Locus 2946

Sequence ID X_DroMel_CAF1
Location 7,889,021 – 7,889,165
Length 144
Max. P 0.999987
window4834 window4835 window4836 window4837

overview

Window 4

Location 7,889,021 – 7,889,129
Length 108
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 67.42
Mean single sequence MFE -26.02
Consensus MFE -12.61
Energy contribution -14.99
Covariance contribution 2.38
Combinations/Pair 1.14
Mean z-score -3.86
Structure conservation index 0.48
SVM decision value 4.00
SVM RNA-class probability 0.999752
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7889021 108 + 22224390
--------ACACACUUUACACGAAUAUGUAUAUAUGGUUUACAGAGAUCUCUGGCCUAUGAUA--GCCAUAACAUAAGAUUUGGUAAUCACAAAUCUCUGUAAACAUAUACACCGACU
--------..................(((((((...((((((((((((...((((........--))))........((((....))))....)))))))))))))))))))...... ( -26.60)
>DroSec_CAF1 2909 109 + 1
--------ACACACUUCACACGAAUAUGUAUAUAUGGUUCACAGAGAUCGAUGGCCUACAAUAUGGCUAU-ACAUAAGAUUUGGUGAUCACAAAUCUCUGUGAACAUAUACACCGACU
--------..................(((((((...((((((((((((..((((((........))))))-......((((....))))....)))))))))))))))))))...... ( -32.80)
>DroEre_CAF1 2940 83 + 1
--------ACACACUUCACACGAAUC-GGGCGCAUGGUUCACAGAAACCUCUGGACUA--------------------------UAAUAACAAAUCUCUGUGACCAUAUACACCGACU
--------................((-((....(((((.((((((.............--------------------------............))))))))))).....)))).. ( -17.11)
>DroYak_CAF1 3008 100 + 1
AAAGAAAAACACAUUUUACACAAAUC-GGGCGUAUGGUGCACAGAAAUCGCUGGAAUA-------UCC-----ACCA-----GUUAAUAACAAAUCUCUGUGCCCAUAAACGCCGACU
..........................-.(((((((((.(((((((....(((((....-------...-----.)))-----))............)))))))))))..))))).... ( -27.59)
>consensus
________ACACACUUCACACGAAUA_GGACAUAUGGUUCACAGAAAUCGCUGGACUA_______GCC_____AUAA_____GGUAAUAACAAAUCUCUGUGAACAUAUACACCGACU
...........................((((((((((.((((((((((...((.....................................)).))))))))))))))))))))..... (-12.61 = -14.99 +   2.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 7,889,021 – 7,889,129
Length 108
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 67.42
Mean single sequence MFE -32.48
Consensus MFE -21.02
Energy contribution -22.15
Covariance contribution 1.13
Combinations/Pair 1.25
Mean z-score -3.62
Structure conservation index 0.65
SVM decision value 5.47
SVM RNA-class probability 0.999987
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7889021 108 - 22224390
AGUCGGUGUAUAUGUUUACAGAGAUUUGUGAUUACCAAAUCUUAUGUUAUGGC--UAUCAUAGGCCAGAGAUCUCUGUAAACCAUAUAUACAUAUUCGUGUAAAGUGUGU--------
.....((((((((((((((((((((((..((((....))))........((((--(......))))).))))))))))))).)))))))))...................-------- ( -34.10)
>DroSec_CAF1 2909 109 - 1
AGUCGGUGUAUAUGUUCACAGAGAUUUGUGAUCACCAAAUCUUAUGU-AUAGCCAUAUUGUAGGCCAUCGAUCUCUGUGAACCAUAUAUACAUAUUCGUGUGAAGUGUGU--------
.....(((((((((((((((((((((.(((..(..(((....((((.-.....)))))))..)..))).)))))))))))).)))))))))...................-------- ( -33.90)
>DroEre_CAF1 2940 83 - 1
AGUCGGUGUAUAUGGUCACAGAGAUUUGUUAUUA--------------------------UAGUCCAGAGGUUUCUGUGAACCAUGCGCCC-GAUUCGUGUGAAGUGUGU--------
((((((.(..(((((((((((((((((.(.....--------------------------......).))))))))))).))))))..)))-))))..............-------- ( -28.00)
>DroYak_CAF1 3008 100 - 1
AGUCGGCGUUUAUGGGCACAGAGAUUUGUUAUUAAC-----UGGU-----GGA-------UAUUCCAGCGAUUUCUGUGCACCAUACGCCC-GAUUUGUGUAAAAUGUGUUUUUCUUU
((((((.((.((((((((((((((((.((.....))-----.(.(-----((.-------....))).)))))))))))).))))).))))-))))...................... ( -33.90)
>consensus
AGUCGGUGUAUAUGGUCACAGAGAUUUGUGAUUACC_____UUAU_____GGC_______UAGGCCAGAGAUCUCUGUGAACCAUACACAC_GAUUCGUGUAAAGUGUGU________
((((.((((((((((((((((((((((.((...................................)).)))))))))))).)))))))))).))))...................... (-21.02 = -22.15 +   1.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 7,889,051 – 7,889,165
Length 114
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 74.15
Mean single sequence MFE -28.75
Consensus MFE -16.35
Energy contribution -16.66
Covariance contribution 0.31
Combinations/Pair 1.15
Mean z-score -2.44
Structure conservation index 0.57
SVM decision value 2.27
SVM RNA-class probability 0.991456
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7889051 114 + 22224390
UUACAGAGAUCUCUGGCCUAUGAUA--GCCAUAACAUAAGAUUUGGUAAUCACAAAUCUCUGUAAACAUAUACACCGACUAUGCUCUACUUACACAUUUGUGAUGUGGGCGUGUUG
((((((((((...((((........--))))........((((....))))....))))))))))..........((((.((((.(((((((((....))))).)))))))))))) ( -32.10)
>DroSec_CAF1 2939 115 + 1
UCACAGAGAUCGAUGGCCUACAAUAUGGCUAU-ACAUAAGAUUUGGUGAUCACAAAUCUCUGUGAACAUAUACACCGACUAUGCUCUACUUACACAUUUGUGAUGUGGGCGUGUUG
((((((((((..((((((........))))))-......((((....))))....))))))))))..........((((.((((.(((((((((....))))).)))))))))))) ( -38.30)
>DroEre_CAF1 2969 90 + 1
UCACAGAAACCUCUGGACUA--------------------------UAAUAACAAAUCUCUGUGACCAUAUACACCGACUAUGUUGUACUUACACAUUUGUGAUGUGGGCGUGUUA
(((((((.............--------------------------............)))))))((((((.(((.....((((.((....))))))..)))))))))........ ( -17.01)
>DroYak_CAF1 3045 99 + 1
GCACAGAAAUCGCUGGAAUA-------UCC-----ACCA-----GUUAAUAACAAAUCUCUGUGCCCAUAAACGCCGACUAUGUGGUACUUACACAUUUGCGAUGUGGGCGUAUUG
(((((((....(((((....-------...-----.)))-----))............)))))))......(((((.((.(((((.......))))).......)).))))).... ( -27.59)
>consensus
UCACAGAAAUCGCUGGACUA_______GCC_____AUAA_____GGUAAUAACAAAUCUCUGUGAACAUAUACACCGACUAUGCUCUACUUACACAUUUGUGAUGUGGGCGUGUUG
((((((((((...((.....................................)).))))))))))..............(((((.(((((((((....))))).)))))))))... (-16.35 = -16.66 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 7,889,051 – 7,889,165
Length 114
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 74.15
Mean single sequence MFE -27.03
Consensus MFE -20.44
Energy contribution -19.88
Covariance contribution -0.56
Combinations/Pair 1.24
Mean z-score -1.65
Structure conservation index 0.76
SVM decision value 1.20
SVM RNA-class probability 0.929250
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7889051 114 - 22224390
CAACACGCCCACAUCACAAAUGUGUAAGUAGAGCAUAGUCGGUGUAUAUGUUUACAGAGAUUUGUGAUUACCAAAUCUUAUGUUAUGGC--UAUCAUAGGCCAGAGAUCUCUGUAA
....((((((((((.....)))))......((......)))))))......((((((((((((..((((....))))........((((--(......))))).)))))))))))) ( -29.80)
>DroSec_CAF1 2939 115 - 1
CAACACGCCCACAUCACAAAUGUGUAAGUAGAGCAUAGUCGGUGUAUAUGUUCACAGAGAUUUGUGAUCACCAAAUCUUAUGU-AUAGCCAUAUUGUAGGCCAUCGAUCUCUGUGA
....((((((((((.....)))))......((......)))))))......(((((((((((.(((..(..(((....((((.-.....)))))))..)..))).))))))))))) ( -29.60)
>DroEre_CAF1 2969 90 - 1
UAACACGCCCACAUCACAAAUGUGUAAGUACAACAUAGUCGGUGUAUAUGGUCACAGAGAUUUGUUAUUA--------------------------UAGUCCAGAGGUUUCUGUGA
........(((.(((((...(((((.......)))))....))).)).)))((((((((((((.(.....--------------------------......).)))))))))))) ( -20.00)
>DroYak_CAF1 3045 99 - 1
CAAUACGCCCACAUCGCAAAUGUGUAAGUACCACAUAGUCGGCGUUUAUGGGCACAGAGAUUUGUUAUUAAC-----UGGU-----GGA-------UAUUCCAGCGAUUUCUGUGC
......(((((...(((...(((((.......)))))....)))....)))))(((((((((.((.....))-----.(.(-----((.-------....))).)))))))))).. ( -28.70)
>consensus
CAACACGCCCACAUCACAAAUGUGUAAGUACAACAUAGUCGGUGUAUAUGGUCACAGAGAUUUGUGAUUACC_____UUAU_____GGC_______UAGGCCAGAGAUCUCUGUGA
....(((((.((..(((....)))...(.....)...)).)))))......((((((((((((.((...................................)).)))))))))))) (-20.44 = -19.88 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:27 2006