Locus 8948

Sequence ID	3R_DroMel_CAF1
Location	23,993,672 – 23,993,772
Length	100
Max. P	0.847369

overview

Window 1

Location	23,993,672 – 23,993,772
Length	100
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	78.65
Mean single sequence MFE	-12.88
Consensus MFE	-9.58
Energy contribution	-9.92
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-0.92
Structure conservation index	0.74
SVM decision value	-0.05
SVM RNA-class probability	0.509966
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23993672 100 + 27905053
CAGCGCUAUUUUACUUAUUUAGUACGUAACUACAAUUUACGCCAUGCAUCUGCAUAUAAAAUGCAUUUUUUUGCAGCAUUUC--UUUUUCACUUUUUUGGUU----
....(((((((((...........(((((.......)))))..((((....)))).))))))(((......)))))).....--..................---- ( -12.80)
>DroVir_CAF1 215427 82 + 1
CAGCGCAAUUUUACUUAUUUAGUACGUAACUGCAAUUUACGCCAUGCAUCUGCAUAUAAAAUGCAUUUUUUUGCAGCCUUUU------------------------
..((((((...((((.....))))......((((.((((....((((....)))).)))).)))).....)))).)).....------------------------ ( -13.40)
>DroPse_CAF1 209812 102 + 1
CAGCGCUAUUUUACUUAUUUAGUACGUAACUACAAUUUACGCCAUGCAUCUGCAUAUAAAAUGCAUUU-UUUGCAGCAUUUC--UCUU-GACUUUUUGGAUACCCU
..((((.....((((.....)))).((((.......))))))..((((..(((((.....)))))...-..)))))).....--....-........((....)). ( -13.50)
>DroWil_CAF1 243978 78 + 1
CAGUGCUAUUUUACUUAUUUAGUACGUAACUACAAUUUACGCCAUGCAUCUGCAUAUAAAAUGCAUUUUUUU------------------------UUUGCU----
.(((((.((((((...........(((((.......)))))..((((....)))).))))))))))).....------------------------......---- ( -11.80)
>DroMoj_CAF1 221388 100 + 1
CAGCGCGAUUUUACUUAUUUAGUACGUAACUGCAAUUUACGCCAUGCAUCUGCAUACAAAAUGCAUUUUUU--CAGCUUUAUUUUCUUUUCUUCAUUUUGUU----
.((((((....((((.....))))(((((.......)))))...)))...(((((.....)))))......--..)))........................---- ( -12.30)
>DroPer_CAF1 211668 102 + 1
CAGCGCUAUUUUACUUAUUUAGUACGUAACUACAAUUUACGCCAUGCAUCUGCAUAUAAAAUGCAUUU-UUUGCAGCAUUUC--UCUU-GACUUUUUGGAUACCCU
..((((.....((((.....)))).((((.......))))))..((((..(((((.....)))))...-..)))))).....--....-........((....)). ( -13.50)
>consensus
CAGCGCUAUUUUACUUAUUUAGUACGUAACUACAAUUUACGCCAUGCAUCUGCAUAUAAAAUGCAUUUUUUUGCAGCAUUUC__UCUU__ACUUUUUUGGUU____
..((((.....((((.....))))(((((.......)))))....))...(((((.....)))))..........))............................. ( -9.58 =  -9.92 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	23,993,672 – 23,993,772
Length	100
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	78.65
Mean single sequence MFE	-16.55
Consensus MFE	-13.23
Energy contribution	-12.95
Covariance contribution	-0.28
Combinations/Pair	1.10
Mean z-score	-1.41
Structure conservation index	0.80
SVM decision value	0.77
SVM RNA-class probability	0.847369
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23993672 100 - 27905053
----AACCAAAAAAGUGAAAAA--GAAAUGCUGCAAAAAAAUGCAUUUUAUAUGCAGAUGCAUGGCGUAAAUUGUAGUUACGUACUAAAUAAGUAAAAUAGCGCUG
----.........((((.....--(((((((...........))))))).(((((....)))))((((((.......))))))..................)))). ( -17.10)
>DroVir_CAF1 215427 82 - 1
------------------------AAAAGGCUGCAAAAAAAUGCAUUUUAUAUGCAGAUGCAUGGCGUAAAUUGCAGUUACGUACUAAAUAAGUAAAAUUGCGCUG
------------------------....(((.((......((((((((.......)))))))).)).......((((((...((((.....)))).))))))))). ( -18.30)
>DroPse_CAF1 209812 102 - 1
AGGGUAUCCAAAAAGUC-AAGA--GAAAUGCUGCAAA-AAAUGCAUUUUAUAUGCAGAUGCAUGGCGUAAAUUGUAGUUACGUACUAAAUAAGUAAAAUAGCGCUG
..(((.........(((-....--(((((((......-....)))))))..((((....)))))))..........((((..((((.....))))...))))))). ( -17.20)
>DroWil_CAF1 243978 78 - 1
----AGCAAA------------------------AAAAAAAUGCAUUUUAUAUGCAGAUGCAUGGCGUAAAUUGUAGUUACGUACUAAAUAAGUAAAAUAGCACUG
----......------------------------.......((((((((((((((....)))).((((((.......)))))).........))))))).)))... ( -14.00)
>DroMoj_CAF1 221388 100 - 1
----AACAAAAUGAAGAAAAGAAAAUAAAGCUG--AAAAAAUGCAUUUUGUAUGCAGAUGCAUGGCGUAAAUUGCAGUUACGUACUAAAUAAGUAAAAUCGCGCUG
----........................(((((--(....((((((((.(....))))))))).((((((.......))))))...............))).))). ( -15.50)
>DroPer_CAF1 211668 102 - 1
AGGGUAUCCAAAAAGUC-AAGA--GAAAUGCUGCAAA-AAAUGCAUUUUAUAUGCAGAUGCAUGGCGUAAAUUGUAGUUACGUACUAAAUAAGUAAAAUAGCGCUG
..(((.........(((-....--(((((((......-....)))))))..((((....)))))))..........((((..((((.....))))...))))))). ( -17.20)
>consensus
____AACCAAAAAAGU__AAGA__GAAAUGCUGCAAAAAAAUGCAUUUUAUAUGCAGAUGCAUGGCGUAAAUUGUAGUUACGUACUAAAUAAGUAAAAUAGCGCUG
.........................................((((((((((((((....)))))((((((.......))))))..........)))))).)))... (-13.23 = -12.95 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:23:18 2006