Locus 7656

Sequence ID	3R_DroMel_CAF1
Location	20,518,228 – 20,518,328
Length	100
Max. P	0.996789

overview

Window 8

Location	20,518,228 – 20,518,328
Length	100
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	72.79
Mean single sequence MFE	-33.67
Consensus MFE	-17.98
Energy contribution	-18.88
Covariance contribution	0.91
Combinations/Pair	1.21
Mean z-score	-5.56
Structure conservation index	0.53
SVM decision value	2.23
SVM RNA-class probability	0.990798
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20518228 100 + 27905053
-------------UCGGU--CUACAAACUGAAGCUUAAUUGUGAUUUAUGGAUGUGUAUUUUUUAGCAGUUAAAAAUCACAAUUUAGCCACU-UUGUAG-GUCGAUGAAACAGCUCA
-------------(((..--(((((((.((..(((.(((((((((((.(((.(((..........))).))).))))))))))).))))).)-))))))-..)))............ ( -31.40)
>DroSec_CAF1 720 100 + 1
-------------UCGGU--CUACAAACUGAAGCUUAAUUGUGAUUUAAGGAUGUGUAUUUUUUUGCACUAAAAAAUCACAAUUUAGCCAAU-UUGUAG-GUCGAUGAAAAACCACA
-------------(((..--(((((((.((..(((.(((((((((((......(((((......)))))....))))))))))).))))).)-))))))-..)))............ ( -34.40)
>DroSim_CAF1 740 99 + 1
-------------UCGGU--CUACAAACUGAAGCUUAAUUGUGAUUUAAGGAUGUGUAUUUUUUAGCACUAAAAAAUCACAAUUUAGCCAAU-UUGUAG-GUCGAU-AAAAACCACA
-------------(((..--(((((((.((..(((.(((((((((((......((((........))))....))))))))))).))))).)-))))))-..))).-.......... ( -32.60)
>DroEre_CAF1 742 99 + 1
-------------UCGGC--CUACAAACAUAAGCAUAAUUGUGAUUUAAGGAUGUAUAUUU-CAAGUAGUAAUACAUCACAAUUUAGCCAAU-UUGUAG-GCCGAUGAAAAACCUCA
-------------(((((--(((((((.....((..(((((((((....(((.......))-)..(((....))))))))))))..))...)-))))))-)))))............ ( -32.00)
>DroYak_CAF1 789 100 + 1
-------------UCGGC--AUACAAACUUGAGCUUAAUUGUGAUUUAAGGAUGUGAAUUU-CAAGCAACGAAAAAUCACAAUGAAGCCAAUUUUGUAG-GCCGAUGGAACACCUCA
-------------(((((--.((((((.(((.((((.((((((((((..(..(((......-...))).)...)))))))))).))))))).)))))).-)))))............ ( -32.40)
>DroPer_CAF1 831 108 + 1
UACACACGUUUCUCUGGUUUAUACAAAAUGAAGUUUCAUUGUGAUUGGAGCCUA--UAUGUUCUGGGAUAAUCCAAUCACAAUCAAGCUUC--CUGUACAACCCAUGAGAG-----A
........(((((((((.((.((((....(((((((.((((((((((((.((((--.......))))....)))))))))))).)))))))--.)))).)).))).)))))-----) ( -39.20)
>consensus
_____________UCGGU__CUACAAACUGAAGCUUAAUUGUGAUUUAAGGAUGUGUAUUUUCUAGCACUAAAAAAUCACAAUUUAGCCAAU_UUGUAG_GCCGAUGAAAAACCUCA
.............((((((.((((((......(((.(((((((((((.....(((..........))).....))))))))))).))).....))))))))))))............ (-17.98 = -18.88 +   0.91)

alignment

secondary structure

dotplot

Window 9

Location	20,518,228 – 20,518,328
Length	100
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	72.79
Mean single sequence MFE	-30.47
Consensus MFE	-17.95
Energy contribution	-18.20
Covariance contribution	0.25
Combinations/Pair	1.21
Mean z-score	-4.50
Structure conservation index	0.59
SVM decision value	2.75
SVM RNA-class probability	0.996789
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20518228 100 - 27905053
UGAGCUGUUUCAUCGAC-CUACAA-AGUGGCUAAAUUGUGAUUUUUAACUGCUAAAAAAUACACAUCCAUAAAUCACAAUUAAGCUUCAGUUUGUAG--ACCGA-------------
............(((..-((((((-(.(((((.(((((((((((.....((............)).....))))))))))).)))..)).)))))))--..)))------------- ( -24.60)
>DroSec_CAF1 720 100 - 1
UGUGGUUUUUCAUCGAC-CUACAA-AUUGGCUAAAUUGUGAUUUUUUAGUGCAAAAAAAUACACAUCCUUAAAUCACAAUUAAGCUUCAGUUUGUAG--ACCGA-------------
............(((..-((((((-(((((((.(((((((((((....(((..........)))......))))))))))).)))..))))))))))--..)))------------- ( -28.30)
>DroSim_CAF1 740 99 - 1
UGUGGUUUUU-AUCGAC-CUACAA-AUUGGCUAAAUUGUGAUUUUUUAGUGCUAAAAAAUACACAUCCUUAAAUCACAAUUAAGCUUCAGUUUGUAG--ACCGA-------------
..........-.(((..-((((((-(((((((.(((((((((((....(((..........)))......))))))))))).)))..))))))))))--..)))------------- ( -28.30)
>DroEre_CAF1 742 99 - 1
UGAGGUUUUUCAUCGGC-CUACAA-AUUGGCUAAAUUGUGAUGUAUUACUACUUG-AAAUAUACAUCCUUAAAUCACAAUUAUGCUUAUGUUUGUAG--GCCGA-------------
............(((((-((((((-((.(((..((((((((((((((.(.....)-.)))))..........)))))))))..)))...))))))))--)))))------------- ( -33.00)
>DroYak_CAF1 789 100 - 1
UGAGGUGUUCCAUCGGC-CUACAAAAUUGGCUUCAUUGUGAUUUUUCGUUGCUUG-AAAUUCACAUCCUUAAAUCACAAUUAAGCUCAAGUUUGUAU--GCCGA-------------
...((....)).(((((-.((((((.(((((((.((((((((((.....((..((-.....)))).....)))))))))).)))).))).)))))).--)))))------------- ( -32.80)
>DroPer_CAF1 831 108 - 1
U-----CUCUCAUGGGUUGUACAG--GAAGCUUGAUUGUGAUUGGAUUAUCCCAGAACAUA--UAGGCUCCAAUCACAAUGAAACUUCAUUUUGUAUAAACCAGAGAAACGUGUGUA
.-----.((((.(((.(((((((.--((((.((.((((((((((((....((.........--..)).)))))))))))).)).))))....))))))).))))))).......... ( -35.80)
>consensus
UGAGGUUUUUCAUCGAC_CUACAA_AUUGGCUAAAUUGUGAUUUUUUACUGCUAAAAAAUACACAUCCUUAAAUCACAAUUAAGCUUCAGUUUGUAG__ACCGA_____________
............(((...((((((....((((.(((((((((((..........................))))))))))).)))).....))))))....)))............. (-17.95 = -18.20 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:21 2006