Locus 2729

Sequence ID	2R_DroMel_CAF1
Location	9,558,687 – 9,558,814
Length	127
Max. P	0.897724

overview

Window 3

Location	9,558,687 – 9,558,784
Length	97
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	80.72
Mean single sequence MFE	-21.52
Consensus MFE	-13.86
Energy contribution	-14.78
Covariance contribution	0.92
Combinations/Pair	1.15
Mean z-score	-1.82
Structure conservation index	0.64
SVM decision value	0.36
SVM RNA-class probability	0.704283
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9558687 97 - 20766785
AAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGUACAAAAAUUAGCUUGUUUUAGUUUUACAU------------GCCAAAAGAUGCAAAGUAU
.........((((((((.(((((((.((((((........))))))..........))))))).....)))))))).(------------((........)))...... ( -21.00)
>DroSec_CAF1 35255 109 - 1
AAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGUAGAGAAAUUAGAGUGUUUUAGUUUUACAUAAAAAUUUACACACCAAAAGAUUCAAAGUAU
.......((((..........(((..((((((........))))))..)))..........((((...((((((.....)))))).))))))))............... ( -20.90)
>DroSim_CAF1 35098 109 - 1
AAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGUAGAAAAAUUAGAGUGUUUUAGUUUUACAUACAAAUUUACACACCAAAAGGUACAAAGUAU
.........((((((((....(((..((((((........))))))..))).(((((......)))))))))))))..............(((....)))......... ( -20.80)
>DroEre_CAF1 37491 106 - 1
AAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAGGGUGCACGGUGAAAAAUCAACAUGGAUUAGUUGCACAUAAAGGUGAACAUACCAAA--AAAC-AUAUAC
.((((((((...........(((...(((((((......))))))).)))..........)))))))).(((.(((......))))))........--....-...... ( -24.80)
>DroYak_CAF1 36673 108 - 1
AAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGGUGGAAAAUCAACUUGGUUUGGAUUUACAUAAAAAUGAACAUAGCAUAGAAAAC-AAGUAU
...(((((.(((((..(..((((((.((((((........)))))).(((.....)))...))))))..).)))))......)))))...............-...... ( -20.10)
>consensus
AAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGUAGAAAAAUUAGCGUGUUUUAGUUUUACAUAAAAAUGAACACACCAAAAGAUACAAAGUAU
.........((((((((.((((....((((((........))))))....((....)).....)))).))))))))................................. (-13.86 = -14.78 +   0.92)

alignment

secondary structure

dotplot

Window 4

Location	9,558,715 – 9,558,814
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	93.13
Mean single sequence MFE	-20.68
Consensus MFE	-18.34
Energy contribution	-18.10
Covariance contribution	-0.24
Combinations/Pair	1.11
Mean z-score	-1.20
Structure conservation index	0.89
SVM decision value	0.19
SVM RNA-class probability	0.624513
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9558715 99 + 20766785
UAAAACAAGCUAAUUUUUGUACGUGCACCUUUUCCUGGGCGCAUUUAGCUCAAGUUUUACCAUGAAUUUCGUUCAUGCAUUAACCCUCGGUUGCCUGAG
((((((.((((((.........((((.(((......))).))))))))))...)))))).(((((((...)))))))........(((((....))))) ( -23.10)
>DroSec_CAF1 35295 99 + 1
UAAAACACUCUAAUUUCUCUACGUGCACCUUUUCCUGGGCGCAUUUAGCUCAAGUUUUACCAUGAAUUUCGUUCAUGCAUUAACCCUCGGUUGCCUGAG
..................(((.((((.(((......))).)))).))).....(((....(((((((...)))))))....))).(((((....))))) ( -19.60)
>DroSim_CAF1 35138 99 + 1
UAAAACACUCUAAUUUUUCUACGUGCACCUUUUCCUGGGCGCAUUUAGCUCAAGUUUUACCAUGAAUUUCGUUCAUGCAUUAACCCUCGGUUGCCUGAG
..................(((.((((.(((......))).)))).))).....(((....(((((((...)))))))....))).(((((....))))) ( -19.60)
>DroEre_CAF1 37528 99 + 1
UAAUCCAUGUUGAUUUUUCACCGUGCACCCUUUCCUGGGCGCAUUUAGCUCAAGUUUUACCAUGAAUUUCGUUCAUGCAUUAACCCUCGGUUGCCUGAG
((((.((((.(((...((((..((((.(((......))).))))..(((....)))......))))..)))..)))).))))...(((((....))))) ( -21.50)
>DroYak_CAF1 36712 99 + 1
CAAACCAAGUUGAUUUUCCACCGUGCACCUUUUCCUGGGCGCAUUUAGCUCAAGUUUUACCAUGAAUUUCGUUCAUGCAUUAACCCUCGGUUGCCUGAG
..((((.((((((.........((((.(((......))).))))))))))...(((....(((((((...)))))))....)))....))))....... ( -19.60)
>consensus
UAAAACAAGCUAAUUUUUCUACGUGCACCUUUUCCUGGGCGCAUUUAGCUCAAGUUUUACCAUGAAUUUCGUUCAUGCAUUAACCCUCGGUUGCCUGAG
........(((((.........((((.(((......))).)))))))))....(((....(((((((...)))))))....))).(((((....))))) (-18.34 = -18.10 +  -0.24)

alignment

secondary structure

dotplot

Window 5

Location	9,558,715 – 9,558,814
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	93.13
Mean single sequence MFE	-25.00
Consensus MFE	-20.98
Energy contribution	-20.98
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.84
SVM decision value	1.00
SVM RNA-class probability	0.897724
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9558715 99 - 20766785
CUCAGGCAACCGAGGGUUAAUGCAUGAACGAAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGUACAAAAAUUAGCUUGUUUUA
..(((((...((((..(((...((((((.....)))))).)))..)))).......((((((........)))))).............)))))..... ( -24.90)
>DroSec_CAF1 35295 99 - 1
CUCAGGCAACCGAGGGUUAAUGCAUGAACGAAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGUAGAGAAAUUAGAGUGUUUUA
(((.......((((..(((...((((((.....)))))).)))..))))..(((..((((((........))))))..)))........)))....... ( -24.20)
>DroSim_CAF1 35138 99 - 1
CUCAGGCAACCGAGGGUUAAUGCAUGAACGAAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGUAGAAAAAUUAGAGUGUUUUA
(((.......((((..(((...((((((.....)))))).)))..))))..(((..((((((........))))))..)))........)))....... ( -24.20)
>DroEre_CAF1 37528 99 - 1
CUCAGGCAACCGAGGGUUAAUGCAUGAACGAAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAGGGUGCACGGUGAAAAAUCAACAUGGAUUA
.((((((...((((..(((...((((((.....)))))).)))..)))).)))...(((((((......)))))))...)))..((((......)))). ( -26.30)
>DroYak_CAF1 36712 99 - 1
CUCAGGCAACCGAGGGUUAAUGCAUGAACGAAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGGUGGAAAAUCAACUUGGUUUG
.......(((((((((((....((((((.....))))))....))))(((.(((..((((((........))))))...)))....))).))))))).. ( -25.40)
>consensus
CUCAGGCAACCGAGGGUUAAUGCAUGAACGAAAUUCAUGGUAAAACUUGAGCUAAAUGCGCCCAGGAAAAGGUGCACGUAGAAAAAUUAGCGUGUUUUA
....(((...((((..(((...((((((.....)))))).)))..)))).)))...((((((........))))))....................... (-20.98 = -20.98 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:01 2006