Locus 2167

Sequence ID	X_DroMel_CAF1
Location	5,876,035 – 5,876,261
Length	226
Max. P	0.697745

overview

Window 9

Location	5,876,035 – 5,876,143
Length	108
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	82.11
Mean single sequence MFE	-36.48
Consensus MFE	-23.77
Energy contribution	-25.90
Covariance contribution	2.13
Combinations/Pair	1.14
Mean z-score	-1.81
Structure conservation index	0.65
SVM decision value	0.31
SVM RNA-class probability	0.681267
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5876035 108 + 22224390
GCGCCCACAAGAUCGCCAGAUUCCUGCCAAUAAGGAAUUGCAUUUGUGCGCAGCGCACUGCGAUGGCGAAUGAGUUGGCCAA--AACCGGUUGCCGCACUUGGUUAACUU
.((((((((((...((..(((((((.......))))))))).))))))(((((....)))))..))))...(((((((((((--...(((...)))...))))))))))) ( -39.10)
>DroSec_CAF1 80817 108 + 1
GCGCCCACAAGAUCGCCAGAUUCCUGCCAAUAAGGAUUUGCAUUUGUGCGCAGCGCACUGCGAUGGCGAAUGAGUUGGGCAA--AACCGGUUGCCGCACUUGGUUAACUU
..((((((..(.((((((...((((.......)))).(((((...(((((...)))))))))))))))).)..).)))))..--....((((((((....))).))))). ( -36.30)
>DroSim_CAF1 83507 108 + 1
GCGCCCGCAAGAUCGCCAGAUUCCUGCCAAUAAGGAUUUGCAUUUGUGCGCAGCGCACUGCGAUGGCGAAUGAGUUGGCCAA--AACCGGUUGCCGCACUUGGUUAACUU
.(((((....)((((((((((.(((.......)))))))).....(((((...))))).)))))))))...(((((((((((--...(((...)))...))))))))))) ( -38.40)
>DroYak_CAF1 86748 88 + 1
GCGCCCACAAGUUGGCCAGAUUCCUGCCAACAAGGAUCUGCAUUCGCGC------------CAU------GGAGUUGGCCAAAAAACCGGUUA----ACUUGGCCAGCUU
((((......((((((.((....))))))))..((((....))))))))------------...------.(((((((((((...........----..))))))))))) ( -32.12)
>consensus
GCGCCCACAAGAUCGCCAGAUUCCUGCCAAUAAGGAUUUGCAUUUGUGCGCAGCGCACUGCGAUGGCGAAUGAGUUGGCCAA__AACCGGUUGCCGCACUUGGUUAACUU
.((((((((((...((.((((.(((.......))))))))).))))))(((((....)))))..))))...(((((((((((.....((.....))...))))))))))) (-23.77 = -25.90 +   2.13)

alignment

secondary structure

dotplot

Window 0

Location	5,876,143 – 5,876,261
Length	118
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	70.88
Mean single sequence MFE	-28.52
Consensus MFE	-13.76
Energy contribution	-14.82
Covariance contribution	1.06
Combinations/Pair	1.19
Mean z-score	-1.92
Structure conservation index	0.48
SVM decision value	0.34
SVM RNA-class probability	0.697745
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5876143 118 - 22224390
UUUAAUGUCCAAUGUCCACUUUAAUCGUAGUGUAAAAUGAAAAGUUUAACUUGACUUAGUGACUUAGUGACUCAUGCGCGGGGUUUGUGGUUAGACUUUCGUGUGGCGCAAGCUGGAA
.......(((......((((........))))....((((((.((((((((.((((..(((.....(((...))).)))..))))...))))))))))))))..(((....)))))). ( -29.40)
>DroSec_CAF1 80925 93 - 1
U--------------------UAAGCGUAGUGUAAAAUGAAAAGUUUAACUUGGCUUGGGGAC---GUGACUCAUGCCCG--GUUUGUGGUUAGACUUUCGUGUGGCGCAAGCUGGAA
.--------------------..(((...((((...((((((.((((((((.((((..(((.(---(((...))))))))--)))...))))))))))))))...))))..))).... ( -30.40)
>DroSim_CAF1 83615 93 - 1
U--------------------UAAGCGUAGUGUAAAAUGAAAAGUUUAACUUGGCUUGGUGAC---AUGACUCAUGCCCG--GUUUGUGGUUAGACUUUCGUGUGGCGCAAGCUGGAA
.--------------------..(((...((((...((((((.((((((((.((((.((.(.(---(((...))))))))--)))...))))))))))))))...))))..))).... ( -27.90)
>DroYak_CAF1 86836 99 - 1
UUUAUGACUCCAUAUUUACUAGAAUUCUAGUGUAAAACUAAAAGUUUAACC----------AU---AUGACGCAUG------UUUUGUGCUUAGACUUUCGAGUGGCGCAAGCUGGAA
........(((.....((((((....))))))....(((.(((((((((.(----------((---(.(((....)------)).)))).)))))))))..)))(((....)))))). ( -26.40)
>consensus
U____________________UAAGCGUAGUGUAAAAUGAAAAGUUUAACUUGGCUUGGUGAC___AUGACUCAUGCCCG__GUUUGUGGUUAGACUUUCGUGUGGCGCAAGCUGGAA
.............................((((...((((((.((((((((.(((...(((.....(((...))).)))...)))...))))))))))))))...))))......... (-13.76 = -14.82 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:42 2006