Locus 1847

Sequence ID 2L_DroMel_CAF1
Location 5,087,051 – 5,087,300
Length 249
Max. P 0.951116
window2971 window2972 window2973 window2974

overview

Window 1

Location 5,087,051 – 5,087,170
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.44
Mean single sequence MFE -22.95
Consensus MFE -17.89
Energy contribution -18.58
Covariance contribution 0.69
Combinations/Pair 1.05
Mean z-score -1.80
Structure conservation index 0.78
SVM decision value 0.18
SVM RNA-class probability 0.621462
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5087051 119 + 22407834
CUU-UCCCACUGUCCCACUUUUAUCGCACUCUCCUCUCGACUUACCGACUCGUAUAGGGGACAAUUGUGUCGCCACAGCCGCACCAUAUGCACACUUAUGUUCAAUAAAAUAGCAAUUAA
...-......((((((....................(((......)))((.....))))))))...((((.((....)).))))....(((....((((.....))))....)))..... ( -17.60)
>DroSec_CAF1 16457 118 + 1
CUU-CCCCACUGUCCCACUUUUAUCGCACUCUCUUCUCGACUUACCGACUCGUAUAGGGGACAAUUGUGUCCCCAUAGCCGCA-CAUAUGCACACUUCGGUACAAUAAAAUAGCAAUUAA
...-.....................((....((.....))..((((((........(((((((....)))))))......(((-....))).....))))))..........))...... ( -23.60)
>DroSim_CAF1 19063 118 + 1
CUU-CCCCACUGUCCCACUUUUAUCGCACUCUCUUCUCGACUUACCGACUCGUAUAGGGGACAAUUGUGUCCCCAUAGCCGCA-CAUAUGCACACUUCGGUGCAAUAAAAUAGCAAUUAA
...-..............((((((.(((((......(((......)))...((...(((((((....)))))))......(((-....))))).....))))).)))))).......... ( -25.60)
>DroYak_CAF1 17982 119 + 1
UUUCCCCCAAUUUCCCACUUCUAUCGCACUCUCUUCUCGGCUUACCGACUCGUAUAGGGGACAAUUGUGUCCCCACAGCCGCA-CAUAUGCACAAUUGUGUUCAAUAAAAUAGCAAUUUA
.........................((..........((((((((......)))..(((((((....)))))))..)))))..-.....((((....))))...........))...... ( -25.00)
>consensus
CUU_CCCCACUGUCCCACUUUUAUCGCACUCUCUUCUCGACUUACCGACUCGUAUAGGGGACAAUUGUGUCCCCACAGCCGCA_CAUAUGCACACUUCGGUUCAAUAAAAUAGCAAUUAA
.........................((.........(((......)))...((((.(((((((....)))))))......(((.....)))........)))).........))...... (-17.89 = -18.58 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,087,090 – 5,087,206
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.09
Mean single sequence MFE -27.12
Consensus MFE -18.59
Energy contribution -21.41
Covariance contribution 2.81
Combinations/Pair 1.04
Mean z-score -2.59
Structure conservation index 0.69
SVM decision value 0.78
SVM RNA-class probability 0.847809
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5087090 116 + 22407834
CUUACCGACUCGUAUAGGGGACAAUUGUGUCGCCACAGCCGCACCAUAUGCACACUUAUGUUCAAUAAAAUAGCAAUUAAUAUUUUUAUAUCA----UUACUUUGAAUUGCUCGUUUACA
......((..((((..((.((((....)))).))......(((.....))).....)))).))..((((..(((((((.((((....))))((----......)))))))))..)))).. ( -17.70)
>DroSec_CAF1 16496 115 + 1
CUUACCGACUCGUAUAGGGGACAAUUGUGUCCCCAUAGCCGCA-CAUAUGCACACUUCGGUACAAUAAAAUAGCAAUUAAUAUUUUUAUGUCA----UUACAUUGAAUAGCUGUUUUACA
..((((((........(((((((....)))))))......(((-....))).....))))))...(((((((((......(((((..((((..----..)))).)))))))))))))).. ( -31.60)
>DroSim_CAF1 19102 119 + 1
CUUACCGACUCGUAUAGGGGACAAUUGUGUCCCCAUAGCCGCA-CAUAUGCACACUUCGGUGCAAUAAAAUAGCAAUUAAUAUUUUUAUGUCAUUCAUUACAUUGAAUUGCUGUUUUACA
..((((((........(((((((....)))))))......(((-....))).....))))))...(((((((((((((.........(((.....))).......))))))))))))).. ( -34.99)
>DroYak_CAF1 18022 114 + 1
CUUACCGACUCGUAUAGGGGACAAUUGUGUCCCCACAGCCGCA-CAUAUGCACAAUUGUGUUCAAUAAAAUAGCAAUUUAUAUU-UUAUGUCU----UUGCUUUAGCCUACUGCUUUACA
...........(((..(((((((....))))))).(((..((.-.....((((....))))...((((((((........))))-))))....----........))...)))...))). ( -24.20)
>consensus
CUUACCGACUCGUAUAGGGGACAAUUGUGUCCCCACAGCCGCA_CAUAUGCACACUUCGGUUCAAUAAAAUAGCAAUUAAUAUUUUUAUGUCA____UUACAUUGAAUUGCUGUUUUACA
...(((((........(((((((....)))))))......(((.....))).....)))))....(((((((((((((...........................))))))))))))).. (-18.59 = -21.41 +   2.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 5,087,090 – 5,087,206
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.09
Mean single sequence MFE -28.75
Consensus MFE -21.67
Energy contribution -22.86
Covariance contribution 1.19
Combinations/Pair 1.13
Mean z-score -1.77
Structure conservation index 0.75
SVM decision value 0.42
SVM RNA-class probability 0.731283
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5087090 116 - 22407834
UGUAAACGAGCAAUUCAAAGUAA----UGAUAUAAAAAUAUUAAUUGCUAUUUUAUUGAACAUAAGUGUGCAUAUGGUGCGGCUGUGGCGACACAAUUGUCCCCUAUACGAGUCGGUAAG
........((((((.........----((((((....))))))))))))...(((((((......(((((.....((..(((.((((....)))).)))..)).)))))...))))))). ( -22.10)
>DroSec_CAF1 16496 115 - 1
UGUAAAACAGCUAUUCAAUGUAA----UGACAUAAAAAUAUUAAUUGCUAUUUUAUUGUACCGAAGUGUGCAUAUG-UGCGGCUAUGGGGACACAAUUGUCCCCUAUACGAGUCGGUAAG
.((((((.(((.(((.(((((..----..........)))))))).))).))))))..((((((.(((((((....-)))......(((((((....))))))).))))...)))))).. ( -31.50)
>DroSim_CAF1 19102 119 - 1
UGUAAAACAGCAAUUCAAUGUAAUGAAUGACAUAAAAAUAUUAAUUGCUAUUUUAUUGCACCGAAGUGUGCAUAUG-UGCGGCUAUGGGGACACAAUUGUCCCCUAUACGAGUCGGUAAG
.((((((.(((((((.(((((.(((.....)))....)))))))))))).))))))...(((((.(((((((....-)))......(((((((....))))))).))))...)))))... ( -34.50)
>DroYak_CAF1 18022 114 - 1
UGUAAAGCAGUAGGCUAAAGCAA----AGACAUAA-AAUAUAAAUUGCUAUUUUAUUGAACACAAUUGUGCAUAUG-UGCGGCUGUGGGGACACAAUUGUCCCCUAUACGAGUCGGUAAG
.....(((.....)))..(((((----........-........)))))...(((((((..(((.(((..(....)-..))).)))(((((((....)))))))........))))))). ( -26.89)
>consensus
UGUAAAACAGCAAUUCAAAGUAA____UGACAUAAAAAUAUUAAUUGCUAUUUUAUUGAACAGAAGUGUGCAUAUG_UGCGGCUAUGGGGACACAAUUGUCCCCUAUACGAGUCGGUAAG
.((((((.(((((((...........................))))))).))))))(((((......))))).......(((((..(((((((....)))))))......)))))..... (-21.67 = -22.86 +   1.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,087,206 – 5,087,300
Length 94
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 78.86
Mean single sequence MFE -18.75
Consensus MFE -13.88
Energy contribution -13.77
Covariance contribution -0.10
Combinations/Pair 1.21
Mean z-score -2.01
Structure conservation index 0.74
SVM decision value 1.41
SVM RNA-class probability 0.951116
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5087206 94 - 22407834
UGCAACUUCAGGUGAACACUUUAACAACUUUUAC------CUCCAAUGUUUAUUUUUU--UUACAACAUAGGAGCUGUGUAAUAAUUCACUUAAGGAAAUAU
.....(((.(((((((....(((...((......------((((.(((((((......--.)).))))).))))..)).)))...))))))).)))...... ( -15.00)
>DroSec_CAF1 16611 96 - 1
UGUAACUUCAGGUGAACACUUUAACGGCUUCUAC------CUCAAAAAUUUAUUUUUUUUUUACAAUAUAGGAGCUGUAUAAUAAUUCACUUAAGGAAAAAU
.....(((.(((((((....(((((((((((((.------...(((((........))))).......)))))))))).)))...))))))).)))...... ( -19.80)
>DroYak_CAF1 18136 99 - 1
AACAACUUCAGGUGAACACUUUUACGGCUUAUACUCGUAUAUCAAAUAUUUGAUUUU---UUAUAAUAUGGGAGCUGUAUAACAAGUCACUUAGGAAAAUAU
.....(((.((((((.......(((((((....((((((((((((....)))))...---.....)))))))))))))).......)))))))))....... ( -21.44)
>consensus
UGCAACUUCAGGUGAACACUUUAACGGCUUAUAC______CUCAAAUAUUUAUUUUUU__UUACAAUAUAGGAGCUGUAUAAUAAUUCACUUAAGGAAAUAU
.....(((.((((((........((((((((((...................................))))))))))........)))))))))....... (-13.88 = -13.77 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:49 2006