Locus 6061

Sequence ID	3R_DroMel_CAF1
Location	15,929,477 – 15,929,608
Length	131
Max. P	0.999698

overview

Window 6

Location	15,929,477 – 15,929,596
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.62
Mean single sequence MFE	-29.02
Consensus MFE	-20.99
Energy contribution	-21.97
Covariance contribution	0.97
Combinations/Pair	1.13
Mean z-score	-2.23
Structure conservation index	0.72
SVM decision value	0.12
SVM RNA-class probability	0.594538
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15929477 119 - 27905053
CAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUUUUGCUGGACGAACAACAAUAGCAACAAUAAUGUUAAUGAAAGCAAACAUUACCGAGAACAGC-GUCACAGCAGCAGGGA
.....(((((....)))))(((((....((((((((((((.(((.((......)).))).))))))))(((((((..(....)..))))))).........))-))....)))))..... ( -26.40)
>DroSec_CAF1 46465 119 - 1
CAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUGUUGCUGGACGAACAACAAUAGCAACAAUAAUGUUAAUGAAAGCAAACAUUACCGAGAACAGC-GUCACAGCAGCAGGGA
.....(((((....)))))(((((....((((((((((((((((.((......)).))))))))))))(((((((..(....)..))))))).........))-))....)))))..... ( -30.30)
>DroSim_CAF1 36551 119 - 1
CAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUGUUGCUGGACGAACAACAAUAGCAACAAUAAUGUUAAUGAAAGCAAACAUUACCGAGAACAGC-GUCACAGCAGCAGGGA
.....(((((....)))))(((((....((((((((((((((((.((......)).))))))))))))(((((((..(....)..))))))).........))-))....)))))..... ( -30.30)
>DroEre_CAF1 35763 99 - 1
CAAAAUGCAUUGAAGUGUAGUUGCGUCAGUGUUUGGUGUUGUUGCUGGGCGAGCAACAAUAGCAACAAUAAUGUUAAUGAAAGCAAACAUUACCGAGAA---------------------
......(((((((.((......)).)))))))(((.((((((((((.....)))))))))).)))...(((((((..(....)..))))))).......--------------------- ( -26.50)
>DroYak_CAF1 48684 116 - 1
CAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUGUUGCGGGGCGAACAACAAUAGCAACAAUAAUUUUAAUGAAAGCAAACAUUACCGGGAACAGC-GUCGCAC---CAGGGA
.....(((((....)))))(.((((.(..(((((((((((((((..(......)..))))))))))........(((((........)))))....)))))..-).)))).---)..... ( -27.60)
>DroAna_CAF1 30457 108 - 1
UAAAAUGCAUUCAAGUGUAGUUGCGUCAAUGUUUGUUGCAGUUG---------CAACAACAGCAACAAUAAUGGUAAUGAAAACAAACAUUACCAAGAACAGCAGUUGAAA---CUGUAA
.....(((((((((.(((.(((((.....((((.(((((....)---------))))))))))))).....((((((((........))))))))......))).))))).---.)))). ( -33.00)
>consensus
CAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUGUUGCUGGACGAACAACAAUAGCAACAAUAAUGUUAAUGAAAGCAAACAUUACCGAGAACAGC_GUCACAG___CAGGGA
......(((((((.((......)).)))))))((((((((((((.((......)).))))))))))))(((((((..(....)..)))))))............................ (-20.99 = -21.97 +   0.97)

alignment

secondary structure

dotplot

Window 7

Location	15,929,516 – 15,929,608
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	96.30
Mean single sequence MFE	-18.68
Consensus MFE	-16.66
Energy contribution	-17.50
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-2.99
Structure conservation index	0.89
SVM decision value	3.91
SVM RNA-class probability	0.999698
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15929516 92 + 27905053
UCAUUAACAUUAUUGUUGCUAUUGUUGUUCGUCCAGCAAAAACAACAAACAUUGACGCAACUACACUUCAAUGCAUUUUGUGCAACAGCUAC
............(((((((..((((((......)))))).....(((((((((((.(........).))))))...)))))))))))).... ( -18.50)
>DroSec_CAF1 46504 92 + 1
UCAUUAACAUUAUUGUUGCUAUUGUUGUUCGUCCAGCAACAACAACAAACAUUGACGCAACUACACUUCAAUGCAUUUUGUCCAACAGCUAC
............((((((...((((((((.....))))))))..(((((((((((.(........).))))))...))))).)))))).... ( -15.70)
>DroSim_CAF1 36590 92 + 1
UCAUUAACAUUAUUGUUGCUAUUGUUGUUCGUCCAGCAACAACAACAAACAUUGACGCAACUACACUUCAAUGCAUUUUGUGCAACAGCUAC
............(((((((..((((((((.....))))))))..(((((((((((.(........).))))))...)))))))))))).... ( -20.20)
>DroEre_CAF1 35782 92 + 1
UCAUUAACAUUAUUGUUGCUAUUGUUGCUCGCCCAGCAACAACACCAAACACUGACGCAACUACACUUCAAUGCAUUUUGUGCAACAGCUAC
............(((((((..((((((((.....))))))))......(((..((.(((............))).)).)))))))))).... ( -18.00)
>DroYak_CAF1 48720 92 + 1
UCAUUAAAAUUAUUGUUGCUAUUGUUGUUCGCCCCGCAACAACAACAAACAUUGACGCAACUACACUUCAAUGCAUUUUGUGCAACAGCUAC
............(((((((...(((((((.((...)))))))))(((((((((((.(........).))))))...)))))))))))).... ( -21.00)
>consensus
UCAUUAACAUUAUUGUUGCUAUUGUUGUUCGUCCAGCAACAACAACAAACAUUGACGCAACUACACUUCAAUGCAUUUUGUGCAACAGCUAC
............(((((((..((((((((.....))))))))..(((((((((((.(........).))))))...)))))))))))).... (-16.66 = -17.50 +   0.84)

alignment

secondary structure

dotplot

Window 8

Location	15,929,516 – 15,929,608
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	96.30
Mean single sequence MFE	-25.48
Consensus MFE	-22.54
Energy contribution	-22.82
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-2.57
Structure conservation index	0.88
SVM decision value	3.29
SVM RNA-class probability	0.998944
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15929516 92 - 27905053
GUAGCUGUUGCACAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUUUUGCUGGACGAACAACAAUAGCAACAAUAAUGUUAAUGA
.....((((((.......(((((((.((......)).)))))))(((((((((.........)))))))))..))))))............. ( -22.60)
>DroSec_CAF1 46504 92 - 1
GUAGCUGUUGGACAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUGUUGCUGGACGAACAACAAUAGCAACAAUAAUGUUAAUGA
..........((((....(((((((.((......)).)))))))((((((((((((.((......)).))))))))))))...))))..... ( -24.80)
>DroSim_CAF1 36590 92 - 1
GUAGCUGUUGCACAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUGUUGCUGGACGAACAACAAUAGCAACAAUAAUGUUAAUGA
.....((((((.......(((((((.((......)).))))))).((((((((((........))))))))))))))))............. ( -25.30)
>DroEre_CAF1 35782 92 - 1
GUAGCUGUUGCACAAAAUGCAUUGAAGUGUAGUUGCGUCAGUGUUUGGUGUUGUUGCUGGGCGAGCAACAAUAGCAACAAUAAUGUUAAUGA
.....((((((.(((...(((((((.((......)).)))))))))).((((((((((.....))))))))))))))))............. ( -28.50)
>DroYak_CAF1 48720 92 - 1
GUAGCUGUUGCACAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUGUUGCGGGGCGAACAACAAUAGCAACAAUAAUUUUAAUGA
.....((((((.......(((((((.((......)).))))))).((((((((((((...)).))))))))))))))))............. ( -26.20)
>consensus
GUAGCUGUUGCACAAAAUGCAUUGAAGUGUAGUUGCGUCAAUGUUUGUUGUUGUUGCUGGACGAACAACAAUAGCAACAAUAAUGUUAAUGA
.....((((((.......(((((((.((......)).))))))).((((((((((........))))))))))))))))............. (-22.54 = -22.82 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:41 2006