Locus 3232

Sequence ID	2R_DroMel_CAF1
Location	11,042,299 – 11,042,477
Length	178
Max. P	0.980654

overview

Window 8

Location	11,042,299 – 11,042,405
Length	106
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	76.47
Mean single sequence MFE	-29.22
Consensus MFE	-11.75
Energy contribution	-13.80
Covariance contribution	2.05
Combinations/Pair	1.30
Mean z-score	-2.30
Structure conservation index	0.40
SVM decision value	0.51
SVM RNA-class probability	0.765566
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11042299 106 + 20766785
CGAAUGCGAAUGUCUUUGGUUGUUUUCUGUAUUAAAACGAAGGUUGAAAGG--CAUUAAGCAAA------CCGU--U--UGGCAUUACAAAGGCAUUACAGCGCGGCUAUAAGCCGCU
.....((.((((((((((.((((((..(((.....(((....))).....)--))..)))))).------((..--.--.)).....))))))))))...))(((((.....))))). ( -35.40)
>DroSec_CAF1 164920 106 + 1
CGAAUGCGAAUGUCUUUGGUUGUUUUCUGUAUUAAAACGAAGGUUGAAAGG--CAUUAAGCAAG------CCGU--U--UGGCAUUAAAAAGGCACUACAGUGUGGCUAUAGGCCGCU
.....((.((((((..(((((((((..(((.....(((....))).....)--))..)))).))------))).--.--.)))))).....(((.(((.((.....)).)))))))). ( -30.60)
>DroSim_CAF1 159168 106 + 1
CGAAUGCGAAUGUCUUUGGUUGUUUUCUGUAUUAAAACGAAGGUUGAAACG--CAUUAAGCAAG------CCGU--U--UGGCAUUAAAAAGGCAUUACAGUGUGGCUAUAAGCCGCU
.....((.(((((((((..((((((..((..((..(((....)))..))..--))..))))))(------((..--.--.))).....)))))))))...))(((((.....))))). ( -31.70)
>DroEre_CAF1 162131 102 + 1
CGAAGGCAAAUGUCUUUGGUUGUUUUCUGUAUUA-AACGAAGGUUGAGA-----UUUUAGCAAU------CCGU--U--UGGUAUUACAUAGGCAUUACAAUGUGGCUAUAAGCCACU
(((((((....)))))))..(((((...((((((-((((..(((((...-----......))))------))))--)--)))))).....))))).......(((((.....))))). ( -28.20)
>DroYak_CAF1 164110 105 + 1
CGAAUGCAAAUGUCUUUGGUUGUUUUCUGCAUUA-AACGAAGGUUGAAAAG--CAUUUAGCAAU------CAGU--U--UGGUAUUACAAAGGCAUUACAAUAUGGCUAUAAGCCACU
........((((((.(((((((((...(((....-(((....))).....)--))...))))))------)))(--(--((......))))))))))......((((.....)))).. ( -25.90)
>DroPer_CAF1 150440 106 + 1
CGAAUGCAAAUGUCUUUGGUUGUUUUCUGUUUUUAGAUUGUGAAUCAAAAGAUCAUUAAUCAUAGAUACACUGUAUUUGUGAUAUCGUGACAUUAUUAUAGCAUGC------------
...((((.(((((((((..(..(..((((....))))..)..)....))))).)))).(((((((((((...))))))))))).................))))..------------ ( -23.50)
>consensus
CGAAUGCAAAUGUCUUUGGUUGUUUUCUGUAUUAAAACGAAGGUUGAAAAG__CAUUAAGCAAA______CCGU__U__UGGCAUUACAAAGGCAUUACAGUGUGGCUAUAAGCCGCU
........((((((((((.((((((..........(((....)))............)))))).......(((......))).....)))))))))).....(((((.....))))). (-11.75 = -13.80 +   2.05)

alignment

secondary structure

dotplot

Window 9

Location	11,042,339 – 11,042,440
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	85.64
Mean single sequence MFE	-19.65
Consensus MFE	-13.87
Energy contribution	-14.51
Covariance contribution	0.64
Combinations/Pair	1.21
Mean z-score	-1.80
Structure conservation index	0.71
SVM decision value	0.21
SVM RNA-class probability	0.637207
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11042339 101 - 20766785
AUUCACUGUAUGUUUCACAAUCAAUUUAAUUAUACAGCGGCUUAUAGCCGCGCUGUAAUGCCUUUGUAAUGCCAAACGGUUUGCUUAAUGCCUUUCAACCU
...........((((..((..(((....((((((..(((((.....)))))..))))))....)))...))..))))((((.((.....)).....)))). ( -20.30)
>DroSec_CAF1 164960 101 - 1
AUUCGCUGUAUGUUUCAUAAUCAAUUUAAUUAAACAGCGGCCUAUAGCCACACUGUAGUGCCUUUUUAAUGCCAAACGGCUUGCUUAAUGCCUUUCAACCU
....(((((..(((..((.....))..)))...)))))(((((((((.....)))))).)))........(((....)))..((.....)).......... ( -20.70)
>DroSim_CAF1 159208 101 - 1
AUUCGCUGUAUGUUUCAUAAUCAAUUUAAUUAAACAGCGGCUUAUAGCCACACUGUAAUGCCUUUUUAAUGCCAAACGGCUUGCUUAAUGCGUUUCAACCU
....(((((..(((..((.....))..)))...)))))(((((((((.....)))))).)))........(((....)))..((.....)).......... ( -19.20)
>DroEre_CAF1 162170 98 - 1
AUCAGCUGUAUGUUACACAACCAAUUAAAUUAUACAGUGGCUUAUAGCCACAUUGUAAUGCCUAUGUAAUACCAAACGGAUUGCUAAAA---UCUCAACCU
....((((((((..................))))))))(((((((((.....)))))).)))...(((((.((....))))))).....---......... ( -17.17)
>DroYak_CAF1 164149 101 - 1
GUCAGUUGUAUGUUACACAACCAAUUAAAUUAUACAGUGGCUUAUAGCCAUAUUGUAAUGCCUUUGUAAUACCAAACUGAUUGCUAAAUGCUUUUCAACCU
(((((((...(((((((...........((((((..(((((.....)))))..)))))).....)))))))...))))))).((.....)).......... ( -20.89)
>consensus
AUUCGCUGUAUGUUUCACAAUCAAUUUAAUUAUACAGCGGCUUAUAGCCACACUGUAAUGCCUUUGUAAUGCCAAACGGAUUGCUUAAUGCCUUUCAACCU
....((((((((..................))))))))(((((((((.....)))))).)))...((((.(((....)))))))................. (-13.87 = -14.51 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	11,042,366 – 11,042,477
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	80.09
Mean single sequence MFE	-25.60
Consensus MFE	-14.40
Energy contribution	-15.00
Covariance contribution	0.60
Combinations/Pair	1.24
Mean z-score	-2.70
Structure conservation index	0.56
SVM decision value	1.87
SVM RNA-class probability	0.980654
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11042366 111 + 20766785
UGGCAUUACAAAGGCAUUACAGCGCGGCUAUAAGCCGCUGUAUAAUUAAAUUGAUUGUGAAACAUACAGUGAAUUAAAUAAUGCAGUAAAACGCACAUCAAAAUAUUGAGU
..((........(((.(((.(((...))).))))))(((((((.(((.((((.((((((.....)))))).)))).))).))))))).....))...((((....)))).. ( -25.60)
>DroSec_CAF1 164987 111 + 1
UGGCAUUAAAAAGGCACUACAGUGUGGCUAUAGGCCGCUGUUUAAUUAAAUUGAUUAUGAAACAUACAGCGAAUUAAAUAAUGCAGCAAAACGCACAUCAAAAUAUUGAGU
..((((((....(((.(((.((.....)).))))))(((((.(((((.....)))))........)))))........)))))).((.....))...((((....)))).. ( -22.80)
>DroSim_CAF1 159235 111 + 1
UGGCAUUAAAAAGGCAUUACAGUGUGGCUAUAAGCCGCUGUUUAAUUAAAUUGAUUAUGAAACAUACAGCGAAUUAAAUAAUGCAUUAAAACGCACAUCAAAAUAUUGAGU
..((((((...((.(((......))).)).(((..((((((.(((((.....)))))........))))))..)))..)))))).............((((....)))).. ( -19.30)
>DroEre_CAF1 162194 91 + 1
UGGUAUUACAUAGGCAUUACAAUGUGGCUAUAAGCCACUGUAUAAUUUAAUUGGUUGUGUAACAUACAGCUGAUUAAAUAAUG--------------------UAAGCAGU
.............((.(((((..(((((.....)))))......(((((((..(((((((...)))))))..)))))))..))--------------------)))))... ( -28.00)
>DroYak_CAF1 164176 111 + 1
UGGUAUUACAAAGGCAUUACAAUAUGGCUAUAAGCCACUGUAUAAUUUAAUUGGUUGUGUAACAUACAACUGACUAAAUAAUGCAGUGAAACGCACUUGAAUGUGUGGAGU
...........((.(((......))).))......((((((((.(((((.(..(((((((...)))))))..).))))).))))))))...(((((......))))).... ( -32.30)
>consensus
UGGCAUUACAAAGGCAUUACAGUGUGGCUAUAAGCCGCUGUAUAAUUAAAUUGAUUGUGAAACAUACAGCGAAUUAAAUAAUGCAGUAAAACGCACAUCAAAAUAUUGAGU
..((((((.........((((..(((((.....)))))))))......((((.((((((.....)))))).))))...))))))........................... (-14.40 = -15.00 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	11,042,366 – 11,042,477
Length	111
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	80.09
Mean single sequence MFE	-21.85
Consensus MFE	-15.85
Energy contribution	-16.17
Covariance contribution	0.32
Combinations/Pair	1.17
Mean z-score	-2.23
Structure conservation index	0.73
SVM decision value	1.54
SVM RNA-class probability	0.962516
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11042366 111 - 20766785
ACUCAAUAUUUUGAUGUGCGUUUUACUGCAUUAUUUAAUUCACUGUAUGUUUCACAAUCAAUUUAAUUAUACAGCGGCUUAUAGCCGCGCUGUAAUGCCUUUGUAAUGCCA
..((((....))))((.(((((.....(((((((.........((((((..................))))))(((((.....)))))...)))))))......))))))) ( -24.47)
>DroSec_CAF1 164987 111 - 1
ACUCAAUAUUUUGAUGUGCGUUUUGCUGCAUUAUUUAAUUCGCUGUAUGUUUCAUAAUCAAUUUAAUUAAACAGCGGCCUAUAGCCACACUGUAGUGCCUUUUUAAUGCCA
((((((....)))).))((.....)).((((((........(((((..(((..((.....))..)))...)))))(((((((((.....)))))).)))....)))))).. ( -23.30)
>DroSim_CAF1 159235 111 - 1
ACUCAAUAUUUUGAUGUGCGUUUUAAUGCAUUAUUUAAUUCGCUGUAUGUUUCAUAAUCAAUUUAAUUAAACAGCGGCUUAUAGCCACACUGUAAUGCCUUUUUAAUGCCA
..((((....))))((.(((((..((.(((((((.......(((((..(((..((.....))..)))...)))))(((.....))).....)))))))..))..))))))) ( -22.70)
>DroEre_CAF1 162194 91 - 1
ACUGCUUA--------------------CAUUAUUUAAUCAGCUGUAUGUUACACAACCAAUUAAAUUAUACAGUGGCUUAUAGCCACAUUGUAAUGCCUAUGUAAUACCA
...(((((--------------------((...........((((((((..................))))))))(((.....)))....))))).))............. ( -15.97)
>DroYak_CAF1 164176 111 - 1
ACUCCACACAUUCAAGUGCGUUUCACUGCAUUAUUUAGUCAGUUGUAUGUUACACAACCAAUUAAAUUAUACAGUGGCUUAUAGCCAUAUUGUAAUGCCUUUGUAAUACCA
.........(((((((.(((((.(((((.((.(((((((..(((((.......)))))..))))))).)).))))(((.....))).....).))))).)))).))).... ( -22.80)
>consensus
ACUCAAUAUUUUGAUGUGCGUUUUACUGCAUUAUUUAAUUCGCUGUAUGUUUCACAAUCAAUUUAAUUAUACAGCGGCUUAUAGCCACACUGUAAUGCCUUUGUAAUGCCA
...........................((((((........((((((((..................))))))))(((((((((.....)))))).)))....)))))).. (-15.85 = -16.17 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:39 2006