGGCGG-GUCCAGUUAACGCUUCAAUGGUGGCAAAUGGCUAAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCU-----------------------
.(((((-(((((((((..(((........)))...))))).......(((((((((((.......)))))))))))))))(((.....))).)))))----------------------- ( -33.50)
>DroYak_CAF1 102492 112 + 1
UGGCGG-GUCCAGUUAACGCUUCAAUGGUGGCAAAUGGCUAAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCCGGCGAAAUGCUUUCUCCGCUGCCU-------GGGCGCCAAGUU
((((..-((((((....((((.....))))......(((.......((((((((((((.......))))))))))))((.(((.....))).)))))..))-------)))))))).... ( -42.40)
>consensus
UGGCGGAGUCCAGUUAACGCUUCAAUGGUGGCAAAUGGCUAAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCUGCCUUUUU_CUUGGCGCCGAGUU
.(((((((...(((...(((((......((((.....))))......(((((((((((.......))))))))))))))))....)))..)))))))(((.........)))........ (-34.37 = -35.52 +   1.15)

alignment

secondary structure

dotplot

Window 6

Location	13,114,793 – 13,114,913
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.93
Mean single sequence MFE	-33.44
Consensus MFE	-28.63
Energy contribution	-29.38
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.86
SVM decision value	1.83
SVM RNA-class probability	0.979069
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13114793 120 - 23771897
AACUCGGCGCCAAGAAAAAAGGCAGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUUAGCCAUUUGCCACCAUUGAAGCGUUAACUGGACUCCGCCA
.....((((((.........)))...((((...((..((((...((((((((((.........))))))))))))))....)).........(((((((....)))).))).))))))). ( -35.70)
>DroSec_CAF1 102465 120 - 1
AACUCGGCGCCAAGUAAAAAGGCAGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCCCCCGAAUUUAGCCAUUUGCCACCAUUGAAGCGUUAACUGGACUCCGCCA
.....((((((.........)))...((((...((..((((...((.(((((((.........))))))))).))))....)).........(((((((....)))).))).))))))). ( -29.90)
>DroSim_CAF1 100192 120 - 1
AACUCGGCGCCAAGUAAAAAGGCAGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUUAGCCAUUUGCCACCAUUGAAGCGUUAACUGGACUCCGCAA
........(((.........))).((((((...((..((((...((((((((((.........))))))))))))))....)).........(((((((....)))).))).)))))).. ( -35.30)
>DroEre_CAF1 99088 96 - 1
-----------------------AGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUUAGCCAUUUGCCACCAUUGAAGCGUUAACUGGAC-CCGCCA
-----------------------.((((.....((..((((...((((((((((.........))))))))))))))....)).........(((((((....)))).)))..-)))).. ( -25.90)
>DroYak_CAF1 102492 112 - 1
AACUUGGCGCCC-------AGGCAGCGGAGAAAGCAUUUCGCCGGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUUAGCCAUUUGCCACCAUUGAAGCGUUAACUGGAC-CCGCCA
....(((((...-------.((((((((((......))))))((((((((((((.........))))))))))))............)))).(((((((....)))).)))..-.))))) ( -40.40)
>consensus
AACUCGGCGCCAAG_AAAAAGGCAGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUUAGCCAUUUGCCACCAUUGAAGCGUUAACUGGACUCCGCCA
........(((.........))).((((((...((..((((...((((((((((.........))))))))))))))....)).........(((((((....)))).))).)))))).. (-28.63 = -29.38 +   0.75)

alignment

secondary structure

dotplot

Window 7

Location	13,114,833 – 13,114,949
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.72
Mean single sequence MFE	-33.24
Consensus MFE	-24.57
Energy contribution	-26.12
Covariance contribution	1.55
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.74
SVM decision value	0.45
SVM RNA-class probability	0.741081
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13114833 116 + 23771897
AAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCUGCCUUUUUUCUUGGCGCCGAGUUU----UCUUUUUUGAAAAACGAGUUACACACGUGUCGCAA
.....(.(((((((((((.......))))))))))).)((((.(((....(((.((.(((.........))))).)))(((----((......)))))............))).)))).. ( -35.30)
>DroSec_CAF1 102505 116 + 1
AAAUUCGGGGGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCUGCCUUUUUACUUGGCGCCGAGUUU----UCUUUUUUGAAAAACGAGUUACACACGUGUCGCAA
.....(.((.((((((((.......)))))))).)).)((((.(((....(((.((.(((.........))))).)))(((----((......)))))............))).)))).. ( -31.20)
>DroSim_CAF1 100232 116 + 1
AAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCUGCCUUUUUACUUGGCGCCGAGUUU----UCUUUUUUGAAAAACGAGUUACACACGUGUCGCAA
.....(.(((((((((((.......))))))))))).)((((.(((....(((.((.(((.........))))).)))(((----((......)))))............))).)))).. ( -35.30)
>DroEre_CAF1 99127 94 + 1
AAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCU--------------------------UUCUUUUUUUGAAAAACGAGUUACACACGUGUCGCAA
.....(.(((((((((((.......))))))))))).)((((.(((....(((...(--------------------------(((.......))))...))).......))).)))).. ( -26.40)
>DroYak_CAF1 102531 113 + 1
AAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCCGGCGAAAUGCUUUCUCCGCUGCCU-------GGGCGCCAAGUUUUGUUUUUUUUUUGAAAAACGAGUUACACACGUGUCGCAA
.....(((((((((((((.......)))))))))))))((((.(((........((.((..-------..)))).....((((((((((....)))))))))).......))).)))).. ( -38.00)
>consensus
AAAUUCGGGCGCAUAAAGUGAAUUGUUUUAUGCGCCGGGCGAAAUGCUUUCUCCGCUGCCUUUUU_CUUGGCGCCGAGUUU____UCUUUUUUGAAAAACGAGUUACACACGUGUCGCAA
.....(.(((((((((((.......))))))))))).)((((........(((.((.(((.........))))).)))....................(((.(.....).))).)))).. (-24.57 = -26.12 +   1.55)

alignment

secondary structure

dotplot

Window 8

Location	13,114,833 – 13,114,949
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.72
Mean single sequence MFE	-31.96
Consensus MFE	-24.07
Energy contribution	-25.30
Covariance contribution	1.23
Combinations/Pair	1.03
Mean z-score	-2.57
Structure conservation index	0.75
SVM decision value	1.60
SVM RNA-class probability	0.966636
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13114833 116 - 23771897
UUGCGACACGUGUGUAACUCGUUUUUCAAAAAAGA----AAACUCGGCGCCAAGAAAAAAGGCAGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUU
..((((...((((.........(((((......))----)))(((.(((((.........))).)).)))...)))).))))..((((((((((.........))))))))))....... ( -33.50)
>DroSec_CAF1 102505 116 - 1
UUGCGACACGUGUGUAACUCGUUUUUCAAAAAAGA----AAACUCGGCGCCAAGUAAAAAGGCAGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCCCCCGAAUUU
..((((...((((.........(((((......))----)))(((.(((((.........))).)).)))...)))).)))).(((.(((((((.........)))))))..)))..... ( -27.90)
>DroSim_CAF1 100232 116 - 1
UUGCGACACGUGUGUAACUCGUUUUUCAAAAAAGA----AAACUCGGCGCCAAGUAAAAAGGCAGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUU
..((((...((((.........(((((......))----)))(((.(((((.........))).)).)))...)))).))))..((((((((((.........))))))))))....... ( -33.50)
>DroEre_CAF1 99127 94 - 1
UUGCGACACGUGUGUAACUCGUUUUUCAAAAAAAGAA--------------------------AGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUU
..((((...((((.....((((((((........)))--------------------------))))).....)))).))))..((((((((((.........))))))))))....... ( -26.80)
>DroYak_CAF1 102531 113 - 1
UUGCGACACGUGUGUAACUCGUUUUUCAAAAAAAAAACAAAACUUGGCGCCC-------AGGCAGCGGAGAAAGCAUUUCGCCGGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUU
..((((...((((.......((((((......))))))....(((.((((..-------..)).)).)))...)))).))))((((((((((((.........))))))))))))..... ( -38.10)
>consensus
UUGCGACACGUGUGUAACUCGUUUUUCAAAAAAGA____AAACUCGGCGCCAAG_AAAAAGGCAGCGGAGAAAGCAUUUCGCCCGGCGCAUAAAACAAUUCACUUUAUGCGCCCGAAUUU
.(((((.(((.(.....).)))...))...............(((.(((((.........))).)).)))...))).((((...((((((((((.........))))))))))))))... (-24.07 = -25.30 +   1.23)

alignment

secondary structure

dotplot

Window 9

Location	13,114,873 – 13,114,977
Length	104
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	85.21
Mean single sequence MFE	-27.20
Consensus MFE	-21.81
Energy contribution	-23.04
Covariance contribution	1.23
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.80
SVM decision value	0.16
SVM RNA-class probability	0.610619
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13114873 104 - 23771897
UGGAUGGAUUGAGGGGCAACCCUACCAUUUGCGACACGUGUGUAACUCGUUUUUCAAAAAAGA----AAACUCGGCGCCAAGAAAAAAGGCAGCGGAGAAAGCAUUUC
.((((((....((((....)))).))))))((...(((.(.....).)))(((((......))----)))(((.(((((.........))).)).)))...))..... ( -29.60)
>DroSec_CAF1 102545 104 - 1
UGGAUGGAUUGAGGGGCAACCCUACCAUUUGCGACACGUGUGUAACUCGUUUUUCAAAAAAGA----AAACUCGGCGCCAAGUAAAAAGGCAGCGGAGAAAGCAUUUC
.((((((....((((....)))).))))))((...(((.(.....).)))(((((......))----)))(((.(((((.........))).)).)))...))..... ( -29.60)
>DroSim_CAF1 100272 104 - 1
UGGAUGGAUUGAGGGGCAACCCUACCAUUUGCGACACGUGUGUAACUCGUUUUUCAAAAAAGA----AAACUCGGCGCCAAGUAAAAAGGCAGCGGAGAAAGCAUUUC
.((((((....((((....)))).))))))((...(((.(.....).)))(((((......))----)))(((.(((((.........))).)).)))...))..... ( -29.60)
>DroEre_CAF1 99167 82 - 1
CGGAUGGAUUGAGGGGCAACCCUACCAUUUGCGACACGUGUGUAACUCGUUUUUCAAAAAAAGAA--------------------------AGCGGAGAAAGCAUUUC
(((((((....((((....)))).)))))))......((((.....((((((((........)))--------------------------))))).....))))... ( -23.00)
>DroYak_CAF1 102571 101 - 1
UGGAUGAAUUGAGGGGCAACCCUACCAUUUGCGACACGUGUGUAACUCGUUUUUCAAAAAAAAAACAAAACUUGGCGCCC-------AGGCAGCGGAGAAAGCAUUUC
.(((((.....((((....))))..)))))((.(((....))).....((((((......))))))....(((.((((..-------..)).)).)))...))..... ( -24.20)
>consensus
UGGAUGGAUUGAGGGGCAACCCUACCAUUUGCGACACGUGUGUAACUCGUUUUUCAAAAAAGA____AAACUCGGCGCCAAG_AAAAAGGCAGCGGAGAAAGCAUUUC
.((((((....((((....)))).))))))((((.(((.(.....).)))...))...............(((.(((((.........))).)).)))...))..... (-21.81 = -23.04 +   1.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:41 2006