Locus 1067

Sequence ID	2R_DroMel_CAF1
Location	4,350,538 – 4,350,629
Length	91
Max. P	0.782192

overview

Window 2

Location	4,350,538 – 4,350,629
Length	91
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	77.08
Mean single sequence MFE	-28.00
Consensus MFE	-18.04
Energy contribution	-20.28
Covariance contribution	2.24
Combinations/Pair	1.04
Mean z-score	-1.72
Structure conservation index	0.64
SVM decision value	0.56
SVM RNA-class probability	0.782192
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4350538 91 + 20766785
GGAACG-------GGAAACG-------AAGAAUGGGAGUUCAUAAAUUCAUCGCCGGUCGCAGAAACAAUGCGCG-AAAUAGCUCAGCACCCGGCACAUUCAAAUG
......-------(....).-------..(((((.(((((....)))))...(((((..(((.......)))((.-.....)).......))))).)))))..... ( -23.80)
>DroSec_CAF1 21068 105 + 1
GGAACGGGGAACGGGGAACGUAGAAUGGAGAAUGGGAGUUCAUAAAUUCAUCGCCGGGCGCUGAAACAAUGCGCG-AAAUAGCUCAGCACCCGGCACAUUCAAAUG
..........(((.....))).(((((..((((....))))...........((((((.(((((......((...-.....))))))).)))))).)))))..... ( -32.50)
>DroSim_CAF1 21369 98 + 1
GGAACG-------GGGAACGUAGAAUGGAGAAUGGGAGUUCAUAAAUUCAUCGCCGGGCGCUGAAACAAUGCGCG-AAAUAGCUCAGCACCCGGCACAUUCAAACG
...(((-------.....))).(((((..((((....))))...........((((((.(((((......((...-.....))))))).)))))).)))))..... ( -32.50)
>DroYak_CAF1 19328 91 + 1
GGAACG-------GGUAAC-------CGAGAAUGGGAGUUCAUAAAUUCAUCGCCGGGAGCAAAAACAAUGCGCG-AAAUAGCUCAGCACCCGGCGCAUUCAAACG
....((-------(....)-------)).(((((.(((((....)))))..(((((((.(((.......)))((.-.....))......))))))))))))..... ( -30.10)
>DroAna_CAF1 27380 84 + 1
GCUAC------------------UAGGGGGUAUGGGAGUUCAUAAA----UCGCCUGGCACUGAAACAAAGCGGGGCUAUAGCUCAGCGCCUCUUUCAUUCAAAUG
.....------------------.(((((((....(((((.(((..----..((((.((...........)).))))))))))))...)))))))........... ( -21.10)
>consensus
GGAACG_______GGGAACG____A_GGAGAAUGGGAGUUCAUAAAUUCAUCGCCGGGCGCUGAAACAAUGCGCG_AAAUAGCUCAGCACCCGGCACAUUCAAAUG
.............................(((((.(((((....)))))...((((((.(((((......((.........))))))).)))))).)))))..... (-18.04 = -20.28 +   2.24)

alignment

secondary structure

dotplot

Window 3

Location	4,350,538 – 4,350,629
Length	91
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	77.08
Mean single sequence MFE	-26.47
Consensus MFE	-19.10
Energy contribution	-20.54
Covariance contribution	1.44
Combinations/Pair	1.20
Mean z-score	-1.47
Structure conservation index	0.72
SVM decision value	0.46
SVM RNA-class probability	0.744573
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4350538 91 - 20766785
CAUUUGAAUGUGCCGGGUGCUGAGCUAUUU-CGCGCAUUGUUUCUGCGACCGGCGAUGAAUUUAUGAACUCCCAUUCUU-------CGUUUCC-------CGUUCC
.....(((((.(((((((((.(((....))-))))).((((....)))))))))((((((...(((......)))..))-------))))...-------))))). ( -24.00)
>DroSec_CAF1 21068 105 - 1
CAUUUGAAUGUGCCGGGUGCUGAGCUAUUU-CGCGCAUUGUUUCAGCGCCCGGCGAUGAAUUUAUGAACUCCCAUUCUCCAUUCUACGUUCCCCGUUCCCCGUUCC
.....((((((((((((((((((((.....-........).)))))))))))))...((((....(((......)))...)))).))))))............... ( -31.62)
>DroSim_CAF1 21369 98 - 1
CGUUUGAAUGUGCCGGGUGCUGAGCUAUUU-CGCGCAUUGUUUCAGCGCCCGGCGAUGAAUUUAUGAACUCCCAUUCUCCAUUCUACGUUCCC-------CGUUCC
.....((((((((((((((((((((.....-........).)))))))))))))...((((....(((......)))...)))).))))))..-------...... ( -31.62)
>DroYak_CAF1 19328 91 - 1
CGUUUGAAUGCGCCGGGUGCUGAGCUAUUU-CGCGCAUUGUUUUUGCUCCCGGCGAUGAAUUUAUGAACUCCCAUUCUCG-------GUUACC-------CGUUCC
.((((((((.(((((((.((.((((.....-........))))..)).)))))))....))))..)))).........((-------(....)-------)).... ( -24.82)
>DroAna_CAF1 27380 84 - 1
CAUUUGAAUGAAAGAGGCGCUGAGCUAUAGCCCCGCUUUGUUUCAGUGCCAGGCGA----UUUAUGAACUCCCAUACCCCCUA------------------GUAGC
...............(((((((((.((.(((...))).)).)))))))))(((.(.----..((((......))))..)))).------------------..... ( -20.30)
>consensus
CAUUUGAAUGUGCCGGGUGCUGAGCUAUUU_CGCGCAUUGUUUCAGCGCCCGGCGAUGAAUUUAUGAACUCCCAUUCUCC_U____CGUUCCC_______CGUUCC
....(((((.(((((((((((((((..............).))))))))))))))....))))).......................................... (-19.10 = -20.54 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:33 2006