Locus 375

Sequence ID X_DroMel_CAF1
Location 1,128,492 – 1,128,629
Length 137
Max. P 0.987851
window565 window566 window567 window568

overview

Window 5

Location 1,128,492 – 1,128,595
Length 103
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 75.89
Mean single sequence MFE -20.16
Consensus MFE -13.86
Energy contribution -13.46
Covariance contribution -0.40
Combinations/Pair 1.12
Mean z-score -2.20
Structure conservation index 0.69
SVM decision value 2.10
SVM RNA-class probability 0.987851
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1128492 103 + 22224390
UUAUUCUAGUAU-UUUCUCUCUUUACUCUCCUGCUGCUUCUU-UUUCGGUAUCAUUUGA--------AAAGAAUUGUUAUUUGUGAAGCUUUUAC-GGCUUCGCAUUUUGGACU
............-...............(((......(((((-((.(((......))))--------))))))........(((((((((.....-)))))))))....))).. ( -18.60)
>DroSim_CAF1 26553 103 + 1
UUAUUCUAGUAU-UUUCUCUCUUUACUCUCCUGCUGCUUCUU-UUUCGGUUUCAUUUGA--------AAAGAAUUGUUAUUUGUGAAGCUUUUAC-GGCUUCGCAUUUUGGACU
............-...............(((......(((((-((.(((......))))--------))))))........(((((((((.....-)))))))))....))).. ( -18.60)
>DroEre_CAF1 26359 105 + 1
UUAUUCUAGUAUACUUCGGUCUGUAUUCGCCUGCUGCUUCUUUUUUCAGUUUCAUUUGA--------AAAGAAUUGUUAUUUGUGAAGCUUUUAC-GGCUUCGCAUUUUGGACU
.................(((((..................(((((((((......))))--------))))).........(((((((((.....-)))))))))....))))) ( -21.90)
>DroYak_CAF1 25965 99 + 1
CGAUUCU-------------CUUUAUUCGCCUGCUGCUUCUU-UUUCAGUUUCAUUUGAACAUUUGGAAAGAAUUGUUAUUUGUGAAGCUUUUAC-GGCUUCGCAUUUUGGACU
(((((((-------------.((((((((..((..(((....-....)))..))..))))....)))).))))))).....(((((((((.....-)))))))))......... ( -20.60)
>DroAna_CAF1 48895 79 + 1
----------------------UUC---UAAGACUGUUUCC--UCUCGGUUUCAGUUAA--------AGAGAAUUGUUAUUUGUGAAGCUCUUACUGGCUUCGCAUUUUCGACU
----------------------(((---(..(((((...((--....))...)))))..--------))))..(((.....(((((((((......)))))))))....))).. ( -21.10)
>consensus
UUAUUCUAGUAU__UUC__UCUUUACUCUCCUGCUGCUUCUU_UUUCGGUUUCAUUUGA________AAAGAAUUGUUAUUUGUGAAGCUUUUAC_GGCUUCGCAUUUUGGACU
................................((((..........)))).........................(((...(((((((((......))))))))).....))). (-13.86 = -13.46 +  -0.40) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 1,128,492 – 1,128,595
Length 103
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 75.89
Mean single sequence MFE -15.42
Consensus MFE -10.11
Energy contribution -10.03
Covariance contribution -0.08
Combinations/Pair 1.20
Mean z-score -1.50
Structure conservation index 0.66
SVM decision value 0.21
SVM RNA-class probability 0.635985
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1128492 103 - 22224390
AGUCCAAAAUGCGAAGCC-GUAAAAGCUUCACAAAUAACAAUUCUUU--------UCAAAUGAUACCGAAA-AAGAAGCAGCAGGAGAGUAAAGAGAGAAA-AUACUAGAAUAA
..(((....((((((((.-......)))))...........((((((--------((..........).))-))))))))...)))...............-............ ( -14.90)
>DroSim_CAF1 26553 103 - 1
AGUCCAAAAUGCGAAGCC-GUAAAAGCUUCACAAAUAACAAUUCUUU--------UCAAAUGAAACCGAAA-AAGAAGCAGCAGGAGAGUAAAGAGAGAAA-AUACUAGAAUAA
..(((....((((((((.-......)))))...........((((((--------((..........).))-))))))))...)))...............-............ ( -14.90)
>DroEre_CAF1 26359 105 - 1
AGUCCAAAAUGCGAAGCC-GUAAAAGCUUCACAAAUAACAAUUCUUU--------UCAAAUGAAACUGAAAAAAGAAGCAGCAGGCGAAUACAGACCGAAGUAUACUAGAAUAA
.(((.....((((((((.-......)))))...........((((((--------(((........)))..)))))))))...)))..((((........)))).......... ( -16.10)
>DroYak_CAF1 25965 99 - 1
AGUCCAAAAUGCGAAGCC-GUAAAAGCUUCACAAAUAACAAUUCUUUCCAAAUGUUCAAAUGAAACUGAAA-AAGAAGCAGCAGGCGAAUAAAG-------------AGAAUCG
.(((.....((((((((.-......)))))...........((((((.......(((....)))......)-))))))))...)))........-------------....... ( -15.42)
>DroAna_CAF1 48895 79 - 1
AGUCGAAAAUGCGAAGCCAGUAAGAGCUUCACAAAUAACAAUUCUCU--------UUAACUGAAACCGAGA--GGAAACAGUCUUA---GAA----------------------
.........((.(((((........))))).))...........(((--------...((((...((....--))...))))...)---)).---------------------- ( -15.80)
>consensus
AGUCCAAAAUGCGAAGCC_GUAAAAGCUUCACAAAUAACAAUUCUUU________UCAAAUGAAACCGAAA_AAGAAGCAGCAGGAGAAUAAAGA__GAA__AUACUAGAAUAA
.........((((((((........)))))...........(((((.........((....)).........)))))...)))............................... (-10.11 = -10.03 +  -0.08) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 1,128,528 – 1,128,629
Length 101
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 93.42
Mean single sequence MFE -28.00
Consensus MFE -24.15
Energy contribution -24.82
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.86
SVM decision value 1.25
SVM RNA-class probability 0.935698
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1128528 101 + 22224390
UUCUU-UUUCGGUAUCAUUUGA--------AAAGAAUUGUUAUUUGUGAAGCUUUUAC-GGCUUCGCAUUUUGGACUGUCGACAAGUUGACAAAUGGCAAACCGGUUUGGC
..((.-..(((((....(((..--------..))).(((((((((((((((((.....-))))))))..........(((((....)))))))))))))))))))...)). ( -28.00)
>DroSec_CAF1 25160 101 + 1
UUCUU-UUUCGGUUUCAUUUGA--------AAAGAAUUGUUAUUUGUGAAGCUUUUAC-GGCUUCGCAUUUUGGACUGUCGACAAGUUGACAAAUGGCAAACCGGUUUGGC
..((.-..((((((((((((..--------........(((...(((((((((.....-))))))))).....))).(((((....)))))))))))..))))))...)). ( -27.60)
>DroSim_CAF1 26589 101 + 1
UUCUU-UUUCGGUUUCAUUUGA--------AAAGAAUUGUUAUUUGUGAAGCUUUUAC-GGCUUCGCAUUUUGGACUGUCGACAAGUUGACAAAUGGCAAACCGGUUUGGC
..((.-..((((((((((((..--------........(((...(((((((((.....-))))))))).....))).(((((....)))))))))))..))))))...)). ( -27.60)
>DroEre_CAF1 26396 102 + 1
UUCUUUUUUCAGUUUCAUUUGA--------AAAGAAUUGUUAUUUGUGAAGCUUUUAC-GGCUUCGCAUUUUGGACUGUCGACAAGUUGACAAAUGGCAAACCGGUUUGGC
...(((((((((......))))--------))))).(((((((((((((((((.....-))))))))..........(((((....))))))))))))))........... ( -28.10)
>DroYak_CAF1 25989 109 + 1
UUCUU-UUUCAGUUUCAUUUGAACAUUUGGAAAGAAUUGUUAUUUGUGAAGCUUUUAC-GGCUUCGCAUUUUGGACUGUCGACAAGUUGACAAAUGGCAAACCGGUUUGGC
(((((-((..((((((....))).)))..)))))))(((((((((((((((((.....-))))))))..........(((((....))))))))))))))........... ( -28.50)
>DroAna_CAF1 48907 101 + 1
UUCC--UCUCGGUUUCAGUUAA--------AGAGAAUUGUUAUUUGUGAAGCUCUUACUGGCUUCGCAUUUUCGACUGUCGACAAGUUGACAAAUGGCAAACCGGUUUGGC
..((--..((((((((......--------.)))).(((((((((((((((((......))))))))....((((((.......)))))).))))))))).))))...)). ( -28.20)
>consensus
UUCUU_UUUCGGUUUCAUUUGA________AAAGAAUUGUUAUUUGUGAAGCUUUUAC_GGCUUCGCAUUUUGGACUGUCGACAAGUUGACAAAUGGCAAACCGGUUUGGC
........((((((((((((..................(((...(((((((((......))))))))).....))).(((((....)))))))))))..))))))...... (-24.15 = -24.82 +   0.67) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 1,128,528 – 1,128,629
Length 101
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 93.42
Mean single sequence MFE -17.02
Consensus MFE -16.92
Energy contribution -16.87
Covariance contribution -0.06
Combinations/Pair 1.06
Mean z-score -0.66
Structure conservation index 0.99
SVM decision value 0.00
SVM RNA-class probability 0.534377
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1128528 101 - 22224390
GCCAAACCGGUUUGCCAUUUGUCAACUUGUCGACAGUCCAAAAUGCGAAGCC-GUAAAAGCUUCACAAAUAACAAUUCUUU--------UCAAAUGAUACCGAAA-AAGAA
.......((((....((((((((........))).........((.(((((.-......))))).))..............--------..)))))..))))...-..... ( -16.40)
>DroSec_CAF1 25160 101 - 1
GCCAAACCGGUUUGCCAUUUGUCAACUUGUCGACAGUCCAAAAUGCGAAGCC-GUAAAAGCUUCACAAAUAACAAUUCUUU--------UCAAAUGAAACCGAAA-AAGAA
.......((((((..((((((((........))).........((.(((((.-......))))).))..............--------..)))))))))))...-..... ( -17.90)
>DroSim_CAF1 26589 101 - 1
GCCAAACCGGUUUGCCAUUUGUCAACUUGUCGACAGUCCAAAAUGCGAAGCC-GUAAAAGCUUCACAAAUAACAAUUCUUU--------UCAAAUGAAACCGAAA-AAGAA
.......((((((..((((((((........))).........((.(((((.-......))))).))..............--------..)))))))))))...-..... ( -17.90)
>DroEre_CAF1 26396 102 - 1
GCCAAACCGGUUUGCCAUUUGUCAACUUGUCGACAGUCCAAAAUGCGAAGCC-GUAAAAGCUUCACAAAUAACAAUUCUUU--------UCAAAUGAAACUGAAAAAAGAA
.......((((((..((((((((........))).........((.(((((.-......))))).))..............--------..)))))))))))......... ( -15.70)
>DroYak_CAF1 25989 109 - 1
GCCAAACCGGUUUGCCAUUUGUCAACUUGUCGACAGUCCAAAAUGCGAAGCC-GUAAAAGCUUCACAAAUAACAAUUCUUUCCAAAUGUUCAAAUGAAACUGAAA-AAGAA
.......((((((..((((((.((..(((....))).......((.(((((.-......))))).))...................))..))))))))))))...-..... ( -15.80)
>DroAna_CAF1 48907 101 - 1
GCCAAACCGGUUUGCCAUUUGUCAACUUGUCGACAGUCGAAAAUGCGAAGCCAGUAAGAGCUUCACAAAUAACAAUUCUCU--------UUAACUGAAACCGAGA--GGAA
.((....((((((.....(((((........))))).......((.(((((........))))).))..............--------.......))))))...--)).. ( -18.40)
>consensus
GCCAAACCGGUUUGCCAUUUGUCAACUUGUCGACAGUCCAAAAUGCGAAGCC_GUAAAAGCUUCACAAAUAACAAUUCUUU________UCAAAUGAAACCGAAA_AAGAA
.......((((((.....(((((........))))).......((.(((((........))))).)).............................))))))......... (-16.92 = -16.87 +  -0.06) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:57 2006