Locus 6741

Sequence ID	3L_DroMel_CAF1
Location	18,063,252 – 18,063,381
Length	129
Max. P	0.911057

overview

Window 1

Location	18,063,252 – 18,063,344
Length	92
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	80.50
Mean single sequence MFE	-28.80
Consensus MFE	-18.26
Energy contribution	-19.24
Covariance contribution	0.97
Combinations/Pair	1.14
Mean z-score	-2.17
Structure conservation index	0.63
SVM decision value	0.79
SVM RNA-class probability	0.851091
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18063252 92 + 23771897
AAAAGUGCCCAACGAUGCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGAUUGGGAUUGCGAUUGUGUCAGCCG--UG-GCAAUGCAA
.....(((.....((((((((((...((((.....((((.............)))).....)))).)))))))))).((..--..-))...))). ( -26.52)
>DroSec_CAF1 8841 92 + 1
AAAAGUGCCAAGCGAUGCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGAUUGGGAUUGCGAUUGUGUCAGCCG--UG-GCAAUGCAA
.....(((((.((((((((((((...((((.....((((.............)))).....)))).)))))))))).))..--))-)))...... ( -30.72)
>DroSim_CAF1 9175 92 + 1
AAAAGUGCCCAGCGAUGCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGAUUGUGAUUGUGAUUGUGUCAGCCG--UG-GCAAUGCAA
.....(((((.((((((((((((...(((((((..((((.............))))..))))))).)))))))))).)).)--.)-)))...... ( -32.92)
>DroEre_CAF1 8787 92 + 1
AAAAGUGCCCAGCGAUGCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAUGGGCGAUUGUGAUUGCGAUUGUGUCAGCCG--UG-GCAAUGCGA
.....(((((.((((((((((((...(((((((.....(((((((....)))))))..))))))).)))))))))).)).)--.)-)))...... ( -36.00)
>DroYak_CAF1 9655 95 + 1
AAAAGUGCCCAGCGAUGCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGACUGUGAUUGUGAUUGCGAUUGCAAAAUGCAAAAUGCAA
...........((((((((((((...(((((((..((((.............))))..))))))).))))))).)))))....(((.....))). ( -29.72)
>DroAna_CAF1 7556 73 + 1
CUGAGUCUC---CGAUGCAGUCGAUAAAUCACGUUCGGCACUCAUCUCAGAGUGCGAUUAUGAUUAAAAUUCUGUU-------------------
.........---....((((......(((((...(((.(((((......))))))))...)))))......)))).------------------- ( -16.90)
>consensus
AAAAGUGCCCAGCGAUGCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGAUUGUGAUUGCGAUUGUGUCAGCCG__UG_GCAAUGCAA
.............((((((((((...(((((((..((((.............))))..))))))).))))))))))................... (-18.26 = -19.24 +   0.97)

alignment

secondary structure

dotplot

Window 2

Location	18,063,268 – 18,063,381
Length	113
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	89.51
Mean single sequence MFE	-38.62
Consensus MFE	-28.00
Energy contribution	-28.16
Covariance contribution	0.16
Combinations/Pair	1.15
Mean z-score	-2.61
Structure conservation index	0.73
SVM decision value	1.07
SVM RNA-class probability	0.911057
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18063268 113 + 23771897
GCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGAUUGGGAUUGCGAUUGUGUCAGCCG--UG-GCAAUGCAAAAUUAAAAGGAGCUGUUGCCAUGGCUAAGACUUU-UUG
(((((((...((((.....((((.............)))).....)))).)))))))((((((((--((-(((((((.............)).))))))))))))..)))...-... ( -39.44)
>DroSec_CAF1 8857 113 + 1
GCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGAUUGGGAUUGCGAUUGUGUCAGCCG--UG-GCAAUGCAAAAUGAAAAGGAGCUGUUGCCAUGGCUCAGACUUU-UUG
(((((((...((((.....((((.............)))).....)))).)))))))((((((((--((-(((((((....(....)...)).))))))))))))..)))...-... ( -39.72)
>DroSim_CAF1 9191 113 + 1
GCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGAUUGUGAUUGUGAUUGUGUCAGCCG--UG-GCAAUGCAAAAUUAAAAGGAGCUGUUGCCAUGGCUCAGACUUU-UUG
(((((((...(((((((..((((.............))))..))))))).)))))))((((((((--((-(((((((.............)).))))))))))))..)))...-... ( -42.24)
>DroEre_CAF1 8803 111 + 1
GCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAUGGGCGAUUGUGAUUGCGAUUGUGUCAGCCG--UG-GCAAUGCGAAAUUGAAAU--GUUGUUGCCAUGGCUCAGACUUU-UUG
(((((((...(((((((.....(((((((....)))))))..))))))).)))))))((((((((--((-(((((.............--...))))))))))))..)))...-... ( -43.29)
>DroYak_CAF1 9671 115 + 1
GCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGACUGUGAUUGUGAUUGCGAUUGCAAAAUGCAAAAUGCAAAAUGAAAAU--GCUGUUUCCAGGGCUCAGACUUUUUUG
(((((((...(((((((..(((.(.((..((....))..))).)))..))))))).)))))))....(((.....)))....(((((.--.(((...(....)..)))...))))). ( -28.40)
>consensus
GCAGUCGAUAAAUCACGUGCGCUGCUCAUCUCAAAAGGCGAUUGUGAUUGCGAUUGUGUCAGCCG__UG_GCAAUGCAAAAUUAAAAGGAGCUGUUGCCAUGGCUCAGACUUU_UUG
(((((((...(((((((..((((.............))))..))))))).)))))))(((((((...((.(((((((.............)).))))))).))))..)))....... (-28.00 = -28.16 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:54 2006