Locus 4765

Sequence ID	2L_DroMel_CAF1
Location	13,580,388 – 13,580,548
Length	160
Max. P	0.999945

overview

Window 1

Location	13,580,388 – 13,580,508
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-36.66
Consensus MFE	-34.08
Energy contribution	-34.12
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.45
Structure conservation index	0.93
SVM decision value	1.36
SVM RNA-class probability	0.945758
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13580388 120 + 22407834
UAUGUGUAUGGGAGCCAUGUCAGUGCCAUUGCAGUUACAUUUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCGUGGCCUGGUCGUUGCCAUUGGC
.....(.((.((.(((((((((((.....((((....((((.((((((...(((....)))))))))....)))).......)))).....))))))))))))).)))...(((...))) ( -37.50)
>DroSec_CAF1 13493 120 + 1
UGUAUGUAUGGGAGCCAUGGCAGUGCCAUUGCAGUUACAUUUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCGUGGCCUGGUCGUUGCCAUUGGC
.((....((((.(((((.(((..(((((..((((........((((((...(((....)))))))))....(((((.......))))).)))))))))..)))))))...).))))..)) ( -37.10)
>DroSim_CAF1 12207 116 + 1
----UGUAUGGGAGUCAUGGCAGUGCCAUUGCAGUUACAUUUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCGUGGCCUGGUCGUUGCCAUUGGC
----.........(((((((((((((((..((((........((((((...(((....)))))))))....(((((.......))))).)))).(((...)))))).)))))))).)))) ( -33.70)
>DroEre_CAF1 13842 120 + 1
CACGUGUAUGGAAGCCAUGGCAGUGCCAUUGCAGUUACAUUUUGCUGUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCCUGGCCUGGUCGUUGCCAUUGGC
.............((((((((((..((((.(((((........))))).))))..........((((....(((((.......)))))..))))((((......)))).)))))).)))) ( -38.10)
>DroYak_CAF1 10634 120 + 1
CACGUGUAAGGGAGCCAUGGCAGUGCCAUUGCAGUUACAAUUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCCUGGCCUGGUCGUUGCCAUUGGC
...(.((((.(..((((.(((((.((((..((((....((..((((((...(((....)))))))))..))(((((.......))))).)))))))))).)))))))).)))))...... ( -36.90)
>consensus
CACGUGUAUGGGAGCCAUGGCAGUGCCAUUGCAGUUACAUUUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCGUGGCCUGGUCGUUGCCAUUGGC
.............(((((((((((((((..((((.......)))).....((((....)))).((((....(((((.......)))))..))))(((...)))))).)))))))).)))) (-34.08 = -34.12 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	13,580,388 – 13,580,508
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-32.94
Consensus MFE	-31.42
Energy contribution	-31.82
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.60
Structure conservation index	0.95
SVM decision value	4.74
SVM RNA-class probability	0.999945
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13580388 120 - 22407834
GCCAAUGGCAACGACCAGGCCACGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAAAUGUAACUGCAAUGGCACUGACAUGGCUCCCAUACACAUA
((((.((((.........)))).(((((((....(((((...((((((....)))))).(((....)))...........)))))..)))..)))).......))))............. ( -30.70)
>DroSec_CAF1 13493 120 - 1
GCCAAUGGCAACGACCAGGCCACGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAAAUGUAACUGCAAUGGCACUGCCAUGGCUCCCAUACAUACA
((((.(((((..(.((((((...))).(((....(((((...((((((....)))))).(((....)))...........)))))..)))..))))..)))))))))............. ( -34.90)
>DroSim_CAF1 12207 116 - 1
GCCAAUGGCAACGACCAGGCCACGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAAAUGUAACUGCAAUGGCACUGCCAUGACUCCCAUACA----
....((((((..(.((((((...))).(((....(((((...((((((....)))))).(((....)))...........)))))..)))..))))..))))))............---- ( -29.20)
>DroEre_CAF1 13842 120 - 1
GCCAAUGGCAACGACCAGGCCAGGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGACAGCAAAAUGUAACUGCAAUGGCACUGCCAUGGCUUCCAUACACGUG
((((.(((((..(.((((((...))).(((....(((((...((((((....)))))).(((....)))...........)))))..)))..))))..)))))))))............. ( -34.90)
>DroYak_CAF1 10634 120 - 1
GCCAAUGGCAACGACCAGGCCAGGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAAUUGUAACUGCAAUGGCACUGCCAUGGCUCCCUUACACGUG
((((.(((((..(.(((...(((....((((...(((.....((((((....)))))).(((....)))......)))..))))..)))...))))..)))))))))............. ( -35.00)
>consensus
GCCAAUGGCAACGACCAGGCCACGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAAAUGUAACUGCAAUGGCACUGCCAUGGCUCCCAUACACAUA
((((.(((((..(.((((((...))).(((..(((((.......)))))....(((((((((....)))..)).)))).........)))..))))..)))))))))............. (-31.42 = -31.82 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	13,580,428 – 13,580,548
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.83
Mean single sequence MFE	-31.48
Consensus MFE	-29.30
Energy contribution	-29.34
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.75
Structure conservation index	0.93
SVM decision value	1.83
SVM RNA-class probability	0.979237
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13580428 120 + 22407834
UUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCGUGGCCUGGUCGUUGCCAUUGGCAUUACAACUGCCGCCGAAUCCACCCACUCCUGUUUUAUUA
..........(((((((......((((....(((((.......)))))..))))((((((((.........))))).((((.......)))))))))))))).................. ( -30.60)
>DroSec_CAF1 13533 120 + 1
UUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCGUGGCCUGGUCGUUGCCAUUGGCAUUACAACUGCCGCCGAAUCCACCCACUCCUGUUUUAUUA
..........(((((((......((((....(((((.......)))))..))))((((((((.........))))).((((.......)))))))))))))).................. ( -30.60)
>DroSim_CAF1 12243 120 + 1
UUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCGUGGCCUGGUCGUUGCCAUUGGCAUUACAACUGCCGCCGAAUCCACCCACUCCUGCUUUAUUA
...((.....(((((........((((....(((((.......)))))..))))((((((((.........))))).((((.......)))))))......))))).....))....... ( -32.20)
>DroEre_CAF1 13882 120 + 1
UUUGCUGUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCCUGGCCUGGUCGUUGCCAUUGGCAUUACAACUGCCGCCGCGUCCACCCACUCCUGUUUUAUUA
..........((((....)))).((((....(((((.......)))))..))))((..(((..(((.(((.((....((((.......)))))).))).))).)))..)).......... ( -31.50)
>DroYak_CAF1 10674 120 + 1
UUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCCUGGCCUGGUCGUUGCCAUUGGCAUUACAACGGCCGCCGAAUCCACCCACUCCUGUUUUAUUA
..........(((((........((((....(((((.......)))))..))))((..((((..((((((((((...)))).....))))))))))...))))))).............. ( -32.50)
>consensus
UUUGCUUUCAUGGGUUUACCCGAAGCAUUUUAAUGCUCAUUAUGCAUUUUUGCUGGCGUGGCCUGGUCGUUGCCAUUGGCAUUACAACUGCCGCCGAAUCCACCCACUCCUGUUUUAUUA
...((.....(((((........((((....(((((.......)))))..))))((..((((.((((....))))..((((.......))))))))...))))))).....))....... (-29.30 = -29.34 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	13,580,428 – 13,580,548
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-38.06
Consensus MFE	-36.00
Energy contribution	-36.04
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-3.35
Structure conservation index	0.95
SVM decision value	4.43
SVM RNA-class probability	0.999897
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13580428 120 - 22407834
UAAUAAAACAGGAGUGGGUGGAUUCGGCGGCAGUUGUAAUGCCAAUGGCAACGACCAGGCCACGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAA
.............((((((..((((((((((.(((((..((((...)))))))))...)))..)))((((..(((((.......)))))....))))..))))..))))))......... ( -36.50)
>DroSec_CAF1 13533 120 - 1
UAAUAAAACAGGAGUGGGUGGAUUCGGCGGCAGUUGUAAUGCCAAUGGCAACGACCAGGCCACGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAA
.............((((((..((((((((((.(((((..((((...)))))))))...)))..)))((((..(((((.......)))))....))))..))))..))))))......... ( -36.50)
>DroSim_CAF1 12243 120 - 1
UAAUAAAGCAGGAGUGGGUGGAUUCGGCGGCAGUUGUAAUGCCAAUGGCAACGACCAGGCCACGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAA
.......((....((((((..((((((((((.(((((..((((...)))))))))...)))..)))((((..(((((.......)))))....))))..))))..))))))....))... ( -39.40)
>DroEre_CAF1 13882 120 - 1
UAAUAAAACAGGAGUGGGUGGACGCGGCGGCAGUUGUAAUGCCAAUGGCAACGACCAGGCCAGGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGACAGCAAA
..........(..((((((..((.(((((((.(((((..((((...)))))))))...)))..)))((((..(((((.......)))))....))))..).))..))))))..)...... ( -39.30)
>DroYak_CAF1 10674 120 - 1
UAAUAAAACAGGAGUGGGUGGAUUCGGCGGCCGUUGUAAUGCCAAUGGCAACGACCAGGCCAGGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAA
.............((((((..((((((((((((((((..((((...)))))))))..))))..)))((((..(((((.......)))))....))))..))))..))))))......... ( -38.60)
>consensus
UAAUAAAACAGGAGUGGGUGGAUUCGGCGGCAGUUGUAAUGCCAAUGGCAACGACCAGGCCACGCCAGCAAAAAUGCAUAAUGAGCAUUAAAAUGCUUCGGGUAAACCCAUGAAAGCAAA
.............((((((..((((((((((.(((((..((((...)))))))))...)))..)))((((..(((((.......)))))....))))..))))..))))))......... (-36.00 = -36.04 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:48 2006