Locus 2227

Sequence ID	X_DroMel_CAF1
Location	6,003,155 – 6,003,290
Length	135
Max. P	0.999971

overview

Window 0

Location	6,003,155 – 6,003,252
Length	97
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	90.33
Mean single sequence MFE	-36.32
Consensus MFE	-33.32
Energy contribution	-33.56
Covariance contribution	0.24
Combinations/Pair	1.10
Mean z-score	-3.42
Structure conservation index	0.92
SVM decision value	5.06
SVM RNA-class probability	0.999971
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6003155 97 + 22224390
---------AUUCAGGUGCUCGCUAGCAAAAACAAAGAGCACGUGCAGCACAAAGGCGGCUAAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGA
---------...((.((((((...............)))))).))..(((((..(((((((((...((((.....))))....))))))))))))))......... ( -35.06)
>DroSec_CAF1 23253 101 + 1
-----GUGAACUCAGGUGCUCGCUGGCAAAAACAAAGAGCAUGUGCAGCACAAAGGCGGCUAAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGA
-----((...((((.((((((..((.......))..)))))).)...(((((..(((((((((...((((.....))))....)))))))))))))).))).)).. ( -37.70)
>DroSim_CAF1 19878 106 + 1
GAUGGGUGAACUCAGGUGCUCGCUGGCAAAAACAAAGAGCACGUGCAGCACAAAGGCGGCUAAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGA
..((((....)))).((((((..((.......))..))))))((.(.(((((..(((((((((...((((.....))))....)))))))))))))).)...)).. ( -40.00)
>DroEre_CAF1 17953 106 + 1
GAUGGGUGGUUUCAGGUGCUCACUAGCAGAAACAAAGAGCACGAGCAGCACAAAGGCGGCGGAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGA
......((.((((..((((((...............)))))).....(((((..((((((.((...((((.....))))....)).))))))))))).)))).)). ( -35.26)
>DroYak_CAF1 20280 106 + 1
GGUGGGUGGUUUCAGGUGCUCACUGGCAGAAACAAAGAGCACGUGCAGCACAAAGGAGGCUAAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGA
......((.((((..((((((..((.......))..)))))).....(((((..(..((((((...((((.....))))....))))))..)))))).)))).)). ( -33.60)
>consensus
G_UGGGUGAAUUCAGGUGCUCGCUGGCAAAAACAAAGAGCACGUGCAGCACAAAGGCGGCUAAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGA
..........(((..((((((..((.......))..)))))).....(((((..(((((((((...((((.....))))....)))))))))))))).)))..... (-33.32 = -33.56 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	6,003,155 – 6,003,252
Length	97
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	90.33
Mean single sequence MFE	-24.39
Consensus MFE	-23.46
Energy contribution	-23.70
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.25
Structure conservation index	0.96
SVM decision value	0.55
SVM RNA-class probability	0.779429
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6003155 97 - 22224390
UCGCUCUCUGCACAGACAGCCAACUUUUGCCUUUGAAGCACUUUUAGCCGCCUUUGUGCUGCACGUGCUCUUUGUUUUUGCUAGCGAGCACCUGAAU---------
..((((.(((((.(((((((........))......(((((...((((((....)).))))...)))))...))))).))).)).))))........--------- ( -24.80)
>DroSec_CAF1 23253 101 - 1
UCGCUCUCUGCACAGACAGCCAACUUUUGCCUUUGAAGCACUUUUAGCCGCCUUUGUGCUGCACAUGCUCUUUGUUUUUGCCAGCGAGCACCUGAGUUCAC-----
..((((.(((((.((((((.................(((((..............)))))((....))...)))))).)).))).))))............----- ( -22.74)
>DroSim_CAF1 19878 106 - 1
UCGCUCUCUGCACAGACAGCCAACUUUUGCCUUUGAAGCACUUUUAGCCGCCUUUGUGCUGCACGUGCUCUUUGUUUUUGCCAGCGAGCACCUGAGUUCACCCAUC
..((((.(((((.(((((((........))......(((((...((((((....)).))))...)))))...))))).)).))).))))................. ( -24.80)
>DroEre_CAF1 17953 106 - 1
UCGCUCUCUGCACAGACAGCCAACUUUUGCCUUUGAAGCACUUUCCGCCGCCUUUGUGCUGCUCGUGCUCUUUGUUUCUGCUAGUGAGCACCUGAAACCACCCAUC
..((((.(((((.(((((((........))......(((((.....((.((......)).))..)))))...))))).))).)).))))................. ( -23.90)
>DroYak_CAF1 20280 106 - 1
UCGCUCUCUGCACAGACAGCCAACUUUUGCCUUUGAAGCACUUUUAGCCUCCUUUGUGCUGCACGUGCUCUUUGUUUCUGCCAGUGAGCACCUGAAACCACCCACC
..((((.(((((.(((((((........))......(((((...(((((......).))))...)))))...))))).)).))).))))................. ( -25.70)
>consensus
UCGCUCUCUGCACAGACAGCCAACUUUUGCCUUUGAAGCACUUUUAGCCGCCUUUGUGCUGCACGUGCUCUUUGUUUUUGCCAGCGAGCACCUGAAUCCACCCA_C
..((((.(((((.(((((((........))......(((((...(((((......).))))...)))))...))))).))).)).))))................. (-23.46 = -23.70 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	6,003,175 – 6,003,290
Length	115
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	89.18
Mean single sequence MFE	-31.60
Consensus MFE	-28.92
Energy contribution	-28.70
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-3.68
Structure conservation index	0.92
SVM decision value	2.11
SVM RNA-class probability	0.988151
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6003175 115 + 22224390
AAACAAAGAGCACGUGCAGCACAAAGGCGGCUAAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGAAAAACACAAAUGCUUUAAAUACGAAAAACACACACUGC
.........(((.(((..(((((..(((((((((...((((.....))))....))))))))))))))..((((((...........))))))................)))))) ( -31.20)
>DroSec_CAF1 23277 100 + 1
AAACAAAGAGCAUGUGCAGCACAAAGGCGGCUAAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGAAAAACACAAAUGCUUUAAAUGCG---------------
.........((((.....(((((..(((((((((...((((.....))))....))))))))))))))..((((((...........))))))..)))).--------------- ( -31.00)
>DroSim_CAF1 19907 112 + 1
AAACAAAGAGCACGUGCAGCACAAAGGCGGCUAAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGAAAAACACAAAUGCUUUAAAUGCGGGAAA---AAACUGC
......(((((((((.(.(((((..(((((((((...((((.....))))....)))))))))))))).)...)))...........))))))....((((....---...)))) ( -32.60)
>consensus
AAACAAAGAGCACGUGCAGCACAAAGGCGGCUAAAAGUGCUUCAAAGGCAAAAGUUGGCUGUCUGUGCAGAGAGCGAAAAACACAAAUGCUUUAAAUGCG__AAA___A_ACUGC
......(((((((((.(.(((((..(((((((((...((((.....))))....)))))))))))))).)...)))...........))))))...................... (-28.92 = -28.70 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:16 2006