Locus 757

Sequence ID	2R_DroMel_CAF1
Location	3,676,695 – 3,676,888
Length	193
Max. P	0.914080

overview

Window 6

Location	3,676,695 – 3,676,811
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.49
Mean single sequence MFE	-32.03
Consensus MFE	-24.34
Energy contribution	-23.70
Covariance contribution	-0.64
Combinations/Pair	1.14
Mean z-score	-1.87
Structure conservation index	0.76
SVM decision value	0.62
SVM RNA-class probability	0.801068
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3676695 116 - 20766785
CUUCGAUGGUGCCUAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUUGAAGCAAAGAACUAUUCAAAACUCCACCAGCGCGUGUUUACAAUUUAAAACACACGUGUGGCGU----GUUAG
((((((.(((((..((((((........)))))).))))).....))))))................((.((((..(((.((((((........)))))).))))))).))----..... ( -32.80)
>DroSim_CAF1 8955 116 - 1
CCUCGAUGGUGCCUAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUUGCAGCAAAGAACUAUUAAAAACUACACCAGCGCGUGUUUACAAUUUAAAACACACGUGUGGCUU----GUUAG
((.....))...(((.((((.((((((((((.((((((........)))))).)))))))................(((.((((((........)))))).))).))))))----).))) ( -33.30)
>DroEre_CAF1 7914 104 - 1
CCUCAAUGGUGCCUAUCAAGUCUAGGUUCUUGGUUGCGCCCAUUUUUGCAGUAAAGAAC------------CACCAGCGCGUGUUUACAAUUUAAAAUACACGUGUGGAGU----GUUAG
.(((..((((..((....))....(((((((..(((((........)))))..))))))------------)))))((((((((..............)))))))).))).----..... ( -28.94)
>DroYak_CAF1 5685 116 - 1
CCUCGAUGGUGCCAAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUUGCAGCAAAGAACUAUUUAAAACUCCACCAGCGCGUGUUUACAAUUUAAAACACACGUGUGGCGU----GUUAG
......((((....))))......(((((((.((((((........)))))).)))))))...(((.((.((((..(((.((((((........)))))).))))))).))----.))). ( -32.70)
>DroAna_CAF1 2608 116 - 1
CCUCGAUGGUGCCAAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUAUCGUUAAAAAUCAAUGAUCAAAU---GCAGCGCGUGUUUACAAAUCA-AACGCACGUGUGCAGCAGCGGUUAG
....((((((((.(((((((........))))))))))))..(((((....))))))))..(((((...(---((.((((((((..........-...))))))))...)))..))))). ( -32.42)
>consensus
CCUCGAUGGUGCCUAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUUGCAGCAAAGAACUAUUAAAAACU_CACCAGCGCGUGUUUACAAUUUAAAACACACGUGUGGCGU____GUUAG
.......(((((..((((((........)))))).))))).................................(((.(((((((..............))))))))))............ (-24.34 = -23.70 +  -0.64)

alignment

secondary structure

dotplot

Window 7

Location	3,676,731 – 3,676,851
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.99
Mean single sequence MFE	-34.68
Consensus MFE	-26.60
Energy contribution	-27.36
Covariance contribution	0.76
Combinations/Pair	1.18
Mean z-score	-2.15
Structure conservation index	0.77
SVM decision value	1.09
SVM RNA-class probability	0.914080
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3676731 120 - 20766785
GCAUCGGAGUCCUCCGACAAGUUCUCCACCUCGGCAUCGUCUUCGAUGGUGCCUAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUUGAAGCAAAGAACUAUUCAAAACUCCACCAGCGC
((.(((((....)))))..((((((((.....))....(.((((((.(((((..((((((........)))))).))))).....)))))))..))))))................)).. ( -32.50)
>DroSim_CAF1 8991 120 - 1
GCAUCGGAGUCCUCCGACAAGUUCUCCACCUCGGCAUCGUCCUCGAUGGUGCCUAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUUGCAGCAAAGAACUAUUAAAAACUACACCAGCGC
((.(((((....)))))..((((.........(((((((((...)))))))))...........(((((((.((((((........)))))).)))))))......))))......)).. ( -37.80)
>DroEre_CAF1 7950 108 - 1
GCAUCGGAGUCCUCCGACAAGUUCUCGACCUCGGCAUCGUCCUCAAUGGUGCCUAUCAAGUCUAGGUUCUUGGUUGCGCCCAUUUUUGCAGUAAAGAAC------------CACCAGCGC
((.(((((....))))).........(((...((((((((.....))))))))......)))..(((((((..(((((........)))))..))))))------------)....)).. ( -34.40)
>DroYak_CAF1 5721 120 - 1
GCAUCGGAGUCCUCCGACAAGUUCUCGACCUCGGCAUCGUCCUCGAUGGUGCCAAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUUGCAGCAAAGAACUAUUUAAAACUCCACCAGCGC
((...(((((.....(((........(....)(((((((((...)))))))))......)))..(((((((.((((((........)))))).))))))).......)))))....)).. ( -37.70)
>DroAna_CAF1 2647 117 - 1
GCAUCGGAGUCCUCUGAAAGGUUCUCUACCUCUGCAUCAUCCUCGAUGGUGCCAAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUAUCGUUAAAAAUCAAUGAUCAAAU---GCAGCGC
((.(((((....))))).((((.....))))((((............(((((.(((((((........)))))))))))).((((.((((((.......)))))).))))---)))).)) ( -31.00)
>consensus
GCAUCGGAGUCCUCCGACAAGUUCUCCACCUCGGCAUCGUCCUCGAUGGUGCCUAUCAAGUCCAGGUUCUUGGUUGCACCCAUUUUUGCAGCAAAGAACUAUUAAAAACU_CACCAGCGC
((.(((((....)))))...............(((((((((...)))))))))............((((((.((((((........)))))).)))))).................)).. (-26.60 = -27.36 +   0.76)

alignment

secondary structure

dotplot

Window 8

Location	3,676,771 – 3,676,888
Length	117
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	87.21
Mean single sequence MFE	-35.63
Consensus MFE	-27.42
Energy contribution	-27.66
Covariance contribution	0.24
Combinations/Pair	1.17
Mean z-score	-1.94
Structure conservation index	0.77
SVM decision value	0.77
SVM RNA-class probability	0.845926
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3676771 117 - 20766785
UCGUUUUUAAAAGUGUGAG-CAACCUACCUCGACCUCCGCAUCGGAGUCCUCCGACAAGUUCUCCACCUCGGCAUCGUCUUCGAUGGUGCCUAUCAAGUCCAGGUUCUUGGUUGCACC
..................(-(((((.((((.(((.........((((..((......))..)))).....(((((((((...)))))))))......))).))))....))))))... ( -38.80)
>DroSim_CAF1 9031 117 - 1
UCGUUUUUAAAAGUGCGAG-CUACCUACCUCGACCUCCGCAUCGGAGUCCUCCGACAAGUUCUCCACCUCGGCAUCGUCCUCGAUGGUGCCUAUCAAGUCCAGGUUCUUGGUUGCACC
............((((.((-(((...((((.(((.........((((..((......))..)))).....(((((((((...)))))))))......))).))))...))))))))). ( -38.10)
>DroEre_CAF1 7978 116 - 1
UCGGU-GUAAAAGUGUGAG-UAACCUACCUCGACCUCCGCAUCGGAGUCCUCCGACAAGUUCUCGACCUCGGCAUCGUCCUCAAUGGUGCCUAUCAAGUCUAGGUUCUUGGUUGCGCC
..(((-((((..(((.(((-..............)))))).(((((....)))))((((.(((.(((...((((((((.....))))))))......))).)))..)))).))))))) ( -34.94)
>DroYak_CAF1 5761 116 - 1
UCGGA-UUAAAAGUGUGAG-UAACCUACCUCGACCUCCGCAUCGGAGUCCUCCGACAAGUUCUCGACCUCGGCAUCGUCCUCGAUGGUGCCAAUCAAGUCCAGGUUCUUGGUUGCACC
(((.(-(.....)).)))(-(((((.((((.(((.......(((((....)))))...............(((((((((...)))))))))......))).))))....))))))... ( -37.20)
>DroAna_CAF1 2684 112 - 1
-----UGUAACAGC-UGAUUUCUCUCACCUCCACUUCGGCAUCGGAGUCCUCUGAAAGGUUCUCUACCUCUGCAUCAUCCUCGAUGGUGCCAAUCAAGUCCAGGUUCUUGGUUGCACC
-----.......((-(((.................))))).(((((....))))).((((.....))))..((((((((...))))))))((((((((........)))))))).... ( -29.13)
>consensus
UCGGUUUUAAAAGUGUGAG_UAACCUACCUCGACCUCCGCAUCGGAGUCCUCCGACAAGUUCUCCACCUCGGCAUCGUCCUCGAUGGUGCCUAUCAAGUCCAGGUUCUUGGUUGCACC
............((((((.....((.((((.(((.......(((((....)))))...............(((((((((...)))))))))......))).))))....)))))))). (-27.42 = -27.66 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:23 2006