Locus 5463

Sequence ID	X_DroMel_CAF1
Location	14,204,695 – 14,204,878
Length	183
Max. P	0.986102

overview

Window 9

Location	14,204,695 – 14,204,809
Length	114
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	85.10
Mean single sequence MFE	-35.58
Consensus MFE	-24.20
Energy contribution	-26.07
Covariance contribution	1.87
Combinations/Pair	1.17
Mean z-score	-1.89
Structure conservation index	0.68
SVM decision value	0.44
SVM RNA-class probability	0.737393
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14204695 114 + 22224390
UGAACCUUCUCUGCAGAUGGUUCGCUCUCAUUACUCCUCGUACAUGUCGCAUUUAGUUGGCUGCCGGCUGGCGCAUUAAGCAGCAGCUUGUGCCAUAUGCCACAUGCCACAUGC
.(((((.(((....))).)))))((...((((((.....))).)))..)).....((.(((((..((((((((((...(((....))))))))))...))).)).))))).... ( -34.60)
>DroSec_CAF1 116013 112 + 1
CGAACCUU--CUGCAGAUGGUUCGCUCUCAUUACUACUCGUACAUGUCGCAUUUAGUUGGCUAGCGGCUGGUGCAUUAAGCAGCAGCUUGUGCCAUAUGCCACAUGCCACAUGC
((((((.(--(....)).))))))...............((.(((((.((((.....((((....(((((.(((.....))).)))))...)))).)))).)))))..)).... ( -37.90)
>DroSim_CAF1 92039 112 + 1
CGAACCUU--CUGCAGAUGGUUCGCUCUCAUUACUACUCGUACAUGUCGCAUUUAGUUGGCUGGCGGCUGGUGCAUUAAGCAGCAGCUUGUGCCAUAUGCCACAUGCCACAUGC
((((((.(--(....)).))))))..................(((((.((((...((.((((((((((((.(((.....))).)))))...))))...))))))))).))))). ( -39.90)
>DroYak_CAF1 105976 96 + 1
UGGACCGU--CUGCAGAUAGUU------CAUUACUCCUCGUACAUGUCGCAUUUAGCUGACUGGCGGCUGGUGCAUUAAGCAG---CCAGU-------GCCGUAUGCCAUAUGC
(((((..(--(....))..)))------))........(((((..(((((.....)).))).((((.(((((((.....))).---)))))-------))))))))........ ( -29.90)
>consensus
CGAACCUU__CUGCAGAUGGUUCGCUCUCAUUACUACUCGUACAUGUCGCAUUUAGUUGGCUGGCGGCUGGUGCAUUAAGCAGCAGCUUGUGCCAUAUGCCACAUGCCACAUGC
((((((............))))))..................(((((.((((...((((((....(((((.(((.....))).)))))...))))...))...)))).))))). (-24.20 = -26.07 +   1.87)

alignment

secondary structure

dotplot

Window 0

Location	14,204,695 – 14,204,809
Length	114
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	85.10
Mean single sequence MFE	-38.80
Consensus MFE	-25.34
Energy contribution	-27.65
Covariance contribution	2.31
Combinations/Pair	1.13
Mean z-score	-2.57
Structure conservation index	0.65
SVM decision value	1.04
SVM RNA-class probability	0.905630
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14204695 114 - 22224390
GCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAUGCGCCAGCCGGCAGCCAACUAAAUGCGACAUGUACGAGGAGUAAUGAGAGCGAACCAUCUGCAGAGAAGGUUCA
((((((.((((.((((.....(((.((((....))))..)))(((....))).)))).....)))).))))))..................(((((.(((....))).))))). ( -40.80)
>DroSec_CAF1 116013 112 - 1
GCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAUGCACCAGCCGCUAGCCAACUAAAUGCGACAUGUACGAGUAGUAAUGAGAGCGAACCAUCUGCAG--AAGGUUCG
((((((.((((.((((...((((....((((.(((.....))).)))).)))))))).....)))).)))))).................((((((.((....)--).)))))) ( -40.10)
>DroSim_CAF1 92039 112 - 1
GCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAUGCACCAGCCGCCAGCCAACUAAAUGCGACAUGUACGAGUAGUAAUGAGAGCGAACCAUCUGCAG--AAGGUUCG
((((((.((((.((((...((((....((((.(((.....))).)))).)))))))).....)))).)))))).................((((((.((....)--).)))))) ( -42.40)
>DroYak_CAF1 105976 96 - 1
GCAUAUGGCAUACGGC-------ACUGG---CUGCUUAAUGCACCAGCCGCCAGUCAGCUAAAUGCGACAUGUACGAGGAGUAAUG------AACUAUCUGCAG--ACGGUCCA
((((.((((..(((((-------.((((---.(((.....)))))))..))).))..)))).))))(((.((((.((..(((....------.))).)))))).--...))).. ( -31.90)
>consensus
GCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAUGCACCAGCCGCCAGCCAACUAAAUGCGACAUGUACGAGGAGUAAUGAGAGCGAACCAUCUGCAG__AAGGUUCA
((((((.((((.((((...((((....((((.(((.....))).)))).)))))))).....)))).))))))..................(((((............))))). (-25.34 = -27.65 +   2.31)

alignment

secondary structure

dotplot

Window 1

Location	14,204,729 – 14,204,838
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	77.54
Mean single sequence MFE	-34.30
Consensus MFE	-19.38
Energy contribution	-22.76
Covariance contribution	3.38
Combinations/Pair	1.07
Mean z-score	-2.48
Structure conservation index	0.57
SVM decision value	2.03
SVM RNA-class probability	0.986102
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14204729 109 - 22224390
GCGUUUUUAAACGCGUCAUUUGCCAAAUUGCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAUGCGCCAGCCGGCAGCCAACUAAAUGCGACAUGUACGAGGA
(((((....)))))........((....(((((((.((((.((((.....(((.((((....))))..)))(((....))).)))).....)))).)))))))...)). ( -38.80)
>DroSec_CAF1 116045 109 - 1
GCGUUUUUAAACGCGUCAUUUGCCAAAUUGCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAUGCACCAGCCGCUAGCCAACUAAAUGCGACAUGUACGAGUA
(((((....)))))...(((((......(((((((.((((.((((...((((....((((.(((.....))).)))).)))))))).....)))).)))))))))))). ( -37.70)
>DroSim_CAF1 92071 109 - 1
GCGUUUUUAAACGCGUCAUUUGCCAAAUUGCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAUGCACCAGCCGCCAGCCAACUAAAUGCGACAUGUACGAGUA
(((((....)))))...(((((......(((((((.((((.((((...((((....((((.(((.....))).)))).)))))))).....)))).)))))))))))). ( -40.00)
>DroEre_CAF1 103710 87 - 1
GCGUUUUUAAAGCCCUCAUUUGCCAAAUUGCAUGUGCCAUGUGGCAU-----ACUAG---CUGCUUCAUGCACC--------------GAAAUGCGGCAUGUACGAGGA
.............((((...(((......))).((((.((((.((((-----....(---.(((.....))).)--------------...)))).)))))))))))). ( -25.30)
>DroYak_CAF1 106002 85 - 1
GCGUUUUUAAACGC--------------GGCAUAUGGCAUACGGC-------ACUGG---CUGCUUAAUGCACCAGCCGCCAGUCAGCUAAAUGCGACAUGUACGAGGA
(((((....)))))--------------.((((.((((..(((((-------.((((---.(((.....)))))))..))).))..)))).)))).............. ( -29.70)
>consensus
GCGUUUUUAAACGCGUCAUUUGCCAAAUUGCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAUGCACCAGCCGCCAGCCAACUAAAUGCGACAUGUACGAGGA
(((((....)))))..............(((((((.((((.(((....((((....((((.(((.....))).)))).....)))).))).)))).)))))))...... (-19.38 = -22.76 +   3.38)

alignment

secondary structure

dotplot

Window 2

Location	14,204,769 – 14,204,878
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	82.35
Mean single sequence MFE	-29.42
Consensus MFE	-16.76
Energy contribution	-19.56
Covariance contribution	2.80
Combinations/Pair	1.11
Mean z-score	-2.40
Structure conservation index	0.57
SVM decision value	0.76
SVM RNA-class probability	0.843235
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14204769 109 + 22224390
AUUAAGCAGCAGCUUGUGCCAUAUGCCACAUGCCACAUGCAAUUUGGCAAAUGACGCGUUUAAAAACGCGACAGUGGCAAUAAACACGCGCAAAACGUUUGAAAAUGAG
.((((((....((.((((.....((((((.(((((.........)))))..((.((((((....)))))).)))))))).....)))).)).....))))))....... ( -32.40)
>DroSec_CAF1 116085 109 + 1
AUUAAGCAGCAGCUUGUGCCAUAUGCCACAUGCCACAUGCAAUUUGGCAAAUGACGCGUUUAAAAACGCGACAGUGGCAAUAAACACGCGCGAAACGUUUGAAAAUGAG
.((((((....((.((((.....((((((.(((((.........)))))..((.((((((....)))))).)))))))).....)))).)).....))))))....... ( -33.50)
>DroSim_CAF1 92111 109 + 1
AUUAAGCAGCAGCUUGUGCCAUAUGCCACAUGCCACAUGCAAUUUGGCAAAUGACGCGUUUAAAAACGCGACAGUGGCAAUAAACACGCGCGGAACGUUUGAAAAUGAG
.((((((..(.((.((((.....((((((.(((((.........)))))..((.((((((....)))))).)))))))).....)))).)).)...))))))....... ( -33.70)
>DroEre_CAF1 103736 101 + 1
AUGAAGCAG---CUAGU-----AUGCCACAUGGCACAUGCAAUUUGGCAAAUGAGGGCUUUAAAAACGCGACAUUGGCAAUAAACACGCGCGAAGCGUUUGGAAAUGAG
.((((((..---((.((-----.(((((.((.((....)).)).))))).)).)).)))))).((((((....(((((.........)).))).))))))......... ( -25.50)
>DroYak_CAF1 106042 85 + 1
AUUAAGCAG---CCAGU-------GCCGUAUGCCAUAUGCC--------------GCGUUUAAAAACGCGACAGCGGCAAUAAACACGCGCAAAACGUUUGAAAACGCG
.....((..---....(-------(((((..((.....))(--------------(((((....))))))...)))))).....((.(((.....))).)).....)). ( -22.00)
>consensus
AUUAAGCAGCAGCUUGUGCCAUAUGCCACAUGCCACAUGCAAUUUGGCAAAUGACGCGUUUAAAAACGCGACAGUGGCAAUAAACACGCGCGAAACGUUUGAAAAUGAG
.((((((....((.((((.....((((((.(((((.........)))))......(((((....)))))....)))))).....)))).)).....))))))....... (-16.76 = -19.56 +   2.80)

alignment

secondary structure

dotplot

Window 3

Location	14,204,769 – 14,204,878
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	82.35
Mean single sequence MFE	-30.98
Consensus MFE	-17.26
Energy contribution	-20.18
Covariance contribution	2.92
Combinations/Pair	1.07
Mean z-score	-2.43
Structure conservation index	0.56
SVM decision value	0.74
SVM RNA-class probability	0.838227
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14204769 109 - 22224390
CUCAUUUUCAAACGUUUUGCGCGUGUUUAUUGCCACUGUCGCGUUUUUAAACGCGUCAUUUGCCAAAUUGCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAU
......................(((((...((((((....(((((....)))))(((((.(((......))).)))))..))))))...)))))((((....))))... ( -34.60)
>DroSec_CAF1 116085 109 - 1
CUCAUUUUCAAACGUUUCGCGCGUGUUUAUUGCCACUGUCGCGUUUUUAAACGCGUCAUUUGCCAAAUUGCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAU
......................(((((...((((((....(((((....)))))(((((.(((......))).)))))..))))))...)))))((((....))))... ( -34.60)
>DroSim_CAF1 92111 109 - 1
CUCAUUUUCAAACGUUCCGCGCGUGUUUAUUGCCACUGUCGCGUUUUUAAACGCGUCAUUUGCCAAAUUGCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAU
......................(((((...((((((....(((((....)))))(((((.(((......))).)))))..))))))...)))))((((....))))... ( -34.60)
>DroEre_CAF1 103736 101 - 1
CUCAUUUCCAAACGCUUCGCGCGUGUUUAUUGCCAAUGUCGCGUUUUUAAAGCCCUCAUUUGCCAAAUUGCAUGUGCCAUGUGGCAU-----ACUAG---CUGCUUCAU
..................((((((((.....((.((((..((.........))...)))).))......))))))))...(..((..-----....)---)..)..... ( -21.80)
>DroYak_CAF1 106042 85 - 1
CGCGUUUUCAAACGUUUUGCGCGUGUUUAUUGCCGCUGUCGCGUUUUUAAACGC--------------GGCAUAUGGCAUACGGC-------ACUGG---CUGCUUAAU
.(((((....)))))...(((((((((...(((((.(((((((((....)))))--------------))))..)))))...)))-------))..)---).))..... ( -29.30)
>consensus
CUCAUUUUCAAACGUUUCGCGCGUGUUUAUUGCCACUGUCGCGUUUUUAAACGCGUCAUUUGCCAAAUUGCAUGUGGCAUGUGGCAUAUGGCACAAGCUGCUGCUUAAU
.............((...((..(((((...(((((((((((((((....)))))......(((......)))...)))).))))))...)))))..))....))..... (-17.26 = -20.18 +   2.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:33 2006