Locus 4509

Sequence ID	2L_DroMel_CAF1
Location	12,926,663 – 12,926,782
Length	119
Max. P	0.870246

overview

Window 2

Location	12,926,663 – 12,926,782
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.23
Mean single sequence MFE	-39.82
Consensus MFE	-23.67
Energy contribution	-24.90
Covariance contribution	1.23
Combinations/Pair	1.24
Mean z-score	-2.39
Structure conservation index	0.59
SVM decision value	0.62
SVM RNA-class probability	0.803519
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12926663 119 + 22407834
UCUCCCUGCCCCUGCAGAAAGACAUUCAGGGCAGGAUCGUAAUGGCAAAGCAAGG-UAUUCACUCCUGGACCGCCAUGGAGCGCACAAUGGCCAUACAGAUCCAUCCCGAUGUCUCCAUC
.....((((....))))..(((((((..(((..(((((...(((((....((..(-(...(.(((((((....))).)))).).))..)))))))...)))))..))))))))))..... ( -38.20)
>DroSec_CAF1 105841 119 + 1
UCUCGCUGCCCCUGCAGAAACACAUUCAGGGCAGGAUCAUAAUGGCCAAGCAAGG-UAUUCACUCCUGGACCGCCAUGGAGCGCACAAUGGCCAUACAGAUCCAUCCCGAUGUCUCCAUC
.....((((....))))....(((((..(((..(((((...(((((((.((...(-....).(((((((....))).)))).))....)))))))...)))))..))))))))....... ( -36.50)
>DroSim_CAF1 109850 119 + 1
UCUCGCUGCCCCUGCAGAAAGACAUUCAGGGCAGGAUCAUAAUGGCCAAGCAAGG-UAUUCACUCCUGGACCGCCAUGGAGCGCAGAAUGGCCAUACAGAUCCAUCCCGAUGUCUCCAUC
.....((((....))))..(((((((..(((..(((((...(((((((..(...(-(.....(((((((....))).)))).)).)..)))))))...)))))..))))))))))..... ( -41.20)
>DroEre_CAF1 113012 119 + 1
UCUCGCUGCCCCUGCAGAAGCACAUUCAGGGCAGGAUUAUAAUGGCCAAUCAAGG-UGUUCACUCCUGGACCGCCUUGGAGCGCACAAUGGCCAUCCAAAUCCAUCCCGAUGUCUCCAUC
.....((((....)))).((.(((((..(((..(((((...(((((((.((((((-((((((....)))).)))))))).(....)..)))))))...)))))..))))))))))..... ( -38.20)
>DroYak_CAF1 108210 119 + 1
UUUCGCUGCCCCUGCAGAAAAACAUUCAGGGCAAGAUCGUAAUGGCCAGGCAAGG-CAUUCACUCCUGGACAGCCAUGGAGCGCACAAUGGCCAUACAGAUCCAUCCCGAUGUCUCCAUC
(((..((((....))))..)))......(((...((((...(((((((.((..(.-....).(((((((....))).)))).))....)))))))...))))...)))((((....)))) ( -36.30)
>DroAna_CAF1 126287 113 + 1
UAUCAGAGCAGUUGCAAAGGGUAAUCCAAAACAGGAUUA-----GCCAGGCCGGGGCGCGGAGUUU--UAGCGUUUUGGACCGCAGCAUGACCAUCCAGGUGCACCCGGAUGUCAGCAUC
.......((.(((((...((.((((((......))))))-----.)).(((((((((((.......--..))))))))).))))))).((((.((((.((....)).))))))))))... ( -48.50)
>consensus
UCUCGCUGCCCCUGCAGAAAGACAUUCAGGGCAGGAUCAUAAUGGCCAAGCAAGG_UAUUCACUCCUGGACCGCCAUGGAGCGCACAAUGGCCAUACAGAUCCAUCCCGAUGUCUCCAUC
.....((((....))))...........(((..(((((...(((((((.((((.....))..(((((((....))).)))).))....)))))))...)))))..)))((((....)))) (-23.67 = -24.90 +   1.23)

alignment

secondary structure

dotplot

Window 3

Location	12,926,663 – 12,926,782
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.23
Mean single sequence MFE	-46.25
Consensus MFE	-32.58
Energy contribution	-34.53
Covariance contribution	1.95
Combinations/Pair	1.26
Mean z-score	-2.22
Structure conservation index	0.70
SVM decision value	0.87
SVM RNA-class probability	0.870246
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12926663 119 - 22407834
GAUGGAGACAUCGGGAUGGAUCUGUAUGGCCAUUGUGCGCUCCAUGGCGGUCCAGGAGUGAAUA-CCUUGCUUUGCCAUUACGAUCCUGCCCUGAAUGUCUUUCUGCAGGGGCAGGGAGA
((((....))))(((..(((((.(((((((((..(((((((((.(((....)))))))))..))-)..))....)))).))))))))..)))......(((..((((....))))..))) ( -50.00)
>DroSec_CAF1 105841 119 - 1
GAUGGAGACAUCGGGAUGGAUCUGUAUGGCCAUUGUGCGCUCCAUGGCGGUCCAGGAGUGAAUA-CCUUGCUUGGCCAUUAUGAUCCUGCCCUGAAUGUGUUUCUGCAGGGGCAGCGAGA
((((....)))).....(((((...(((((((..(((((((((.(((....)))))))))..))-)......)))))))...)))))((((((...(((......)))))))))...... ( -47.70)
>DroSim_CAF1 109850 119 - 1
GAUGGAGACAUCGGGAUGGAUCUGUAUGGCCAUUCUGCGCUCCAUGGCGGUCCAGGAGUGAAUA-CCUUGCUUGGCCAUUAUGAUCCUGCCCUGAAUGUCUUUCUGCAGGGGCAGCGAGA
((((....))))(((..(((((...(((((((..(..((((((.(((....)))))))))....-....)..)))))))...)))))..)))......((((.((((....)))).)))) ( -50.60)
>DroEre_CAF1 113012 119 - 1
GAUGGAGACAUCGGGAUGGAUUUGGAUGGCCAUUGUGCGCUCCAAGGCGGUCCAGGAGUGAACA-CCUUGAUUGGCCAUUAUAAUCCUGCCCUGAAUGUGCUUCUGCAGGGGCAGCGAGA
((((....))))(((..(((((..((((((((.....((((....))))(((.(((.(....).-))).)))))))))))..)))))..)))......((((((....))))))...... ( -46.80)
>DroYak_CAF1 108210 119 - 1
GAUGGAGACAUCGGGAUGGAUCUGUAUGGCCAUUGUGCGCUCCAUGGCUGUCCAGGAGUGAAUG-CCUUGCCUGGCCAUUACGAUCUUGCCCUGAAUGUUUUUCUGCAGGGGCAGCGAAA
((((....))))(((..(((((.(((((((((.....((((((.(((....)))))))))...(-(...)).)))))).))))))))..)))......((((.((((....)))).)))) ( -45.90)
>DroAna_CAF1 126287 113 - 1
GAUGCUGACAUCCGGGUGCACCUGGAUGGUCAUGCUGCGGUCCAAAACGCUA--AAACUCCGCGCCCCGGCCUGGC-----UAAUCCUGUUUUGGAUUACCCUUUGCAACUGCUCUGAUA
...(((((((((((((....))))))).)))).))(((((((.....(((..--.......)))....)))).((.-----((((((......)))))).))...)))............ ( -36.50)
>consensus
GAUGGAGACAUCGGGAUGGAUCUGUAUGGCCAUUGUGCGCUCCAUGGCGGUCCAGGAGUGAAUA_CCUUGCUUGGCCAUUAUGAUCCUGCCCUGAAUGUCUUUCUGCAGGGGCAGCGAGA
((((....))))(((..(((((...(((((((.(((.((((((.(((....))))))))).)))........)))))))...)))))..)))...........((((....))))..... (-32.58 = -34.53 +   1.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:32 2006