Locus 5398

Sequence ID	2L_DroMel_CAF1
Location	15,389,957 – 15,390,082
Length	125
Max. P	0.874522

overview

Window 9

Location	15,389,957 – 15,390,053
Length	96
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	76.90
Mean single sequence MFE	-22.67
Consensus MFE	-9.22
Energy contribution	-9.38
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.50
Structure conservation index	0.41
SVM decision value	0.89
SVM RNA-class probability	0.874522
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15389957 96 + 22407834
---UGUCUAAAAUGGCCCAAAAGGCAGCCCCCA-AGUCAAAUGACACUAACAACAACAAUAAACUACUGUUGACACAGUGUUUUUGUUGUUAUGGCCGUU
---.......(((((((.....((......)).-.(((....)))......((((((((.((((.(((((....)))))))))))))))))..))))))) ( -26.80)
>DroVir_CAF1 161036 90 + 1
AACUGUCGAGU-UGGCCCAAAAGGCAGCU-CCA-ACUCAAAUGACACUAACAACAACAAUAAACUACUGUAGACAU-------UUGUUGUUGUUGUUGCU
...((((((((-(((.((....)).....-)))-))))....)))).((((((((((((((((....((....)))-------))))))))))))))).. ( -27.00)
>DroWil_CAF1 239542 93 + 1
---UGUCUAAAAUGGCCCAAAAGGCAGUCGCCACAGUCAAAUGACACUAACAACAACAAUAAACUACUGUUGACAU----UUGUUGCUGUUGUUGCUGGA
---.(((......)))(((...(((....)))...(((....)))..((((((((.(((((((....((....)))----)))))).)))))))).))). ( -22.20)
>DroMoj_CAF1 169858 91 + 1
AACUGUCGACUGUGGCCCAAAAGGCAGCU-CCA-AGUCAAAUGACACUAACAACAACAAUAAACUACUGUUGACAU-------UUGUUGUUGCUGUUGUU
.......(((((..((((....))..)).-.).-)))).((..(((.(((((((((.....(((....))).....-------))))))))).)))..)) ( -23.20)
>DroAna_CAF1 142699 87 + 1
---UGUCUAAAAUGGCCCAAAAGGCAGCCCCCA-AGUCAAAUGACACUUAAAACAACAAUAAACUACUGUUGACAUACUGUUUUUGUUUU---------U
---.(((......)))...((((((((......-.(((....)))........(((((.........))))).....)))))))).....---------. ( -13.50)
>DroPer_CAF1 137430 84 + 1
---UGUCGAAAAUGGCCCAAAAGGCAGCCCCCG-AGUCAAAUGACACCAGCAGCAACAAUAAACAAAAGGCGACA-------UUUGUUG---GGGCUG--
---...........(((.....)))((((((..-.(((....)))................((((((.(....).-------)))))))---))))).-- ( -23.30)
>consensus
___UGUCGAAAAUGGCCCAAAAGGCAGCCCCCA_AGUCAAAUGACACUAACAACAACAAUAAACUACUGUUGACAU______UUUGUUGUUGUUGCUG_U
...((((.......(((.....)))..........(((....)))..........................))))......................... ( -9.22 =  -9.38 +   0.17)

alignment

secondary structure

dotplot

Window 0

Location	15,389,992 – 15,390,082
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	89.70
Mean single sequence MFE	-20.12
Consensus MFE	-16.31
Energy contribution	-17.37
Covariance contribution	1.06
Combinations/Pair	1.08
Mean z-score	-2.48
Structure conservation index	0.81
SVM decision value	0.60
SVM RNA-class probability	0.794954
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15389992 90 + 22407834
AAUGACACUAACAACAACAAUAAACUACUGUUGACACAGUGUUUUUGUUGUUAUGGCCGUUGUUGCCAUUUUGCUCUCUAGUCCAUUCAA
...(((......((((((((.((((.(((((....)))))))))))))))))(((((.......)))))...........)))....... ( -21.60)
>DroSec_CAF1 135801 90 + 1
AAUGACACUAACAACAACAAUAAACUACUGUUGACACAGUGUUUUUGUUGUUAUGGCCGUUGUUGCCAUUUUGCUCUCUAGUCCAUUCAA
...(((......((((((((.((((.(((((....)))))))))))))))))(((((.......)))))...........)))....... ( -21.60)
>DroSim_CAF1 140723 90 + 1
AAUGACACUAACAACAACAAUAAACUACUGUUGACACAGUGUUUUUGUUGUUAUGGCCGUAGUUGCCAUUUUGCUCUCUAGUCCAUUCAA
...(((......((((((((.((((.(((((....)))))))))))))))))(((((.......)))))...........)))....... ( -21.60)
>DroEre_CAF1 142132 90 + 1
AAUGACACUAACAACAACAAUAAACUACUGUUGACACAGUGUUUUUGUUGUUAUGGCCGUUGUUGCCAUUUUGCUCCCCAGUCCAUUCAA
...(((......((((((((.((((.(((((....)))))))))))))))))(((((.......)))))...........)))....... ( -21.60)
>DroYak_CAF1 142763 90 + 1
AAUGACACUAACAACAACAAUAAACUACUGUUGACACAGUGUUUUUGUUGUUAUGGCCGUUGUUGCCAUUUGGCUCUCCAGUCCAUUCAA
..(((.......((((((((.((((.(((((....)))))))))))))))))((((.(......(((....)))......).))))))). ( -22.90)
>DroAna_CAF1 142734 81 + 1
AAUGACACUUAAAACAACAAUAAACUACUGUUGACAUACUGUUUUUGUUUU---------UGUUGCCAUUUGGCUCUUACGUUCGAAUAC
...(((......(((((.((((((..((.((......)).)).)))))).)---------))))(((....)))......)))....... ( -11.40)
>consensus
AAUGACACUAACAACAACAAUAAACUACUGUUGACACAGUGUUUUUGUUGUUAUGGCCGUUGUUGCCAUUUUGCUCUCUAGUCCAUUCAA
...(((......((((((((.((((.(((((....)))))))))))))))))(((((.......)))))...........)))....... (-16.31 = -17.37 +   1.06)

alignment

secondary structure

dotplot

Window 1

Location	15,389,992 – 15,390,082
Length	90
Sequences	6
Columns	90
Reading direction	reverse
Mean pairwise identity	89.70
Mean single sequence MFE	-24.40
Consensus MFE	-19.30
Energy contribution	-20.75
Covariance contribution	1.45
Combinations/Pair	1.12
Mean z-score	-3.05
Structure conservation index	0.79
SVM decision value	0.84
SVM RNA-class probability	0.864684
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15389992 90 - 22407834
UUGAAUGGACUAGAGAGCAAAAUGGCAACAACGGCCAUAACAACAAAAACACUGUGUCAACAGUAGUUUAUUGUUGUUGUUAGUGUCAUU
...((((((((((........(((((.......)))))(((((((((((((((((....))))).)))).)))))))).))))).))))) ( -26.50)
>DroSec_CAF1 135801 90 - 1
UUGAAUGGACUAGAGAGCAAAAUGGCAACAACGGCCAUAACAACAAAAACACUGUGUCAACAGUAGUUUAUUGUUGUUGUUAGUGUCAUU
...((((((((((........(((((.......)))))(((((((((((((((((....))))).)))).)))))))).))))).))))) ( -26.50)
>DroSim_CAF1 140723 90 - 1
UUGAAUGGACUAGAGAGCAAAAUGGCAACUACGGCCAUAACAACAAAAACACUGUGUCAACAGUAGUUUAUUGUUGUUGUUAGUGUCAUU
...((((((((((........(((((.......)))))(((((((((((((((((....))))).)))).)))))))).))))).))))) ( -26.50)
>DroEre_CAF1 142132 90 - 1
UUGAAUGGACUGGGGAGCAAAAUGGCAACAACGGCCAUAACAACAAAAACACUGUGUCAACAGUAGUUUAUUGUUGUUGUUAGUGUCAUU
...((((((((((........(((((.......)))))(((((((((((((((((....))))).)))).)))))))).))))).))))) ( -26.10)
>DroYak_CAF1 142763 90 - 1
UUGAAUGGACUGGAGAGCCAAAUGGCAACAACGGCCAUAACAACAAAAACACUGUGUCAACAGUAGUUUAUUGUUGUUGUUAGUGUCAUU
...(((((((((..(.(((...((....))..))))(((((((((((((((((((....))))).)))).)))))))))))))).))))) ( -28.10)
>DroAna_CAF1 142734 81 - 1
GUAUUCGAACGUAAGAGCCAAAUGGCAACA---------AAAACAAAAACAGUAUGUCAACAGUAGUUUAUUGUUGUUUUAAGUGUCAUU
.........(....).....(((((((...---------((((((...((((((....(((....)))))))))))))))...))))))) ( -12.70)
>consensus
UUGAAUGGACUAGAGAGCAAAAUGGCAACAACGGCCAUAACAACAAAAACACUGUGUCAACAGUAGUUUAUUGUUGUUGUUAGUGUCAUU
...((((((((((........(((((.......)))))(((((((((((((((((....))))).)))).)))))))).))))).))))) (-19.30 = -20.75 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:12 2006