Locus 8662

Sequence ID X_DroMel_CAF1
Location 21,950,879 – 21,951,182
Length 303
Max. P 0.997958
window14234 window14235 window14236 window14237 window14238

overview

Window 4

Location 21,950,879 – 21,950,989
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.73
Mean single sequence MFE -22.93
Consensus MFE -17.36
Energy contribution -17.08
Covariance contribution -0.28
Combinations/Pair 1.15
Mean z-score -1.48
Structure conservation index 0.76
SVM decision value -0.05
SVM RNA-class probability 0.505737
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21950879 110 - 22224390
UGG--------CAACUUUUUCACCAUCUCCACUUUUCGACCACACAUCGGGGACAAACUUUACUUUGUAUUUGAGUGUGUG--UUUGCCAGUUGAUGAUUCUCGAAUUUCAUUUCUUUUU
.(.--------...)........((((...(((...(((.(((((((((((.(((((......))))).))))).))))))--.)))..))).))))......(((......)))..... ( -20.20)
>DroSec_CAF1 9407 111 - 1
UGG--------CAACUUU-UCCCCAUCUCUACUUUUCGGCCACACAUCGAGGACAAACUUUACUUUGUAUUUGAGUGUGUGUUUUUGCCAGUUGAUGAUUCUCGAAUUUCAUUCCUUUUU
(((--------(((....-...((.............)).(((((((((((.(((((......))))).))))).))))))...))))))...(((((..........)))))....... ( -21.52)
>DroSim_CAF1 1068 111 - 1
UGG--------CAACUUU-UCCCCAUCUCUACUUUUCGGCCACACAUCGAGGACAAACUUUACUUUGUAUUUGAGUGUGUGUGUUUGCCAGUUGAUGAUUCUCGAAUUUCAUUCCUUUUU
(((--------(((....-...((.............)).(((((((((((.(((((......))))).))))).))))))...))))))...(((((..........)))))....... ( -21.52)
>DroEre_CAF1 1018 109 - 1
CGG--------CAACUUUUUCCCCAUCUCCACUUUUCGACCACACAUCGAGGACAAACUUUACUUUGUAUUUGAGUGUGU--G-UUGCCAGUUGAUGAUUCUCGAAUUUCAUUUCUGUUU
.(.--------...)........((((...(((...(((((((((.(((((.(((((......))))).)))))))))).--)-)))..))).))))......(((......)))..... ( -23.10)
>DroYak_CAF1 8965 119 - 1
CGGCAACUCGGCAACUUUUUCCCCAUCUCCACUUUUCGACCACACAUCGAGGACAAACUUUACUUUGUAUCCGAGUGUGUGCG-UUGCCGGUUGAUGAUUCUCGAAUUUCAUUUAUAUUU
(((((((..(....)......................(..(((((.(((.(((((((......))))).))))))))))..))-))))))((.(((((..........))))).)).... ( -28.30)
>consensus
UGG________CAACUUUUUCCCCAUCUCCACUUUUCGACCACACAUCGAGGACAAACUUUACUUUGUAUUUGAGUGUGUG_GUUUGCCAGUUGAUGAUUCUCGAAUUUCAUUUCUUUUU
.......................((((...(((...(((.(((((((((((.(((((......))))).))))).))))))...)))..))).))))....................... (-17.36 = -17.08 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 21,950,989 – 21,951,109
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.17
Mean single sequence MFE -25.80
Consensus MFE -24.32
Energy contribution -24.16
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.47
Structure conservation index 0.94
SVM decision value 0.99
SVM RNA-class probability 0.895939
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21950989 120 - 22224390
ACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAAUUACUCGGCUGCUCUUUUGAAAGACUUUUUGCCUAAUGCU
.....((((((((((..((((......))))......)))))...((((((..((..((.(((((((........))))))).))..))..))..)))).........)))))....... ( -26.90)
>DroSec_CAF1 9518 120 - 1
ACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAAUUACUCGGCUGCUCUUUAGAAAGACUUUUUGCCUAAUGCC
.....((((((((((..((((......))))......))))).......((..((..((.(((((((........))))))).))..))..))...............)))))....... ( -25.10)
>DroSim_CAF1 1179 120 - 1
ACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAAUUACUCGGCUGCUCUUUUGAAAGACUUUUUGCCUAAUGCC
.....((((((((((..((((......))))......)))))...((((((..((..((.(((((((........))))))).))..))..))..)))).........)))))....... ( -26.90)
>DroEre_CAF1 1127 120 - 1
ACUUUGGCAACGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAAUUACUCGGCUGCUCUUUUGAAAGACUUUUUGCCUAAUGCU
.....(((((.((((..((((......))))......))))....((((((..((..((.(((((((........))))))).))..))..))..)))).........)))))....... ( -26.40)
>DroYak_CAF1 9084 120 - 1
ACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAAUUACUCGGUUGCUCUUUUAAAAGACUUUUUGCCUAAUGCU
.....((((((((((..((((......))))......))))).......((..((..((.(((((((........))))))).))..))..))...............)))))....... ( -23.70)
>consensus
ACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAAUUACUCGGCUGCUCUUUUGAAAGACUUUUUGCCUAAUGCU
.....(((((.((((..((((......))))......))))........((..((..((.(((((((........))))))).))..))..))...............)))))....... (-24.32 = -24.16 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 21,951,029 – 21,951,142
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.80
Mean single sequence MFE -25.42
Consensus MFE -21.98
Energy contribution -21.82
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.15
Structure conservation index 0.86
SVM decision value 2.56
SVM RNA-class probability 0.995331
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21951029 113 + 22224390
UUUCAUUGUUGUUCGAAAUUUCUUAGCCACUUUUGUCGUGCACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGC-------UUUUAUUUUUUUCUUUCCCAAGGAGAA
.......................((((((((((.((.((((.(..((.....))..)((......)))))).)).)))))))))).-------.......((((((((....)))))))) ( -23.90)
>DroSec_CAF1 9558 120 + 1
UUUCAUUGUUGUUCGAAAUUUCUUAGCCACUUUUGUCGUGCACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGCAUUUAUUUUUUAUUUUUUUCUUUCCCAAGGAGAA
..............(((((....((((((((((.((.((((.(..((.....))..)((......)))))).)).)))))))))).....))))).....((((((((....)))))))) ( -24.20)
>DroSim_CAF1 1219 120 + 1
UUUCAUUGUUGUUCGAAAUUUCUUAGCCACUUUUGUCGUGCACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGCAUUUAUUUUUUAUUUUUUUCGUUCCCAAGGAGAA
((((.(((..(..(((((.....((((((((((.((.((((.(..((.....))..)((......)))))).)).))))))))))....((.....))....)))))..).))).)))). ( -25.30)
>DroEre_CAF1 1167 114 + 1
UUUCAUUGUUGUUCGAAAUUUCUUAGCCACUUUUGUCGUGCACUUAUUUAUUAUUUGGCUAAUUCGCGCGUUGCCAAAGUGGCUGCAUUUA--UU----UUUUUGGCUUCCCAAGGAGAA
.......................((((((((((.(((((((..(((.(((.....))).)))...)))))..)).))))))))))......--((----(((((((....))))))))). ( -26.80)
>DroYak_CAF1 9124 116 + 1
UUUCAUUGUUGUUCGAAAUUUCUUAGCCACUUUUGUCGUGCACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGCAUUUGGUUU----UUUUUGCUUUGCCAAGGAGAA
..................(((((((((((((((.((.((((.(..((.....))..)((......)))))).)).)))))))))(((...(((..----.....))).)))..)))))). ( -26.90)
>consensus
UUUCAUUGUUGUUCGAAAUUUCUUAGCCACUUUUGUCGUGCACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGCAUUUA_UUUUUAUUUUUUUCUUUCCCAAGGAGAA
((((.(((......((....)).((((((((((.((.((((.(..((.....))..)((......)))))).)).))))))))))..........................))).)))). (-21.98 = -21.82 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 21,951,029 – 21,951,142
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.80
Mean single sequence MFE -21.90
Consensus MFE -19.44
Energy contribution -19.64
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 0.89
SVM decision value 2.97
SVM RNA-class probability 0.997958
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21951029 113 - 22224390
UUCUCCUUGGGAAAGAAAAAAAUAAAA-------GCAGCCACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAA
((((.....))))..............-------..(((((((((.....(((((..((((......))))......))))).....)))))))))........................ ( -21.00)
>DroSec_CAF1 9558 120 - 1
UUCUCCUUGGGAAAGAAAAAAAUAAAAAAUAAAUGCAGCCACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAA
((((.....)))).......................(((((((((.....(((((..((((......))))......))))).....)))))))))........................ ( -21.00)
>DroSim_CAF1 1219 120 - 1
UUCUCCUUGGGAACGAAAAAAAUAAAAAAUAAAUGCAGCCACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAA
((((..(((....)))....................(((((((((.....(((((..((((......))))......))))).....))))))))).))))................... ( -21.60)
>DroEre_CAF1 1167 114 - 1
UUCUCCUUGGGAAGCCAAAAA----AA--UAAAUGCAGCCACUUUGGCAACGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAA
((((..((((....))))...----..--.......((((((((((....)((((..((((......))))......))))......))))))))).))))................... ( -23.80)
>DroYak_CAF1 9124 116 - 1
UUCUCCUUGGCAAAGCAAAAA----AAACCAAAUGCAGCCACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAA
...((.(((.....(((....----........)))(((((((((.....(((((..((((......))))......))))).....)))))))))................))).)).. ( -22.10)
>consensus
UUCUCCUUGGGAAAGAAAAAAAUAAAAA_UAAAUGCAGCCACUUUGGCAAUGCGCGAAUUAGCCAAAUAAUAAAUAAGUGCACGACAAAAGUGGCUAAGAAAUUUCGAACAACAAUGAAA
...((.(((...........................(((((((((.....(((((..((((......))))......))))).....)))))))))..((....))......))).)).. (-19.44 = -19.64 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 21,951,069 – 21,951,182
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.80
Mean single sequence MFE -28.96
Consensus MFE -22.96
Energy contribution -25.24
Covariance contribution 2.28
Combinations/Pair 1.03
Mean z-score -1.45
Structure conservation index 0.79
SVM decision value 0.04
SVM RNA-class probability 0.551968
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21951069 113 + 22224390
CACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGC-------UUUUAUUUUUUUCUUUCCCAAGGAGAAAAGUAAUGAAAGUGCAAGGGAUAACUUUUUCGGUGGCCAA
..............(((((((....((((...(((.....)))...-------..(((((((((((((.....))))))))))))).....))))..(..(......)..)..))))))) ( -29.10)
>DroSec_CAF1 9598 120 + 1
CACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGCAUUUAUUUUUUAUUUUUUUCUUUCCCAAGGAGAAAAGUAAUGAAAGUGCAAGGGAUAACUUUUUCGGUGGCCAA
..............(((((((....((((...(((.....)))........(((.(((((((((((((.....))))))))))))).))).))))..(..(......)..)..))))))) ( -29.90)
>DroSim_CAF1 1259 120 + 1
CACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGCAUUUAUUUUUUAUUUUUUUCGUUCCCAAGGAGAAAAGUAAUGAAAGUGCAAGGGAUAACUUUUUCGGUGGCCAA
..............(((((((....((((...(((.....)))........(((.(((((((((((.(.....).))))))))))).))).))))..(..(......)..)..))))))) ( -28.20)
>DroEre_CAF1 1207 114 + 1
CACUUAUUUAUUAUUUGGCUAAUUCGCGCGUUGCCAAAGUGGCUGCAUUUA--UU----UUUUUGGCUUCCCAAGGAGAAAAGUAAUGAAAGUGCAAGGGAUAACUUUUUCGGUGGCCAA
..............(((((((....((((((.(((.....))).))((((.--((----(((((((....))))))))).)))).......))))..(..(......)..)..))))))) ( -29.80)
>DroYak_CAF1 9164 116 + 1
CACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGCAUUUGGUUU----UUUUUGCUUUGCCAAGGAGAAAAGUAAUGAAAGUGCAAGGGAUAACUUUUUCGGUGGCCAA
..............(((((((....((((...((((((((....)).))))))((----((.(((((((.(....)...))))))).))))))))..(..(......)..)..))))))) ( -27.80)
>consensus
CACUUAUUUAUUAUUUGGCUAAUUCGCGCAUUGCCAAAGUGGCUGCAUUUA_UUUUUAUUUUUUUCUUUCCCAAGGAGAAAAGUAAUGAAAGUGCAAGGGAUAACUUUUUCGGUGGCCAA
..............(((((((....((((...(((.....)))............(((((((((((((.....))))))))))))).....))))..(..(......)..)..))))))) (-22.96 = -25.24 +   2.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:42 2006