Locus 1773

Sequence ID	3R_DroMel_CAF1
Location	5,101,882 – 5,102,041
Length	159
Max. P	0.936480

overview

Window 1

Location	5,101,882 – 5,102,001
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.89
Mean single sequence MFE	-27.58
Consensus MFE	-19.48
Energy contribution	-20.64
Covariance contribution	1.16
Combinations/Pair	1.10
Mean z-score	-1.80
Structure conservation index	0.71
SVM decision value	0.02
SVM RNA-class probability	0.546070
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5101882 119 + 27905053
GCGAAAACAUUGGUAAUAACUUCAUAAAACACGAUAGUCGACUAAUUUGAUUGCGCUUUGCAAUUAAACUUGCCCCA-AAUGGGGGCACAAUCCCAUUUCAGGGUUGGCCAAACUCGUUC
((((.....(((((.................((.....)).....(((((((((.....)))))))))..((((((.-....))))))((((((.......)))))))))))..)))).. ( -31.20)
>DroSec_CAF1 8813 110 + 1
GCGAAAACAUUUGUAAUAACUUCAUAAAACACGAUAGUCGACUAAUUUGAUUGCGCUUCGCAAUUAAACUUGCCCCA-AAUGGGGGCACAAUCCCAUUUCAGGGCACCUGA---------
(((((.((....)).................((.(((((((.....))))))))).))))).........(((((.(-(((((((......))))))))..))))).....--------- ( -28.10)
>DroSim_CAF1 8847 119 + 1
GCGAAAACAUUUGUAAUAACUUCAUAAAACACGAUAGUCGACUAAUUUGAUUGCGCUUUGCAAUUAAACUUGCCCCA-AAUGGGGGCACAAUCCCAUUUCAGGGUUGGCCAAACUCGUUC
(((((....)))))................((((..(((((((..(((((((((.....)))))))))..((((((.-....))))))..............))))))).....)))).. ( -29.30)
>DroEre_CAF1 8895 120 + 1
GCGAAAACAUUUGUAAUUACUUCAUAAAACACGGUAGUCCACUAAUUUGAUUGCAUUUUGCAAUUAAACUUGCCCCAAAAUGGUAGCACAACCCCAUUUCAGGGUUGGCCGAACCCGUUC
(((((....)))))................((((...((......(((((((((.....)))))))))..((((.......))))((.((((((.......)))))))).))..)))).. ( -26.50)
>DroYak_CAF1 9792 120 + 1
GCGAAAACAUUUGUAAUAACUUCAUAAAACACGAUAGUCGACUAAUUUGAUUGCAUUUUGCAAUUAAACUUGCCCCAAAAUGCGAGCACAACCCCAUUUCGGUGUUGGCCAAACUCGUUC
(((((....)))))................(((((((....))).((((.(((((((((((((......))))...)))))))))((.((((.((.....)).)))))))))).)))).. ( -22.80)
>consensus
GCGAAAACAUUUGUAAUAACUUCAUAAAACACGAUAGUCGACUAAUUUGAUUGCGCUUUGCAAUUAAACUUGCCCCA_AAUGGGGGCACAAUCCCAUUUCAGGGUUGGCCAAACUCGUUC
(((((....)))))....................(((....))).((((((((((...))))))))))..((((((......))))))((((((.......))))))............. (-19.48 = -20.64 +   1.16)

alignment

secondary structure

dotplot

Window 2

Location	5,101,922 – 5,102,041
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.78
Mean single sequence MFE	-29.57
Consensus MFE	-25.68
Energy contribution	-26.24
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.99
Structure conservation index	0.87
SVM decision value	1.11
SVM RNA-class probability	0.916200
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5101922 119 + 27905053
ACUAAUUUGAUUGCGCUUUGCAAUUAAACUUGCCCCA-AAUGGGGGCACAAUCCCAUUUCAGGGUUGGCCAAACUCGUUCGUGUACCUUAGCCCUUUGCCUAAUUAAACGAAAUUGUUUC
.....(((((((((.....)))))))))..((((((.-....))))))((((((.......))))))...((((...(((((.....((((........))))....)))))...)))). ( -32.00)
>DroSim_CAF1 8887 119 + 1
ACUAAUUUGAUUGCGCUUUGCAAUUAAACUUGCCCCA-AAUGGGGGCACAAUCCCAUUUCAGGGUUGGCCAAACUCGUUCGUGUACCUUAGCCCUUUGCAUAAUUAAACGAAAUUGUUUC
.....(((((((((.....)))))))))..((((((.-....))))))((((((.......))))))...((((...(((((........((.....))........)))))...)))). ( -31.79)
>DroEre_CAF1 8935 119 + 1
ACUAAUUUGAUUGCAUUUUGCAAUUAAACUUGCCCCAAAAUGGUAGCACAACCCCAUUUCAGGGUUGGCCGAACCCGUUCGUGUACC-CAGUCCUUUGCCUAAUUAAACGAAAUUGUUUC
.....(((((((((.....)))))))))..((((.......))))((.((((((.......)))))))).((((...(((((.((..-(((....)))..)).....)))))...)))). ( -26.40)
>DroYak_CAF1 9832 119 + 1
ACUAAUUUGAUUGCAUUUUGCAAUUAAACUUGCCCCAAAAUGCGAGCACAACCCCAUUUCGGUGUUGGCCAAACUCGUUCGUGGGCC-CAGUCCUUUGCCUAAUUAAACGAAAUUGUUUC
.....((((.(((((((((((((......))))...)))))))))((.((((.((.....)).)))))))))).(((((..(((((.-.........)))))....)))))......... ( -28.10)
>consensus
ACUAAUUUGAUUGCACUUUGCAAUUAAACUUGCCCCA_AAUGGGAGCACAACCCCAUUUCAGGGUUGGCCAAACUCGUUCGUGUACC_CAGCCCUUUGCCUAAUUAAACGAAAUUGUUUC
.....(((((((((.....)))))))))..((((((......))))))((((((.......))))))...((((...(((((........((.....))........)))))...)))). (-25.68 = -26.24 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	5,101,922 – 5,102,041
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.78
Mean single sequence MFE	-35.00
Consensus MFE	-29.36
Energy contribution	-28.99
Covariance contribution	-0.37
Combinations/Pair	1.15
Mean z-score	-2.25
Structure conservation index	0.84
SVM decision value	1.25
SVM RNA-class probability	0.936480
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5101922 119 - 27905053
GAAACAAUUUCGUUUAAUUAGGCAAAGGGCUAAGGUACACGAACGAGUUUGGCCAACCCUGAAAUGGGAUUGUGCCCCCAUU-UGGGGCAAGUUUAAUUGCAAAGCGCAAUCAAAUUAGU
...(((((..((((...(((((.....(((((((.(.(......)).)))))))...)))))))))..)))))(((((....-.))))).(((((.(((((.....))))).)))))... ( -37.90)
>DroSim_CAF1 8887 119 - 1
GAAACAAUUUCGUUUAAUUAUGCAAAGGGCUAAGGUACACGAACGAGUUUGGCCAACCCUGAAAUGGGAUUGUGCCCCCAUU-UGGGGCAAGUUUAAUUGCAAAGCGCAAUCAAAUUAGU
...(((((..(((((..........((((....(((..((......))...)))..)))).)))))..)))))(((((....-.))))).(((((.(((((.....))))).)))))... ( -34.20)
>DroEre_CAF1 8935 119 - 1
GAAACAAUUUCGUUUAAUUAGGCAAAGGACUG-GGUACACGAACGGGUUCGGCCAACCCUGAAAUGGGGUUGUGCUACCAUUUUGGGGCAAGUUUAAUUGCAAAAUGCAAUCAAAUUAGU
.((((......)))).....(((...(((((.-(.........).))))).)))..(((..((((((((.....)).))))))..)))..(((((.(((((.....))))).)))))... ( -34.90)
>DroYak_CAF1 9832 119 - 1
GAAACAAUUUCGUUUAAUUAGGCAAAGGACUG-GGCCCACGAACGAGUUUGGCCAACACCGAAAUGGGGUUGUGCUCGCAUUUUGGGGCAAGUUUAAUUGCAAAAUGCAAUCAAAUUAGU
....(((.(((((((.....(((..(....).-.)))...))))))).)))(((....(((((((((((.....))).))))))))))).(((((.(((((.....))))).)))))... ( -33.00)
>consensus
GAAACAAUUUCGUUUAAUUAGGCAAAGGACUA_GGUACACGAACGAGUUUGGCCAACCCUGAAAUGGGAUUGUGCCCCCAUU_UGGGGCAAGUUUAAUUGCAAAACGCAAUCAAAUUAGU
...(((((..(((((.....(((...(((((..............))))).))).......)))))..)))))(((((......))))).(((((.(((((.....))))).)))))... (-29.36 = -28.99 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:00 2006