Locus 2826

Sequence ID	3R_DroMel_CAF1
Location	7,575,130 – 7,575,275
Length	145
Max. P	0.998969

overview

Window 4

Location	7,575,130 – 7,575,237
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	90.27
Mean single sequence MFE	-25.60
Consensus MFE	-21.00
Energy contribution	-21.56
Covariance contribution	0.56
Combinations/Pair	1.16
Mean z-score	-2.28
Structure conservation index	0.82
SVM decision value	2.05
SVM RNA-class probability	0.986527
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7575130 107 + 27905053
CAACUUAUUACUAAUUAAGUUCAGCAGUUCUUUAUUUUAGCCAACGCAAUAGGGAUGAGCGUUGUAUCGAUAUGUCAGCAUAUCGAUAUGUCUAAGCUGAUAUUAAG
..(((((........)))))(((((................((((((...........))))))((((((((((....)))))))))).......)))))....... ( -28.40)
>DroSec_CAF1 7148 107 + 1
CAACUUAUUAUUAAUUAAGUUCAGCAGUUUUUUUUUUUAGCCAACGCAAUAGGGAUGAACGUUGUAUCGAUAUGUCAGCAUAUCGAUAUGUCUAAGCUGAUAUUAAG
..(((((........)))))(((((.((((.(((((...((....))...))))).))))...(((((((((((....)))))))))))......)))))....... ( -27.30)
>DroSim_CAF1 7584 107 + 1
CAACUUAUUAUUAAUUAAGUUCAGCAGUUCUUUUUUUUAGCCAACGCAAUAGGGAUGAACGUUGUAUCGAUAUGUCAGCAUAUCGAUAUGUCUAGGCUGAUAUUAAG
..(((((........)))))(((((.((((.(((((...((....))...))))).))))...(((((((((((....)))))))))))......)))))....... ( -28.80)
>DroEre_CAF1 7570 104 + 1
CAACUUAUUAUUAAUUAAGUUCAUCAGUUUU---UUUCAGUCAACGUAAUAGGGAUGAGCGCAAUAUCGAUAUGCCAGCAUAUCGAUAUGUCUAGGCUGAUAUUAAA
.((((((........))))))..........---..((((((..(((.......)))((.(((.((((((((((....))))))))))))))).))))))....... ( -24.40)
>DroYak_CAF1 7238 106 + 1
CAACUUAUUAUUAAUUAAGUUCAUCAGUUUUU-UUUUUAGUUAACGCAAUAGGGAUGAGCGCAGUAUCGAUAUUACAGCAUAUCGAUAUGUCUAAGCUGUUAUUUAA
((.((((...........(((((((.(((..(-(....))..)))........)))))))...((((((((((......))))))))))...)))).))........ ( -19.10)
>consensus
CAACUUAUUAUUAAUUAAGUUCAGCAGUUUUUUUUUUUAGCCAACGCAAUAGGGAUGAGCGUUGUAUCGAUAUGUCAGCAUAUCGAUAUGUCUAAGCUGAUAUUAAG
.((((((........))))))((((.((((.(((((...((....))...))))).))))...(((((((((((....)))))))))))......))))........ (-21.00 = -21.56 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	7,575,130 – 7,575,237
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	90.27
Mean single sequence MFE	-23.62
Consensus MFE	-20.08
Energy contribution	-20.96
Covariance contribution	0.88
Combinations/Pair	1.12
Mean z-score	-2.76
Structure conservation index	0.85
SVM decision value	3.31
SVM RNA-class probability	0.998969
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7575130 107 - 27905053
CUUAAUAUCAGCUUAGACAUAUCGAUAUGCUGACAUAUCGAUACAACGCUCAUCCCUAUUGCGUUGGCUAAAAUAAAGAACUGCUGAACUUAAUUAGUAAUAAGUUG
........(((((((....((((((((((....))))))))))((((((...........))))))...............((((((......)))))).))))))) ( -27.60)
>DroSec_CAF1 7148 107 - 1
CUUAAUAUCAGCUUAGACAUAUCGAUAUGCUGACAUAUCGAUACAACGUUCAUCCCUAUUGCGUUGGCUAAAAAAAAAAACUGCUGAACUUAAUUAAUAAUAAGUUG
.......(((((.......((((((((((....))))))))))((((((...........))))))................)))))(((((........))))).. ( -25.40)
>DroSim_CAF1 7584 107 - 1
CUUAAUAUCAGCCUAGACAUAUCGAUAUGCUGACAUAUCGAUACAACGUUCAUCCCUAUUGCGUUGGCUAAAAAAAAGAACUGCUGAACUUAAUUAAUAAUAAGUUG
.......(((((.......((((((((((....))))))))))((((((...........))))))................)))))(((((........))))).. ( -25.00)
>DroEre_CAF1 7570 104 - 1
UUUAAUAUCAGCCUAGACAUAUCGAUAUGCUGGCAUAUCGAUAUUGCGCUCAUCCCUAUUACGUUGACUGAAA---AAAACUGAUGAACUUAAUUAAUAAUAAGUUG
.....((((((.......(((((((((((....)))))))))))..((.(((............))).))...---....))))))((((((........)))))). ( -21.20)
>DroYak_CAF1 7238 106 - 1
UUAAAUAACAGCUUAGACAUAUCGAUAUGCUGUAAUAUCGAUACUGCGCUCAUCCCUAUUGCGUUAACUAAAAA-AAAAACUGAUGAACUUAAUUAAUAAUAAGUUG
........(((((((....(((((((((......)))))))))..((((...........))))..........-.........................))))))) ( -18.90)
>consensus
CUUAAUAUCAGCUUAGACAUAUCGAUAUGCUGACAUAUCGAUACAACGCUCAUCCCUAUUGCGUUGGCUAAAAAAAAAAACUGCUGAACUUAAUUAAUAAUAAGUUG
........((((.......((((((((((....))))))))))((((((...........))))))................))))((((((........)))))). (-20.08 = -20.96 +   0.88)

alignment

secondary structure

dotplot

Window 6

Location	7,575,162 – 7,575,275
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	84.77
Mean single sequence MFE	-28.66
Consensus MFE	-22.78
Energy contribution	-22.58
Covariance contribution	-0.20
Combinations/Pair	1.19
Mean z-score	-2.92
Structure conservation index	0.79
SVM decision value	2.53
SVM RNA-class probability	0.995024
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7575162 113 + 27905053
UAUUUUAGCCAACGCAAUAGGGAUGAGCGUUGUAUCGAUAUGUCAGCAUAUCGAUAUGUCUAAGCUGAUAUUAAGCUGAUGCGUUUAUUUUGUAUUAACUUAAAUUAAAAUUU
....(((((((((((...........))))))((((((((((....)))))))))).......)))))..(((((.(((((((.......))))))).))))).......... ( -31.60)
>DroSec_CAF1 7180 113 + 1
UUUUUUAGCCAACGCAAUAGGGAUGAACGUUGUAUCGAUAUGUCAGCAUAUCGAUAUGUCUAAGCUGAUAUUAAGCUGAUGCGUUUAUUUUGUAUUAACUUAAAUUAAAAUUU
..(((((((....))(((((((((((((((.(((((((((((....)))))))))))(((..((((.......)))))))))))))))))).)))).........)))))... ( -27.90)
>DroSim_CAF1 7616 113 + 1
UUUUUUAGCCAACGCAAUAGGGAUGAACGUUGUAUCGAUAUGUCAGCAUAUCGAUAUGUCUAGGCUGAUAUUAAGCUGAUGCGUUUAUUUUGUAUUAACUUAAAUUAAAAUUU
....((((((((((.............))))(((((((((((....))))))))))).....))))))..(((((.(((((((.......))))))).))))).......... ( -30.82)
>DroEre_CAF1 7601 111 + 1
--UUUCAGUCAACGUAAUAGGGAUGAGCGCAAUAUCGAUAUGCCAGCAUAUCGAUAUGUCUAGGCUGAUAUUAAAUUGAUGCGUUUAUUUUGUAUUAAGCUGAAUUAUUAUUU
--.((((((.....((((((((((((((((((((((((((((....)))))))))))(((......)))..........)))))))))))).))))).))))))......... ( -34.50)
>DroYak_CAF1 7270 101 + 1
-UUUUUAGUUAACGCAAUAGGGAUGAGCGCAGUAUCGAUAUUACAGCAUAUCGAUAUGUCUAAGCUGUUAUUUAAUUGUGCCGUUUAUUUUUUAAUAAG-----------UUU
-...........((((((..((((((((...((((((((((......))))))))))......)))..))))).))))))...((((((....))))))-----------... ( -18.50)
>consensus
UUUUUUAGCCAACGCAAUAGGGAUGAGCGUUGUAUCGAUAUGUCAGCAUAUCGAUAUGUCUAAGCUGAUAUUAAGCUGAUGCGUUUAUUUUGUAUUAACUUAAAUUAAAAUUU
...................(((((((((((.(((((((((((....))))))))))).....((((.......))))...)))))))))))...................... (-22.78 = -22.58 +  -0.20)

alignment

secondary structure

dotplot

Window 7

Location	7,575,162 – 7,575,275
Length	113
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	84.77
Mean single sequence MFE	-21.30
Consensus MFE	-15.44
Energy contribution	-15.76
Covariance contribution	0.32
Combinations/Pair	1.21
Mean z-score	-2.83
Structure conservation index	0.72
SVM decision value	1.86
SVM RNA-class probability	0.980448
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7575162 113 - 27905053
AAAUUUUAAUUUAAGUUAAUACAAAAUAAACGCAUCAGCUUAAUAUCAGCUUAGACAUAUCGAUAUGCUGACAUAUCGAUACAACGCUCAUCCCUAUUGCGUUGGCUAAAAUA
..((((((..(((((((.((.(.........).)).))))))).....((.......((((((((((....))))))))))((((((...........)))))))))))))). ( -24.00)
>DroSec_CAF1 7180 113 - 1
AAAUUUUAAUUUAAGUUAAUACAAAAUAAACGCAUCAGCUUAAUAUCAGCUUAGACAUAUCGAUAUGCUGACAUAUCGAUACAACGUUCAUCCCUAUUGCGUUGGCUAAAAAA
..........(((((((.((.(.........).)).)))))))....(((.......((((((((((....))))))))))((((((...........)))))))))...... ( -21.70)
>DroSim_CAF1 7616 113 - 1
AAAUUUUAAUUUAAGUUAAUACAAAAUAAACGCAUCAGCUUAAUAUCAGCCUAGACAUAUCGAUAUGCUGACAUAUCGAUACAACGUUCAUCCCUAUUGCGUUGGCUAAAAAA
..........(((((((.((.(.........).)).)))))))....((((......((((((((((....)))))))))).(((((...........)))))))))...... ( -21.60)
>DroEre_CAF1 7601 111 - 1
AAAUAAUAAUUCAGCUUAAUACAAAAUAAACGCAUCAAUUUAAUAUCAGCCUAGACAUAUCGAUAUGCUGGCAUAUCGAUAUUGCGCUCAUCCCUAUUACGUUGACUGAAA--
..........(((((.(((((.........((((...........((......)).(((((((((((....)))))))))))))))........))))).)))))......-- ( -22.43)
>DroYak_CAF1 7270 101 - 1
AAA-----------CUUAUUAAAAAAUAAACGGCACAAUUAAAUAACAGCUUAGACAUAUCGAUAUGCUGUAAUAUCGAUACUGCGCUCAUCCCUAUUGCGUUAACUAAAAA-
...-----------.................(((.((((........(((.(((...(((((((((......)))))))))))).))).......)))).))).........- ( -16.76)
>consensus
AAAUUUUAAUUUAAGUUAAUACAAAAUAAACGCAUCAGCUUAAUAUCAGCUUAGACAUAUCGAUAUGCUGACAUAUCGAUACAACGCUCAUCCCUAUUGCGUUGGCUAAAAAA
...................................................(((...((((((((((....))))))))))((((((...........)))))).)))..... (-15.44 = -15.76 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:35 2006