Locus 5379

Sequence ID	3L_DroMel_CAF1
Location	14,788,032 – 14,788,264
Length	232
Max. P	0.979640

overview

Window 7

Location	14,788,032 – 14,788,146
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-30.37
Consensus MFE	-26.68
Energy contribution	-26.82
Covariance contribution	0.14
Combinations/Pair	1.07
Mean z-score	-2.17
Structure conservation index	0.88
SVM decision value	1.84
SVM RNA-class probability	0.979640
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14788032 114 - 23771897
GUCCG--CUCUACGUUCACAUUUUUCUUUUUAAUAGGAAAAACACGUCUUCAGUCUC--CUGGCCAUGGAGU--GCGUGUUUGGCCAGCUUUGUUUUCGCAUGUGAAAGUAUUUAAUUCA
.....--...(((.(((((((..............((..((((((((((((((((..--..)))..))))).--))))))))..)).((.........))))))))).)))......... ( -29.50)
>DroSec_CAF1 31184 114 - 1
GUCCG--CUCUACGUUCACAUUUUUCUUUUUAAUAGGAAAAACACGUCUUCAGUCUC--CUGGCCAUGGAGU--GCGUGUUUGGCCAGCUUUGUUUUCGCAUGUGAAAGUAUUUAAUUCA
.....--...(((.(((((((..............((..((((((((((((((((..--..)))..))))).--))))))))..)).((.........))))))))).)))......... ( -29.50)
>DroSim_CAF1 23428 114 - 1
GUCCG--CUCUACGUUCACAUUUUUCUUUUUAAUAGGAAAAACACGUCUUCAGUCUC--CUGGCCAUGGAGU--GCGUGUUUGGCCAGCUUUGUUUUCGCAUGUGAAAGUAUUUAAUUCA
.....--...(((.(((((((..............((..((((((((((((((((..--..)))..))))).--))))))))..)).((.........))))))))).)))......... ( -29.50)
>DroEre_CAF1 30677 114 - 1
GUCCU--CUCUACGUUCACAUUUUUCUUUUUAAUAGGAAAAACACGUCUUCGGUCUC--CUGGCCAUGGAGU--GCGUGUUUGGCCAGCUUUGUUUUCGCAUGUGAAAGUAUUUAAUUCA
.....--...(((.(((((((..............((..((((((((((((((((..--..))))..)))).--))))))))..)).((.........))))))))).)))......... ( -31.20)
>DroYak_CAF1 33011 114 - 1
GUCCU--CUCUACGUUCACAUUUUUCUUUUUAAUAGGAAAAACACGUCUUCAGUCUC--CUGGCCAUGGAGU--GCGUGUUUGGCCAGCUUUGUUUUCGCAUGUGAAAGUAUUUAAUUCA
.....--...(((.(((((((..............((..((((((((((((((((..--..)))..))))).--))))))))..)).((.........))))))))).)))......... ( -29.50)
>DroAna_CAF1 30010 120 - 1
GUCCUUUCUCUCCUUUCACAUUUUUCUUUUUAAUAGGAAAAACACGUCUUCGAGCCCCACAGGCCCCGGAGUGUGCGUGUUUGGCCAGCUUUGUUUUCGCAUGUGAAAGUAUUUAAUUCA
............(((((((((..............((..(((((((((((((.(((.....)))..)))))...))))))))..)).((.........)))))))))))........... ( -33.00)
>consensus
GUCCG__CUCUACGUUCACAUUUUUCUUUUUAAUAGGAAAAACACGUCUUCAGUCUC__CUGGCCAUGGAGU__GCGUGUUUGGCCAGCUUUGUUUUCGCAUGUGAAAGUAUUUAAUUCA
..........(((.(((((((..............((..((((((((((((((((......)))..)))))...))))))))..)).((.........))))))))).)))......... (-26.68 = -26.82 +   0.14)

alignment

secondary structure

dotplot

Window 8

Location	14,788,146 – 14,788,264
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.01
Mean single sequence MFE	-30.87
Consensus MFE	-17.73
Energy contribution	-19.15
Covariance contribution	1.42
Combinations/Pair	1.17
Mean z-score	-2.18
Structure conservation index	0.57
SVM decision value	0.37
SVM RNA-class probability	0.710135
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14788146 118 + 23771897
UUGAAAGGCUGGCUCCGAAGGGAAA--CGGCCAUGAAUCUGUGCCAGAUGAAACAAUGGCAGGCACAAGCCUGGGAUUCAAUGAUAACAAAUUGAACGUGUGCUGGGAAAAUGUAUAGGG
(((...(((((..(((....)))..--))))).(((((((..((((..........))))((((....)))).))))))).......)))......(.(((((.........))))).). ( -38.80)
>DroSec_CAF1 31298 118 + 1
UUGAAAGGCUGGCUCCGAAGGGAAA--UGGCCAUGAAUCUGUGCCAGAUGAAACAAUGGCAGGCACAAGCCUGGGAUUCAAUGAUAACAAAUUGAACGUGUGAUGGGAAAAUUUAUAGGG
(((...(((((..(((....)))..--))))).(((((((..((((..........))))((((....)))).))))))).......)))......(.(((((.........))))).). ( -33.60)
>DroSim_CAF1 23542 118 + 1
UUGAAAGGCUGGCUCCGAAGGGAAA--CGGCCAUGAAUCUGUGCCAGAUGAAACAAUGGCAGGCACAAGCCUGGGAUUCAAUGAUAACAAAUUGAACGUGUGAUGGGAAAAUUUAUAGGG
(((...(((((..(((....)))..--))))).(((((((..((((..........))))((((....)))).))))))).......)))......(.(((((.........))))).). ( -36.70)
>DroEre_CAF1 30791 118 + 1
UUGAAAGGCUGGCUCCGAAGGGAAA--UGGCUAUGAAUCUGUGCCAGAUGAAACAAUGGCAGGCAAAAGCCUGGGAUUCAAUGAUAACAAAUUGAACGUGUGCUGGGGAAAUUUAUAGGG
......(((((..(((....)))..--)))))((((((...(.((((.....(((.((.(((((....)))))...((((((........))))))))))).)))).)..)))))).... ( -32.10)
>DroYak_CAF1 33125 120 + 1
UUGAAAGGCUGACUCCAAAGGGAAACACGACUGUGAAUCUGUGCCAGAUGAAACAAUGGCAGGCAAAAGCCUGGGAUUCAAUGAUAACAAAUUGAACGUGUGCUGGGAAAAUUUAUAGGG
..............((....(....)....((((((((...(.((((.....(((.((.(((((....)))))...((((((........))))))))))).)))).)..)))))))))) ( -28.30)
>DroAna_CAF1 30130 93 + 1
CUGAAAAGCU----------------------ACGAAUGUGUGUUAGAUGAAUUAAUAGCCUA-AUAUGGUCAGAAUACAAGGAUAACAAAUAGAUCGUA----GGGCAAGUGUGGAAUG
........((----------------------((((.(((.(((((..((.(((....(((..-....)))...))).))....))))).)))..)))))----)............... ( -15.70)
>consensus
UUGAAAGGCUGGCUCCGAAGGGAAA__CGGCCAUGAAUCUGUGCCAGAUGAAACAAUGGCAGGCACAAGCCUGGGAUUCAAUGAUAACAAAUUGAACGUGUGCUGGGAAAAUUUAUAGGG
......(((((..(((....)))....))))).(((((((..((((..........))))((((....)))).)))))))........................................ (-17.73 = -19.15 +   1.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:48 2006