Locus 6400

Sequence ID	3R_DroMel_CAF1
Location	16,777,411 – 16,777,603
Length	192
Max. P	0.569518

overview

Window 5

Location	16,777,411 – 16,777,523
Length	112
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	90.03
Mean single sequence MFE	-32.22
Consensus MFE	-24.59
Energy contribution	-26.22
Covariance contribution	1.63
Combinations/Pair	1.03
Mean z-score	-1.53
Structure conservation index	0.76
SVM decision value	0.05
SVM RNA-class probability	0.556909
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16777411 112 - 27905053
CCAUUGUUGAGCUCCGGCUCAGCUACUUCAGGUAGCUGGACAAUAAACUACCCCUUCGGAACUAAGCCACCCCUGAAGGGUAAUGAUCGAUGGACCUUGAGAGACCUACAAG
((((((..((((....))))((((((.....))))))..............((((((((.............)))))))).......))))))..((((((....)).)))) ( -32.72)
>DroSec_CAF1 9811 104 - 1
CCAUUGUUGAGCCCCGGCUCAGCUACUUCAGGUA----GACAAUAAACCACCCCUUCGGAACUGAGCCACCCCUGAAGGGUAUUGAUCGAUGGACCUUGAGAGA----CAAG
.....(((((((....)))))))..(((.((((.----(((((((......((((((((.............))))))))))))).)).....)))).)))...----.... ( -31.52)
>DroSim_CAF1 11464 112 - 1
CCAUUGUUGAGCCCCGGCUCAGCUACUUCAGGUAGCUGGACAAUAAACCACCCCUUCGGAACUAAGCCACCCCUGAAGCGAAUUGAUCGAUGGACCUUGAGAGACCUACAAG
((((((((((((....)))))))..(((((((..(((((........))....(....).....)))....)))))))..........)))))..((((((....)).)))) ( -31.70)
>DroEre_CAF1 5630 111 - 1
CCAUUGUUGAGCUCCGGCUCAGCUACUUCAGGUAGCUGGACAAUAAACCACC-CUUCUAACUUAAGCCACCCCUGAAGGGUAUUGAUCGGUAGACCUUGAGAAACCUACAAG
.....(((((((....)))))))..(((.((((.(((((.((((.....(((-((((.................))))))))))).)))))..)))).)))........... ( -32.93)
>consensus
CCAUUGUUGAGCCCCGGCUCAGCUACUUCAGGUAGCUGGACAAUAAACCACCCCUUCGGAACUAAGCCACCCCUGAAGGGUAUUGAUCGAUGGACCUUGAGAGACCUACAAG
.....(((((((....)))))))..(((.((((...(.(((((((......((((((((.............))))))))))))).)).)...)))).)))........... (-24.59 = -26.22 +   1.63)

alignment

secondary structure

dotplot

Window 6

Location	16,777,483 – 16,777,603
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.47
Mean single sequence MFE	-39.35
Consensus MFE	-32.74
Energy contribution	-33.43
Covariance contribution	0.69
Combinations/Pair	1.08
Mean z-score	-1.58
Structure conservation index	0.83
SVM decision value	0.07
SVM RNA-class probability	0.569518
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16777483 120 + 27905053
UCCAGCUACCUGAAGUAGCUGAGCCGGAGCUCAACAAUGGCUCAAUUGUUCCUGUUCGCCACCGGUUCAAACGAGUUUCGGGCGGUAAGACGAGAUUUGUGAAUCUCCAGAACUCUGAAC
...((((((.....))))))(((((((.((..((((..(((......)))..)))).))..)))))))..((((((((((..(.....).)))))))))).......(((....)))... ( -36.70)
>DroSec_CAF1 9879 116 + 1
UC----UACCUGAAGUAGCUGAGCCGGGGCUCAACAAUGGCUCAAUUGUUCCUGUUCGCCACUGGUUCAAACGAGUUUCGGGCGGUAAGACGAGAUUCGUGGAUCUCCAGAACUCUGAAC
.(----..(((((((....(((((((((((..((((..(((......)))..)))).))).))))))))......)))))))..)......((((((....))))))(((....)))... ( -37.10)
>DroSim_CAF1 11536 120 + 1
UCCAGCUACCUGAAGUAGCUGAGCCGGGGCUCAACAAUGGCUCAAUUGUUCCUGUUCGCCACCGGUUCAAACGAGUUUCGGGCGGUAAGACGAGAUUCGUGGAUCUCCAGAACUCUGAAC
(((((((((.....))))))((((((((((..((((..(((......)))..)))).))).)))))))..((((((((((..(.....).)))))))))))))....(((....)))... ( -46.20)
>DroEre_CAF1 5701 119 + 1
UCCAGCUACCUGAAGUAGCUGAGCCGGAGCUCAACAAUGGCUCAAUUGUUCCUGUUCACCACCGGUUUAAACGAGUUUUGGGCGGCAAGACGAGAUUUCUAGAUCUCCAGAACUCUGAA-
..(((((((.....)))))))(((((((((..((((((......))))))...))).....)))))).....(((((((((.((......))(((((....))))))))))))))....- ( -37.40)
>consensus
UCCAGCUACCUGAAGUAGCUGAGCCGGAGCUCAACAAUGGCUCAAUUGUUCCUGUUCGCCACCGGUUCAAACGAGUUUCGGGCGGUAAGACGAGAUUCGUGGAUCUCCAGAACUCUGAAC
....(((((.....)))))(((((((((((..((((..(((......)))..)))).))).))))))))...((((((.((.((......))(((((....))))))).))))))..... (-32.74 = -33.43 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:37 2006