Locus 8244

Sequence ID	3L_DroMel_CAF1
Location	21,656,678 – 21,656,896
Length	218
Max. P	0.938347

overview

Window 0

Location	21,656,678 – 21,656,790
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	76.16
Mean single sequence MFE	-30.93
Consensus MFE	-17.08
Energy contribution	-19.70
Covariance contribution	2.62
Combinations/Pair	1.10
Mean z-score	-2.30
Structure conservation index	0.55
SVM decision value	1.29
SVM RNA-class probability	0.938347
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21656678 112 + 23771897
AAC-------AGCAAUGAUAUUGUCCUCCUGUAUACAACUGAACAAGUUUUCACAUAUAGCCGAUGGAUCGAGUG-UGACUGCUCUCUAACCAGCAGAGGCAUUCCGUCCGUCGGCCCAA
.((-------((....(((...)))...))))....((((.....))))..........((((((((((.(((((-(..(((((........)))))..)))))).)))))))))).... ( -35.70)
>DroEre_CAF1 32924 119 + 1
AACAACACC-AGUAAUAAUAUUGUCCUCCUGGAACAAACUGAACAAGUUUUCACAUAUAGCCGAUGGAUCGAGUGCUUACUGCUCUCUAACCAGCAGAGGCAUUCUGUCCGUCGGCCCAA
........(-(((.......((((((....)).))))))))..................((((((((((.((((((((.(((((........))))))))))))).)))))))))).... ( -42.41)
>DroYak_CAF1 42058 118 + 1
AACAACACC-AGCAAUGAUAUUGUCAUCCUGUAACUAACUGAACAAGUUUUCACAUAUAGCCGCUAGAUCGAGUG-UGACUGCUCUCUAACCAGCAGAGGCAUUCUGUCCGUCGGCCCAA
........(-((..(((((...))))).))).....((((.....))))..........((((...(((.(((((-(..(((((........)))))..)))))).)))...)))).... ( -26.20)
>DroAna_CAF1 33107 110 + 1
GA--ACUUGAUGGAAUAGUAUUGA-------GUACAAACUGAACAAAAUAUCAUUUAUAUCCUAUUCCCCAAGUG-UGUCCAAGCUCUAAGCAGCAGUGGCAUUCUGUCCAUCGGUCCAA
..--(((((..(((((((..((.(-------((....))).))....(((.....)))...))))))).)))))(-.(.((..(((......))).(((((.....).)))).)).)).. ( -19.40)
>consensus
AAC_ACACC_AGCAAUAAUAUUGUCCUCCUGGAACAAACUGAACAAGUUUUCACAUAUAGCCGAUGGAUCGAGUG_UGACUGCUCUCUAACCAGCAGAGGCAUUCUGUCCGUCGGCCCAA
...........................................................((((((((((.(((((.(..(((((........)))))..)))))).)))))))))).... (-17.08 = -19.70 +   2.62)

alignment

secondary structure

dotplot

Window 1

Location	21,656,711 – 21,656,825
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.04
Mean single sequence MFE	-30.65
Consensus MFE	-21.52
Energy contribution	-24.40
Covariance contribution	2.88
Combinations/Pair	1.07
Mean z-score	-1.49
Structure conservation index	0.70
SVM decision value	0.04
SVM RNA-class probability	0.552964
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21656711 114 + 23771897
GAACAAGUUUUCACAUAUAGCCGAUGGAUCGAGUG-UGACUGCUCUCUAACCAGCAGAGGCAUUCCGUCCGUCGGCCCAAACAUGGCAAAAGGCAUGUCC-----AUCCUUCCUAUCGCA
((.................((((((((((.(((((-(..(((((........)))))..)))))).))))))))))....(((((.(....).)))))..-----..........))... ( -38.50)
>DroEre_CAF1 32963 115 + 1
GAACAAGUUUUCACAUAUAGCCGAUGGAUCGAGUGCUUACUGCUCUCUAACCAGCAGAGGCAUUCUGUCCGUCGGCCCAAACAUGGCAAAAGGCAUGUCC-----AUCCUUCCUAUCGCA
((.................((((((((((.((((((((.(((((........))))))))))))).))))))))))....(((((.(....).)))))..-----..........))... ( -42.20)
>DroYak_CAF1 42097 114 + 1
GAACAAGUUUUCACAUAUAGCCGCUAGAUCGAGUG-UGACUGCUCUCUAACCAGCAGAGGCAUUCUGUCCGUCGGCCCAAACAUGGCAAAAGGCAUGUCC-----AUCCUUCCUAUCGCA
((.................((((...(((.(((((-(..(((((........)))))..)))))).)))...))))....(((((.(....).)))))..-----..........))... ( -28.00)
>DroAna_CAF1 33138 119 + 1
GAACAAAAUAUCAUUUAUAUCCUAUUCCCCAAGUG-UGUCCAAGCUCUAAGCAGCAGUGGCAUUCUGUCCAUCGGUCCAAACAAGGCAAAAGGCAUGUCCAUUCCAUCCUUCCUAUCGUA
................(((((((.((((.....((-.(.((..(((......))).(((((.....).)))).)).))).....)).)).))).))))...................... ( -13.90)
>consensus
GAACAAGUUUUCACAUAUAGCCGAUGGAUCGAGUG_UGACUGCUCUCUAACCAGCAGAGGCAUUCUGUCCGUCGGCCCAAACAUGGCAAAAGGCAUGUCC_____AUCCUUCCUAUCGCA
((.................((((((((((.(((((.(..(((((........)))))..)))))).))))))))))....(((((.(....).))))).................))... (-21.52 = -24.40 +   2.88)

alignment

secondary structure

dotplot

Window 2

Location	21,656,790 – 21,656,896
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.96
Mean single sequence MFE	-31.61
Consensus MFE	-22.17
Energy contribution	-22.57
Covariance contribution	0.40
Combinations/Pair	1.09
Mean z-score	-1.64
Structure conservation index	0.70
SVM decision value	0.56
SVM RNA-class probability	0.782167
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21656790 106 + 23771897
ACAUGGCAAAAGGCAUGUCC-----AUCCUUCCUAUCGCAACAAGAGCAAUUUGUUCUAAUGCGCCAUGGCAGCGGCAGCUGCU---GGAAAUGGC-----GAGACU-AAAUCUGUGGAA
.((((.(....).))))(((-----((........(((((...(((((.....)))))..)))(((((((((((....))))))---....)))))-----))....-......))))). ( -34.07)
>DroVir_CAF1 19607 85 + 1
ACAAGGCAAAAGGCAUGUCC-----AUCC-UCCUAUCGUAACAAGAACAAUUUGUUCUAAUGCGCCAUGGCAGCAGUUGCAGCAGCGGCAG-----------------------------
...(((....(((.((....-----))))-))))...(((((.(((((.....)))))..(((((....)).)))))))).((....))..----------------------------- ( -19.20)
>DroEre_CAF1 33043 106 + 1
ACAUGGCAAAAGGCAUGUCC-----AUCCUUCCUAUCGCAACAAGAGCAAUUUGUUCUAAUGCACCAUGGCAGCGGCAGCUGCU---GGAAAUGGC-----GAGACU-AAAUCUGUGGAA
.((((.(....).))))(((-----((........((((....(((((.....)))))......(((..(((((....))))))---)).....))-----))....-......))))). ( -30.57)
>DroYak_CAF1 42176 106 + 1
ACAUGGCAAAAGGCAUGUCC-----AUCCUUCCUAUCGCAACAAGAGCAAUUUGUUCUAAUGCGCCAUGGCAGCGGCAGCUGCU---GAAAAUGGC-----GAGACU-AAAUGUGUGGAA
(((((.(....).)))))..-----.....(((...((((...(((((.....)))))....((((((((((((....))))))---....)))))-----).....-...)))).))). ( -35.00)
>DroAna_CAF1 33217 117 + 1
ACAAGGCAAAAGGCAUGUCCAUUCCAUCCUUCCUAUCGUAACAAGAGCAAUUUGUUCUAAUGCGCCAUGGCAGCAGCAGCUGCC---GGAGUUGGGAUGCUGGGCCCAGAAUCUCAAGCU
....(((....(((((.((.(((((...........((((...(((((.....)))))..))))....((((((....))))))---))))).)).)))))..))).............. ( -39.20)
>consensus
ACAUGGCAAAAGGCAUGUCC_____AUCCUUCCUAUCGCAACAAGAGCAAUUUGUUCUAAUGCGCCAUGGCAGCGGCAGCUGCU___GGAAAUGGC_____GAGACU_AAAUCUGUGGAA
.((((((...(((..................)))...(((...(((((.....)))))..)))))))))(((((....)))))..................................... (-22.17 = -22.57 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:20 2006