Locus 427

Sequence ID 2L_DroMel_CAF1
Location 1,254,244 – 1,254,369
Length 125
Max. P 0.963250
window692 window693 window694 window695

overview

Window 2

Location 1,254,244 – 1,254,344
Length 100
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 76.72
Mean single sequence MFE -21.24
Consensus MFE -11.20
Energy contribution -11.96
Covariance contribution 0.76
Combinations/Pair 1.15
Mean z-score -1.84
Structure conservation index 0.53
SVM decision value 0.30
SVM RNA-class probability 0.679582
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1254244 100 + 22407834
AAUGCGAA--AAGUGCCUUCAACUUUUUAUGAAAUAUGGGUUGACAGACGGCUCAUCUGUCAUCUAAUAAAUGCAUUUAAAAUUAAACAAAUGCGCGCAUA-------A
.(((((((--((((.......)))))))........(((((.((((((.......)))))))))))......((((((..........))))))..)))).-------. ( -22.60)
>DroSec_CAF1 13969 100 + 1
AAUGCGAA--AAGUGCUCUCUACUUUUUAUGAAAUAUGGGUUGACAGAUGGCUCAUCUGUCAUCUAAUAAAUGCAUUUAAAAUUAAACAAAUGCGCGAAGA-------A
..((((((--(((((.....))))))))........(((((.((((((((...)))))))))))))......((((((..........)))))))))....-------. ( -24.30)
>DroSim_CAF1 14471 100 + 1
AAUGCGAA--AAGUGCUUCCUACUUUUUAUGAAAUAUGGGAUGACAGAUGGCUCAUCUGUCAACUAAGAAAUGCAUUUAAAAUUAAACAAAUGCGCGCAAA-------A
..((((..--.(((...(((((..(((....)))..)))))(((((((((...)))))))))))).......((((((..........)))))).))))..-------. ( -25.60)
>DroEre_CAF1 26783 81 + 1
AAUGCGGAGGAAGUGCUCCCUACUUUUUAUG------------ACAGACGGCUCAUCUGCCAUCCAAUAAACGCGUUUCGAACUAAA----UU-----AAA-------A
((((((.((((((((.....))))))))...------------...((.(((......))).)).......))))))..........----..-----...-------. ( -15.70)
>DroYak_CAF1 14628 102 + 1
AAUGCGGA--AAGUGCUUCCUACUUUUUAUGAAAUAUGGGUUGACAGGCGGCUCAUCUGUCAUCUAAGAAACGCGAUUGAAAUUAAACGAAUU-----AAAAUAUGAAG
..((((((--(((((.....))))))).((((...((((((((.....))))))))...))))........))))..................-----........... ( -18.00)
>consensus
AAUGCGAA__AAGUGCUUCCUACUUUUUAUGAAAUAUGGGUUGACAGACGGCUCAUCUGUCAUCUAAUAAAUGCAUUUAAAAUUAAACAAAUGCGCG_AAA_______A
((((((....(((((.....))))).............((.(((((((.......))))))).))......))))))................................ (-11.20 = -11.96 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 1,254,244 – 1,254,344
Length 100
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 76.72
Mean single sequence MFE -21.26
Consensus MFE -11.92
Energy contribution -12.00
Covariance contribution 0.08
Combinations/Pair 1.29
Mean z-score -1.73
Structure conservation index 0.56
SVM decision value 0.14
SVM RNA-class probability 0.604440
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1254244 100 - 22407834
U-------UAUGCGCGCAUUUGUUUAAUUUUAAAUGCAUUUAUUAGAUGACAGAUGAGCCGUCUGUCAACCCAUAUUUCAUAAAAAGUUGAAGGCACUU--UUCGCAUU
.-------.(((((.(((((((........)))))))..........(((((((((...))))))))).......(((((........)))))......--..))))). ( -24.30)
>DroSec_CAF1 13969 100 - 1
U-------UCUUCGCGCAUUUGUUUAAUUUUAAAUGCAUUUAUUAGAUGACAGAUGAGCCAUCUGUCAACCCAUAUUUCAUAAAAAGUAGAGAGCACUU--UUCGCAUU
.-------((((..((((((((........)))))))..........(((((((((...)))))))))..................)..))))((....--...))... ( -24.30)
>DroSim_CAF1 14471 100 - 1
U-------UUUGCGCGCAUUUGUUUAAUUUUAAAUGCAUUUCUUAGUUGACAGAUGAGCCAUCUGUCAUCCCAUAUUUCAUAAAAAGUAGGAAGCACUU--UUCGCAUU
.-------..((((.(((((((........)))))))........(((((((((((...))))))))...((.(((((......))))))).)))....--..)))).. ( -24.30)
>DroEre_CAF1 26783 81 - 1
U-------UUU-----AA----UUUAGUUCGAAACGCGUUUAUUGGAUGGCAGAUGAGCCGUCUGU------------CAUAAAAAGUAGGGAGCACUUCCUCCGCAUU
.-------...-----..----.............((..(((((..((((((((((...)))))))------------)))....)))))((((......))))))... ( -20.70)
>DroYak_CAF1 14628 102 - 1
CUUCAUAUUUU-----AAUUCGUUUAAUUUCAAUCGCGUUUCUUAGAUGACAGAUGAGCCGCCUGUCAACCCAUAUUUCAUAAAAAGUAGGAAGCACUU--UCCGCAUU
...........-----...................(((.........((((((.........))))))..((.(((((......)))))))........--..)))... ( -12.70)
>consensus
U_______UUU_CGCGCAUUUGUUUAAUUUUAAAUGCAUUUAUUAGAUGACAGAUGAGCCGUCUGUCAACCCAUAUUUCAUAAAAAGUAGGAAGCACUU__UUCGCAUU
................................(((((..........(((((((((...))))))))).....................(((.........)))))))) (-11.92 = -12.00 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 1,254,278 – 1,254,369
Length 91
Sequences 3
Columns 91
Reading direction forward
Mean pairwise identity 91.58
Mean single sequence MFE -22.33
Consensus MFE -18.27
Energy contribution -18.60
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.46
Structure conservation index 0.82
SVM decision value 0.54
SVM RNA-class probability 0.773496
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1254278 91 + 22407834
UGGGUUGACAGACGGCUCAUCUGUCAUCUAAUAAAUGCAUUUAAAAUUAAACAAAUGCGCGCAUAAGUGCUGCAAUCAGUUAGACAUUAUG
.....(((((((.......)))))))((((((....((((((..........))))))((((....))))........))))))....... ( -20.70)
>DroSec_CAF1 14003 91 + 1
UGGGUUGACAGAUGGCUCAUCUGUCAUCUAAUAAAUGCAUUUAAAAUUAAACAAAUGCGCGAAGAAGUGCUGCAAUAAGUUAGAUACCAUG
(((...((((((((...))))))))(((((((...((((((((....)))).....((((......))))))))....))))))).))).. ( -25.30)
>DroSim_CAF1 14505 91 + 1
UGGGAUGACAGAUGGCUCAUCUGUCAACUAAGAAAUGCAUUUAAAAUUAAACAAAUGCGCGCAAAAGUGCUGCAAUAAGUAAGACAUUAUG
..((.(((((((((...))))))))).)).......((((((..........))))))((((....))))..................... ( -21.00)
>consensus
UGGGUUGACAGAUGGCUCAUCUGUCAUCUAAUAAAUGCAUUUAAAAUUAAACAAAUGCGCGCAAAAGUGCUGCAAUAAGUUAGACAUUAUG
..((.(((((((((...))))))))).))......((((((((....)))).....((((......))))))))................. (-18.27 = -18.60 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 1,254,278 – 1,254,369
Length 91
Sequences 3
Columns 91
Reading direction reverse
Mean pairwise identity 91.58
Mean single sequence MFE -23.83
Consensus MFE -20.57
Energy contribution -21.13
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -3.42
Structure conservation index 0.86
SVM decision value 1.55
SVM RNA-class probability 0.963250
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1254278 91 - 22407834
CAUAAUGUCUAACUGAUUGCAGCACUUAUGCGCGCAUUUGUUUAAUUUUAAAUGCAUUUAUUAGAUGACAGAUGAGCCGUCUGUCAACCCA
......((((((..(((.((.(((....)))))(((((((........))))))))))..))))))((((((((...))))))))...... ( -25.10)
>DroSec_CAF1 14003 91 - 1
CAUGGUAUCUAACUUAUUGCAGCACUUCUUCGCGCAUUUGUUUAAUUUUAAAUGCAUUUAUUAGAUGACAGAUGAGCCAUCUGUCAACCCA
...(((((((((.........((........))(((((((........))))))).....))))))((((((((...)))))))).))).. ( -24.60)
>DroSim_CAF1 14505 91 - 1
CAUAAUGUCUUACUUAUUGCAGCACUUUUGCGCGCAUUUGUUUAAUUUUAAAUGCAUUUCUUAGUUGACAGAUGAGCCAUCUGUCAUCCCA
..................((.(((....)))))(((((((........)))))))..........(((((((((...)))))))))..... ( -21.80)
>consensus
CAUAAUGUCUAACUUAUUGCAGCACUUAUGCGCGCAUUUGUUUAAUUUUAAAUGCAUUUAUUAGAUGACAGAUGAGCCAUCUGUCAACCCA
......((((((......((.(((....)))))(((((((........))))))).....))))))((((((((...))))))))...... (-20.57 = -21.13 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:58 2006