Locus 3305

Sequence ID	X_DroMel_CAF1
Location	8,826,342 – 8,826,535
Length	193
Max. P	0.997921

overview

Window 6

Location	8,826,342 – 8,826,433
Length	91
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	81.35
Mean single sequence MFE	-25.30
Consensus MFE	-11.77
Energy contribution	-13.03
Covariance contribution	1.25
Combinations/Pair	1.14
Mean z-score	-2.96
Structure conservation index	0.47
SVM decision value	0.24
SVM RNA-class probability	0.647656
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8826342 91 - 22224390
GAAAACUGGCACAGGAAAC-----------UGGCUAUUAAAAAGCAUUCUGCGAAAGUAGAUGUCAGGGGUCAGAGAAAAGUUGACUGCAGGGCUCAAAAAG
.....(((((((((....)-----------))(((.......)))..(((((....)))))))))))(((((...(...((....)).)..)))))...... ( -28.20)
>DroSec_CAF1 67605 91 - 1
GGCAACUGGCACAGGAAAC-----------UGGCUAUUAAAAAGCAUCCAGCGAAAAUAGAUGUCAGGGGUCCGAGAAAAGUUGACUGCAGGGCUCAAAAAG
.....(((((((((....)-----------)).(((((.....((.....))...))))).))))))((((((..(...((....)).).))))))...... ( -25.50)
>DroSim_CAF1 59659 91 - 1
GGCAACUGGCACAGGAAAC-----------UGGCUAUUAAAAAGCAUCCAGCGAAAAUAGAUGUCAGGGGUCCGAGAAAAGUUGACUGCAGGGCUCAAAAAG
.....(((((((((....)-----------)).(((((.....((.....))...))))).))))))((((((..(...((....)).).))))))...... ( -25.50)
>DroEre_CAF1 63149 93 - 1
GGAAAAUGGAAAUGGAAACAGGUAGGCGAAUGGCUUUUA-AAAGCAUCCUGCGAAAAG-AAUGUCUGGGGUCAGAGAAAAGUUGACUGCAGGACU-------
............((....)).(((((......((((...-.))))..)))))......-....((((.((((((.......)))))).))))...------- ( -22.00)
>consensus
GGAAACUGGCACAGGAAAC___________UGGCUAUUAAAAAGCAUCCAGCGAAAAUAGAUGUCAGGGGUCAGAGAAAAGUUGACUGCAGGGCUCAAAAAG
.....((((((..(....)..............(((((.....((.....))...))))).))))))((((((......((....))...))))))...... (-11.77 = -13.03 +   1.25)

alignment

secondary structure

dotplot

Window 7

Location	8,826,367 – 8,826,473
Length	106
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	74.10
Mean single sequence MFE	-30.94
Consensus MFE	-12.21
Energy contribution	-13.74
Covariance contribution	1.53
Combinations/Pair	1.05
Mean z-score	-2.67
Structure conservation index	0.39
SVM decision value	2.96
SVM RNA-class probability	0.997921
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8826367 106 - 22224390
UAGUCAUUUCAGAGGAUGCCAUGGCAACCACGCCUAAAAUGAAAACUGGCACAGGAAAC-----------UGGCUAUUAAAAAGCAUUCUGCGAAAGUAGAUGUCAGGGGUCAGAGA
......((((...((.(((....))).))..........(((...(((((((((....)-----------))(((.......)))..(((((....)))))))))))...))))))) ( -34.00)
>DroSec_CAF1 67630 106 - 1
UAGGCACUGCAGAGGAUGCCAUGGCAACCACGCCUAAAAUGGCAACUGGCACAGGAAAC-----------UGGCUAUUAAAAAGCAUCCAGCGAAAAUAGAUGUCAGGGGUCCGAGA
(((((.(....).((.(((....))).))..)))))...((((..(((((((((....)-----------)).(((((.....((.....))...))))).))))))..).)))... ( -33.80)
>DroSim_CAF1 59684 106 - 1
UAGUCACUGCAGAGGAUGCCAUGGCAACCACGCCUAAAAUGGCAACUGGCACAGGAAAC-----------UGGCUAUUAAAAAGCAUCCAGCGAAAAUAGAUGUCAGGGGUCCGAGA
.............((((.((.(((((.....(((......)))..((((..(((....)-----------))(((.......)))..))))..........))))))).)))).... ( -33.00)
>DroEre_CAF1 63167 104 - 1
-----------GCGGAUGCCAUGGCAACCAAGUCCAAAAUGGAAAAUGGAAAUGGAAACAGGUAGGCGAAUGGCUUUUA-AAAGCAUCCUGCGAAAAG-AAUGUCUGGGGUCAGAGA
-----------...(((.(((.((((.(((..(((.....)))...)))...((....)).(((((......((((...-.))))..)))))......-..))))))).)))..... ( -29.20)
>DroYak_CAF1 63910 88 - 1
UAGUCAUUUCAGCGGAUGCCAUGGCAACCACGGCCAAA-U---------------------------GGAUGGCUAUUAAAAAGCAUCCUGCGAAAAG-GAUGUCAGAGGUCCAAGC
.....(((((.(.((.(((....))).)).)(((((..-.---------------------------...)))))........(((((((......))-)))))..)))))...... ( -24.70)
>consensus
UAGUCACUGCAGAGGAUGCCAUGGCAACCACGCCUAAAAUGGAAACUGGCACAGGAAAC___________UGGCUAUUAAAAAGCAUCCUGCGAAAAUAGAUGUCAGGGGUCCGAGA
.............((((.((.(((((.(((.(((.............)))...(....)...........)))..........((.....)).........))))))).)))).... (-12.21 = -13.74 +   1.53)

alignment

secondary structure

dotplot

Window 8

Location	8,826,433 – 8,826,535
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.11
Mean single sequence MFE	-29.16
Consensus MFE	-21.45
Energy contribution	-21.21
Covariance contribution	-0.24
Combinations/Pair	1.13
Mean z-score	-1.70
Structure conservation index	0.74
SVM decision value	1.03
SVM RNA-class probability	0.903304
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8826433 102 + 22224390
AUUUUAGGCGUGGUUGCCAUGGCAUCCUCUGAAAUGACUAGAUGCAUGUGCAGCCUGAAAAGAGUUCGAAUCGUAAUUAAGUCGCCAGUACA------------------ACGAAUUCGA
.((((((((.....(((((((.((((.((......))...)))))))).))))))))))).(((((((....(((.............))).------------------.))))))).. ( -26.12)
>DroSec_CAF1 67696 102 + 1
AUUUUAGGCGUGGUUGCCAUGGCAUCCUCUGCAGUGCCUAGGUGCAUUUGCAGCCUGAAAAGAGUUCGAAUCGUAAUUAAGUCGCCAUUACA------------------ACGAAUUCGA
.(((((((((.((.(((....))).)).)((((((((......))).))))))))))))).(((((((....(((((.........))))).------------------.))))))).. ( -33.00)
>DroSim_CAF1 59750 102 + 1
AUUUUAGGCGUGGUUGCCAUGGCAUCCUCUGCAGUGACUAGGUGCAUUUGCAGCCUGAAAAGAGUUCGAAUCGUAAUUAAGUCGCCAUUACA------------------ACGAAUUCGA
.(((((((((.((.(((....))).)).)(((((((.(.....))).))))))))))))).(((((((....(((((.........))))).------------------.))))))).. ( -30.20)
>DroEre_CAF1 63242 79 + 1
AUUUUGGACUUGGUUGCCAUGGCAUCCGC-------------UGCAUGUGCAGUCUGAAAAGAGUUCGA----------AGUCGUCAAUGCA------------------ACGAAUUUGA
.((((((((((((.(((....))).))((-------------(((....))))).......))))))))----------))((((.......------------------))))...... ( -23.70)
>DroYak_CAF1 63959 119 + 1
A-UUUGGCCGUGGUUGCCAUGGCAUCCGCUGAAAUGACUAGCUGCAUGUGCAGCCUGAAAAGAGUUCGAACCAUAAUUAAGUCGACAGUACAACGAAAUCAACGAUUUCAACGAAUUCAA
(-(((((((((((...)))))))....((((...(((((.(((((....)))))((....)).................))))).)))).....((((((...))))))..))))).... ( -32.80)
>consensus
AUUUUAGGCGUGGUUGCCAUGGCAUCCUCUGAAAUGACUAGGUGCAUGUGCAGCCUGAAAAGAGUUCGAAUCGUAAUUAAGUCGCCAGUACA__________________ACGAAUUCGA
.((((((((..((.(((....))).))...............(((....))))))))))).(((((((...........................................))))))).. (-21.45 = -21.21 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:00 2006