Locus 1153

Sequence ID	X_DroMel_CAF1
Location	3,445,412 – 3,445,547
Length	135
Max. P	0.835464

overview

Window 2

Location	3,445,412 – 3,445,512
Length	100
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	80.52
Mean single sequence MFE	-30.52
Consensus MFE	-19.40
Energy contribution	-21.04
Covariance contribution	1.64
Combinations/Pair	1.19
Mean z-score	-1.80
Structure conservation index	0.64
SVM decision value	0.30
SVM RNA-class probability	0.680080
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3445412 100 + 22224390
AAAGGGUUCCACAACUGAGAUUGCUGGAGAUUGCU-AGGUGUACGGCACCAAAACCAAAUGG--GGGCUUAAAGGGCUUCAAAAUGGG----------GCCUGGAUGUUUUUA
...((.((((((((......))).)))))......-.((((.....))))....))...(((--((((.....(((((((.....)))----------))))....))))))) ( -26.10)
>DroSec_CAF1 17671 99 + 1
AAAGGGUUCCAGAACUGAGAUUGCAGGA-----CU-AGGUGUACGGCACC------AAAUGG--GGGCUUAAAGGGCUUCAAAAUGGGGCCCAAAGGGGCCUGGAUUUUGUUU
...(((((((((..(((......)))..-----))-.((((.....))))------......--.........(((((((.....)))))))...)))))))........... ( -32.10)
>DroSim_CAF1 17440 99 + 1
AAAGGGUUCCAGAACUGAGAUUGCAGGA-----CU-AGGUGUACGGCACC------AAAUGG--GGGCUUAAAGGGCUUCAAAAUGGGGCCCAAAGGGGCCUGGAUUUUGUUU
...(((((((((..(((......)))..-----))-.((((.....))))------......--.........(((((((.....)))))))...)))))))........... ( -32.10)
>DroEre_CAF1 20161 97 + 1
AAAGGGUUCCAGAACCGAGAUUGCAGGA-----CU-AGGUGUACGGCACC------AAAUGGGGGGGCUUAAAAGGCUUGAAAUGAGGGCCCAAAGGGGCCCGGGUUUU----
...(((((((....((.........)).-----..-.((((.....))))------.......))))))).........(((((..((((((....))))))..)))))---- ( -31.00)
>DroYak_CAF1 18938 96 + 1
AAAGGGUUCCCAAACUGAGAUUGCAGAA-----CUGAGGUGCACGGCACC------AAAUGG--AGGCUUAAAGGGCUUUAAAUGGGGGCCCAAAGUUGCCAGGAUUUU----
...(((((((((..(((......)))..-----....(((((...)))))------.....(--(((((.....))))))...))))))))).................---- ( -31.30)
>consensus
AAAGGGUUCCAGAACUGAGAUUGCAGGA_____CU_AGGUGUACGGCACC______AAAUGG__GGGCUUAAAGGGCUUCAAAAUGGGGCCCAAAGGGGCCUGGAUUUU_UU_
.......(((...........................(((((...)))))..............((((((...(((((((.....)))))))....)))))))))........ (-19.40 = -21.04 +   1.64)

alignment

secondary structure

dotplot

Window 3

Location	3,445,447 – 3,445,547
Length	100
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	76.34
Mean single sequence MFE	-32.50
Consensus MFE	-16.79
Energy contribution	-18.19
Covariance contribution	1.40
Combinations/Pair	1.24
Mean z-score	-1.98
Structure conservation index	0.52
SVM decision value	0.73
SVM RNA-class probability	0.835464
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3445447 100 + 22224390
AGGUGUACGGCACCAAAACCAAAUGG--GGGCUUAAAGGGCUUCAAAAUGGG----------GCCUGGAUGUUUUUAUUUUUUUUUCGAAACACAGAUUC-----GAGGUUGCUUUG
.((((.....))))..((((((((((--((((.....(((((((.....)))----------))))....)))))))))).....(((((.......)))-----))))))...... ( -28.90)
>DroSec_CAF1 17701 101 + 1
AGGUGUACGGCACC------AAAUGG--GGGCUUAAAGGGCUUCAAAAUGGGGCCCAAAGGGGCCUGGAUUUUGUUUUUUUUUU---UUAACACAGAUUC-----GAGGUUGCUUUG
.((((.....))))------......--.........(((((((.....)))))))((((.(((((.((.(((((.((......---..)).))))).))-----.))))).)))). ( -34.90)
>DroSim_CAF1 17470 100 + 1
AGGUGUACGGCACC------AAAUGG--GGGCUUAAAGGGCUUCAAAAUGGGGCCCAAAGGGGCCUGGAUUUUGUUUUUU-UUU---UCAACACAGAUUC-----GAGGUUGCUUUG
.((((.....))))------......--.........(((((((.....)))))))((((.(((((.((.(((((.((..-...---..)).))))).))-----.))))).)))). ( -33.90)
>DroEre_CAF1 20191 105 + 1
AGGUGUACGGCACC------AAAUGGGGGGGCUUAAAAGGCUUGAAAUGAGGGCCCAAAGGGGCCCGGGUUUU------UUGUUUUCGAAACACAAGCCCACGAGGAGGUUGCUUUG
.((((.....))))------....((((.(((((....((((((......((((((....))))))..(((((------........))))).)))))).......))))).)))). ( -37.20)
>DroYak_CAF1 18969 95 + 1
AGGUGCACGGCACC------AAAUGG--AGGCUUAAAGGGCUUUAAAUGGGGGCCCAAAGUUGCCAGGAUUUU------U---UUUCGAAACGCAGAUUC-----GAGGUUGCUUUG
.(((((...)))))------...(((--..((((...(((((((.....))))))).))))..))).......------.---(((((((.......)))-----))))........ ( -27.60)
>consensus
AGGUGUACGGCACC______AAAUGG__GGGCUUAAAGGGCUUCAAAAUGGGGCCCAAAGGGGCCUGGAUUUU_UU_UUUUUUUUUCGAAACACAGAUUC_____GAGGUUGCUUUG
........((((((..............((((((...(((((((.....)))))))....))))))((((((......................)))))).......)).))))... (-16.79 = -18.19 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:37 2006