Locus 376

Sequence ID	X_DroMel_CAF1
Location	1,129,666 – 1,129,841
Length	175
Max. P	0.996344

overview

Window 9

Location	1,129,666 – 1,129,761
Length	95
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	96.53
Mean single sequence MFE	-28.64
Consensus MFE	-24.52
Energy contribution	-24.92
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.56
Structure conservation index	0.86
SVM decision value	2.64
SVM RNA-class probability	0.996022
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1129666 95 + 22224390
UUCCAGCUUCAGUCCGGGGUUCAUUAAUGCGCACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUC-UUUUGU
...(((((.(((((.((......((((.((((.....))))))))((((((.....))))))..))))))).......)))))......-...... ( -26.90)
>DroSec_CAF1 26288 93 + 1
UUCCAGCUUCAGUC-GGGGUUCAUUAAUGCGCACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGCCUGUCUUUCCAGCUGUCUCU--UUUUGU
...(((((..((.(-(((.....((((.((((.....))))))))((((((.....)))))).....)))).))....))))).....--...... ( -26.70)
>DroSim_CAF1 27736 93 + 1
UUCCAGCUUCAGUC-GGGGUUCAUUAAUGCGCACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGCCUGUCUUUCCAGCUGUCUCU--UUUUGU
...(((((..((.(-(((.....((((.((((.....))))))))((((((.....)))))).....)))).))....))))).....--...... ( -26.70)
>DroEre_CAF1 27601 95 + 1
UCCCAGCUUCAGUC-GGUGUUCAUUAAUGCGCACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUCUUUUUGU
...(((((.(((((-(((.....((((.((((.....))))))))((((((.....)))))).)))))))).......)))))............. ( -32.20)
>DroYak_CAF1 27196 95 + 1
UGCCAGCUUCAGUC-GGGGUUCAUUAAUGCGCACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUCUUUUUGU
...(((((.(((((-((......((((.((((.....))))))))((((((.....))))))..))))))).......)))))............. ( -30.70)
>consensus
UUCCAGCUUCAGUC_GGGGUUCAUUAAUGCGCACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUC_UUUUGU
...(((((.(((((.((......((((.((((.....))))))))((((((.....))))))..))))))).......)))))............. (-24.52 = -24.92 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	1,129,666 – 1,129,761
Length	95
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	96.53
Mean single sequence MFE	-26.04
Consensus MFE	-22.30
Energy contribution	-22.70
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.86
SVM decision value	1.90
SVM RNA-class probability	0.981850
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1129666 95 - 22224390
ACAAAA-GAGAGACAGCUGGAAAGACAGUCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUGCGCAUUAAUGAACCCCGGACUGAAGCUGGAA
......-......(((((.......((((((((....)))....(((.((((...((((...))))........)))).)))))))).)))))... ( -25.30)
>DroSec_CAF1 26288 93 - 1
ACAAAA--AGAGACAGCUGGAAAGACAGGCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUGCGCAUUAAUGAACCCC-GACUGAAGCUGGAA
......--.....(((((....((...((.((..((((((.....))))))....((((...))))...........))))-..))..)))))... ( -23.70)
>DroSim_CAF1 27736 93 - 1
ACAAAA--AGAGACAGCUGGAAAGACAGGCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUGCGCAUUAAUGAACCCC-GACUGAAGCUGGAA
......--.....(((((....((...((.((..((((((.....))))))....((((...))))...........))))-..))..)))))... ( -23.70)
>DroEre_CAF1 27601 95 - 1
ACAAAAAGAGAGACAGCUGGAAAGACAGUCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUGCGCAUUAAUGAACACC-GACUGAAGCUGGGA
.............(((((.......(((((((..((((((.....))))))....((((...)))).............))-))))).)))))... ( -28.50)
>DroYak_CAF1 27196 95 - 1
ACAAAAAGAGAGACAGCUGGAAAGACAGUCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUGCGCAUUAAUGAACCCC-GACUGAAGCUGGCA
...............((..(.....(((((((..((((((.....))))))....((((...)))).............))-)))))...)..)). ( -29.00)
>consensus
ACAAAA_GAGAGACAGCUGGAAAGACAGUCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUGCGCAUUAAUGAACCCC_GACUGAAGCUGGAA
.............(((((.......(((((((..((((((.....))))))....((((...)))).............)).))))).)))))... (-22.30 = -22.70 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	1,129,697 – 1,129,801
Length	104
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	95.41
Mean single sequence MFE	-33.06
Consensus MFE	-28.22
Energy contribution	-28.90
Covariance contribution	0.68
Combinations/Pair	1.07
Mean z-score	-2.45
Structure conservation index	0.85
SVM decision value	2.68
SVM RNA-class probability	0.996344
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1129697 104 + 22224390
CACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUC-UUUUGUGAACAGAAGUGGAUCUCAGACACUCGGAAAAAUGGCUCAA
.....((.(((...((((((.....))))))..((((.(((((.((((.((((.((.(-....).))))))...))))....))))).))))......))).)). ( -32.80)
>DroSec_CAF1 26318 103 + 1
CACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGCCUGUCUUUCCAGCUGUCUCU--UUUUGUGAGCAGAAGUGGAUCUCAGACACUCGCAAAAAUGGCUCAA
.................(((((((.(((....)))((.(((((.((((.(((.(((.--......))))))...))))....)))))...))..))))))).... ( -30.80)
>DroSim_CAF1 27766 103 + 1
CACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGCCUGUCUUUCCAGCUGUCUCU--UUUUGUGAGCAGAAGUGGAUCUCAGACACUCGCAAAAAUGGCUCAA
.................(((((((.(((....)))((.(((((.((((.(((.(((.--......))))))...))))....)))))...))..))))))).... ( -30.80)
>DroEre_CAF1 27631 105 + 1
CACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUCUUUUUGUGAGCAGAAGUGGAUCUCAGACACUUGGAAAAAUGGUCCAA
......(.(((...((((((.....))))))))))((((((.(((((((.(((((((.((((((....)))))).))).....)))).))))))).))))))... ( -33.30)
>DroYak_CAF1 27226 105 + 1
CACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUCUUUUUGUGAGCAGCCGUGGAUCUCAGACACUCGGAAAAAUGGCUCAA
.....((.(((...((((((.....))))))..((((.(((((.((((((((.(((.(.....).)))))))..))))....))))).))))......))).)). ( -37.60)
>consensus
CACUAUGUGCUUAAAACGCCAUUUGGGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUC_UUUUGUGAGCAGAAGUGGAUCUCAGACACUCGGAAAAAUGGCUCAA
.....((.(((...((((((.....))))))..((((.(((((.((((.(((.(((.........))))))...))))....))))).))))......))).)). (-28.22 = -28.90 +   0.68)

alignment

secondary structure

dotplot

Window 2

Location	1,129,697 – 1,129,801
Length	104
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	95.41
Mean single sequence MFE	-31.76
Consensus MFE	-27.24
Energy contribution	-27.88
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.86
SVM decision value	1.73
SVM RNA-class probability	0.974653
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1129697 104 - 22224390
UUGAGCCAUUUUUCCGAGUGUCUGAGAUCCACUUCUGUUCACAAAA-GAGAGACAGCUGGAAAGACAGUCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUG
....(((((((....((.(((((....(((((((((.(((......-)))))).)).)))).))))).))(((....))).)))))))................. ( -31.00)
>DroSec_CAF1 26318 103 - 1
UUGAGCCAUUUUUGCGAGUGUCUGAGAUCCACUUCUGCUCACAAAA--AGAGACAGCUGGAAAGACAGGCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUG
....(((((((....(..(((((....((((...((((((......--.))).))).)))).)))))..)(((....))).)))))))................. ( -30.00)
>DroSim_CAF1 27766 103 - 1
UUGAGCCAUUUUUGCGAGUGUCUGAGAUCCACUUCUGCUCACAAAA--AGAGACAGCUGGAAAGACAGGCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUG
....(((((((....(..(((((....((((...((((((......--.))).))).)))).)))))..)(((....))).)))))))................. ( -30.00)
>DroEre_CAF1 27631 105 - 1
UUGGACCAUUUUUCCAAGUGUCUGAGAUCCACUUCUGCUCACAAAAAGAGAGACAGCUGGAAAGACAGUCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUG
...(((..((((((((..(((((.(((......))).(((.......))))))))..))))))))..))).(((((((((.....))))))...)))........ ( -31.60)
>DroYak_CAF1 27226 105 - 1
UUGAGCCAUUUUUCCGAGUGUCUGAGAUCCACGGCUGCUCACAAAAAGAGAGACAGCUGGAAAGACAGUCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUG
....(((((((....((.(((((....((((..(((((((.(.....).))).)))))))).))))).))(((....))).)))))))................. ( -36.20)
>consensus
UUGAGCCAUUUUUCCGAGUGUCUGAGAUCCACUUCUGCUCACAAAA_GAGAGACAGCUGGAAAGACAGUCGGCUAACGCCCAAAUGGCGUUUUAAGCACAUAGUG
....(((((((....((.(((((....((((...((((((.........))).))).)))).))))).))(((....))).)))))))................. (-27.24 = -27.88 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	1,129,722 – 1,129,841
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.92
Mean single sequence MFE	-31.98
Consensus MFE	-24.20
Energy contribution	-24.48
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.52
Structure conservation index	0.76
SVM decision value	0.27
SVM RNA-class probability	0.660349
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1129722 119 + 22224390
GGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUC-UUUUGUGAACAGAAGUGGAUCUCAGACACUCGGAAAAAUGGCUCAAGGGCCAGAAGAAAACUGUGCAUUCUUUUAGCUCUAAAUGU
(((....)))((((((.(((((((.((((((((-(((((....)))))).))).....)))))).))))).)))).)).(((((.(((((((.........))))))).)))))...... ( -35.40)
>DroSec_CAF1 26343 117 + 1
GGCGUUAGCCGCCUGUCUUUCCAGCUGUCUCU--UUUUGUGAGCAGAAGUGGAUCUCAGACACUCGCAAAAAUGGCUCAAGUGCCAGAAGAACACUUUU-GCUUUUUAAGCUCUAAAUAA
(((....)))((.(((((.((((.(((.(((.--......))))))...))))....)))))...((((((.((((......)))).........))))-)).......))......... ( -30.40)
>DroSim_CAF1 27791 117 + 1
GGCGUUAGCCGCCUGUCUUUCCAGCUGUCUCU--UUUUGUGAGCAGAAGUGGAUCUCAGACACUCGCAAAAAUGGCUCAAGUGCCAGAAGAAAACUUUU-GCUUUUUAAGCUCUAAAUAA
(((....)))((.(((((.((((.(((.(((.--......))))))...))))....)))))...((((((.((((......)))).........))))-)).......))......... ( -30.40)
>DroEre_CAF1 27656 109 + 1
GGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUCUUUUUGUGAGCAGAAGUGGAUCUCAGACACUUGGAAAAAUGGUCCAAGUGCCAGUGGGAAAAA-----------UAAAACUUAAUAC
(((....)))...(((.(((((.((((..(((.((((((....)))))).))).......((((((((.......)))))))).)))).))))).)-----------))........... ( -31.00)
>DroYak_CAF1 27251 95 + 1
GGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUCUUUUUGUGAGCAGCCGUGGAUCUCAGACACUCGGAAAAAUGGCUCAAGUGCCAGAUG-------------------------AAAAC
..((((..((((.(((((.((((((((.(((.(.....).)))))))..))))....))))).)))).....((((......))))))))-------------------------..... ( -32.70)
>consensus
GGCGUUAGCCGACUGUCUUUCCAGCUGUCUCUC_UUUUGUGAGCAGAAGUGGAUCUCAGACACUCGGAAAAAUGGCUCAAGUGCCAGAAGAAAACU_U____U_UUUAAGCUCUAAAUAA
(((....)))((.(((((.((((.(((.(((.........))))))...))))....))))).)).......((((......)))).................................. (-24.20 = -24.48 +   0.28)

alignment

secondary structure

dotplot

Window 4

Location	1,129,722 – 1,129,841
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.92
Mean single sequence MFE	-31.48
Consensus MFE	-22.72
Energy contribution	-23.36
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.64
Structure conservation index	0.72
SVM decision value	0.39
SVM RNA-class probability	0.715182
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1129722 119 - 22224390
ACAUUUAGAGCUAAAAGAAUGCACAGUUUUCUUCUGGCCCUUGAGCCAUUUUUCCGAGUGUCUGAGAUCCACUUCUGUUCACAAAA-GAGAGACAGCUGGAAAGACAGUCGGCUAACGCC
...((.((.((((.(((((.((...)).))))).)))).)).))...........((.(((((....(((((((((.(((......-)))))).)).)))).))))).))(((....))) ( -29.50)
>DroSec_CAF1 26343 117 - 1
UUAUUUAGAGCUUAAAAAGC-AAAAGUGUUCUUCUGGCACUUGAGCCAUUUUUGCGAGUGUCUGAGAUCCACUUCUGCUCACAAAA--AGAGACAGCUGGAAAGACAGGCGGCUAACGCC
.........((((.....((-((((((((((...........))).)))))))))....((((....((((...((((((......--.))).))).)))).))))))))(((....))) ( -33.10)
>DroSim_CAF1 27791 117 - 1
UUAUUUAGAGCUUAAAAAGC-AAAAGUUUUCUUCUGGCACUUGAGCCAUUUUUGCGAGUGUCUGAGAUCCACUUCUGCUCACAAAA--AGAGACAGCUGGAAAGACAGGCGGCUAACGCC
.........((((.....((-(((((........((((......)))))))))))....((((....((((...((((((......--.))).))).)))).))))))))(((....))) ( -31.70)
>DroEre_CAF1 27656 109 - 1
GUAUUAAGUUUUA-----------UUUUUCCCACUGGCACUUGGACCAUUUUUCCAAGUGUCUGAGAUCCACUUCUGCUCACAAAAAGAGAGACAGCUGGAAAGACAGUCGGCUAACGCC
.......(((((.-----------..((((.....((((((((((.......)))))))))).))))(((((((((.(((.......)))))).)).)))))))))....(((....))) ( -31.50)
>DroYak_CAF1 27251 95 - 1
GUUUU-------------------------CAUCUGGCACUUGAGCCAUUUUUCCGAGUGUCUGAGAUCCACGGCUGCUCACAAAAAGAGAGACAGCUGGAAAGACAGUCGGCUAACGCC
.....-------------------------....((((......)))).......((.(((((....((((..(((((((.(.....).))).)))))))).))))).))(((....))) ( -31.60)
>consensus
GUAUUUAGAGCUAAAA_A____A_AGUUUUCUUCUGGCACUUGAGCCAUUUUUCCGAGUGUCUGAGAUCCACUUCUGCUCACAAAA_GAGAGACAGCUGGAAAGACAGUCGGCUAACGCC
..................................((((......)))).......((.(((((....((((...((((((.........))).))).)))).))))).))(((....))) (-22.72 = -23.36 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:03 2006