Locus 9739

Sequence ID	3R_DroMel_CAF1
Location	25,775,365 – 25,775,488
Length	123
Max. P	0.932987

overview

Window 7

Location	25,775,365 – 25,775,466
Length	101
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	78.50
Mean single sequence MFE	-21.48
Consensus MFE	-12.43
Energy contribution	-13.55
Covariance contribution	1.12
Combinations/Pair	1.17
Mean z-score	-2.05
Structure conservation index	0.58
SVM decision value	0.53
SVM RNA-class probability	0.770560
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25775365 101 + 27905053
AAUGUUUAUGCACAAAAUGCACU--------UGUUAUGGGUACCAUAAAUGUGUUAGAAAACUUUUUAAACACGAUUGUUCAAGUUAUGUUUAAAAUUUAUGAGUGUUU
.........((((.....((((.--------..((((((...))))))..)))).........(((((((((..(((.....)))..))))))))).......)))).. ( -20.80)
>DroSim_CAF1 19182 101 + 1
AAUGUUUAUGAACAAAAUGCACU--------UGUUAUGGUUACCACAAAUGUGUUAACAAACUUUUUAAACACGAUUUUUCAAGUUAUGUUUAAAAUUUAUGAGCACUU
..((((((((((...........--------.(((...((((.(((....))).)))).))).(((((((((..(((.....)))..)))))))))))))))))))... ( -21.00)
>DroEre_CAF1 20481 93 + 1
AGUGUUUAUGCACAAAA--------------CGUUAUGGGUGCCAUAAAU--GUUGGCAAACUCCUUAACAAAGAUUUGCCAAGUUUUCUUUAACAUUUACGAGUACUU
.((((....))))....--------------......(((((((.(((((--(((((((((...(((....))).))))))(((....))).)))))))).).)))))) ( -21.10)
>DroYak_CAF1 17834 107 + 1
GUUGUUUAUGCACAAAAUGCACUUGGACAAAUGUUAUGGGUACCAUAAAU--GUUAGCAAACUUUUUAAACAAGAUUUUCCAAGUUUUGUUUAAAAUUUAUGAGUAACU
.(((((((((((.....))))..)))))))...((((((...))))))..--((((.((....((((((((((((((.....))))))))))))))....))..)))). ( -23.00)
>consensus
AAUGUUUAUGCACAAAAUGCACU________UGUUAUGGGUACCAUAAAU__GUUAGCAAACUUUUUAAACAAGAUUUUCCAAGUUAUGUUUAAAAUUUAUGAGUACUU
((((((((((.......................((((((...))))))...............((((((((((((((.....))))))))))))))..)))))))))). (-12.43 = -13.55 +   1.12)

alignment

secondary structure

dotplot

Window 8

Location	25,775,388 – 25,775,488
Length	100
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	78.82
Mean single sequence MFE	-22.02
Consensus MFE	-10.76
Energy contribution	-12.20
Covariance contribution	1.44
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.49
SVM decision value	0.13
SVM RNA-class probability	0.598556
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25775388 100 + 27905053
-UGUUAUGGGUACCAUAAAUGUGUUAGAAAACUUUUUAAACACGAUUGUUCAAGUUAUGUUUAAAAUUUAUGAGUGUUUCUUUCAUCGGAAGCCCAUCG----------CU
-.((.(((((((((((((((..(((....)))..((((((((..(((.....)))..))))))))))))))).))..((((......)))))))))).)----------). ( -23.20)
>DroSec_CAF1 19035 100 + 1
-UGUUAUGGUUACCAUAAAUGUGUUAACAAACUUUUUAAACACGAUUUUUCAAGUUAUGUUUAAAAUUUAUGAGUACUUCUUUCAACAGAAGCCCAUCG----------CU
-.((.((((.((((((((((((....)))....(((((((((..(((.....)))..))))))))))))))).)))(((((......))))).)))).)----------). ( -21.30)
>DroSim_CAF1 19205 100 + 1
-UGUUAUGGUUACCACAAAUGUGUUAACAAACUUUUUAAACACGAUUUUUCAAGUUAUGUUUAAAAUUUAUGAGCACUUCUUUCAACAGAAGCCCAUCG----------CU
-.((.(((((((.(((....))).)))).....(((((((((..(((.....)))..)))))))))..........(((((......)))))..))).)----------). ( -17.80)
>DroEre_CAF1 20498 108 + 1
-CGUUAUGGGUGCCAUAAAU--GUUGGCAAACUCCUUAACAAAGAUUUGCCAAGUUUUCUUUAACAUUUACGAGUACUUCGUUCAAAAGCAACCCAUCUCUGUGGCCUGCU
-.(..(((((((((.(((((--(((((((((...(((....))).))))))(((....))).)))))))).).)))).)))).)...((((..((((....))))..)))) ( -24.40)
>DroYak_CAF1 17864 109 + 1
AUGUUAUGGGUACCAUAAAU--GUUAGCAAACUUUUUAAACAAGAUUUUCCAAGUUUUGUUUAAAAUUUAUGAGUAACUCGUUCACAAGAAACCCAUUGCUGUCGCCUGUU
..((.(((((((((((((((--(((....)))..(((((((((((((.....)))))))))))))))))))).))......(((....))))))))).))........... ( -23.40)
>consensus
_UGUUAUGGGUACCAUAAAUGUGUUAGCAAACUUUUUAAACACGAUUUUUCAAGUUAUGUUUAAAAUUUAUGAGUACUUCUUUCAACAGAAGCCCAUCG__________CU
.....(((((((((((((((..(((....)))..((((((((.((((.....)))).))))))))))))))).))......(((....))))))))).............. (-10.76 = -12.20 +   1.44)

alignment

secondary structure

dotplot

Window 9

Location	25,775,388 – 25,775,488
Length	100
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	78.82
Mean single sequence MFE	-23.42
Consensus MFE	-13.48
Energy contribution	-12.80
Covariance contribution	-0.68
Combinations/Pair	1.26
Mean z-score	-2.24
Structure conservation index	0.58
SVM decision value	1.23
SVM RNA-class probability	0.932987
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25775388 100 - 27905053
AG----------CGAUGGGCUUCCGAUGAAAGAAACACUCAUAAAUUUUAAACAUAACUUGAACAAUCGUGUUUAAAAAGUUUUCUAACACAUUUAUGGUACCCAUAACA-
.(----------..(((((...((.((((((((((.(((......((((((((((.............))))))))))))))))))......)))))))..)))))..).- ( -17.12)
>DroSec_CAF1 19035 100 - 1
AG----------CGAUGGGCUUCUGUUGAAAGAAGUACUCAUAAAUUUUAAACAUAACUUGAAAAAUCGUGUUUAAAAAGUUUGUUAACACAUUUAUGGUAACCAUAACA-
.(----------..((((((((((......))))))((.((((((((((((((((...((....))..)))))))))).(((....)))...))))))))..))))..).- ( -22.40)
>DroSim_CAF1 19205 100 - 1
AG----------CGAUGGGCUUCUGUUGAAAGAAGUGCUCAUAAAUUUUAAACAUAACUUGAAAAAUCGUGUUUAAAAAGUUUGUUAACACAUUUGUGGUAACCAUAACA-
.(----------..((((((((((......))))))((.((((((((((((((((...((....))..)))))))))).(((....)))...))))))))..))))..).- ( -22.70)
>DroEre_CAF1 20498 108 - 1
AGCAGGCCACAGAGAUGGGUUGCUUUUGAACGAAGUACUCGUAAAUGUUAAAGAAAACUUGGCAAAUCUUUGUUAAGGAGUUUGCCAAC--AUUUAUGGCACCCAUAACG-
...........(..((((((((((((.....)))))).(((((((((((.(((....)))((((((.((((.....)))))))))))))--)))))))).))))))..).- ( -29.10)
>DroYak_CAF1 17864 109 - 1
AACAGGCGACAGCAAUGGGUUUCUUGUGAACGAGUUACUCAUAAAUUUUAAACAAAACUUGGAAAAUCUUGUUUAAAAAGUUUGCUAAC--AUUUAUGGUACCCAUAACAU
....(((((..((.((((((..((((....))))..))))))...((((((((((...((....))..)))))))))).)))))))...--..((((((...))))))... ( -25.80)
>consensus
AG__________CGAUGGGCUUCUGUUGAAAGAAGUACUCAUAAAUUUUAAACAUAACUUGAAAAAUCGUGUUUAAAAAGUUUGCUAACACAUUUAUGGUACCCAUAACA_
..............(((((((((........)))))..(((((((((((((((((...((....))..)))))))))).(((....)))...)))))))...))))..... (-13.48 = -12.80 +  -0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:41:06 2006