Locus 6679

Sequence ID	3L_DroMel_CAF1
Location	17,754,833 – 17,755,073
Length	240
Max. P	0.999544

overview

Window 7

Location	17,754,833 – 17,754,953
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.72
Mean single sequence MFE	-22.45
Consensus MFE	-18.78
Energy contribution	-18.22
Covariance contribution	-0.56
Combinations/Pair	1.17
Mean z-score	-1.50
Structure conservation index	0.84
SVM decision value	0.61
SVM RNA-class probability	0.798817
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17754833 120 - 23771897
UAUAGUUACACACAUAGUAUAUCUUUUGUGGCGCCCCAUCAUCAAUAUUGAAAAGUGCACUCGCAGGAGCAAAAACAGCAAGAAAAACAAUUGAAAAGCACAAUAAAGUGUGCAACGUGA
..........(((...((.(.((((((((.((.((...(((.......)))....(((....))))).))....)))).)))).).)).........(((((......)))))...))). ( -22.00)
>DroSec_CAF1 777 117 - 1
UAUAGUUACACACAU---AUAUCUUUUGUGGCGCCCCAUCAUCAAUACUGAAAAGUGCACUCGCAGGAGCAAAAACAGCAAGAAAAACAAUUGAAAAGCACAAUAAAGUGUGCAACGUGA
..........(((..---...((((((((.((.((...........(((....)))((....)).)).))....)))).))))..............(((((......)))))...))). ( -22.70)
>DroSim_CAF1 3962 117 - 1
UAUAGUUACACACAU---AUAUCUUUUGUGGCGCCCCAUCAUCAAUAUUGAAAAGUGCACUCGCAGGAGCAAAAACAGCAAGAAAAACAAUUGAAAAGCACAAUAAAGUGUGCAACGUGA
..........(((..---...((((((((.((.((...(((.......)))....(((....))))).))....)))).))))..............(((((......)))))...))). ( -21.90)
>DroEre_CAF1 3510 116 - 1
UAUAGUUACAUA-AU---AUAUCUUUUGUGGCGCCCCAUCAUCAAUAUUGGAAAGUGCAAUUGCAAGAGCAAAAAUAACAAGAGAAACAAUUGAAAAGCACAAUACAGUGUGCAACGUGA
.....((((...-..---...((((((((.((((.(((..........)))...))))..((((....)))).....))))))))............(((((......)))))...)))) ( -25.50)
>DroYak_CAF1 20004 116 - 1
UAUAGUUACAUA-AU---AUAUCUUUUGUGGCGCCCCAUCAUCAAUAUUGGAAAGUGCACUUGCAAGCUUAAAAAUAACAAGAAAAACAAUUGAAAUGCACAAUAAAGUGUGCAACGUGA
.....((((...-..---...((..((((.((((.(((..........)))...)))).((((...............))))....))))..))..((((((......))))))..)))) ( -20.16)
>consensus
UAUAGUUACACACAU___AUAUCUUUUGUGGCGCCCCAUCAUCAAUAUUGAAAAGUGCACUCGCAGGAGCAAAAACAGCAAGAAAAACAAUUGAAAAGCACAAUAAAGUGUGCAACGUGA
........(((...........((((((((((((....(((.......)))...))))...))))))))............................(((((......)))))...))). (-18.78 = -18.22 +  -0.56)

alignment

secondary structure

dotplot

Window 8

Location	17,754,913 – 17,755,033
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.47
Mean single sequence MFE	-21.36
Consensus MFE	-19.03
Energy contribution	-19.03
Covariance contribution	-0.00
Combinations/Pair	1.08
Mean z-score	-1.44
Structure conservation index	0.89
SVM decision value	1.00
SVM RNA-class probability	0.898198
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17754913 120 - 23771897
CUUCACGUUUCACAUUUCAAUUCAUUGAUUAAGCAAAUGCAUUCAAUUUUCGAUUGGCUCUUAAUCAAUGAAGCGUUAAAUAUAGUUACACACAUAGUAUAUCUUUUGUGGCGCCCCAUC
....................(((((((((((((.....((..((.......))...)).)))))))))))))((((((.....((.(((.......)))...))....))))))...... ( -23.20)
>DroSec_CAF1 857 114 - 1
CUUCACGUUU---AUUUCAAUUCAUUGAUUAAGCAAAUGCAUUCAAUUUUCGAUUGGCUCUUAAUCAAUGAAGCGUUAAAUAUAGUUACACACAU---AUAUCUUUUGUGGCGCCCCAUC
..........---.......(((((((((((((.....((..((.......))...)).)))))))))))))((((((.(((((((.....)).)---))))......))))))...... ( -21.30)
>DroSim_CAF1 4042 114 - 1
CUUCACGUUU---AUUUCAAUUCAUUGAUUAAGCAAAUGCAUUCAAUUUUCGAUUGGCUCUUAAUCAAUGAAGCGUUAAAUAUAGUUACACACAU---AUAUCUUUUGUGGCGCCCCAUC
..........---.......(((((((((((((.....((..((.......))...)).)))))))))))))((((((.(((((((.....)).)---))))......))))))...... ( -21.30)
>DroEre_CAF1 3590 112 - 1
CUUUACGUUU---GUUUCAAUUCAUUGAUUUGGCAAAAGCGUUCAAUUUUCGAUUGGC-CUUAAUCAAUGAUGCGUUAAAUAUAGUUACAUA-AU---AUAUCUUUUGUGGCGCCCCAUC
....((((..---........(((((((((.(((.....((.........))....))-)..))))))))).))))........((((((..-..---........))))))........ ( -20.40)
>DroYak_CAF1 20084 113 - 1
CUUCACGUUU---AUUUCAAUUCAUUGAUUAGGCAAAUGCGUUCAAUUUUCGAUUGGCUCUUGAUCAAUGAAGCGUUAAAUAUAGUUACAUA-AU---AUAUCUUUUGUGGCGCCCCAUC
......((((---(...(..(((((((((((((.....((...(((((...))))))).)))))))))))))..).)))))...((((((..-..---........))))))........ ( -20.60)
>consensus
CUUCACGUUU___AUUUCAAUUCAUUGAUUAAGCAAAUGCAUUCAAUUUUCGAUUGGCUCUUAAUCAAUGAAGCGUUAAAUAUAGUUACACACAU___AUAUCUUUUGUGGCGCCCCAUC
....................(((((((((((((.....((..((.......))...)).)))))))))))))((((((.....((.................))....))))))...... (-19.03 = -19.03 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	17,754,953 – 17,755,073
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.20
Mean single sequence MFE	-28.20
Consensus MFE	-21.38
Energy contribution	-22.98
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-1.85
Structure conservation index	0.76
SVM decision value	0.54
SVM RNA-class probability	0.775177
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17754953 120 + 23771897
UUUAACGCUUCAUUGAUUAAGAGCCAAUCGAAAAUUGAAUGCAUUUGCUUAAUCAAUGAAUUGAAAUGUGAAACGUGAAGCCAGCAACAAAGAAUGGGCUGGCUGUUUGUGAAAUGGGCU
......(((((((((((((((...((.((((...)))).))......))))))))))))........((...(((...(((((((..((.....)).)))))))...)))...)).))). ( -30.80)
>DroSec_CAF1 894 117 + 1
UUUAACGCUUCAUUGAUUAAGAGCCAAUCGAAAAUUGAAUGCAUUUGCUUAAUCAAUGAAUUGAAAU---AAACGUGAAGCCAGCAACAAAGAAUGGGCUGGCUGUUUGUGAAAUGCGCU
.....((((((((((((((((...((.((((...)))).))......))))))))))))).....((---((((....(((((((..((.....)).))))))))))))).....))).. ( -32.50)
>DroSim_CAF1 4079 117 + 1
UUUAACGCUUCAUUGAUUAAGAGCCAAUCGAAAAUUGAAUGCAUUUGCUUAAUCAAUGAAUUGAAAU---AAACGUGAAGCCAGCAACAAAGAAUGGGCUGGCUGUUUGUGAAAUGCGCU
.....((((((((((((((((...((.((((...)))).))......))))))))))))).....((---((((....(((((((..((.....)).))))))))))))).....))).. ( -32.50)
>DroEre_CAF1 3626 112 + 1
UUUAACGCAUCAUUGAUUAAG-GCCAAUCGAAAAUUGAACGCUUUUGCCAAAUCAAUGAAUUGAAAC---AAACGUAAAGCCCACAAUGGAGAAUGAGGUGGCU----GCGAAAUGCGCU
.....(((((((((((((..(-((.((.((.........))..)).))).)))))))))........---...(((..((((.((.((.....))...))))))----)))...)))).. ( -24.20)
>DroYak_CAF1 20120 113 + 1
UUUAACGCUUCAUUGAUCAAGAGCCAAUCGAAAAUUGAACGCAUUUGCCUAAUCAAUGAAUUGAAAU---AAACGUGAAGCCAACUAUAUGGAAUGAGGUGGCU----CUGAAAUUCGCU
................(((.((((((.((((..(((((..((....))....)))))...))))...---...(((....(((......))).)))...)))))----))))........ ( -21.00)
>consensus
UUUAACGCUUCAUUGAUUAAGAGCCAAUCGAAAAUUGAAUGCAUUUGCUUAAUCAAUGAAUUGAAAU___AAACGUGAAGCCAGCAACAAAGAAUGGGCUGGCUGUUUGUGAAAUGCGCU
......(((((((((((((((.((...((((...))))..)).....)))))))))))))..................(((((((............))))))).............)). (-21.38 = -22.98 +   1.60)

alignment

secondary structure

dotplot

Window 0

Location	17,754,953 – 17,755,073
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.20
Mean single sequence MFE	-29.78
Consensus MFE	-25.36
Energy contribution	-26.36
Covariance contribution	1.00
Combinations/Pair	1.07
Mean z-score	-3.22
Structure conservation index	0.85
SVM decision value	3.71
SVM RNA-class probability	0.999544
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17754953 120 - 23771897
AGCCCAUUUCACAAACAGCCAGCCCAUUCUUUGUUGCUGGCUUCACGUUUCACAUUUCAAUUCAUUGAUUAAGCAAAUGCAUUCAAUUUUCGAUUGGCUCUUAAUCAAUGAAGCGUUAAA
.((.............(((((((.((.....))..)))))))..................(((((((((((((.....((..((.......))...)).)))))))))))))))...... ( -29.10)
>DroSec_CAF1 894 117 - 1
AGCGCAUUUCACAAACAGCCAGCCCAUUCUUUGUUGCUGGCUUCACGUUU---AUUUCAAUUCAUUGAUUAAGCAAAUGCAUUCAAUUUUCGAUUGGCUCUUAAUCAAUGAAGCGUUAAA
(((((.......(((((((((((.((.....))..)))))))....))))---.......(((((((((((((.....((..((.......))...)).))))))))))))))))))... ( -34.30)
>DroSim_CAF1 4079 117 - 1
AGCGCAUUUCACAAACAGCCAGCCCAUUCUUUGUUGCUGGCUUCACGUUU---AUUUCAAUUCAUUGAUUAAGCAAAUGCAUUCAAUUUUCGAUUGGCUCUUAAUCAAUGAAGCGUUAAA
(((((.......(((((((((((.((.....))..)))))))....))))---.......(((((((((((((.....((..((.......))...)).))))))))))))))))))... ( -34.30)
>DroEre_CAF1 3626 112 - 1
AGCGCAUUUCGC----AGCCACCUCAUUCUCCAUUGUGGGCUUUACGUUU---GUUUCAAUUCAUUGAUUUGGCAAAAGCGUUCAAUUUUCGAUUGGC-CUUAAUCAAUGAUGCGUUAAA
((((((......----((((....((........))..))))........---........(((((((((.(((.....((.........))....))-)..)))))))))))))))... ( -26.90)
>DroYak_CAF1 20120 113 - 1
AGCGAAUUUCAG----AGCCACCUCAUUCCAUAUAGUUGGCUUCACGUUU---AUUUCAAUUCAUUGAUUAGGCAAAUGCGUUCAAUUUUCGAUUGGCUCUUGAUCAAUGAAGCGUUAAA
.((((((....(----(((((.((.((.....)))).))))))...))))---.......(((((((((((((.....((...(((((...))))))).)))))))))))))))...... ( -24.30)
>consensus
AGCGCAUUUCACAAACAGCCAGCCCAUUCUUUGUUGCUGGCUUCACGUUU___AUUUCAAUUCAUUGAUUAAGCAAAUGCAUUCAAUUUUCGAUUGGCUCUUAAUCAAUGAAGCGUUAAA
(((((...........(((((((............)))))))..................(((((((((((((.....((..((.......))...)).))))))))))))))))))... (-25.36 = -26.36 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:23 2006