Locus 125

Sequence ID	4_DroMel_CAF1
Location	854,477 – 854,628
Length	151
Max. P	0.985094

overview

Window 1

Location	854,477 – 854,590
Length	113
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	97.64
Mean single sequence MFE	-37.38
Consensus MFE	-36.57
Energy contribution	-36.13
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-2.85
Structure conservation index	0.98
SVM decision value	2.00
SVM RNA-class probability	0.985094
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 854477 113 + 1281640
UGUGUACAACUUGUGUGUGCAACCAAAUCUUUGCAAUCGGUGCAUUGCAGGCUUUGAGUCAAAAGUCAUUCUGUUCCGACUCAAAGUCGUGUGGUCUUAUGCAGCAUAGGUUA
.......(((((((((.((((((((......((((((......))))))(((((((((((...((.....)).....)))))))))))...))))....))))))))))))). ( -37.50)
>DroSec_CAF1 34559 113 + 1
UGUGUACAACUUGUGUGUGCAACCAAAUCUUUGCAAUCGGUGCAUUGCGGGCUUUGAGUCAAAAGUCAUUUUGUUCCGACUCAAAGUCGUGUGGUCUUAUGCAGCAUAGGUUA
.......(((((((((.((((((((......((((((......))))))(((((((((((.................)))))))))))...))))....))))))))))))). ( -35.93)
>DroSim_CAF1 29349 113 + 1
UGUGUACAACUUGUGUGUGCAACCAAAUCUUUGCGAUCGGUGCAUUGCGGGCUUUGAGUCAAAAGUCAUUUUGUUCCGACUCAAAGUCGUUUGGUCUUAUGCAGCAUAGGUUA
.......(((((((((.((((((((((((((((.(.((((.(((.....((((((......))))))....))).))))).)))))..)))))))....))))))))))))). ( -38.70)
>consensus
UGUGUACAACUUGUGUGUGCAACCAAAUCUUUGCAAUCGGUGCAUUGCGGGCUUUGAGUCAAAAGUCAUUUUGUUCCGACUCAAAGUCGUGUGGUCUUAUGCAGCAUAGGUUA
.......(((((((((.((((((((......((((((......))))))(((((((((((.................)))))))))))...))))....))))))))))))). (-36.57 = -36.13 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	854,517 – 854,628
Length	111
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	84.90
Mean single sequence MFE	-32.02
Consensus MFE	-26.86
Energy contribution	-25.66
Covariance contribution	-1.20
Combinations/Pair	1.19
Mean z-score	-1.86
Structure conservation index	0.84
SVM decision value	0.88
SVM RNA-class probability	0.872250
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 854517 111 - 1281640
UCGCUACACAGUGGUGGUAACAUUCCACGUGCGCGGGCUAACCUAUGCUGCAUAAGACCACACGACUUUGAGUCGG------AA-CAGAAUGACUUUUGACUCAAAGCCUGCAAUGCA
..((..(((.((((((....))..))))))).(((((((..(.((((...)))).)...........(((((((((------((-.........))))))))))))))))))...)). ( -32.40)
>DroSec_CAF1 34599 111 - 1
UCGCUACACAGUGGUGGUAACAUUCCACGUGCGCGGGCUAACCUAUGCUGCAUAAGACCACACGACUUUGAGUCGG------AA-CAAAAUGACUUUUGACUCAAAGCCCGCAAUGCA
..((..(((.((((((....))..))))))).(((((((..(.((((...)))).)...........(((((((((------((-.........))))))))))))))))))...)). ( -34.60)
>DroSim_CAF1 29389 111 - 1
UCGCUACACAGUGGUGGUAACAUUCCACGUGCGCGGGCUAACCUAUGCUGCAUAAGACCAAACGACUUUGAGUCGG------AA-CAAAAUGACUUUUGACUCAAAGCCCGCAAUGCA
..((..(((.((((((....))..))))))).(((((((..(.((((...)))).)...........(((((((((------((-.........))))))))))))))))))...)). ( -34.60)
>DroEre_CAF1 34980 97 - 1
UCGCUACACAGUGGUGGUAACAUUCCACGUGCGCGGGCUAACUUAUGC--------------CGACUUUGGGUCGG------AAUCAGAAUGACUUUUGACUCAA-GCCUGCAAUGUA
(((((((...))))))).........((((..(((((((........(--------------((((.....)))))------..((((((....))))))....)-)))))).)))). ( -30.90)
>DroYak_CAF1 36929 103 - 1
UCGCUACACAGUGGUGGUAACAUUCCACGUGCGCGGGUAAACUUAUGC--------------CGACUUUGAGUCGAAAACAAAAUCAGAAUGACUUUUGACUCAA-AUCUGCAAUGUA
((((..(((.((((((....))..))))))).)))).........(((--------------.((.((((((((((((................)))))))))))-))).)))..... ( -27.59)
>consensus
UCGCUACACAGUGGUGGUAACAUUCCACGUGCGCGGGCUAACCUAUGCUGCAUAAGACCA_ACGACUUUGAGUCGG______AA_CAGAAUGACUUUUGACUCAAAGCCUGCAAUGCA
..((..(((.((((((....))..))))))).((((((........................((((.....))))..........(((((....))))).......))))))...)). (-26.86 = -25.66 +  -1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:56 2006