Locus 5414

Sequence ID	3L_DroMel_CAF1
Location	14,836,036 – 14,836,141
Length	105
Max. P	0.902316

overview

Window 8

Location	14,836,036 – 14,836,141
Length	105
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	76.29
Mean single sequence MFE	-24.43
Consensus MFE	-15.02
Energy contribution	-15.00
Covariance contribution	-0.02
Combinations/Pair	1.24
Mean z-score	-1.63
Structure conservation index	0.61
SVM decision value	0.69
SVM RNA-class probability	0.824883
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14836036 105 + 23771897
GAACG---GAGGAUAUUGAAUUCAUCGUACAAUAUGGCAAAGUCAAUAACAUGACCAUGUACGAGACAGUUGCCAAAUUGGAAAAUGUGAGUAUAUA--------U--CGGUGUUGGA
.....---...((((((((((((((....((((.((((((.(((....((((....))))....)))..)))))).))))......)))))).....--------)--)))))))... ( -24.20)
>DroVir_CAF1 35162 110 + 1
AUGCUAAUGAUCAUAUUGAAUUCGUUGUUCAAUAUGGCCGAGUCAAUAACAUGACCAUGUACGAGACGAUUGCCAAAUUGGAAAACGUGAGUACAGCUAAACAUAG--UAGU------
.(((((..(..((((((((((.....))))))))))..)(.((((......))))).(((((...(((....((.....))....)))..)))))........)))--))..------ ( -27.40)
>DroPse_CAF1 68801 104 + 1
AAGCG---GAGGAUAUUGAUUUUAUUGUGCAGUAUGGCAGAGUCAAUAACAUGACCAUGUACGAGACAGUUGCCAAAUUGGAAAAUGUGAGUAUAUU--------U--CUGG-AUGGA
...((---(((((((((.((.......(.((((.((((((.(((....((((....))))....)))..)))))).)))).)....)).))))).))--------)--))).-..... ( -23.60)
>DroGri_CAF1 32200 105 + 1
AAGCUAAUGAUAGAAUUGAAUUUGUCGUUCAAUAUGGCCGAGUCAAUAACAUGACCAUGUACGAGACAGUUGCCAAAUUGGAAUAUGUGAGUACAUC-----AUAU--GUGU------
.......(((((((......)))))))((((((.((((...(((....((((....))))....)))....)))).))))))((((((((.....))-----))))--))..------ ( -24.20)
>DroWil_CAF1 160098 105 + 1
CUGCU---GAUGAUAUUGAUUUUAUUGUACAAUACGGCAAAGUCAAUGACAUGACCAUGUAUGAGACAGUUGCCAAAUUAGAAAAUGUAAGUAUCCA--------AGUUAG--CAAUA
.((((---(((((((((.(((((...(((...)))(((((.(((....((((....))))....)))..))))).......)))))...))))))..--------.)))))--))... ( -23.60)
>DroPer_CAF1 66258 104 + 1
AAGCG---GAGGAUAUUGAUUUUAUUGUGCAGUAUGGCAGAGUCAAUAACAUGACCAUGUACGAGACAGUUGCCAAAUUGGAAAAUGUGAGUAUAUU--------U--CUGG-AUGGA
...((---(((((((((.((.......(.((((.((((((.(((....((((....))))....)))..)))))).)))).)....)).))))).))--------)--))).-..... ( -23.60)
>consensus
AAGCG___GAGGAUAUUGAAUUUAUUGUACAAUAUGGCAGAGUCAAUAACAUGACCAUGUACGAGACAGUUGCCAAAUUGGAAAAUGUGAGUAUAUA________U__CUGU__UGGA
......................((((...((((.((((((.(((....((((....))))....)))..)))))).))))...))))............................... (-15.02 = -15.00 +  -0.02)

alignment

secondary structure

dotplot

Window 9

Location	14,836,036 – 14,836,141
Length	105
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	76.29
Mean single sequence MFE	-18.14
Consensus MFE	-13.69
Energy contribution	-14.08
Covariance contribution	0.39
Combinations/Pair	1.12
Mean z-score	-1.35
Structure conservation index	0.76
SVM decision value	1.02
SVM RNA-class probability	0.902316
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14836036 105 - 23771897
UCCAACACCG--A--------UAUAUACUCACAUUUUCCAAUUUGGCAACUGUCUCGUACAUGGUCAUGUUAUUGACUUUGCCAUAUUGUACGAUGAAUUCAAUAUCCUC---CGUUC
.........(--(--------(((.......((((...((((.((((((..(((....((((....))))....))).)))))).))))...))))......)))))...---..... ( -21.12)
>DroVir_CAF1 35162 110 - 1
------ACUA--CUAUGUUUAGCUGUACUCACGUUUUCCAAUUUGGCAAUCGUCUCGUACAUGGUCAUGUUAUUGACUCGGCCAUAUUGAACAACGAAUUCAAUAUGAUCAUUAGCAU
------....--.........(((((((..(((.((.((.....)).)).)))...))))..(((((......))))).(..(((((((((.......)))))))))..)...))).. ( -24.10)
>DroPse_CAF1 68801 104 - 1
UCCAU-CCAG--A--------AAUAUACUCACAUUUUCCAAUUUGGCAACUGUCUCGUACAUGGUCAUGUUAUUGACUCUGCCAUACUGCACAAUAAAAUCAAUAUCCUC---CGCUU
.....-....--.--------......................(((((...(((....((((....))))....)))..)))))..........................---..... ( -12.90)
>DroGri_CAF1 32200 105 - 1
------ACAC--AUAU-----GAUGUACUCACAUAUUCCAAUUUGGCAACUGUCUCGUACAUGGUCAUGUUAUUGACUCGGCCAUAUUGAACGACAAAUUCAAUUCUAUCAUUAGCUU
------....--..((-----((((.............((((.((((....(((....((((....))))....)))...)))).))))...((.....)).....))))))...... ( -18.00)
>DroWil_CAF1 160098 105 - 1
UAUUG--CUAACU--------UGGAUACUUACAUUUUCUAAUUUGGCAACUGUCUCAUACAUGGUCAUGUCAUUGACUUUGCCGUAUUGUACAAUAAAAUCAAUAUCAUC---AGCAG
..(((--((((.(--------((((...........))))).)))))))((((......((.(((((......))))).))..((((((...........))))))....---.)))) ( -19.80)
>DroPer_CAF1 66258 104 - 1
UCCAU-CCAG--A--------AAUAUACUCACAUUUUCCAAUUUGGCAACUGUCUCGUACAUGGUCAUGUUAUUGACUCUGCCAUACUGCACAAUAAAAUCAAUAUCCUC---CGCUU
.....-....--.--------......................(((((...(((....((((....))))....)))..)))))..........................---..... ( -12.90)
>consensus
UCCA__ACAG__A________AAUAUACUCACAUUUUCCAAUUUGGCAACUGUCUCGUACAUGGUCAUGUUAUUGACUCUGCCAUAUUGAACAAUAAAAUCAAUAUCAUC___AGCUU
......................................((((.(((((...(((....((((....))))....)))..))))).))))............................. (-13.69 = -14.08 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:47 2006