Locus 1397

Sequence ID	X_DroMel_CAF1
Location	4,205,066 – 4,205,186
Length	120
Max. P	0.817616

overview

Window 8

Location	4,205,066 – 4,205,186
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.25
Mean single sequence MFE	-42.18
Consensus MFE	-33.72
Energy contribution	-33.12
Covariance contribution	-0.60
Combinations/Pair	1.38
Mean z-score	-1.56
Structure conservation index	0.80
SVM decision value	0.23
SVM RNA-class probability	0.645834
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4205066 120 + 22224390
AGGUUUCGCCGGUGCCGCUAAGCAGCAAAACGAACAGAUGAAGGCACUUGGCAUUGAGGAGCAGAGCGGCGGUGCCGCCCGAGAUGCUGGCAAGGCCAAAGAGGAGGAAAAGAAGGAGCC
.((((((((((((((((((....)))....(.....).....)))))).((((((..((......(((((...)))))))..)))))))))....((.....))..........)))))) ( -39.80)
>DroVir_CAF1 61842 120 + 1
CGGUUUUGCCGGCGCUGCCAAACAGCAGAACGAACAAAUGAAGGCCCUGGGCAUUGAGGAGCAAAGCGGCGGUGCCGCUCGCGAUGCCGGCAAGGCCAAAGAGGAGGAGAAAAAGGAGCC
.((((((((((((((((.....)))).................(((((........))).))...((((((....))).)))...))))))))))))....................... ( -44.90)
>DroGri_CAF1 47786 120 + 1
CGGCUUUGCUGGCGCCGCCAAGCAGCAGAAUGAACAAAUGAAGGCCUUGGGCAUUGAAGAGCAGAGUGGCGGUGCUGCGCGUGAUGCCGGCAAAGCCAAGGAGGAGGAGAAAAAGGAGCC
.(((((((((((((.(((...((((((.((((..(((.........)))..)))).....((......))..))))))..))).)))))))))))))....................... ( -45.30)
>DroWil_CAF1 43522 120 + 1
CGGUUUUGCCGGUGCGGCCAAGCAGCAGAACGAACAGAUGAAGGCUCUUGGAAUUGAGGAGCAAAGCGGCGGUGCCGCUCGUGAUGCCGGCAAGGCCAAGGAGGAGGAGAAAAAAGAGCC
.((((((((((.(((......)))(((..((((..........((((((.......))))))...(((((...)))))))))..)))))))))))))....................... ( -44.90)
>DroYak_CAF1 41522 120 + 1
AGGAUUCGCCGGUGCCGCUAAGCAGCAAAAUGAACAGAUGAAGGCCCUCGGCAUUGAGGAGCAGAGCGGCGGUGCCGCCCGAGAUGCUGGCAAGGCCAAAGAGGAGGAAAAGAAGGAGCC
.((.(((.((....(((((....)))................((((.((((((((..((......(((((...)))))))..))))))))...)))).....)).))....)))....)) ( -36.00)
>consensus
CGGUUUUGCCGGUGCCGCCAAGCAGCAGAACGAACAGAUGAAGGCCCUGGGCAUUGAGGAGCAGAGCGGCGGUGCCGCCCGAGAUGCCGGCAAGGCCAAAGAGGAGGAGAAAAAGGAGCC
.((((((((((((((.((...)).))....((...........((((((......)))).))...(((((...))))).))....))))))))))))....................... (-33.72 = -33.12 +  -0.60)

alignment

secondary structure

dotplot

Window 9

Location	4,205,066 – 4,205,186
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.25
Mean single sequence MFE	-37.82
Consensus MFE	-28.83
Energy contribution	-28.95
Covariance contribution	0.12
Combinations/Pair	1.31
Mean z-score	-1.91
Structure conservation index	0.76
SVM decision value	0.67
SVM RNA-class probability	0.817616
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4205066 120 - 22224390
GGCUCCUUCUUUUCCUCCUCUUUGGCCUUGCCAGCAUCUCGGGCGGCACCGCCGCUCUGCUCCUCAAUGCCAAGUGCCUUCAUCUGUUCGUUUUGCUGCUUAGCGGCACCGGCGAAACCU
(((.................((((((.(((..((((....(((((((...)))))))))))...))).)))))).)))........((((((.((((((...))))))..)))))).... ( -37.07)
>DroVir_CAF1 61842 120 - 1
GGCUCCUUUUUCUCCUCCUCUUUGGCCUUGCCGGCAUCGCGAGCGGCACCGCCGCUUUGCUCCUCAAUGCCCAGGGCCUUCAUUUGUUCGUUCUGCUGUUUGGCAGCGCCGGCAAAACCG
((.....................(((((((..(((((.(((((((((...))))).))))......))))))))))))....(((((..((.(((((....))))).))..))))).)). ( -43.00)
>DroGri_CAF1 47786 120 - 1
GGCUCCUUUUUCUCCUCCUCCUUGGCUUUGCCGGCAUCACGCGCAGCACCGCCACUCUGCUCUUCAAUGCCCAAGGCCUUCAUUUGUUCAUUCUGCUGCUUGGCGGCGCCAGCAAAGCCG
.......................((((((((.(((.....((...)).((((((..(.((.....((((..((((.......))))..))))..)).)..)))))).))).)))))))). ( -37.00)
>DroWil_CAF1 43522 120 - 1
GGCUCUUUUUUCUCCUCCUCCUUGGCCUUGCCGGCAUCACGAGCGGCACCGCCGCUUUGCUCCUCAAUUCCAAGAGCCUUCAUCUGUUCGUUCUGCUGCUUGGCCGCACCGGCAAAACCG
((.....................((((..((.((((..(((((((((...)))))...((((...........))))..........))))..))))))..))))((....))....)). ( -34.90)
>DroYak_CAF1 41522 120 - 1
GGCUCCUUCUUUUCCUCCUCUUUGGCCUUGCCAGCAUCUCGGGCGGCACCGCCGCUCUGCUCCUCAAUGCCGAGGGCCUUCAUCUGUUCAUUUUGCUGCUUAGCGGCACCGGCGAAUCCU
((((...................))))(((((((((....(((((((...))))))).((.((((......)))))).......)))).....((((((...))))))..)))))..... ( -37.11)
>consensus
GGCUCCUUUUUCUCCUCCUCUUUGGCCUUGCCGGCAUCACGAGCGGCACCGCCGCUCUGCUCCUCAAUGCCAAGGGCCUUCAUCUGUUCGUUCUGCUGCUUGGCGGCACCGGCAAAACCG
(((((................(((((.(((..((((....(((((((...)))))))))))...))).))))))))))......((((.((.(((((....))))).)).))))...... (-28.83 = -28.95 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:24 2006