Locus 7544

Sequence ID	3R_DroMel_CAF1
Location	20,208,206 – 20,208,358
Length	152
Max. P	0.984117

overview

Window 5

Location	20,208,206 – 20,208,303
Length	97
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	81.79
Mean single sequence MFE	-23.35
Consensus MFE	-17.33
Energy contribution	-18.17
Covariance contribution	0.83
Combinations/Pair	1.16
Mean z-score	-2.56
Structure conservation index	0.74
SVM decision value	1.03
SVM RNA-class probability	0.903939
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20208206 97 - 27905053
UGCGUGUGGCAAUCAGCGACAUGCAUUUAAUUGGCAUUUUUAUUAAACAGCUGAAAAUGAGCAGUUGGGAAAAGGCAGCGAACAAA--------AAACCAAAAAA
(((((((.((.....)).)))))))........((.(((((......((((((........)))))).))))).))..........--------........... ( -22.90)
>DroSec_CAF1 19473 97 - 1
UGCGUGUGGCAAUCAGCGACAUGCAUUUAAUUGGCAUUUUUAUUAAACAGCUGAAAAUGAGCAGUUGCAAAGAGGCAGCGAACAAA--------AAACCAAAAAA
(((((((.((.....)).))))))).....((((((((((((.........))))))))....(((((......))))).......--------...)))).... ( -26.10)
>DroSim_CAF1 19485 97 - 1
UGCGUGUGGCAAUCAGCGACAUGCAUUUAAUUGGCAUUUUUAUUAAACAGCUGAAAAUGAGCAGUUGCAAAGAGGCAGCGAACAAA--------AAACCAAAAAA
(((((((.((.....)).))))))).....((((((((((((.........))))))))....(((((......))))).......--------...)))).... ( -26.10)
>DroEre_CAF1 19709 88 - 1
UGCGUGUGGCAAUCAGCGACAUGCAUUUAAUUGGCAUUUUUAUUAAACAGCUGAAAAUGAGCAGUUGGGCAAAGGCUGCA-----------------CUAAAAAA
(((((((.((.....)).))))))).....((((((((((((.........)))))))).((((((.......)))))).-----------------)))).... ( -24.70)
>DroYak_CAF1 20155 105 - 1
UGCGUGUGGCAAUCAGCGACAUGCAUUUAAUUGGCAUUUUUAUUAAACAGCUGAAAAUGAGCAGUUGGGCAAAAGCUGCAAACAAAUACAAUCAACACGAAAAAA
(((((((.((.....)).)))))))....((((.((((((((.........)))))))).((((((.......)))))).........))))............. ( -25.70)
>DroPer_CAF1 23134 88 - 1
-UUGCGGUGCAAUCAGCAACAUGCAUUUAAUUGGCAUUAUUAUUAAACAGCUGAAAGUGAGCAGCAAGAAAAAAGG--CGGAUAAG--------GA--C----AA
-.((((.(((.....)))...))))....(((.((.(((....)))...((((........))))..........)--).)))...--------..--.----.. ( -14.60)
>consensus
UGCGUGUGGCAAUCAGCGACAUGCAUUUAAUUGGCAUUUUUAUUAAACAGCUGAAAAUGAGCAGUUGGAAAAAGGCAGCGAACAAA________AAACCAAAAAA
(((((((.((.....)).)))))))((((((((.((((((((.........))))))))..)))))))).................................... (-17.33 = -18.17 +   0.83)

alignment

secondary structure

dotplot

Window 6

Location	20,208,268 – 20,208,358
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	86.33
Mean single sequence MFE	-25.67
Consensus MFE	-19.04
Energy contribution	-19.80
Covariance contribution	0.76
Combinations/Pair	1.19
Mean z-score	-2.92
Structure conservation index	0.74
SVM decision value	1.96
SVM RNA-class probability	0.984117
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20208268 90 + 27905053
GCCAAUUAAAUGCAUGUCGCUGAUUGCCACACGCAGCAUCAGUGGCUGCCGGAAAAACAGAAACACUCAUCCAAAACCUGCAAAUGGCAC
((((.......(((.(((((((((.((........)))))))))))))).(((................)))............)))).. ( -24.79)
>DroSec_CAF1 19535 90 + 1
GCCAAUUAAAUGCAUGUCGCUGAUUGCCACACGCAGCAUCAGCGGCUGCCGGACAAACAGAAACACUCAUCCAAAACCUGCAAAUGGCAC
((((.......(((.(((((((((.((........)))))))))))))).(((................)))............)))).. ( -26.49)
>DroSim_CAF1 19547 90 + 1
GCCAAUUAAAUGCAUGUCGCUGAUUGCCACACGCAGCAUCAGCGGCUGCCGGAAAAACAGAAACACUCAUCCAAAACCUGCAAAUGGCAC
((((.......(((.(((((((((.((........)))))))))))))).(((................)))............)))).. ( -26.69)
>DroEre_CAF1 19762 90 + 1
GCCAAUUAAAUGCAUGUCGCUGAUUGCCACACGCAGGAUCAGCGGCUGCCGGAAAAACAGAAACACUCAUCCAAAACCUGCAAAUGGCAC
((((.......(((.((((((((((((.....)))..)))))))))))).(((................)))............)))).. ( -26.59)
>DroAna_CAF1 20758 82 + 1
GCCAAUUAAAUGCACGGUGCUGAUUGCCAU--------UCGGCGGGUGGAAAAAAUAACGAAGCACUUUGCAAAGUCCUGCAAAUGGCAC
((((......((((.((((((.(((.((((--------(.....)))))....))).....)))))).))))..(.....)...)))).. ( -23.80)
>consensus
GCCAAUUAAAUGCAUGUCGCUGAUUGCCACACGCAGCAUCAGCGGCUGCCGGAAAAACAGAAACACUCAUCCAAAACCUGCAAAUGGCAC
((((.......(((.((((((((((((.....)))..))))))))))))..........((.....))................)))).. (-19.04 = -19.80 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:28 2006