Locus 10000

Sequence ID	3R_DroMel_CAF1
Location	26,774,374 – 26,774,475
Length	101
Max. P	0.828342

overview

Window 1

Location	26,774,374 – 26,774,475
Length	101
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	91.37
Mean single sequence MFE	-26.40
Consensus MFE	-24.04
Energy contribution	-24.23
Covariance contribution	0.19
Combinations/Pair	1.04
Mean z-score	-1.40
Structure conservation index	0.91
SVM decision value	0.71
SVM RNA-class probability	0.828342
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26774374 101 + 27905053
----CGAAGGAGUGGAAGGACCCAGCAGGCCGCAUUUUAUGAAUUAUUCAAAAUGAUCAUAAUAAAUUGCUGCAGCCUUUUACGGCAGCUGGGAAAAAGGGGGGA----
----................((((((..((.(((..((((((.((((.....)))))))))).....))).)).(((......))).))))))............---- ( -27.40)
>DroSec_CAF1 77774 98 + 1
----CGAAGGAGUGGAAGGACCUAGCAGGCCGCAUUUUAUGAAUUAUUCAAAAUGAUCAUAAUAAAUUGCUGCAGCCUUUUACGGCAGCUGGGAAAU---GGGGA----
----................((((((..((.(((..((((((.((((.....)))))))))).....))).)).(((......))).))))))....---.....---- ( -25.10)
>DroSim_CAF1 81483 98 + 1
----CGAAGGAGUGGAAGGACCUAGCAGGCCGCAUUUUAUGAAUUAUUCAAAAUGAUCAUAAUAAAUUGCUGCAGCCUUUUACGGCAGCUGGGAAAU---GGGGA----
----................((((((..((.(((..((((((.((((.....)))))))))).....))).)).(((......))).))))))....---.....---- ( -25.10)
>DroEre_CAF1 79301 98 + 1
----CGAAGGAGUAGAAGGACCUAGCAGGCCGCAUUUUAUGAAUUAUUCAAAAUGAUCAUAAUAAAUUGCUGCAGCCUUUUACGGCAGCUGCAAAAU---GGGGC----
----...(((..........))).....(((.((((((((((.((((.....))))))))))....((((.((.(((......))).)).)))))))---).)))---- ( -23.40)
>DroYak_CAF1 80942 98 + 1
----CGAAGGAGUAGAAGGACCUAGCAGGCCGCAUUUUAUGAAUUAUUCAAAAUGAUCAUAAUAAAUUGCUGCAGCCUUUUACGGCAGCUGGGAAAU---GGGAA----
----................((((((..((.(((..((((((.((((.....)))))))))).....))).)).(((......))).))))))....---.....---- ( -25.10)
>DroAna_CAF1 91833 107 + 1
GUUACGAAGGAAGCCGACGACCUAGCAGGCCGCAUUUUAUGAAUUAUUCAAAAUGAUCAUAAUAAAUUGCUGCAGCCUUUUACGGCAGCUGGGAACAA--GGGGACUUG
....((..((...))..)).((((((..((.(((..((((((.((((.....)))))))))).....))).)).(((......))).))))))..(((--(....)))) ( -32.30)
>consensus
____CGAAGGAGUGGAAGGACCUAGCAGGCCGCAUUUUAUGAAUUAUUCAAAAUGAUCAUAAUAAAUUGCUGCAGCCUUUUACGGCAGCUGGGAAAU___GGGGA____
....................((((((..((.(((..((((((.((((.....)))))))))).....))).)).(((......))).))))))................ (-24.04 = -24.23 +   0.19)

alignment

secondary structure

dotplot

Window 2

Location	26,774,374 – 26,774,475
Length	101
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	91.37
Mean single sequence MFE	-21.69
Consensus MFE	-18.80
Energy contribution	-18.82
Covariance contribution	0.03
Combinations/Pair	1.05
Mean z-score	-1.36
Structure conservation index	0.87
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26774374 101 - 27905053
----UCCCCCCUUUUUCCCAGCUGCCGUAAAAGGCUGCAGCAAUUUAUUAUGAUCAUUUUGAAUAAUUCAUAAAAUGCGGCCUGCUGGGUCCUUCCACUCCUUCG----
----............((((((.((((((....((....))......((((((..............))))))..))))))..))))))................---- ( -26.04)
>DroSec_CAF1 77774 98 - 1
----UCCCC---AUUUCCCAGCUGCCGUAAAAGGCUGCAGCAAUUUAUUAUGAUCAUUUUGAAUAAUUCAUAAAAUGCGGCCUGCUAGGUCCUUCCACUCCUUCG----
----.....---....((.(((.((((((....((....))......((((((..............))))))..))))))..))).))................---- ( -19.54)
>DroSim_CAF1 81483 98 - 1
----UCCCC---AUUUCCCAGCUGCCGUAAAAGGCUGCAGCAAUUUAUUAUGAUCAUUUUGAAUAAUUCAUAAAAUGCGGCCUGCUAGGUCCUUCCACUCCUUCG----
----.....---....((.(((.((((((....((....))......((((((..............))))))..))))))..))).))................---- ( -19.54)
>DroEre_CAF1 79301 98 - 1
----GCCCC---AUUUUGCAGCUGCCGUAAAAGGCUGCAGCAAUUUAUUAUGAUCAUUUUGAAUAAUUCAUAAAAUGCGGCCUGCUAGGUCCUUCUACUCCUUCG----
----(((.(---(((((((.((.(((......))).)).))))....((((((..............)))))))))).)))....((((....))))........---- ( -21.64)
>DroYak_CAF1 80942 98 - 1
----UUCCC---AUUUCCCAGCUGCCGUAAAAGGCUGCAGCAAUUUAUUAUGAUCAUUUUGAAUAAUUCAUAAAAUGCGGCCUGCUAGGUCCUUCUACUCCUUCG----
----.....---....((.(((.((((((....((....))......((((((..............))))))..))))))..))).))................---- ( -19.54)
>DroAna_CAF1 91833 107 - 1
CAAGUCCCC--UUGUUCCCAGCUGCCGUAAAAGGCUGCAGCAAUUUAUUAUGAUCAUUUUGAAUAAUUCAUAAAAUGCGGCCUGCUAGGUCGUCGGCUUCCUUCGUAAC
((((....)--)))...((.((.(((.....((((((((........((((((..............))))))..))))))))....))).)).))............. ( -23.84)
>consensus
____UCCCC___AUUUCCCAGCUGCCGUAAAAGGCUGCAGCAAUUUAUUAUGAUCAUUUUGAAUAAUUCAUAAAAUGCGGCCUGCUAGGUCCUUCCACUCCUUCG____
................((.(((.((((((....((....))......((((((..............))))))..))))))..))).)).................... (-18.80 = -18.82 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:46:46 2006