Locus 517

Sequence ID	3L_DroMel_CAF1
Location	1,527,162 – 1,527,275
Length	113
Max. P	0.891607

overview

Window 4

Location	1,527,162 – 1,527,275
Length	113
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.62
Mean single sequence MFE	-32.23
Consensus MFE	-18.32
Energy contribution	-19.02
Covariance contribution	0.70
Combinations/Pair	1.17
Mean z-score	-1.74
Structure conservation index	0.57
SVM decision value	0.06
SVM RNA-class probability	0.564438
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1527162 113 + 23771897
GAAUAAACC-UUUUACC--AUUACAGCCAAAAUCAAGGAGCUGUUUGAACACAAUCUGCAGAUGGAGCUGGAGGACUCAUCCUCAAGCCUAGACUCCUCGUUUAGCAAUGGAAGCG
.........-.....((--(((...((.(((....(((((((((..((......)).)))).(((.(((.(((((....))))).))))))..)))))..))).)))))))..... ( -27.90)
>DroVir_CAF1 8131 112 + 1
----AAUGCGUGUCUCCAUUUUGCAGCUAAAAUCAAGGAGCUGUUUGAGCAGAAUCUGCAACAGGAGCUGGAUGACUCGGCUUCCAGCAUGGACUCCUCCUUUAGCAAUGGCAGCU
----.......((..(((((.....((((((....((((((((((...((((...)))))))))..((((((.(......).)))))).....)))))..)))))))))))..)). ( -32.50)
>DroPse_CAF1 5646 110 + 1
----AACCCUUAUUUCC--AUUUAAGCCAAGGUUAAAGAGCUUUUUGAGCAGAAUCUGCAGCUGGAGCUGGAGGACUCUGCCUCCAGCAUGGACUCCUCCUUCAGCAAUAGCAGCG
----((((((((.....--...))))....)))).....(((......((((...)))).((((((((((((((......))))))))..(((....)))))))))......))). ( -35.40)
>DroYak_CAF1 6190 111 + 1
CAU--UACU-UUUUACC--UUUACAGCCAAAAUCAAGGAGCUGUUUGAACAAAAUCUGCAGAUGGAGCUGGAGGACUCAUCCUCCAGCUUGGACUCCUCGUUUAGCAAUGGAAGCG
...--....-......(--(((...((.(((....(((((((((..((......)).)))).(.(((((((((((....))))))))))).).)))))..))).))....)))).. ( -33.00)
>DroAna_CAF1 6418 107 + 1
------AAC-UAUUACU--UUUGCAGCCAAAAUCAAAGAACUGUUUGAGCAAAAUCUUCAGCUGGAGCUAGAGGACUCUGCUUCCAGCAUGGACUCCUCCUUUAGCAACGGCAGCG
------...-.......--...((.(((....(((((......)))))((..........((((((((.(((....))))).))))))..(((....)))....))...))).)). ( -29.20)
>DroPer_CAF1 5816 110 + 1
----AACCCUUAUUUCC--AUUUAAGCCAAGGUUAAAGAGCUUUUUGAGCAGAAUCUGCAGCUGGAGCUGGAGGACUCUGCCUCCAGCAUGGACUCCUCCUUCAGCAAUAGCAGCG
----((((((((.....--...))))....)))).....(((......((((...)))).((((((((((((((......))))))))..(((....)))))))))......))). ( -35.40)
>consensus
____AAACC_UAUUACC__AUUACAGCCAAAAUCAAAGAGCUGUUUGAGCAGAAUCUGCAGCUGGAGCUGGAGGACUCUGCCUCCAGCAUGGACUCCUCCUUUAGCAAUGGCAGCG
.........................((.....(((((......)))))............((((((((((((((......))))))))..(((....))))))))).......)). (-18.32 = -19.02 +   0.70)

alignment

secondary structure

dotplot

Window 5

Location	1,527,162 – 1,527,275
Length	113
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.62
Mean single sequence MFE	-35.03
Consensus MFE	-24.94
Energy contribution	-25.08
Covariance contribution	0.14
Combinations/Pair	1.31
Mean z-score	-1.88
Structure conservation index	0.71
SVM decision value	0.97
SVM RNA-class probability	0.891607
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1527162 113 - 23771897
CGCUUCCAUUGCUAAACGAGGAGUCUAGGCUUGAGGAUGAGUCCUCCAGCUCCAUCUGCAGAUUGUGUUCAAACAGCUCCUUGAUUUUGGCUGUAAU--GGUAAAA-GGUUUAUUC
.(((((((((((((((((((((((...((((.(((((....))))).))))............(((......)))))))))))..))))))...)))--))....)-)))...... ( -32.50)
>DroVir_CAF1 8131 112 - 1
AGCUGCCAUUGCUAAAGGAGGAGUCCAUGCUGGAAGCCGAGUCAUCCAGCUCCUGUUGCAGAUUCUGCUCAAACAGCUCCUUGAUUUUAGCUGCAAAAUGGAGACACGCAUU----
.(((((....(((((((((((((.....((((((.(......).))))))..(((((((((...))))...)))))))))))..))))))).)))...((....)).))...---- ( -35.20)
>DroPse_CAF1 5646 110 - 1
CGCUGCUAUUGCUGAAGGAGGAGUCCAUGCUGGAGGCAGAGUCCUCCAGCUCCAGCUGCAGAUUCUGCUCAAAAAGCUCUUUAACCUUGGCUUAAAU--GGAAAUAAGGGUU----
..((((....((((..(((....)))..((((((((......))))))))..)))).)))).....(((.....))).......(((((.((.....--))...)))))...---- ( -35.10)
>DroYak_CAF1 6190 111 - 1
CGCUUCCAUUGCUAAACGAGGAGUCCAAGCUGGAGGAUGAGUCCUCCAGCUCCAUCUGCAGAUUUUGUUCAAACAGCUCCUUGAUUUUGGCUGUAAA--GGUAAAA-AGUA--AUG
......(((((((...((((((((...((((((((((....)))))))))).........((......)).....)))))))).(((((.((....)--).)))))-))))--))) ( -39.20)
>DroAna_CAF1 6418 107 - 1
CGCUGCCGUUGCUAAAGGAGGAGUCCAUGCUGGAAGCAGAGUCCUCUAGCUCCAGCUGAAGAUUUUGCUCAAACAGUUCUUUGAUUUUGGCUGCAAA--AGUAAUA-GUU------
.(((...((.(((((((..((((.....((((..(((((((((.((.(((....))))).)))))))))....)))).))))..))))))).))...--)))....-...------ ( -33.10)
>DroPer_CAF1 5816 110 - 1
CGCUGCUAUUGCUGAAGGAGGAGUCCAUGCUGGAGGCAGAGUCCUCCAGCUCCAGCUGCAGAUUCUGCUCAAAAAGCUCUUUAACCUUGGCUUAAAU--GGAAAUAAGGGUU----
..((((....((((..(((....)))..((((((((......))))))))..)))).)))).....(((.....))).......(((((.((.....--))...)))))...---- ( -35.10)
>consensus
CGCUGCCAUUGCUAAAGGAGGAGUCCAUGCUGGAGGCAGAGUCCUCCAGCUCCAGCUGCAGAUUCUGCUCAAACAGCUCCUUGAUUUUGGCUGAAAA__GGAAAUA_GGUUU____
..........((((((((((((((....((((((((......)))))))).......((((...)))).......)))))))..)))))))......................... (-24.94 = -25.08 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:02 2006