Locus 4834

Sequence ID	X_DroMel_CAF1
Location	12,555,997 – 12,556,088
Length	91
Max. P	0.994558

overview

Window 0

Location	12,555,997 – 12,556,088
Length	91
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	78.74
Mean single sequence MFE	-21.03
Consensus MFE	-10.12
Energy contribution	-9.96
Covariance contribution	-0.16
Combinations/Pair	1.08
Mean z-score	-1.90
Structure conservation index	0.48
SVM decision value	0.04
SVM RNA-class probability	0.552354
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12555997 91 + 22224390
-----------UUGCCUUCGAUAUUUAAGCCAGCUGUUUUUACAGCUGUUCUCCGACCAUUUAGUG--AUAGUCAGCUAAAUUUGCUU--UGGUAUUCUUUCGUUC
-----------........(((((..(((((((((((....)))))))..........(((((((.--.......)))))))..))))--..)))))......... ( -20.70)
>DroSec_CAF1 19747 89 + 1
-----------UUACCACCGAUAUUUAAGCCAGCUGUUUUUACAGCUGUUCU-CGACCUUUUAGUG--AUAGUCAGCAAAAUUUUCGU--UGGGGUUCUUU-GUUC
-----------..(((.(((((........(((((((....)))))))....-.(((..((....)--)..)))............))--)))))).....-.... ( -20.50)
>DroSim_CAF1 18051 89 + 1
-----------UUACCAGCGAUAUUUAAGCCAGCUGUUUUUACAGCUGUUCU-CGACCUUUUAGUG--AUAGUCAGCAAAAUUUUCGU--UGGGGUUCUUU-GUUC
-----------...(((((((.......(((((((((....)))))))....-.(((..((....)--)..))).)).......))))--)))........-.... ( -24.44)
>DroEre_CAF1 20842 97 + 1
UUUUUGGGAUUUUACCUCGGAUAUUUAAGCCAGCUGUUUUUACAGCUGUUCU-CGU-CAUCUAGUG--AUAGUCAGCAA--UUCGCUU--UGGGGUUCUUU-GUUC
......((((...((((((((.........(((((((....)))))))....-.((-...(((...--.)))...))..--.....))--)))))).....-)))) ( -21.80)
>DroYak_CAF1 11558 81 + 1
--------------------GUAUUUUAGCCAGCUGUUUUUACAGCUGUUCU-CAA-CACUUAGUGAGAUAGUCAGCAG--UUUGUUUUCUGGGGUUCUUU-GUUC
--------------------..........(((((((....)))))))....-.((-(.(((((.(((((((.......--.)))))))))))))))....-.... ( -17.70)
>consensus
___________UUACCACCGAUAUUUAAGCCAGCUGUUUUUACAGCUGUUCU_CGACCAUUUAGUG__AUAGUCAGCAAAAUUUGCUU__UGGGGUUCUUU_GUUC
............................(((((((((....)))))))............(((......)))...))............................. (-10.12 =  -9.96 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	12,555,997 – 12,556,088
Length	91
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	78.74
Mean single sequence MFE	-20.18
Consensus MFE	-12.74
Energy contribution	-13.42
Covariance contribution	0.68
Combinations/Pair	1.13
Mean z-score	-2.74
Structure conservation index	0.63
SVM decision value	2.49
SVM RNA-class probability	0.994558
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12555997 91 - 22224390
GAACGAAAGAAUACCA--AAGCAAAUUUAGCUGACUAU--CACUAAAUGGUCGGAGAACAGCUGUAAAAACAGCUGGCUUAAAUAUCGAAGGCAA-----------
((.(....).......--((((....((..((((((((--......))))))))..))(((((((....))))))))))).....))........----------- ( -24.50)
>DroSec_CAF1 19747 89 - 1
GAAC-AAAGAACCCCA--ACGAAAAUUUUGCUGACUAU--CACUAAAAGGUCG-AGAACAGCUGUAAAAACAGCUGGCUUAAAUAUCGGUGGUAA-----------
....-.....(((((.--.(((...(((((.((.....--)).)))))..)))-....(((((((....)))))))...........)).)))..----------- ( -22.40)
>DroSim_CAF1 18051 89 - 1
GAAC-AAAGAACCCCA--ACGAAAAUUUUGCUGACUAU--CACUAAAAGGUCG-AGAACAGCUGUAAAAACAGCUGGCUUAAAUAUCGCUGGUAA-----------
....-........(((--.(((.(.((..(((((((..--........)))))-....(((((((....)))))))))..)).).))).)))...----------- ( -20.40)
>DroEre_CAF1 20842 97 - 1
GAAC-AAAGAACCCCA--AAGCGAA--UUGCUGACUAU--CACUAGAUG-ACG-AGAACAGCUGUAAAAACAGCUGGCUUAAAUAUCCGAGGUAAAAUCCCAAAAA
....-.....(((.(.--.(((...--..)))......--.....((((-...-((..(((((((....)))))))..))...)))).).)))............. ( -17.30)
>DroYak_CAF1 11558 81 - 1
GAAC-AAAGAACCCCAGAAAACAAA--CUGCUGACUAUCUCACUAAGUG-UUG-AGAACAGCUGUAAAAACAGCUGGCUAAAAUAC--------------------
....-....................--..((......((((((.....)-.))-))).(((((((....)))))))))........-------------------- ( -16.30)
>consensus
GAAC_AAAGAACCCCA__AAGCAAAUUUUGCUGACUAU__CACUAAAUGGUCG_AGAACAGCUGUAAAAACAGCUGGCUUAAAUAUCGGAGGUAA___________
.............................((.((((((........))))))......(((((((....)))))))))............................ (-12.74 = -13.42 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:11 2006