Locus 4278

Sequence ID	X_DroMel_CAF1
Location	11,248,965 – 11,249,111
Length	146
Max. P	0.993814

overview

Window 2

Location	11,248,965 – 11,249,085
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.44
Mean single sequence MFE	-24.37
Consensus MFE	-22.88
Energy contribution	-22.96
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.74
Structure conservation index	0.94
SVM decision value	2.43
SVM RNA-class probability	0.993814
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11248965 120 + 22224390
CCCAAAAAAACACACCCACUCACCUCGUCGACACACGUCUCUCUAUAUAUGUAGGUAUAUAGAGUACUAGAUCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAAUGCUUGCAU
.........................(((((((....((..((((((((((....)))))))))).)).(((((((((.......)))))))))))))))).....(((((.....))))) ( -23.60)
>DroSec_CAF1 8398 118 + 1
CCCAAA--AACACACCCACUCACCUCGUCGACACACGUCUCUCUAUAUAUGUAGGUAUAUAGAGUUCUAGACCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAAUGCUUGUAU
......--...(((..((..((...(((((((........((((((((((....))))))))))....(((((((((.......))))))))))))))))......))...))..))).. ( -24.60)
>DroSim_CAF1 9055 118 + 1
CCCAAA--AACACACCCACUCACCUCGUCGACACACGUCUCUCUAUAUAUGCAGGUAUAUAGAGUUCUAGACCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAAUGCUUGUAU
......--...(((..((..((...(((((((........((((((((((....))))))))))....(((((((((.......))))))))))))))))......))...))..))).. ( -24.60)
>DroEre_CAF1 8333 116 + 1
CCCAAU----CACACCUACUCACCUCGUCGACACACGUCUCUCUAUAUGAAUACAUAUAUAGAGUUCUAGACCGAUUCACAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAUUGCUUGUAU
......----......(((......(((((((......((((.((((((....)))))).))))....(((((((((.......)))))))))))))))).......))).......... ( -23.72)
>DroYak_CAF1 8436 117 + 1
CCCAAA-CAACACACCUACUCACCUCGUCGACACACGUCCCUCUAUAUAAAUA--UAUAUAGAGUUCUAGACCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUACUGCUUGUAU
.....(-(((((....(((......(((((((........(((((((((....--)))))))))....(((((((((.......)))))))))))))))).......))).)).)))).. ( -25.32)
>consensus
CCCAAA__AACACACCCACUCACCUCGUCGACACACGUCUCUCUAUAUAUGUAGGUAUAUAGAGUUCUAGACCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAAUGCUUGUAU
.................((......(((((((........((((((((((....))))))))))....(((((((((.......)))))))))))))))).......))........... (-22.88 = -22.96 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	11,249,005 – 11,249,111
Length	106
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	91.47
Mean single sequence MFE	-23.84
Consensus MFE	-21.72
Energy contribution	-21.64
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-1.18
Structure conservation index	0.91
SVM decision value	0.16
SVM RNA-class probability	0.610172
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11249005 106 + 22224390
CUCUAUAUAUGUAGGUAUAUAGAGUACUAGAUCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAAUGCUUGCAUAGU--GUCGUGUCUUUUGCAUGUGCCAC----
((((((((((....))))))))))...((((((((((.......)))))))))).....((...(((((((.....((((...--...))))...))))))).))...---- ( -22.20)
>DroSec_CAF1 8436 108 + 1
CUCUAUAUAUGUAGGUAUAUAGAGUUCUAGACCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAAUGCUUGUAUAGUGUGUCAUGUCUUUUGCAUGUGCCAC----
((((((((((....))))))))))...((((((((((.......))))))))))...((((...((((..(((((.....)))))..))))......)))).......---- ( -24.30)
>DroSim_CAF1 9093 108 + 1
CUCUAUAUAUGCAGGUAUAUAGAGUUCUAGACCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAAUGCUUGUAUAGUGUGUCGUGUCUUUUGCAUGUGCCAC----
.......(((((((((((((((((.((((((((((((.......))))))))))..))....))).))).)))))))))))(((.(((((((.....))))).)))))---- ( -26.20)
>DroEre_CAF1 8369 106 + 1
CUCUAUAUGAAUACAUAUAUAGAGUUCUAGACCGAUUCACAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAUUGCUUGUAUAGU--GUCGUGUCUUUUGCAUGCGCCAC----
...((((((((.((((...(((....)))((((((((.......)))))))).....)))).))))))))...........((--(.(((((.....))))))))...---- ( -22.70)
>DroYak_CAF1 8475 108 + 1
CUCUAUAUAAAUA--UAUAUAGAGUUCUAGACCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUACUGCUUGUAUAGU--GUCGUGUCUUUUGCAUGUGCCACCCUC
(((((((((....--)))))))))...((((((((((.......)))))))))).(((.....)))(((((.....)))))((--(.(((((.....)))))...))).... ( -23.80)
>consensus
CUCUAUAUAUGUAGGUAUAUAGAGUUCUAGACCGAUUCAAAUUCAGUUGGUUUGUUGAUGUUUUCAUGUAAUGCUUGUAUAGU__GUCGUGUCUUUUGCAUGUGCCAC____
((((((((((....))))))))))...((((((((((.......))))))))))...((((...((((....(((.....)))....))))......))))........... (-21.72 = -21.64 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:02 2006