Locus 4659

Sequence ID	3L_DroMel_CAF1
Location	13,192,265 – 13,192,453
Length	188
Max. P	0.989035

overview

Window 4

Location	13,192,265 – 13,192,377
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.55
Mean single sequence MFE	-25.67
Consensus MFE	-19.18
Energy contribution	-19.26
Covariance contribution	0.08
Combinations/Pair	1.12
Mean z-score	-1.52
Structure conservation index	0.75
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13192265 112 - 23771897
CUUAAAACUGGUGCAACACACAUUGGCCUCCUCCUCCGCCGACUCGAACAAAAAAAAUCCCCCGACAUGUGUA-----C---CUCCUGCCCUGAAACCUGGCAGAGCGCCAAACUAGCCG
........((((((...((((((((((..........))))).(((................)))..))))).-----.---...(((((..(....).))))).))))))......... ( -25.69)
>DroSec_CAF1 43538 108 - 1
CUUAAAACUGGUGCAACA--CAUUGGCCUC---CUCCGCCAACUCGAA--AACAAAAUCCCCCGACAUGUGUA-----CCACCUCCUGUCCUGAAACCUGGCAGAGCGCCAAACUAGCCG
........((((((.(((--(((((((...---....))))).(((..--............)))..))))).-----.......(((.((........))))).))))))......... ( -24.74)
>DroSim_CAF1 41952 106 - 1
CUUAAAACUGGUGCAACA--CAUUGGCCUC---CUCCGCCGACUCGAA--A--AAAAUCCCCCGACAUGUGUA-----CCACCUCCUGCCCUGAAACCUGGCAGAGCGCCAAACUAGCCG
........((((((.(((--(((((((...---....))))).(((..--.--.........)))..))))).-----.......(((((..(....).))))).))))))......... ( -26.60)
>DroEre_CAF1 47226 102 - 1
CUUAAAACUGGUGCAACA--CAUUGGCCUC---CUCCGCCGACUCGAA-----AAAAUCCCCCGACAUGUGU--------ACCUCCUGCCCUGAAAGCUGGCAAAGCGCCAAACUAGCCG
........((((((.(((--(((((((...---....))))).(((..-----.........)))..)))))--------......((((.........))))..))))))......... ( -23.40)
>DroYak_CAF1 43262 110 - 1
CUUAAAACUGGUGCAACA--CAUUGGCCUC---CUCCGCCGACUCGAA-----AAAAUCCCCCGACAUGUGUAUGUUCCUACCUCCUUCCCUGGAAGCUGGCAGAGCGCCAAACUAGCCG
........((((((.(((--(((((((...---....))))).(((..-----.........)))..)))))......((.((..((((....))))..)).)).))))))......... ( -27.90)
>consensus
CUUAAAACUGGUGCAACA__CAUUGGCCUC___CUCCGCCGACUCGAA__A__AAAAUCCCCCGACAUGUGUA_____C_ACCUCCUGCCCUGAAACCUGGCAGAGCGCCAAACUAGCCG
........((((((........(((((..........)))))...........................................(((((..(....).))))).))))))......... (-19.18 = -19.26 +   0.08)

alignment

secondary structure

dotplot

Window 5

Location	13,192,337 – 13,192,453
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.86
Mean single sequence MFE	-39.82
Consensus MFE	-35.34
Energy contribution	-35.34
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.26
Structure conservation index	0.89
SVM decision value	0.07
SVM RNA-class probability	0.568477
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13192337 116 + 23771897
GGCGGAGGAGGAGGCCAAUGUGUGUUGCACCAGUUUUAAGGCCACGA----CGCACAGCUGAGCUGCAUUUUGCAACAUGUUUCGGUGUCCCGAAUGCAAUGCCAUGCCUCAAGCCGCAA
.((((..((((.(((((.(((((((((..((........))...)))----))))))..)).)))((((..((((......(((((....)))))))))))))....))))...)))).. ( -43.00)
>DroSec_CAF1 43611 111 + 1
GGCGGAG---GAGGCCAAUG--UGUUGCACCAGUUUUAAGGCCACGA----CGCACAGCUGAGCUGCAUUUUGCAACAUGUUUCGGUGUCCCGAAUGCAAUGCCAUGCCUCAAGCCGCAA
.((((..---(((((.((((--(((((((.((((((....((.....----.))......)))))).....)))))))))))((((....))))............)))))...)))).. ( -38.60)
>DroSim_CAF1 42023 111 + 1
GGCGGAG---GAGGCCAAUG--UGUUGCACCAGUUUUAAGGCCACGA----CGCACAGCUGAGCUGCAUUUUGCAACAUGUUUCGGUGUCCCGAAUGCAAUGCCAUGCCUCAAGCCGCAA
.((((..---(((((.((((--(((((((.((((((....((.....----.))......)))))).....)))))))))))((((....))))............)))))...)))).. ( -38.60)
>DroEre_CAF1 47293 115 + 1
GGCGGAG---GAGGCCAAUG--UGUUGCACCAGUUUUAAGGCCACGACGGACGCACAGCUGAGCUGCAUUUUGCAACAUGUUUCGGUGUCCCGAAUGCAAUGCCAUGCCUCAAGCCGCAA
.((((..---(((((....(--(((((((((........))...((..((((((..(((...(.(((.....))).)..)))...))))))))..))))))))...)))))...)))).. ( -40.30)
>DroYak_CAF1 43337 111 + 1
GGCGGAG---GAGGCCAAUG--UGUUGCACCAGUUUUAAGGCCACGA----CGCACAGCUGAGCUGCAUUUUGCAACAUGUUUCGGUGUCCCGAAUGCAAUGCCAUGCCUCAAGCCGCAA
.((((..---(((((.((((--(((((((.((((((....((.....----.))......)))))).....)))))))))))((((....))))............)))))...)))).. ( -38.60)
>consensus
GGCGGAG___GAGGCCAAUG__UGUUGCACCAGUUUUAAGGCCACGA____CGCACAGCUGAGCUGCAUUUUGCAACAUGUUUCGGUGUCCCGAAUGCAAUGCCAUGCCUCAAGCCGCAA
.((((.....(((((.......(((((((.((((((...(((..((.....))....))))))))).....)))))))((((((((....))))).))).......)))))...)))).. (-35.34 = -35.34 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	13,192,337 – 13,192,453
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.86
Mean single sequence MFE	-40.80
Consensus MFE	-38.90
Energy contribution	-38.90
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.95
SVM decision value	2.15
SVM RNA-class probability	0.989035
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13192337 116 - 23771897
UUGCGGCUUGAGGCAUGGCAUUGCAUUCGGGACACCGAAACAUGUUGCAAAAUGCAGCUCAGCUGUGCG----UCGUGGCCUUAAAACUGGUGCAACACACAUUGGCCUCCUCCUCCGCC
..((((...(((((...((((.((.(((((....)))))....(((((.....)))))...)).))))(----(.((((((........)))....)))))....))))).....)))). ( -40.40)
>DroSec_CAF1 43611 111 - 1
UUGCGGCUUGAGGCAUGGCAUUGCAUUCGGGACACCGAAACAUGUUGCAAAAUGCAGCUCAGCUGUGCG----UCGUGGCCUUAAAACUGGUGCAACA--CAUUGGCCUC---CUCCGCC
..((((...(((((...((((.((.(((((....)))))....(((((.....)))))...)).)))).----..((((((........)))....))--)....)))))---..)))). ( -40.90)
>DroSim_CAF1 42023 111 - 1
UUGCGGCUUGAGGCAUGGCAUUGCAUUCGGGACACCGAAACAUGUUGCAAAAUGCAGCUCAGCUGUGCG----UCGUGGCCUUAAAACUGGUGCAACA--CAUUGGCCUC---CUCCGCC
..((((...(((((...((((.((.(((((....)))))....(((((.....)))))...)).)))).----..((((((........)))....))--)....)))))---..)))). ( -40.90)
>DroEre_CAF1 47293 115 - 1
UUGCGGCUUGAGGCAUGGCAUUGCAUUCGGGACACCGAAACAUGUUGCAAAAUGCAGCUCAGCUGUGCGUCCGUCGUGGCCUUAAAACUGGUGCAACA--CAUUGGCCUC---CUCCGCC
..((((...(((((...((((.((.(((((....)))))....(((((.....)))))...)).)))).......((((((........)))....))--)....)))))---..)))). ( -40.90)
>DroYak_CAF1 43337 111 - 1
UUGCGGCUUGAGGCAUGGCAUUGCAUUCGGGACACCGAAACAUGUUGCAAAAUGCAGCUCAGCUGUGCG----UCGUGGCCUUAAAACUGGUGCAACA--CAUUGGCCUC---CUCCGCC
..((((...(((((...((((.((.(((((....)))))....(((((.....)))))...)).)))).----..((((((........)))....))--)....)))))---..)))). ( -40.90)
>consensus
UUGCGGCUUGAGGCAUGGCAUUGCAUUCGGGACACCGAAACAUGUUGCAAAAUGCAGCUCAGCUGUGCG____UCGUGGCCUUAAAACUGGUGCAACA__CAUUGGCCUC___CUCCGCC
..((((...(((((...((((.((.(((((....)))))....(((((.....)))))...)).)))).......((.(((........)))...))........))))).....)))). (-38.90 = -38.90 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:52 2006