Locus 4170

Sequence ID	3R_DroMel_CAF1
Location	11,330,880 – 11,331,040
Length	160
Max. P	0.999924

overview

Window 8

Location	11,330,880 – 11,331,000
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.00
Mean single sequence MFE	-23.30
Consensus MFE	-20.22
Energy contribution	-20.26
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.52
Structure conservation index	0.87
SVM decision value	0.58
SVM RNA-class probability	0.790325
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11330880 120 + 27905053
AAUCCCCAGCCACAACAAGGACACCAUUUUGAAUACAGUGCUGGAAUCCUUGAAUGCAAAUUGCUGCACAAUCAACGGCAAUCGACAACAAUGCAGCCGCUUGAAAAUCAUUUAAAAAAU
........(((....((((((..(((..(((....)))...)))..))))))..((((......))))........))).........(((.((....)))))................. ( -22.30)
>DroSec_CAF1 70053 120 + 1
AAUCCCCAGCCACAACAAGGACACCAUUUUGAAUACAGUGCUGGAAUCCUUGAAUGCAAAUUGCUGCACAAUCAACGGCAAUCGACAACAAUGCAGCCGCUUGAAAAUCAUUUAAAAAAU
........(((....((((((..(((..(((....)))...)))..))))))..((((......))))........))).........(((.((....)))))................. ( -22.30)
>DroSim_CAF1 68272 120 + 1
AAUCCCCAGCCACAACAAGGACACCAUUUUGAAUACAGUGCUGGAAUCCUCGAAUGCAAAUUGCUGCACAAUCAACGGCAAUCGACAACAAUGCAGCCGCUUGAAAAUCAUUUAAAAAAU
.....(((((.((.....((...))....((....))))))))).......((.((((......))))...((((((((................)))).))))...))........... ( -19.09)
>DroEre_CAF1 65616 120 + 1
AGUCCCCAGCCACAACAAGGACUCCAUGUUGAAUGCAGUGCUGGAAUCCUUGAAUGCAAAUUGCUGCACAAUCAACGGCAAUCGACAACAAUGCAGCCGCUUGAAAAUCAUUUAAAAAAU
.(((....(((....((((((.(((((..((....))..).)))).))))))..((((......))))........)))....)))..(((.((....)))))................. ( -27.60)
>DroYak_CAF1 67316 120 + 1
AAUCCACAGCCACAACAAGGACUCCAUUUUGAAUGCAGUGCUGGAAUCCUUGAAUGCAAAUUGCUGCACAAUCAACGACAAUUGACAACAAUGCAGCCGCUUGAAAAUCAUUUAAAAAAU
....((.(((.....((((((.((((..(((....)))...)))).))))))..........((((((...((((......))))......)))))).)))))................. ( -25.20)
>consensus
AAUCCCCAGCCACAACAAGGACACCAUUUUGAAUACAGUGCUGGAAUCCUUGAAUGCAAAUUGCUGCACAAUCAACGGCAAUCGACAACAAUGCAGCCGCUUGAAAAUCAUUUAAAAAAU
.......(((.....((((((..(((..(((....)))...)))..))))))..........((((((.......((.....)).......)))))).)))................... (-20.22 = -20.26 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	11,330,880 – 11,331,000
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.00
Mean single sequence MFE	-37.96
Consensus MFE	-36.12
Energy contribution	-36.00
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-2.89
Structure conservation index	0.95
SVM decision value	4.58
SVM RNA-class probability	0.999924
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11330880 120 - 27905053
AUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAGCACUGUAUUCAAAAUGGUGUCCUUGUUGUGGCUGGGGAUU
...........((((..((.((.(((((((....((((((....)))))).))))))).....(((..(((((((.(((....((....))...))).))))))).))).))))..)))) ( -37.60)
>DroSec_CAF1 70053 120 - 1
AUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAGCACUGUAUUCAAAAUGGUGUCCUUGUUGUGGCUGGGGAUU
...........((((..((.((.(((((((....((((((....)))))).))))))).....(((..(((((((.(((....((....))...))).))))))).))).))))..)))) ( -37.60)
>DroSim_CAF1 68272 120 - 1
AUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCGAGGAUUCCAGCACUGUAUUCAAAAUGGUGUCCUUGUUGUGGCUGGGGAUU
...........((((..((.((.(((((((....((((((....)))))).))))))).....(((..(((((((.(((....((....))...))).))))))).))).))))..)))) ( -37.30)
>DroEre_CAF1 65616 120 - 1
AUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAGCACUGCAUUCAACAUGGAGUCCUUGUUGUGGCUGGGGACU
.............((..((.((.(((((((....((((((....)))))).))))))).....(((..(((((((((((...............))))))))))).))).))))..)).. ( -39.06)
>DroYak_CAF1 67316 120 - 1
AUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCAAUUGUCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAGCACUGCAUUCAAAAUGGAGUCCUUGUUGUGGCUGUGGAUU
...............(((((((.(((((((....((((((....)))))).))))))).....(((..(((((((((((...............))))))))))).))).))).)))).. ( -38.26)
>consensus
AUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAGCACUGUAUUCAAAAUGGUGUCCUUGUUGUGGCUGGGGAUU
...........((((..((.((.(((((((....((((((....)))))).))))))).....(((..(((((((.(((....((....))...))).))))))).))).))))..)))) (-36.12 = -36.00 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	11,330,920 – 11,331,040
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.42
Mean single sequence MFE	-33.98
Consensus MFE	-32.06
Energy contribution	-32.34
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.25
Structure conservation index	0.94
SVM decision value	0.62
SVM RNA-class probability	0.801749
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11330920 120 - 27905053
CUUCAUUUGUGUCACUCCGCGUGGCAGCGAAGUUUAAGGGAUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAG
.....((((((((((.....)))))).))))......(((((((((..((((.....((((..(((((((....((((((....)))))).)))))))..)))))))).))))))))).. ( -33.70)
>DroSec_CAF1 70093 120 - 1
CUUCAUUUGUGUCACUCCGCGUGGCAGCGAAGUUUAAGGGAUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAG
.....((((((((((.....)))))).))))......(((((((((..((((.....((((..(((((((....((((((....)))))).)))))))..)))))))).))))))))).. ( -33.70)
>DroSim_CAF1 68312 120 - 1
CUUCAUUUGUGUCACUCCGCGUGGCAGCGAAGUUUAAGGGAUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCGAGGAUUCCAG
(((..((((((((((.....)))))).))))....)))(((.((((..((((.....((((..(((((((....((((((....)))))).)))))))..))))))))..)))).))).. ( -34.80)
>DroEre_CAF1 65656 119 - 1
CUUCAUUUGUGUCACUC-CCGCGGCAGCGACGUUGAAGGGAUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAG
(((((....((((.(((-(...)).)).)))).)))))(((.(((((.((((.....((((..(((((((....((((((....)))))).)))))))..)))))))).))))).))).. ( -33.80)
>DroYak_CAF1 67356 120 - 1
CUUCAUUUGUGUCACUCUCCGUGGCAGCGAUGUUAAAGGGAUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCAAUUGUCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAG
...((((..((((((.....))))))..)))).....(((((((((..((((.....((((..(((((((....((((((....)))))).)))))))..)))))))).))))))))).. ( -33.90)
>consensus
CUUCAUUUGUGUCACUCCGCGUGGCAGCGAAGUUUAAGGGAUUUUUUAAAUGAUUUUCAAGCGGCUGCAUUGUUGUCGAUUGCCGUUGAUUGUGCAGCAAUUUGCAUUCAAGGAUUCCAG
(((..((((((((((.....)))))).))))....)))(((.(((((.((((.....((((..(((((((....((((((....)))))).)))))))..)))))))).))))).))).. (-32.06 = -32.34 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:09 2006