Locus 8332

Sequence ID	3R_DroMel_CAF1
Location	22,245,506 – 22,245,666
Length	160
Max. P	0.771733

overview

Window 3

Location	22,245,506 – 22,245,616
Length	110
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	81.75
Mean single sequence MFE	-31.00
Consensus MFE	-20.30
Energy contribution	-19.72
Covariance contribution	-0.58
Combinations/Pair	1.12
Mean z-score	-2.15
Structure conservation index	0.65
SVM decision value	0.53
SVM RNA-class probability	0.771733
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22245506 110 + 27905053
AAACUUUAUUAACAUUUUUCGCAUGCUGCACGUGCAG----CGUUUGUGGCAGGAACGUCGC-GAC-GCGUCGCGUAUUUCGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAU
.(((((((((((.......((((((((((....))))----)))(((((((......)))))-)).-))).((((.....))))....)))))))))))((((.....)))).... ( -34.70)
>DroVir_CAF1 21275 97 + 1
AAACUUUAUUAACAUUUUUCGCAUGCUGCACGUGCA-----CAUU---------GACAACGU-----GGGCCGCGUAUUUUGCGCUUUUUAAUGAAGUUUCAUAAAUUGUGAGAAU
.(((((((((((............(((.(((((.(.-----....---------)...))))-----)))).((((.....))))...)))))))))))((((.....)))).... ( -22.00)
>DroPse_CAF1 25393 116 + 1
AAACUUUAUUAACAUUUUUCGCAUGCUGCACGUGCAGCCCGCAUUUGUGGCAGGGACGACGGGGACGGCGGCGCGCGUUUCGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAU
.(((((((((((............(((((.(((.(...((((....))))...).))).((....)))))))(((((...)))))...)))))))))))((((.....)))).... ( -39.60)
>DroGri_CAF1 46008 98 + 1
AAACUUUAUUAACAUUUUUCGCAUGCUGCACGUGCAG----CACU---------GACAACGU-----GGGCCGCGUAUUUUGUGCUUUUUAAUGAAGUUUCAUAAAUUGUGAGAAU
.(((((((((((........(((((.....)))))((----(((.---------....((((-----(...))))).....)))))..)))))))))))((((.....)))).... ( -25.20)
>DroAna_CAF1 18796 100 + 1
AAACUUUAUUAACAUUUUUCGCAUGCUGCACGUGCAG----CAUUUCUGCCAG-----------CC-GCCUUGCGUAUUUCGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAU
.(((((((((((........(((((((((....))))----))....)))...-----------..-.....((((.....))))...)))))))))))((((.....)))).... ( -24.90)
>DroPer_CAF1 33378 116 + 1
AAACUUUAUUAACAUUUUUCGCAUGCUGCACGUGCAGCCCGCAUUUGUGGCAGGGACGACGGUGACGGCGGCGCGCGUUUCGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAU
.(((((((((((............(((((.(((.(...((((....))))...).))).((....)))))))(((((...)))))...)))))))))))((((.....)))).... ( -39.60)
>consensus
AAACUUUAUUAACAUUUUUCGCAUGCUGCACGUGCAG____CAUUUGUGGCAG_GACGACGG__AC_GCGCCGCGUAUUUCGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAU
...(((((((((........(((((.....))))).....................................((((.....))))...)))))))))((((((.....)))))).. (-20.30 = -19.72 +  -0.58)

alignment

secondary structure

dotplot

Window 4

Location	22,245,576 – 22,245,666
Length	90
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	82.30
Mean single sequence MFE	-23.15
Consensus MFE	-14.68
Energy contribution	-15.02
Covariance contribution	0.34
Combinations/Pair	1.21
Mean z-score	-1.86
Structure conservation index	0.63
SVM decision value	0.09
SVM RNA-class probability	0.576691
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22245576 90 + 27905053
AUUUCGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAUCGAACGUUAAUCAAAUAAGGAGCGG---------AGAGCCAUGUGCAAGAGGUGGCGCC
.((((.(((((((((..((..((((((.....)))))).))((.......))...))))))))))---------)))(((((.(.....).)))))... ( -25.60)
>DroVir_CAF1 21332 94 + 1
AUUUUGCGCUUUUUAAUGAAGUUUCAUAAAUUGUGAGAAUCGAACGUUAAUCAAAUAAGGUGCGAGAGAAAUCAAAAGCCUUGUCCG-----AGACGCC
.....((((((.((((((...((((((.....))))))......))))))....(((((((....((....))....)))))))..)-----)).))). ( -19.40)
>DroGri_CAF1 46066 94 + 1
AUUUUGUGCUUUUUAAUGAAGUUUCAUAAAUUGUGAGAAUCGAACGUUAAUCAAAUAAGGUGCGAGAGAAAUCAAAAGCCUUGUCCC-----AGGCGCC
.....((((((.((((((...((((((.....))))))......))))))....(((((((....((....))....)))))))...-----)))))). ( -20.60)
>DroEre_CAF1 25005 90 + 1
AUUUUGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAUCGAACGUUAAUCAAAUAAGGAGCGG---------AAAGCCAUGUACAAAAGGUGGCCCC
..(((.(((((((((..((..((((((.....)))))).))((.......))...))))))))).---------)))(((((.(.....).)))))... ( -23.40)
>DroYak_CAF1 22884 90 + 1
AUUUCGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAUCGAACGUUAAUCAAAUAAGGAGCGG---------AGAGCCAUGUACACAAGGUGGCGCC
.((((.(((((((((..((..((((((.....)))))).))((.......))...))))))))))---------)))(((((.(.....).)))))... ( -25.40)
>DroAna_CAF1 18856 86 + 1
AUUUCGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAUCGAACGUUAAUCAAAUAAGGAGCGG---------GG---CCCGCACA-AAGGUGGCGCC
......(((((((((..((..((((((.....)))))).))((.......))...))))))))).---------((---(((((...-...)))).))) ( -24.50)
>consensus
AUUUCGCGCUCUUUAAUGAAGUUUCAUAAAUUGUGAAAAUCGAACGUUAAUCAAAUAAGGAGCGG_________AAAGCCAUGUACA_AAGGUGGCGCC
......(((((((((..((..((((((.....)))))).))((.......))...))))))))).............(((((.........)))))... (-14.68 = -15.02 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:04 2006