Locus 3110

Sequence ID	X_DroMel_CAF1
Location	8,289,201 – 8,289,315
Length	114
Max. P	0.950764

overview

Window 9

Location	8,289,201 – 8,289,315
Length	114
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	69.83
Mean single sequence MFE	-21.10
Consensus MFE	-4.19
Energy contribution	-4.83
Covariance contribution	0.64
Combinations/Pair	1.31
Mean z-score	-2.22
Structure conservation index	0.20
SVM decision value	1.30
SVM RNA-class probability	0.939498
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8289201 114 + 22224390
UAUGAAAA-CG----UUGAAAAACGUUCGCUAGAACAUUUCCGCCUUUCGUUACUGGAAAUGCAAUAAUUCCAGAAAUAAUUUUUCCAAAUUGGCUUGCAAUUUUAUUUCAUAACUUUC
((((((((-((----((....)))))..(((((..((((((((...........))))))))...........((((.....))))....)))))...........)))))))...... ( -21.80)
>DroSec_CAF1 4925 101 + 1
CAUGAAAU-UG----UUGAAAA--GUUUGCUAGAACAUUUCCGCA-UUCGCUACUGGAAAUGCA---------GCAAUAAU-UUUCCAAAUUCGUUUGCAAUUUUAUUUCAUAAUAUUC
.(((((((-((----(.(((((--..(((((....(((((((((.-...))....))))))).)---------))))...)-))))...........))))))))))............ ( -20.10)
>DroSim_CAF1 4720 101 + 1
CAUGAAAU-UG----UUGAAAA--GUUUGCUAGAACAUUUCCGCA-UUCGCUGCUGGAAAUGCA---------GCAAUAAU-UUUCGAAAUUGGUUUGCAAUUUUAUUUCAUAAUUUUC
.(((((((-..----..(((((--..(((((....((((((((((-.....))).))))))).)---------))))...)-))))(((((((.....))))))))))))))....... ( -26.60)
>DroEre_CAF1 4924 103 + 1
UAUGCAAU-CAAGAAUCGAGAU--G-CUGCUAGGAUAUUUCCAUA-UUCGCUACUG-A-AUGUA---------GCAUUACUUUUUCAAAAUUUGUAUGCAAUUUUAUUUCAUAAUUUUC
(((((((.-...(((..(.(((--(-((((..(((....)))..(-((((....))-)-)))))---------))))).)...))).....)))))))..................... ( -19.60)
>DroYak_CAF1 4656 96 + 1
AAUAUAUUGCAAUAUUCGU--U--A-CUGA-AAUAUAUUGCAAUA-UUCGUUACUG-AAAUGCG---------GCAA----UUUCC--AAUUUCCAUGCAAUUUUAUGACAUAAUUUUC
...(((((((((((((((.--.--.-.)))-...)))))))))))-)..((((..(-((.((((---------(.((----(....--.))).))..))).)))..))))......... ( -17.40)
>consensus
CAUGAAAU_CG____UUGAAAA__GUUUGCUAGAACAUUUCCGCA_UUCGCUACUGGAAAUGCA_________GCAAUAAUUUUUCCAAAUUGGUUUGCAAUUUUAUUUCAUAAUUUUC
.................((((..............((((((((...........))))))))...........((((..................)))).......))))......... ( -4.19 =  -4.83 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	8,289,201 – 8,289,315
Length	114
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	69.83
Mean single sequence MFE	-21.82
Consensus MFE	-5.22
Energy contribution	-7.26
Covariance contribution	2.04
Combinations/Pair	1.32
Mean z-score	-2.22
Structure conservation index	0.24
SVM decision value	1.40
SVM RNA-class probability	0.950764
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8289201 114 - 22224390
GAAAGUUAUGAAAUAAAAUUGCAAGCCAAUUUGGAAAAAUUAUUUCUGGAAUUAUUGCAUUUCCAGUAACGAAAGGCGGAAAUGUUCUAGCGAACGUUUUUCAA----CG-UUUUCAUA
......(((((((...........((((((((....)))))....((((((.........))))))........)))((((((((((....))))))))))...----..-.))))))) ( -25.40)
>DroSec_CAF1 4925 101 - 1
GAAUAUUAUGAAAUAAAAUUGCAAACGAAUUUGGAAA-AUUAUUGC---------UGCAUUUCCAGUAGCGAA-UGCGGAAAUGUUCUAGCAAAC--UUUUCAA----CA-AUUUCAUG
......((((((((.......((((....))))((((-(...((((---------(((((((((.(((.....-)))))))))))...)))))..--)))))..----..-)))))))) ( -23.20)
>DroSim_CAF1 4720 101 - 1
GAAAAUUAUGAAAUAAAAUUGCAAACCAAUUUCGAAA-AUUAUUGC---------UGCAUUUCCAGCAGCGAA-UGCGGAAAUGUUCUAGCAAAC--UUUUCAA----CA-AUUUCAUG
......((((((((.((((((.....)))))).((((-(...((((---------(((((((((.(((.....-)))))))))))...)))))..--)))))..----..-)))))))) ( -26.50)
>DroEre_CAF1 4924 103 - 1
GAAAAUUAUGAAAUAAAAUUGCAUACAAAUUUUGAAAAAGUAAUGC---------UACAU-U-CAGUAGCGAA-UAUGGAAAUAUCCUAGCAG-C--AUCUCGAUUCUUG-AUUGCAUA
...................((((..(((...((((........(((---------(((..-.-..))))))..-...(((....)))......-.--...))))...)))-..)))).. ( -15.60)
>DroYak_CAF1 4656 96 - 1
GAAAAUUAUGUCAUAAAAUUGCAUGGAAAUU--GGAAA----UUGC---------CGCAUUU-CAGUAACGAA-UAUUGCAAUAUAUU-UCAG-U--A--ACGAAUAUUGCAAUAUAUU
......((((.((......))))))((((((--((...----...)---------)).))))-)........(-(((((((((((...-((..-.--.--..))))))))))))))... ( -18.40)
>consensus
GAAAAUUAUGAAAUAAAAUUGCAAACAAAUUUGGAAAAAUUAUUGC_________UGCAUUUCCAGUAGCGAA_UGCGGAAAUGUUCUAGCAAAC__UUUUCAA____CG_AUUUCAUA
........(((((.....((((.....(((((....)))))...............((((((((.(((......)))))))))))....)))).....)))))................ ( -5.22 =  -7.26 +   2.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:14 2006