Locus 5579

Sequence ID	X_DroMel_CAF1
Location	14,412,992 – 14,413,176
Length	184
Max. P	0.977612

overview

Window 1

Location	14,412,992 – 14,413,112
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.92
Mean single sequence MFE	-34.04
Consensus MFE	-28.69
Energy contribution	-29.37
Covariance contribution	0.69
Combinations/Pair	1.10
Mean z-score	-2.48
Structure conservation index	0.84
SVM decision value	1.39
SVM RNA-class probability	0.948917
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14412992 120 + 22224390
AAUUACGUAUGCAGAAAAUGACCAACAUGUUGCUCCCAGGACUGUGGCAUAAAAAAUUGGCAUAGGAAUGAGGCAGUUGCAAGGGGCAAGGGCAGGAUGUCAUAUAGAAAUGGCAGCAUG
.......(((((.........((....(.(((((((((...(((((.((........)).)))))...))..((....))..))))))).)...)).((((((......))))))))))) ( -32.90)
>DroSec_CAF1 122712 120 + 1
AAUUACGUAUGCAGAAAAUGACCAACAUGUUGCUCCCAGGACUGUGCCAUAAAAAAUUGGCAUAAGAAUGGGGCAGAUGCAAGGGGCAAGGGCAGGAUGCCAUAUAGAAAUGGCAGCAUG
.......(((((......((.((......((((.((((....(((((((........)))))))....)))))))).(((.....))).)).))...((((((......))))))))))) ( -38.10)
>DroSim_CAF1 115909 120 + 1
AAUUACGUAUGCAGAAAAUGACCAACAUGUUGCUCCCAGGACUGUGCCAUAAAAAAUUGGCAUAAGAAUGAGGCAGAUGCAAGGGGCAAGGGCAGGAUGCCAUAUAGAAAUGGCAGCAUG
.......(((((.........((....(.(((((((((....(((((((........)))))))....))..((....))..))))))).)...)).((((((......))))))))))) ( -36.00)
>DroEre_CAF1 107732 117 + 1
AAUUACGUAUGCAGAAAAUGACCAACAUGUUGCUCCCAGGACUCUGCCAUAAAAAAUUGGCAC-AGAAUAAGGCAGAAGU--GGGGCGAGGGCACGAUGCCAUGUAGAAAUUGCAGCAUG
.........................((((((((.((((....((((((...............-.......))))))..)--)))(((..(((.....))).))).......)))))))) ( -29.15)
>consensus
AAUUACGUAUGCAGAAAAUGACCAACAUGUUGCUCCCAGGACUGUGCCAUAAAAAAUUGGCAUAAGAAUGAGGCAGAUGCAAGGGGCAAGGGCAGGAUGCCAUAUAGAAAUGGCAGCAUG
.......(((((.........((....(.((((.(((.....(((((((........)))))))........((....))..))))))).)...)).((((((......))))))))))) (-28.69 = -29.37 +   0.69)

alignment

secondary structure

dotplot

Window 2

Location	14,413,032 – 14,413,152
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.98
Mean single sequence MFE	-32.42
Consensus MFE	-26.41
Energy contribution	-26.72
Covariance contribution	0.31
Combinations/Pair	1.13
Mean z-score	-2.73
Structure conservation index	0.81
SVM decision value	1.80
SVM RNA-class probability	0.977612
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14413032 120 + 22224390
ACUGUGGCAUAAAAAAUUGGCAUAGGAAUGAGGCAGUUGCAAGGGGCAAGGGCAGGAUGUCAUAUAGAAAUGGCAGCAUGCAUACUAAAAAUGCACUUCUGAGAUGCACUGAAAGCAAAC
.(((((.((........)).)))))...(.(((((....((..(((((((.(((...((((((......))))))...)))...)).....))).))..))...))).)).)........ ( -29.70)
>DroSec_CAF1 122752 119 + 1
ACUGUGCCAUAAAAAAUUGGCAUAAGAAUGGGGCAGAUGCAAGGGGCAAGGGCAGGAUGCCAUAUAGAAAUGGCAGCAUGCAUACUAA-AAUGCACUUCUGAGAUGCACUGAAAGCAAAA
..(((((((........)))))))....(.(((((....((..(((((((.(((...((((((......))))))...)))...))..-..))).))..))...))).)).)........ ( -33.90)
>DroSim_CAF1 115949 119 + 1
ACUGUGCCAUAAAAAAUUGGCAUAAGAAUGAGGCAGAUGCAAGGGGCAAGGGCAGGAUGCCAUAUAGAAAUGGCAGCAUGCAUACUAA-AAUGCACUUCUGAGAUGCACUGAAAGCAAAA
..(((((((........)))))))....(.(((((....((..(((((((.(((...((((((......))))))...)))...))..-..))).))..))...))).)).)........ ( -33.90)
>DroEre_CAF1 107772 115 + 1
ACUCUGCCAUAAAAAAUUGGCAC-AGAAUAAGGCAGAAGU--GGGGCGAGGGCACGAUGCCAUGUAGAAAUUGCAGCAUGCAUACUAA-GCUGCACUUCUAAGAUGCACUAAA-GAAGAC
.((.(((((........))))).-))....((((((((((--(.(((...(((.....)))...(((....(((.....)))..))).-))).)))))).....))).))...-...... ( -32.20)
>consensus
ACUGUGCCAUAAAAAAUUGGCAUAAGAAUGAGGCAGAUGCAAGGGGCAAGGGCAGGAUGCCAUAUAGAAAUGGCAGCAUGCAUACUAA_AAUGCACUUCUGAGAUGCACUGAAAGCAAAA
..(((((((........)))))))......(((((....((..(((((((.(((...((((((......))))))...)))...)).....))).))..))...))).)).......... (-26.41 = -26.72 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	14,413,072 – 14,413,176
Length	104
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	77.38
Mean single sequence MFE	-26.92
Consensus MFE	-15.29
Energy contribution	-15.60
Covariance contribution	0.31
Combinations/Pair	1.05
Mean z-score	-2.06
Structure conservation index	0.57
SVM decision value	0.59
SVM RNA-class probability	0.792834
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14413072 104 + 22224390
AAGGGGCAAGGGCAGGAUGUCAUAUAGAAAUGGCAGCAUGCAUACUAAAAAUGCACUUCUGAGAUGCACUGAAAGCAAACUUCUGAGACAAAUAUCU------C-AA-------UCGA
(((..((.((.(((...((((((......))))))...)))...)).....((((((....)).))))......))...))).(((((......)))------)-).-------.... ( -21.40)
>DroSec_CAF1 122792 103 + 1
AAGGGGCAAGGGCAGGAUGCCAUAUAGAAAUGGCAGCAUGCAUACUAA-AAUGCACUUCUGAGAUGCACUGAAAGCAAAAUUCUGAGAAAAACAGCC------C-AA-------AAGA
...((((.((.(((...((((((......))))))...)))...))..-.......((((.((((((.......)))....))).)))).....)))------)-..-------.... ( -29.70)
>DroSim_CAF1 115989 103 + 1
AAGGGGCAAGGGCAGGAUGCCAUAUAGAAAUGGCAGCAUGCAUACUAA-AAUGCACUUCUGAGAUGCACUGAAAGCAAAAAUCUGAGACAAACAGCC------C-AA-------AAGC
...((((.((.(((...((((((......))))))...)))...))..-........(((.((((((.......)))....))).)))......)))------)-..-------.... ( -28.60)
>DroEre_CAF1 107811 109 + 1
--GGGGCGAGGGCACGAUGCCAUGUAGAAAUUGCAGCAUGCAUACUAA-GCUGCACUUCUAAGAUGCACUAAA-GAAGACCUC-----CGAUUGUCUGUGGCCUUAAAUAAGCACAGC
--.....((((.(((..(((....(((((..((((((...........-)))))).)))))....))).....-..((((...-----.....))))))).))))............. ( -28.00)
>consensus
AAGGGGCAAGGGCAGGAUGCCAUAUAGAAAUGGCAGCAUGCAUACUAA_AAUGCACUUCUGAGAUGCACUGAAAGCAAAAUUCUGAGACAAACAGCC______C_AA_______AAGA
.....((.((.(((...((((((......))))))...)))...)).....((((((....)).))))......)).......................................... (-15.29 = -15.60 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:21 2006