Locus 7960

Sequence ID	3R_DroMel_CAF1
Location	21,352,944 – 21,353,087
Length	143
Max. P	0.998651

overview

Window 8

Location	21,352,944 – 21,353,055
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	93.77
Mean single sequence MFE	-25.18
Consensus MFE	-22.94
Energy contribution	-22.90
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-2.10
Structure conservation index	0.91
SVM decision value	3.17
SVM RNA-class probability	0.998651
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21352944 111 + 27905053
GGUGCCAAUGCGAUUUGUCACCUACACCUUCUGAAAUACUAUGUAUGUAUGAAUAUAUUUCGCUUUCAUUUUGUUUGGAUCUCUGUUUUGGCUUUCGCGUUGAUCGCACUA
(((((((((((((...((((...(((...(((.(((((..(((...((..(((.....)))))...)))..))))))))....)))..))))..))))))))...))))). ( -28.10)
>DroSec_CAF1 45899 109 + 1
GGUGCCAAUGCGAUUUGUCACCUACACCUUCUGAAAUACUAUGUAUGAAU--AUAUAUUUCGCUUUCAUUUUGUUUGGAUCUCUGUUUUGGCUUUCGCGUUGAUCGCACUA
(((((((((((((...((((...(((......((((((.(((((....))--)))))))))...((((.......))))....)))..))))..))))))))...))))). ( -27.80)
>DroSim_CAF1 43153 109 + 1
GGUGCCAAUGCUAUUUGUCACCUACACCUUCUGAAAUACUAUGUAUGAAU--AUAUAUUUCGCUUUCAUUUUGUUUGGAUCUCUGUUUUGGCUUUCGCGUUGAUCGCACUA
(((((((((((.....((((...(((......((((((.(((((....))--)))))))))...((((.......))))....)))..))))....))))))...))))). ( -22.40)
>DroEre_CAF1 45158 103 + 1
GGUGCCAAUGCGAUUUGUCACCUACACCUUCUGAAAUACUAUGUA--------UAUAAUUCGCGUUCAUUUUGUUUGGAUCUCUGUUUUGGCUUUCGCGUUGAUCGUACUA
(((((((((((((...((((...(((...((..((.....((((.--------........))))........))..))....)))..))))..))))))))...))))). ( -23.32)
>DroYak_CAF1 45336 103 + 1
GGUGCCAAUGCGAUUUGUCACCUACACCUUCUGAAAUACUAUGUA--------UAUAUUUCGCUUUCAUUUUGUUUGGAUCUCUGUUUUGGCAUUCGCGUUGAUCGUACUA
(((((((((((((..(((((...(((...(((.(((((..(((..--------.............)))..))))))))....)))..))))).))))))))...))))). ( -24.26)
>consensus
GGUGCCAAUGCGAUUUGUCACCUACACCUUCUGAAAUACUAUGUAUG_AU__AUAUAUUUCGCUUUCAUUUUGUUUGGAUCUCUGUUUUGGCUUUCGCGUUGAUCGCACUA
(((((((((((((...((((...(((...(((.(((((..(((.......................)))..))))))))....)))..))))..))))))))...))))). (-22.94 = -22.90 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	21,352,979 – 21,353,087
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	93.60
Mean single sequence MFE	-18.38
Consensus MFE	-17.60
Energy contribution	-17.80
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.24
Structure conservation index	0.96
SVM decision value	0.83
SVM RNA-class probability	0.862275
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21352979 108 - 27905053
GUGGCUAUUGCAAAAACAUUUUGCACAGCUUUUAGUGCGAUCAACGCGAAAGCCAAAACAGAGAUCCAAACAAAAUGAAAGCGAAAUAUAUUCAUACAUACAUAGUAU
...(((((((((((.....))))))..(((((((.((.((((...((....))(......).)))))).......)))))))...................))))).. ( -20.60)
>DroSec_CAF1 45934 106 - 1
GUGGCUAUUGCAAAAACAUUUUGCACAGCUUUUAGUGCGAUCAACGCGAAAGCCAAAACAGAGAUCCAAACAAAAUGAAAGCGAAAUAUAU--AUUCAUACAUAGUAU
...(((((((((((.....))))))..(((((((.((.((((...((....))(......).)))))).......))))))).........--........))))).. ( -20.60)
>DroSim_CAF1 43188 106 - 1
GUGGCUAUUGCAAAAACAUUUUGCACAGCUUUUAGUGCGAUCAACGCGAAAGCCAAAACAGAGAUCCAAACAAAAUGAAAGCGAAAUAUAU--AUUCAUACAUAGUAU
...(((((((((((.....))))))..(((((((.((.((((...((....))(......).)))))).......))))))).........--........))))).. ( -20.60)
>DroEre_CAF1 45193 100 - 1
GUGGCUAUUGCAAAAACAUUUUGCACAGCUUUUAGUACGAUCAACGCGAAAGCCAAAACAGAGAUCCAAACAAAAUGAACGCGAAUUAUA--------UACAUAGUAU
((((((..((((((.....)))))).))).........((((...((....))(......).)))).............)))........--------.......... ( -15.80)
>DroYak_CAF1 45371 100 - 1
GUGGCUAUUGCAAAAACAUUUUGCACGGCUUUUAGUACGAUCAACGCGAAUGCCAAAACAGAGAUCCAAACAAAAUGAAAGCGAAAUAUA--------UACAUAGUAU
...(((((((((((.....))))))..(((((((....((((...((....))(......).)))).........)))))))........--------...))))).. ( -14.32)
>consensus
GUGGCUAUUGCAAAAACAUUUUGCACAGCUUUUAGUGCGAUCAACGCGAAAGCCAAAACAGAGAUCCAAACAAAAUGAAAGCGAAAUAUAU__AU_CAUACAUAGUAU
...(((((((((((.....))))))..(((((((((..((((...((....))(......).))))...))....)))))))...................))))).. (-17.60 = -17.80 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:03 2006