Locus 5360

Sequence ID	2L_DroMel_CAF1
Location	15,189,408 – 15,189,590
Length	182
Max. P	0.784545

overview

Window 0

Location	15,189,408 – 15,189,516
Length	108
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	81.45
Mean single sequence MFE	-20.14
Consensus MFE	-13.14
Energy contribution	-14.03
Covariance contribution	0.89
Combinations/Pair	1.05
Mean z-score	-1.91
Structure conservation index	0.65
SVM decision value	0.40
SVM RNA-class probability	0.722564
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15189408 108 + 22407834
CGACAACAGCCCAAUCCUGUUCAGCAAACCAA--CGAACGAUGGUGUCGACAACACCUCACAAAUCUCAGAAACCCCUGCGAAUAGGAAACUAUAUGCAUAUAUC--UGCUU
(((((((((.......)))))......((((.--(....).))))))))..................((((......((((.((((....)))).))))....))--))... ( -22.30)
>DroSec_CAF1 134344 108 + 1
CGACAACAGCCCAAUCCUGUUCAACAAACCAA--CGAACGAUGGUGUCGACAACACCUCACAAGACUCACAAACCUCUGCGAAUAGGAAACUAUAUGCAUAUAUC--UGCAC
(((((((((.......)))))......((((.--(....).))))))))............................((((.((((....)))).))))......--..... ( -20.30)
>DroSim_CAF1 137679 108 + 1
CGACAACAGCCCAAUCCUGUUCAACAAACCAA--CGAACGAUGGUGUCGACAACACCUCACAAAACUCACAAACCUCUGCGAAUAGGAAACUAUAUGCAUAUAUC--UGCAC
(((((((((.......)))))......((((.--(....).))))))))............................((((.((((....)))).))))......--..... ( -20.30)
>DroEre_CAF1 137336 97 + 1
CGACAACAGCCCAAUCCUGUUCAGCAAACCAG--CGAACGAUGGUGGCGACAACACCUCACAAGACUCAGAGUCC-CGGCGAAUUGGAAACUAUAUG------------CAC
.(((..............((((.((......)--)))))((.((((.......))))))............))).-..(((.((.(....).)).))------------).. ( -19.70)
>DroYak_CAF1 149879 108 + 1
CGACAACAGCCCAAUCCUGUUCAACAAACCAA--CGAAGGACGGUGUCGACAACACCUCACAGAACUCAGAAACCUCUGCGAAUAGGAAACUAUAUGCAUAUAUC--UGCAC
(((((((((.......)))))......(((..--(....)..)))))))...........((((....(((....)))(((.((((....)))).))).....))--))... ( -23.60)
>DroPer_CAF1 171410 98 + 1
CGAGGACAAUCCAAAACCAUCGA--AAACCAAACCAAACGACGAUGUCGACAACAACUCACAAA------------CAGCGAAUAGGAAUCUAUAUGCAUAUAUCCUUGCAA
((((((...........(((((.--................)))))..................------------..(((.((((....)))).))).....))))))... ( -14.63)
>consensus
CGACAACAGCCCAAUCCUGUUCAACAAACCAA__CGAACGAUGGUGUCGACAACACCUCACAAAACUCAGAAACCUCUGCGAAUAGGAAACUAUAUGCAUAUAUC__UGCAC
....(((((.......)))))..................((.(((((.....)))))))...................(((.((((....)))).))).............. (-13.14 = -14.03 +   0.89)

alignment

secondary structure

dotplot

Window 1

Location	15,189,480 – 15,189,590
Length	110
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	81.74
Mean single sequence MFE	-27.00
Consensus MFE	-15.70
Energy contribution	-17.46
Covariance contribution	1.76
Combinations/Pair	1.09
Mean z-score	-2.17
Structure conservation index	0.58
SVM decision value	0.57
SVM RNA-class probability	0.784545
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15189480 110 + 22407834
CCCUGCGAAUAGGAAACUAUAUGCAUAUAUCUGCUUAUAAAUAUAUCUUGAAGUACCUGGGUGUGCGUGAA-AAUAUCUUUGUAACAAGGCUGACGCAGCGAGGAUAACAU
...((((.((((....)))).))))..(((((..............((((...(((..((((((.......-.))))))..))).))))((((...))))..))))).... ( -26.40)
>DroSec_CAF1 134416 111 + 1
CUCUGCGAAUAGGAAACUAUAUGCAUAUAUCUGCACAUAAAUAUAUCUUCAAGUACCUGGGUGCGCGUGAAAAAUAUCUUUGCAACAAUGCUGCCGCUGCGAGGAUAACAU
...((((.((((....)))).))))......................((((.((((....))))...))))...((((((((((.....((....)))))))))))).... ( -28.30)
>DroSim_CAF1 137751 111 + 1
CUCUGCGAAUAGGAAACUAUAUGCAUAUAUCUGCACAUAAAUAUAUCUUCAAGUACCUGGGUGCGCGUGAAAAAUAUCUUCGCAACAAUGCUGCCGCUGCGAGGAUAACAU
...((((.((((....)))).))))......................((((.((((....))))...))))...((((((((((.....((....)))))))))))).... ( -30.40)
>DroEre_CAF1 137408 85 + 1
C-CGGCGAAUUGGAAACUAUAUG----------CACAUAAAUAUUUUUCCAAGUACCCGGCUGUGCGUAAU-AAUAUCUUUGCAACA--------------AGGAUAACAU
(-(((....(((((((..((((.----------.......)))).)))))))....))))...........-..((((((((...))--------------)))))).... ( -19.90)
>DroYak_CAF1 149951 109 + 1
CUCUGCGAAUAGGAAACUAUAUGCAUAUAUCUGCACAUAAAUAUUUCUUUAGGUACCUGUGUGUGCGUAAA-AAUAUCUUUGCAACA-GACUGACGCUGCGAGGAUAACAU
...((((.((((....)))).)))).......(((((((......((....))......))))))).....-..((((((((((.(.-.......).)))))))))).... ( -30.00)
>consensus
CUCUGCGAAUAGGAAACUAUAUGCAUAUAUCUGCACAUAAAUAUAUCUUCAAGUACCUGGGUGUGCGUGAA_AAUAUCUUUGCAACAAGGCUGACGCUGCGAGGAUAACAU
...((((.((((....)))).))))...........................((((......))))........((((((((((.............)))))))))).... (-15.70 = -17.46 +   1.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:14 2006