Locus 685

Sequence ID 2L_DroMel_CAF1
Location 2,001,655 – 2,001,778
Length 123
Max. P 0.860007
window1118 window1119 window1120 window1121

overview

Window 8

Location 2,001,655 – 2,001,752
Length 97
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 73.56
Mean single sequence MFE -21.94
Consensus MFE -13.48
Energy contribution -12.95
Covariance contribution -0.53
Combinations/Pair 1.29
Mean z-score -1.55
Structure conservation index 0.61
SVM decision value 0.82
SVM RNA-class probability 0.860007
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2001655 97 + 22407834
GAUACUA--------UGCUAUGCAGGGUAUAUGUACAUAUAUAACUAAGCAGCUUCUUUGCUGCCUCUGUUU---------ACUUGGUCUCUCUUUGAUUGGAAAGUUGACAGA
((.((((--------.(.((.((((((((((((....)))))).....(((((......))))))))))).)---------)).)))).))((((..(((....)))..).))) ( -23.70)
>DroSec_CAF1 19250 89 + 1
GCUACUA--------UGCUAUGCAGUGUAU--------AUAUAACUAAGCAGCUUCUUUGCUGCCUCUGUUU---------ACUUGGUCUCUCUUUGAUUGGAAAGUUGACAGA
.....((--------(((........))))--------).........(((((......))))).((((((.---------((((.(((.......)))....)))).)))))) ( -20.60)
>DroSim_CAF1 16108 89 + 1
GAUACUA--------UGCAAUGCAGUGUAU--------AUAUAACUAAGCAGCUUCUUUGCUGCCUCUGUUU---------ACUUGGUCUCUCUUUGAUUGGAAAGUUGACAGA
.((((..--------(((...)))..))))--------..........(((((......))))).((((((.---------((((.(((.......)))....)))).)))))) ( -21.30)
>DroEre_CAF1 16198 104 + 1
GAUACUAUGCCACUAUGCUACGCAGUGUAU--------AUAUAACUAAGCAGCUUCUUUGCUGCUCCU--CCACUUGGCUUACUUGGUCCCUUUUUGAUUGGAAAGUUGACAGA
........((((.(((((........))))--------)........((((((......))))))...--.....)))).......(((.((((((....))))))..)))... ( -22.60)
>DroYak_CAF1 20620 103 + 1
GAUACUGUGCCACUAUUCUAUGCAGUAUAU--------AUAUAACUAAGCAGCUUCUUUGCUGCUUCUGUUUACUUGGU---CUUGGUCGCUCUUUGAUUGGAAAGUUGACAGA
.(((((((.............)))))))..--------.........((((((......))))))((((((.((((...---.(..((((.....))))..).)))).)))))) ( -27.82)
>DroAna_CAF1 15885 74 + 1
UAUAC-------------------------------AUGUCCUGUUAGUCAGCUUCUUUGCUGAUUCUGUUU---------ACUUGGUCUCUCUUUGAUUGGUAAGUUGACAAA
.....-------------------------------.((((.....(((((((......)))))))...(((---------(((.((((.......))))))))))..)))).. ( -15.60)
>consensus
GAUACUA________UGCUAUGCAGUGUAU________AUAUAACUAAGCAGCUUCUUUGCUGCCUCUGUUU_________ACUUGGUCUCUCUUUGAUUGGAAAGUUGACAGA
.........................................(((((..(((((......)))))...................(..(((.......)))..)..)))))..... (-13.48 = -12.95 +  -0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 2,001,655 – 2,001,752
Length 97
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 73.56
Mean single sequence MFE -18.10
Consensus MFE -11.85
Energy contribution -11.47
Covariance contribution -0.39
Combinations/Pair 1.29
Mean z-score -1.15
Structure conservation index 0.65
SVM decision value 0.26
SVM RNA-class probability 0.657319
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2001655 97 - 22407834
UCUGUCAACUUUCCAAUCAAAGAGAGACCAAGU---------AAACAGAGGCAGCAAAGAAGCUGCUUAGUUAUAUAUGUACAUAUACCCUGCAUAGCA--------UAGUAUC
(((((..((((.....((.....))....))))---------..)))))((((((......))))))...((((.((((((.........))))))..)--------))).... ( -19.20)
>DroSec_CAF1 19250 89 - 1
UCUGUCAACUUUCCAAUCAAAGAGAGACCAAGU---------AAACAGAGGCAGCAAAGAAGCUGCUUAGUUAUAU--------AUACACUGCAUAGCA--------UAGUAGC
(((((..((((.....((.....))....))))---------..)))))((((((......)))))).........--------.....((((......--------..)))). ( -18.60)
>DroSim_CAF1 16108 89 - 1
UCUGUCAACUUUCCAAUCAAAGAGAGACCAAGU---------AAACAGAGGCAGCAAAGAAGCUGCUUAGUUAUAU--------AUACACUGCAUUGCA--------UAGUAUC
(((((..((((.....((.....))....))))---------..)))))((((((......)))))).........--------((((..(((...)))--------..)))). ( -18.10)
>DroEre_CAF1 16198 104 - 1
UCUGUCAACUUUCCAAUCAAAAAGGGACCAAGUAAGCCAAGUGG--AGGAGCAGCAAAGAAGCUGCUUAGUUAUAU--------AUACACUGCGUAGCAUAGUGGCAUAGUAUC
.((((..(((((((..........)))..))))..((((.((((--..(((((((......)))))))..))))..--------.(((.....)))......)))))))).... ( -23.00)
>DroYak_CAF1 20620 103 - 1
UCUGUCAACUUUCCAAUCAAAGAGCGACCAAG---ACCAAGUAAACAGAAGCAGCAAAGAAGCUGCUUAGUUAUAU--------AUAUACUGCAUAGAAUAGUGGCACAGUAUC
.((((..((((((...((.......))....)---)..))))..))))(((((((......)))))))........--------..(((((((((......)))...)))))). ( -18.40)
>DroAna_CAF1 15885 74 - 1
UUUGUCAACUUACCAAUCAAAGAGAGACCAAGU---------AAACAGAAUCAGCAAAGAAGCUGACUAACAGGACAU-------------------------------GUAUA
..((((.((((.....((.....))....))))---------........(((((......))))).......)))).-------------------------------..... ( -11.30)
>consensus
UCUGUCAACUUUCCAAUCAAAGAGAGACCAAGU_________AAACAGAAGCAGCAAAGAAGCUGCUUAGUUAUAU________AUACACUGCAUAGCA________UAGUAUC
...(((..((((........)))).)))....................(((((((......))))))).............................................. (-11.85 = -11.47 +  -0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 2,001,684 – 2,001,778
Length 94
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -21.92
Consensus MFE -14.78
Energy contribution -14.20
Covariance contribution -0.58
Combinations/Pair 1.35
Mean z-score -1.73
Structure conservation index 0.67
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2001684 94 + 22407834
UAUAUAACUAAGCAGCUUCUUUGCUGCCUCUGUUU---------ACUUGGUCUCUCUUUGAUUGGAAAGUUGACAGAUU-GUGUUCCGGUUCAUUGCCUUACUU
.((((((....(((((......))))).((((((.---------((((.(((.......)))....)))).))))))))-))))...(((.....)))...... ( -22.40)
>DroSec_CAF1 19272 93 + 1
-AUAUAACUAAGCAGCUUCUUUGCUGCCUCUGUUU---------ACUUGGUCUCUCUUUGAUUGGAAAGUUGACAGAUU-GUGUUCUGGUUCAUUGCUUCACUU
-..........(((((......))))).((((((.---------((((.(((.......)))....)))).))))))..-(((....(((.....))).))).. ( -21.40)
>DroSim_CAF1 16130 93 + 1
-AUAUAACUAAGCAGCUUCUUUGCUGCCUCUGUUU---------ACUUGGUCUCUCUUUGAUUGGAAAGUUGACAGAUU-GUGUUCUGGUUCAUUGCCUUACUU
-((((((....(((((......))))).((((((.---------((((.(((.......)))....)))).))))))))-))))...(((.....)))...... ( -21.90)
>DroEre_CAF1 16228 100 + 1
-AUAUAACUAAGCAGCUUCUUUGCUGCUCCU--CCACUUGGCUUACUUGGUCCCUUUUUGAUUGGAAAGUUGACAGAUU-GUGUUCUGGUUCAUUGCCUUACUU
-.........((((((......))))))...--......(((...............(..(((....)))..)((((..-....)))).......)))...... ( -20.60)
>DroYak_CAF1 20650 100 + 1
-AUAUAACUAAGCAGCUUCUUUGCUGCUUCUGUUUACUUGGU---CUUGGUCGCUCUUUGAUUGGAAAGUUGACAGAUUCGUGUUCUGGUUCAUUGCCUUACUU
-.........((((((......))))))((((((.((((...---.(..((((.....))))..).)))).))))))...(((....(((.....))).))).. ( -25.70)
>DroAna_CAF1 15891 94 + 1
UGUCCUGUUAGUCAGCUUCUUUGCUGAUUCUGUUU---------ACUUGGUCUCUCUUUGAUUGGUAAGUUGACAAAUG-GUGUGUUAGUUCAUCGAGUUGCCU
.........(((((((......)))))))......---------....(((..(((.(..(((....)))..).....(-(((........)))))))..))). ( -19.50)
>consensus
_AUAUAACUAAGCAGCUUCUUUGCUGCCUCUGUUU_________ACUUGGUCUCUCUUUGAUUGGAAAGUUGACAGAUU_GUGUUCUGGUUCAUUGCCUUACUU
....(((((..(((((......)))))...................(..(((.......)))..)..)))))........(((....(((.....))).))).. (-14.78 = -14.20 +  -0.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 2,001,684 – 2,001,778
Length 94
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 83.33
Mean single sequence MFE -19.07
Consensus MFE -13.76
Energy contribution -13.35
Covariance contribution -0.41
Combinations/Pair 1.37
Mean z-score -1.93
Structure conservation index 0.72
SVM decision value 0.23
SVM RNA-class probability 0.643457
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2001684 94 - 22407834
AAGUAAGGCAAUGAACCGGAACAC-AAUCUGUCAACUUUCCAAUCAAAGAGAGACCAAGU---------AAACAGAGGCAGCAAAGAAGCUGCUUAGUUAUAUA
......((...(((..((((....-..))))))).(((((........))))).))..((---------((....(((((((......)))))))..))))... ( -19.20)
>DroSec_CAF1 19272 93 - 1
AAGUGAAGCAAUGAACCAGAACAC-AAUCUGUCAACUUUCCAAUCAAAGAGAGACCAAGU---------AAACAGAGGCAGCAAAGAAGCUGCUUAGUUAUAU-
..((...((..(((..((((....-..))))))).(((((........))))).....))---------..))..(((((((......)))))))........- ( -18.40)
>DroSim_CAF1 16130 93 - 1
AAGUAAGGCAAUGAACCAGAACAC-AAUCUGUCAACUUUCCAAUCAAAGAGAGACCAAGU---------AAACAGAGGCAGCAAAGAAGCUGCUUAGUUAUAU-
......((...(((..((((....-..))))))).(((((........))))).))..((---------((....(((((((......)))))))..))))..- ( -19.90)
>DroEre_CAF1 16228 100 - 1
AAGUAAGGCAAUGAACCAGAACAC-AAUCUGUCAACUUUCCAAUCAAAAAGGGACCAAGUAAGCCAAGUGG--AGGAGCAGCAAAGAAGCUGCUUAGUUAUAU-
......(((..(((..((((....-..)))))))(((((((..........)))..))))..)))..((((--..(((((((......)))))))..))))..- ( -25.10)
>DroYak_CAF1 20650 100 - 1
AAGUAAGGCAAUGAACCAGAACACGAAUCUGUCAACUUUCCAAUCAAAGAGCGACCAAG---ACCAAGUAAACAGAAGCAGCAAAGAAGCUGCUUAGUUAUAU-
.......((..(((..((((.......))))))).((((......)))).)).......---.....((((....(((((((......)))))))..))))..- ( -17.40)
>DroAna_CAF1 15891 94 - 1
AGGCAACUCGAUGAACUAACACAC-CAUUUGUCAACUUACCAAUCAAAGAGAGACCAAGU---------AAACAGAAUCAGCAAAGAAGCUGACUAACAGGACA
((....))...............(-(.(((((..((((.....((.....))....))))---------..))))).(((((......)))))......))... ( -14.40)
>consensus
AAGUAAGGCAAUGAACCAGAACAC_AAUCUGUCAACUUUCCAAUCAAAGAGAGACCAAGU_________AAACAGAAGCAGCAAAGAAGCUGCUUAGUUAUAU_
...........(((..((((.......))))))).(((((........)))))......................(((((((......)))))))......... (-13.76 = -13.35 +  -0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:52 2006