Locus 2839

Sequence ID	2R_DroMel_CAF1
Location	9,834,598 – 9,834,700
Length	102
Max. P	0.857213

overview

Window 3

Location	9,834,598 – 9,834,700
Length	102
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	96.56
Mean single sequence MFE	-37.32
Consensus MFE	-29.57
Energy contribution	-32.41
Covariance contribution	2.84
Combinations/Pair	1.04
Mean z-score	-2.24
Structure conservation index	0.79
SVM decision value	0.81
SVM RNA-class probability	0.857213
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9834598 102 + 20766785
GGUCAACAGCAAGAAACGGUGACGGAGACGAAAGAGACUCG--UUCCCAUUGCCG-GAGAUUCAUUCGUCUGGCGGCUGUU-UUGGCCAAAAGUGGCCGCAAACAU
........((..((((((((...((..((((.......)))--)..))..(((((-((((.....)).)))))))))))))-))(((((....)))))))...... ( -37.60)
>DroSec_CAF1 72010 105 + 1
GGUCAACAGCAAGAAACGGUGACGGAGACGAAAGAGACUCGUGUUCCCAUUGCCG-GAGAUUCAUUCGUCUGGCGGCUGUUUUUGGCCAAAAGUGGCCGCAAACAU
........((.(((((((((...((((((((.......)))).))))...(((((-((((.....)).))))))))))))))))(((((....)))))))...... ( -36.80)
>DroSim_CAF1 73844 105 + 1
GGUCAACAGCAAGAAACGGUGACGGAGACGAAAGAGACUCGUGUUCCCAUUGCCG-GAGAUUCAUUCGUCUGGCGGCUGUUUUUGGCCAAAAGUGGCCGCAAACAU
........((.(((((((((...((((((((.......)))).))))...(((((-((((.....)).))))))))))))))))(((((....)))))))...... ( -36.80)
>DroEre_CAF1 76973 103 + 1
GGUCAACAGCAAGAAACGGUGACGGAGACGAGAGAGACUCG--UUCCCAUUGCCGGGAGAUUCAUUCGUCUGGUGGCUGUU-UUGGCCAAAAGUGGCCGCUAACAU
.......(((..((((((((...((..(((((.....))))--)..))...(((((..((.....))..))))).))))))-))(((((....))))))))..... ( -39.50)
>DroYak_CAF1 74483 102 + 1
GGUCAACAGCAAGAAACGGUGACGGAGACGAAAGAGACUCG--UUCCCAUUGCCG-GAGAUUCAUUCGUCUGGUGGCUGUU-UUGGCCAAAAGUGGCCGCAAACAU
(((((.((((......(((..(.((..((((.......)))--)..)).)..)))-..((.....))).))).)))))(((-(((((((....)))))).)))).. ( -35.90)
>consensus
GGUCAACAGCAAGAAACGGUGACGGAGACGAAAGAGACUCG__UUCCCAUUGCCG_GAGAUUCAUUCGUCUGGCGGCUGUU_UUGGCCAAAAGUGGCCGCAAACAU
....((((((......((....)).(((((((.(((.(((................))).))).)))))))....))))))...(((((....)))))........ (-29.57 = -32.41 +   2.84)

alignment

secondary structure

dotplot

Window 4

Location	9,834,598 – 9,834,700
Length	102
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	96.56
Mean single sequence MFE	-31.96
Consensus MFE	-26.06
Energy contribution	-25.90
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.68
Structure conservation index	0.82
SVM decision value	0.27
SVM RNA-class probability	0.662521
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9834598 102 - 20766785
AUGUUUGCGGCCACUUUUGGCCAA-AACAGCCGCCAGACGAAUGAAUCUC-CGGCAAUGGGAA--CGAGUCUCUUUCGUCUCCGUCACCGUUUCUUGCUGUUGACC
........(((((....)))))..-((((((.(((.((.((.....))))-.))).((((..(--((((.....)))))..))))...........)))))).... ( -32.40)
>DroSec_CAF1 72010 105 - 1
AUGUUUGCGGCCACUUUUGGCCAAAAACAGCCGCCAGACGAAUGAAUCUC-CGGCAAUGGGAACACGAGUCUCUUUCGUCUCCGUCACCGUUUCUUGCUGUUGACC
........(((((....)))))...((((((.(((.((.((.....))))-.)))(((((..(((((((.....)))))....))..)))))....)))))).... ( -30.60)
>DroSim_CAF1 73844 105 - 1
AUGUUUGCGGCCACUUUUGGCCAAAAACAGCCGCCAGACGAAUGAAUCUC-CGGCAAUGGGAACACGAGUCUCUUUCGUCUCCGUCACCGUUUCUUGCUGUUGACC
........(((((....)))))...((((((.(((.((.((.....))))-.)))(((((..(((((((.....)))))....))..)))))....)))))).... ( -30.60)
>DroEre_CAF1 76973 103 - 1
AUGUUAGCGGCCACUUUUGGCCAA-AACAGCCACCAGACGAAUGAAUCUCCCGGCAAUGGGAA--CGAGUCUCUCUCGUCUCCGUCACCGUUUCUUGCUGUUGACC
..(((((((((..((..((((...-....))))..))..............(((..((((..(--((((.....)))))..))))..)))......))))))))). ( -34.00)
>DroYak_CAF1 74483 102 - 1
AUGUUUGCGGCCACUUUUGGCCAA-AACAGCCACCAGACGAAUGAAUCUC-CGGCAAUGGGAA--CGAGUCUCUUUCGUCUCCGUCACCGUUUCUUGCUGUUGACC
.(((((..(((((....))))).)-))))..((.(((.(((..(((....-(((..((((..(--((((.....)))))..))))..))).))))))))).))... ( -32.20)
>consensus
AUGUUUGCGGCCACUUUUGGCCAA_AACAGCCGCCAGACGAAUGAAUCUC_CGGCAAUGGGAA__CGAGUCUCUUUCGUCUCCGUCACCGUUUCUUGCUGUUGACC
........(((((....)))))...((((((....((((((.....))....((..((((((...((((.....)))))).))))..))))))...)))))).... (-26.06 = -25.90 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:47 2006