Locus 8663

Sequence ID	X_DroMel_CAF1
Location	21,951,222 – 21,951,506
Length	284
Max. P	0.999758

overview

Window 9

Location	21,951,222 – 21,951,320
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.63
Mean single sequence MFE	-35.86
Consensus MFE	-24.94
Energy contribution	-25.82
Covariance contribution	0.88
Combinations/Pair	1.03
Mean z-score	-1.77
Structure conservation index	0.70
SVM decision value	0.07
SVM RNA-class probability	0.570676
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21951222 98 - 22224390
CUGC--------------AAUCGGAGCCGUUUCUUUGGAGCUUGCGGCAAAGUUUGCAAACUCCCCCAG--------AGCCGCUGUUUAUCGGUUCUGUGGGCUUUGUUCAAAGUUCUGU
((..--------------...(((((((........((((.((((((......)))))).)))).((((--------(((((........)))))))).)))))))).....))...... ( -32.40)
>DroSec_CAF1 9758 106 - 1
CUGC--------------AAUCGGAGCCGUUUCUUUGGAGUUUGCGGCAAAGUUUGCAAACUCCCCCAGCGCUGCAGCGCCGCUGUUUAUCGGUUCUGUGGGCUUUGUUCAAAGUUCUGU
..((--------------(..((((((((.......(((((((((((......)))))))))))..((((((......).))))).....)))))))).(((((((....)))))))))) ( -38.10)
>DroSim_CAF1 1419 106 - 1
CUGC--------------AAUCGGAGCCGUUUCUUUGGAGUUUGCGGCAAAGUUUGCAAACUCCCCCAGCGCUGCAGCGCCGCUGUUUAUCGGUUCUGUGGGCUUUGUUCAAAGUUCUGU
..((--------------(..((((((((.......(((((((((((......)))))))))))..((((((......).))))).....)))))))).(((((((....)))))))))) ( -38.10)
>DroEre_CAF1 1361 112 - 1
CUGCAAGCUGCAAGCAGCAAGCGGAGCCGUUUCUUUGAAGUUUGCGGCGAAGUUUGAAAACUCCCCCAG--------CGCCGCUGUUUAUCGGUUCUGUGGGCUUUGUUUAAAGUUCUGU
((((..((((....))))..)))).(((((..((....))...)))))(((.((((((.....((((((--------.((((........)))).))).))).....)))))).)))... ( -40.20)
>DroYak_CAF1 9320 98 - 1
CUGC--------------AAGCGGAGCCGUUUCUUUGAAGUUUGCGGCAAAGUUUGCCAGCUCCCCCAG--------CGCCGCUGUUUAUCGGUUCUGUGGGCUUUGUUUAAAGUUCUGU
..((--------------((((...(((((..((....))...)))))...))))))(((..(((.(((--------.((((........)))).))).)))..)))............. ( -30.50)
>consensus
CUGC______________AAUCGGAGCCGUUUCUUUGGAGUUUGCGGCAAAGUUUGCAAACUCCCCCAG________CGCCGCUGUUUAUCGGUUCUGUGGGCUUUGUUCAAAGUUCUGU
.....................((((((((.......(((((((((((......)))))))))))..(((.............))).....)))))))).(((((((....)))))))... (-24.94 = -25.82 +   0.88)

alignment

secondary structure

dotplot

Window 0

Location	21,951,320 – 21,951,426
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.87
Mean single sequence MFE	-36.27
Consensus MFE	-24.78
Energy contribution	-24.86
Covariance contribution	0.08
Combinations/Pair	1.15
Mean z-score	-1.81
Structure conservation index	0.68
SVM decision value	0.03
SVM RNA-class probability	0.548015
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21951320 106 - 22224390
AGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAACCCUUCGGUGGCGGGGGCACUUCGAUGGGAUUCGCCAGCCGGGGGUAAGACAAAUUAGUUGCAAGUUGCA--------------CG
.(((....((((......)))).......))).(((((.((((((((((....((.....))..))))))).))))))))...........((.((.....)))--------------). ( -28.70)
>DroSec_CAF1 9864 106 - 1
AGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGCCUUCGGUGGCGGGGGCACUGCGAUGGGACUUGCCAGCCGGGGGUAAGACAAAUUACUUGCAAGUUGCA--------------AG
.(((....((((......)))).......)))..(((((((((((((((..(.(......))..))))))).))))))))...........(((((.....)))--------------)) ( -34.00)
>DroSim_CAF1 1525 106 - 1
AGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGCCUUCGGUGGCGGGGGCACUGCGAUGGGACUUGCCAGCCGGGGGUAAGACAAAUUACUUGCAAGUUGCA--------------AG
.(((....((((......)))).......)))..(((((((((((((((..(.(......))..))))))).))))))))...........(((((.....)))--------------)) ( -34.00)
>DroEre_CAF1 1473 118 - 1
AGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGUCUUCGGUGGCGGGG--ACUCCGGUUGGAUUUGCCAGCCGGGGGUAAGACAAAUUAGUUGGAAGUUGCAAGUUGCAGGCUGCAAG
.((((........(((((((.........(((.((((((((....)))))--)))((((((((.....)))))))).))).........)))))))....(((.....)))))))..... ( -41.77)
>DroYak_CAF1 9418 120 - 1
AGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGCCUUCGGAGGCGGAGGCACUUCGGUGGGAUUUGCCAGCCGGGGGUAAGACAAAUUAGUUGCAAGUUGCAAGUUGCAAGUUGCAAG
.(((....((((......)))).......)))..((((((((.((((((..(((....)))...))))))..))))))))............((((((.((((.....)))).)))))). ( -42.90)
>consensus
AGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGCCUUCGGUGGCGGGGGCACUGCGAUGGGAUUUGCCAGCCGGGGGUAAGACAAAUUAGUUGCAAGUUGCA______________AG
.(((....((((......)))).......)))..(((((((((((((((....((.....))..))))))).)))))))).............(((.....)))................ (-24.78 = -24.86 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	21,951,386 – 21,951,506
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.25
Mean single sequence MFE	-40.82
Consensus MFE	-34.94
Energy contribution	-36.66
Covariance contribution	1.72
Combinations/Pair	1.06
Mean z-score	-3.27
Structure conservation index	0.86
SVM decision value	4.01
SVM RNA-class probability	0.999758
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21951386 120 + 22224390
GAAGGGUUGGCUUUUGUUUACAGCUGAUUGUAUUUGGCCUUUGUUUUCGGUCAUUGCCAAAGUUGUCACAUCGUCGGGCGAAGGCCUAAUGAAUAGAAAGCCAAGCCAGCACGAAAAUCU
...((.(((((((((((..((((((....(((..(((((.........))))).)))...)))))).)).((((..(((....)))..))))...))))))))).))............. ( -41.70)
>DroSec_CAF1 9930 120 + 1
GAAGGCUUGGCUUUUGUUUACAGCUGAUUGUAUUUGGCCUUUGUUUUCGGUCAUUGCCAAAGUUGUCACAUCGUCAGGCGACGGCCUAAUGAAUAGAAAGCCAAGCCAGCACGAAAAUCU
...((((((((((((((..((((((....(((..(((((.........))))).)))...)))))).)).((((.((((....)))).))))...))))))))))))............. ( -43.00)
>DroSim_CAF1 1591 120 + 1
GAAGGCUUGGCUUUUGUUUACAGCUGAUUGUAUUUGGCCUUUGUUUUCGGUCAUUGCCAAAGUUGUCACAUCGUCAGGCGACGGCCUAAUGAAUAGAAAGCCAAGCCAGCACGAAAAUCU
...((((((((((((((..((((((....(((..(((((.........))))).)))...)))))).)).((((.((((....)))).))))...))))))))))))............. ( -43.00)
>DroEre_CAF1 1551 120 + 1
GAAGACUUGGCUUUUGUUUACAGCUGAUUGUAUUUGGCCUUUGUUUUCGGUCAUUGCAAAAGUUGUCACAUCGUCGGGCGGCGGCCUAAUGAAUUGAAAGCCAAGUCAACACGAAAAUCU
...((((((((((((((..((((((..(((((..(((((.........))))).))))).)))))).)).((((..(((....)))..))))...))))))))))))............. ( -44.30)
>DroYak_CAF1 9498 107 + 1
GAAGGCUUGGCUUUUGUUUACAGCUGAUUGUAUUUGGCCUUUGUUUUCGGGCAUUGCAAAAGUUGUCACAUCGUCGGGCAAC-------------GAAAACCAAGCCAACACGAAAAUCU
...(((((((.(((((((.((((((..(((((....((((........))))..))))).))))))......(.....))))-------------)))).)))))))............. ( -32.10)
>consensus
GAAGGCUUGGCUUUUGUUUACAGCUGAUUGUAUUUGGCCUUUGUUUUCGGUCAUUGCCAAAGUUGUCACAUCGUCGGGCGACGGCCUAAUGAAUAGAAAGCCAAGCCAGCACGAAAAUCU
...((((((((((((((..((((((....(((..(((((.........))))).)))...)))))).)).((((.((((....)))).))))...))))))))))))............. (-34.94 = -36.66 +   1.72)

alignment

secondary structure

dotplot

Window 2

Location	21,951,386 – 21,951,506
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.25
Mean single sequence MFE	-31.24
Consensus MFE	-27.44
Energy contribution	-28.60
Covariance contribution	1.16
Combinations/Pair	1.10
Mean z-score	-1.82
Structure conservation index	0.88
SVM decision value	1.85
SVM RNA-class probability	0.980076
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21951386 120 - 22224390
AGAUUUUCGUGCUGGCUUGGCUUUCUAUUCAUUAGGCCUUCGCCCGACGAUGUGACAACUUUGGCAAUGACCGAAAACAAAGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAACCCUUC
.............((.((((((((..........(((((((((........))))....(((((......))))).....)))))...((((......))))....)))))))).))... ( -27.60)
>DroSec_CAF1 9930 120 - 1
AGAUUUUCGUGCUGGCUUGGCUUUCUAUUCAUUAGGCCGUCGCCUGACGAUGUGACAACUUUGGCAAUGACCGAAAACAAAGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGCCUUC
.............(((((((((((..........(((((((((........)))))...(((((......)))))......))))...((((......))))....)))))))))))... ( -38.10)
>DroSim_CAF1 1591 120 - 1
AGAUUUUCGUGCUGGCUUGGCUUUCUAUUCAUUAGGCCGUCGCCUGACGAUGUGACAACUUUGGCAAUGACCGAAAACAAAGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGCCUUC
.............(((((((((((..........(((((((((........)))))...(((((......)))))......))))...((((......))))....)))))))))))... ( -38.10)
>DroEre_CAF1 1551 120 - 1
AGAUUUUCGUGUUGACUUGGCUUUCAAUUCAUUAGGCCGCCGCCCGACGAUGUGACAACUUUUGCAAUGACCGAAAACAAAGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGUCUUC
.............(((((((((((..........((((..((.....)).((..(......)..))...............))))...((((......))))....)))))))))))... ( -28.00)
>DroYak_CAF1 9498 107 - 1
AGAUUUUCGUGUUGGCUUGGUUUUC-------------GUUGCCCGACGAUGUGACAACUUUUGCAAUGCCCGAAAACAAAGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGCCUUC
.............(((((((((((.-------------((((((((.((.((..(......)..)).))..))........)))....((((......))))))).)))))))))))... ( -24.40)
>consensus
AGAUUUUCGUGCUGGCUUGGCUUUCUAUUCAUUAGGCCGUCGCCCGACGAUGUGACAACUUUGGCAAUGACCGAAAACAAAGGCCAAAUACAAUCAGCUGUAAACAAAAGCCAAGCCUUC
.............(((((((((((..........(((((((((........)))))...(((((......)))))......))))...((((......))))....)))))))))))... (-27.44 = -28.60 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:45 2006