Locus 4288

Sequence ID 3L_DroMel_CAF1
Location 12,557,629 – 12,557,813
Length 184
Max. P 0.998944
window6627 window6628 window6629 window6630 window6631

overview

Window 7

Location 12,557,629 – 12,557,722
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 91.51
Mean single sequence MFE -30.02
Consensus MFE -26.02
Energy contribution -26.58
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.52
Structure conservation index 0.87
SVM decision value 3.29
SVM RNA-class probability 0.998944
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12557629 93 + 23771897
GUCCAACGGGCGGAGCACUCAACUUAAUUAUGGGUUCGGUGCGUCGAUAUUUUCGCCCAGAAGACUAAAGUCUUCAGAUUCCAGACCUUAAGA
(((....(((((..(((((.((((((....)))))).)))))..)((.....)))))).((((((....))))))........)))....... ( -31.90)
>DroSec_CAF1 45866 93 + 1
GUCCAACGGGCGGAGCACUCAACUUAAUUAUGGGUUCGGUGCGUCGAUAUUUUCGCCCAGAAGACUAAAGUCUUCAGAUUCCAGACUUCAGAA
(((....(((((..(((((.((((((....)))))).)))))..)((.....)))))).((((((....))))))........)))....... ( -32.30)
>DroSim_CAF1 47112 93 + 1
GUCCAACGGGCGGAGCACUCAACUUAAUUAUGGGUUCGGUGCGUCAAUAUUUUCGCCCAGAAGACUAAAGUCCUCAGAUUCCAGACUUCAGAA
(((....((((((((((((.((((((....)))))).))))).........))))))).((.(((....))).))........)))....... ( -27.50)
>DroEre_CAF1 46583 93 + 1
GUCCAUCAGGCGGAGCACUCAACUUAAUUAUGGGUUCGGUGCUCCGAUAUUUUCGCCCAGAAGACUGAAGUCUUUAGAUUCCAGACUUCAGCA
........(((((((((((.((((((....)))))).))))))))((.....))))).....(.(((((((((.........)))))))))). ( -35.80)
>DroYak_CAF1 47079 93 + 1
GUCCAUCAGGCGGAGCACUCAACUUAAUUAUGGGUUCGAUGCGCCGAUAUUUUCGCCCAGAAGACCGACGUCUUUAGAUUCCAGACUUGAAGA
(((.(((.(((((.(((.((((((((....)))))).))))).))((.....)))))..((((((....)))))).)))....)))....... ( -22.60)
>consensus
GUCCAACGGGCGGAGCACUCAACUUAAUUAUGGGUUCGGUGCGUCGAUAUUUUCGCCCAGAAGACUAAAGUCUUCAGAUUCCAGACUUCAGAA
(((....((((((((((((.((((((....)))))).))))).........))))))).((((((....))))))........)))....... (-26.02 = -26.58 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,557,629 – 12,557,722
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 91.51
Mean single sequence MFE -27.10
Consensus MFE -24.76
Energy contribution -23.84
Covariance contribution -0.92
Combinations/Pair 1.30
Mean z-score -1.40
Structure conservation index 0.91
SVM decision value 0.94
SVM RNA-class probability 0.885588
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12557629 93 - 23771897
UCUUAAGGUCUGGAAUCUGAAGACUUUAGUCUUCUGGGCGAAAAUAUCGACGCACCGAACCCAUAAUUAAGUUGAGUGCUCCGCCCGUUGGAC
...((((((((.........))))))))((((..((((((......(((((...................)))))......))))))..)))) ( -26.21)
>DroSec_CAF1 45866 93 - 1
UUCUGAAGUCUGGAAUCUGAAGACUUUAGUCUUCUGGGCGAAAAUAUCGACGCACCGAACCCAUAAUUAAGUUGAGUGCUCCGCCCGUUGGAC
..(((((((((.........)))))))))(((..((((((......(((((...................)))))......))))))..))). ( -26.71)
>DroSim_CAF1 47112 93 - 1
UUCUGAAGUCUGGAAUCUGAGGACUUUAGUCUUCUGGGCGAAAAUAUUGACGCACCGAACCCAUAAUUAAGUUGAGUGCUCCGCCCGUUGGAC
..(((((((((.........)))))))))(((..((((((........((.((((..(((..........)))..))))))))))))..))). ( -26.10)
>DroEre_CAF1 46583 93 - 1
UGCUGAAGUCUGGAAUCUAAAGACUUCAGUCUUCUGGGCGAAAAUAUCGGAGCACCGAACCCAUAAUUAAGUUGAGUGCUCCGCCUGAUGGAC
.((((((((((.........))))))))))((..(((((((.....))(((((((..(((..........)))..))))))))))))..)).. ( -33.90)
>DroYak_CAF1 47079 93 - 1
UCUUCAAGUCUGGAAUCUAAAGACGUCGGUCUUCUGGGCGAAAAUAUCGGCGCAUCGAACCCAUAAUUAAGUUGAGUGCUCCGCCUGAUGGAC
.......((((.........))))(((.(((....((((((.....))((.((((..(((..........)))..)))).))))))))).))) ( -22.60)
>consensus
UCCUGAAGUCUGGAAUCUGAAGACUUUAGUCUUCUGGGCGAAAAUAUCGACGCACCGAACCCAUAAUUAAGUUGAGUGCUCCGCCCGUUGGAC
...((((((((.........))))))))((((..((((((........((.((((..(((..........)))..))))))))))))..)))) (-24.76 = -23.84 +  -0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,557,659 – 12,557,761
Length 102
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 80.91
Mean single sequence MFE -28.26
Consensus MFE -21.30
Energy contribution -22.02
Covariance contribution 0.72
Combinations/Pair 1.32
Mean z-score -1.58
Structure conservation index 0.75
SVM decision value 0.27
SVM RNA-class probability 0.660013
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12557659 102 - 23771897
GUUUGAAGUCUGGAAGUCUUGAAGUUUG-AAGUCUGGAAGUCUUAAGGUCUGGAAUCUGAAGACUUUAGUCUUCUGGGCGAAAAUAUCGACGCACCGAACCCA
.......((.(((..((.((((.((((.-..(((..((((.((.(((((((.........))))))))).))))..)))..)))).)))).)).))).))... ( -29.70)
>DroSec_CAF1 45896 102 - 1
ACUUGAAGUCUGGAAGUCUUGAAGCUUG-AAGUCUGGAAGUUCUGAAGUCUGGAAUCUGAAGACUUUAGUCUUCUGGGCGAAAAUAUCGACGCACCGAACCCA
.(((.(((.(.....).))).)))....-..(((..((((..(((((((((.........))))))))).))))..))).......(((......)))..... ( -29.00)
>DroSim_CAF1 47142 93 - 1
---------CUGGAAGUCUUGAAGCUUG-AAGUCUGGAAGUUCUGAAGUCUGGAAUCUGAGGACUUUAGUCUUCUGGGCGAAAAUAUUGACGCACCGAACCCA
---------.(((..(((..........-..(((..((((..(((((((((.........))))))))).))))..))).........)))...)))...... ( -26.40)
>DroEre_CAF1 46613 87 - 1
GU----------------UUGAAGUCUGGAAGUCCUGAAGUGCUGAAGUCUGGAAUCUAAAGACUUCAGUCUUCUGGGCGAAAAUAUCGGAGCACCGAACCCA
..----------------.........((..((((.((((.((((((((((.........)))))))))))))).)))).......((((....))))..)). ( -31.70)
>DroYak_CAF1 47109 96 - 1
GU-------CUGGAAGUCUUGAAGUCUGUAAGUCUUAAAGUCUUCAAGUCUGGAAUCUAAAGACGUCGGUCUUCUGGGCGAAAAUAUCGGCGCAUCGAACCCA
((-------(..((((.(((((((.((...........)).))))))).((((..((....))..)))).))))..))).......((((....))))..... ( -24.50)
>consensus
GU_______CUGGAAGUCUUGAAGUUUG_AAGUCUGGAAGUCCUGAAGUCUGGAAUCUGAAGACUUUAGUCUUCUGGGCGAAAAUAUCGACGCACCGAACCCA
...............((.((((.((((....(((((((((..(((((((((.........))))))))).)))))))))..)))).)))).)).......... (-21.30 = -22.02 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 12,557,722 – 12,557,813
Length 91
Sequences 3
Columns 91
Reading direction forward
Mean pairwise identity 86.08
Mean single sequence MFE -24.17
Consensus MFE -19.82
Energy contribution -20.48
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.82
SVM decision value 0.86
SVM RNA-class probability 0.868109
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12557722 91 + 23771897
CUUCCAGACUUCAAACUUCAAGACUUCCAGACUUCAAACUUCCAGACUUCAGUUUGCAGAUUGCAGACUGUGGGGAAAUUGAAGCAGUCCG
......((((.....((((((...((((.(....)...........((.((((((((.....)))))))).)))))).)))))).)))).. ( -23.30)
>DroSec_CAF1 45959 91 + 1
CUUCCAGACUUCAAGCUUCAAGACUUCCAGACUUCAAGUUUCCAGACUUCAGUUUACAGAUUGCAGACUGUGAGGAAAUUGAAGCAGUCCG
......((((....(((((((...((((..(((..(((((....))))).)))((((((........)))))))))).))))))))))).. ( -23.40)
>DroSim_CAF1 47205 76 + 1
CUUCCAGACUUCAAGCUUCAAGACUUCCAG---------------ACUUCAGUUUGCAGAUUGCAGACUGUGAGGAAAUUGAAGCAGUCCG
......((((....(((((((...((((..---------------....((((((((.....))))))))...)))).))))))))))).. ( -25.80)
>consensus
CUUCCAGACUUCAAGCUUCAAGACUUCCAGACUUCAA__UUCCAGACUUCAGUUUGCAGAUUGCAGACUGUGAGGAAAUUGAAGCAGUCCG
......((((....(((((((...((((.....................((((((((.....))))))))...)))).))))))))))).. (-19.82 = -20.48 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 12,557,722 – 12,557,813
Length 91
Sequences 3
Columns 91
Reading direction reverse
Mean pairwise identity 86.08
Mean single sequence MFE -26.57
Consensus MFE -25.24
Energy contribution -24.97
Covariance contribution -0.27
Combinations/Pair 1.07
Mean z-score -2.26
Structure conservation index 0.95
SVM decision value 1.96
SVM RNA-class probability 0.984102
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12557722 91 - 23771897
CGGACUGCUUCAAUUUCCCCACAGUCUGCAAUCUGCAAACUGAAGUCUGGAAGUUUGAAGUCUGGAAGUCUUGAAGUUUGAAGUCUGGAAG
((((((((((((((((((...((((.(((.....))).)))).((.((..........)).))))))))..))))))....)))))).... ( -26.20)
>DroSec_CAF1 45959 91 - 1
CGGACUGCUUCAAUUUCCUCACAGUCUGCAAUCUGUAAACUGAAGUCUGGAAACUUGAAGUCUGGAAGUCUUGAAGCUUGAAGUCUGGAAG
((((((((((((((((((...((((.(((.....))).))))...((.(....)..)).....))))))..))))))....)))))).... ( -27.20)
>DroSim_CAF1 47205 76 - 1
CGGACUGCUUCAAUUUCCUCACAGUCUGCAAUCUGCAAACUGAAGU---------------CUGGAAGUCUUGAAGCUUGAAGUCUGGAAG
((((((((((((((((((...((((.(((.....))).))))....---------------..))))))..))))))....)))))).... ( -26.30)
>consensus
CGGACUGCUUCAAUUUCCUCACAGUCUGCAAUCUGCAAACUGAAGUCUGGAA__UUGAAGUCUGGAAGUCUUGAAGCUUGAAGUCUGGAAG
((((((((((((((((((...((((.(((.....))).)))).((.((..........)).))))))))..))))))....)))))).... (-25.24 = -24.97 +  -0.27)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:38 2006