Locus 540

Sequence ID 2L_DroMel_CAF1
Location 1,676,588 – 1,676,992
Length 404
Max. P 0.995306
window862 window863 window864 window865 window866 window867 window868

overview

Window 2

Location 1,676,588 – 1,676,707
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.61
Mean single sequence MFE -29.95
Consensus MFE -27.67
Energy contribution -27.92
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.92
SVM decision value 0.19
SVM RNA-class probability 0.627607
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1676588 119 - 22407834
CCUUUUUGGCCGGACUUUGUCCGGCGGUCAGAAUGGCA-AGCAAACGUUAUGCCAGAAACUAAAUUAAGAUUGAAAUGUAAAACUGAAAGCGUUUUACACAAUUAUUGAACGCUCGAGAC
...((((((((((((...)))))))(.((((..(((((-(((....))).))))).............(((((...((((((((.......))))))))))))).)))).)...))))). ( -32.40)
>DroSec_CAF1 3045 116 - 1
CCUU-UUGGCCGGACUUUGUCCGGCGGUCAGAAUGGCA-AGCAAACGUUAUGCCAGAAACUAAAUUAAGAUUGAAAUGUAAAACUGAAAGCGUUUUACACAAUUAUUGAACGCUCG--AC
....-...(((((((...))))))).(((....(((((-(((....))).))))).........(((((((((...((((((((.......))))))))))))).))))......)--)) ( -30.90)
>DroSim_CAF1 3932 116 - 1
CCUU-UUGGCCGGACUUUGUCCGGCGGUCAGAAUGGGA-AGCAAACGUUAUGCCAGAAACUAAAUUAAGAUUGAAAUGUAAAACUGAAAGCGUUUUACACAAUUAUUGAACGCUCG--AC
((((-((((((((((...)))))))...))))).))((-.((....(((........)))....(((((((((...((((((((.......))))))))))))).))))..)))).--.. ( -26.90)
>DroYak_CAF1 4074 117 - 1
CCUU-UUAGACGGACUUUGUCCGGCGGUCAGAAAGGCAGAGCAAACGUUAUGCCAGAAACUAAAUUAAGAUUGAAAUGUAAAACUGAAAGCGUUUUACACAAUUAUUGAACGCUCG--AC
....-.....(((((...)))))(((.((((...((((.(((....))).))))..............(((((...((((((((.......))))))))))))).)))).)))...--.. ( -29.60)
>consensus
CCUU_UUGGCCGGACUUUGUCCGGCGGUCAGAAUGGCA_AGCAAACGUUAUGCCAGAAACUAAAUUAAGAUUGAAAUGUAAAACUGAAAGCGUUUUACACAAUUAUUGAACGCUCG__AC
..........(((((...)))))(((.((((...((((.(((....))).))))..............(((((...((((((((.......))))))))))))).)))).)))....... (-27.67 = -27.92 +   0.25)

alignment

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secondary structure

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Window 3

Location 1,676,668 – 1,676,758
Length 90
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 70.00
Mean single sequence MFE -29.83
Consensus MFE -19.59
Energy contribution -19.82
Covariance contribution 0.23
Combinations/Pair 1.10
Mean z-score -1.26
Structure conservation index 0.66
SVM decision value 0.52
SVM RNA-class probability 0.768214
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1676668 90 + 22407834
U-UGCCAUUCUGACCGCCGGACAAAGUCCGGCCAAAAAGGGGUUCCGUCCGAAU----------------------UUGGGUAUUUACGGAUUUAUUGCGAGGGGUAGGCAAA
(-((((((((((((((((((((...)))))))(......))))).(((..((((----------------------(((........)))))))...))).))))).))))). ( -29.30)
>DroSec_CAF1 3123 85 + 1
U-UGCCAUUCUGACCGCCGGACAAAGUCCGGCCAA-AAGGGGUUCCGUCCGAAAAAAUG--------------------------AAGGGAUUUAUUACGAGGGGUAGCCAAA
(-((((.(((.(((.(((((((...)))))))...-..((....))))).)))..((((--------------------------((....))))))......)))))..... ( -23.50)
>DroYak_CAF1 4152 112 + 1
UCUGCCUUUCUGACCGCCGGACAAAGUCCGUCUAA-AAGGGGUUUUGUCCGCAAAAAAUUACGAGGGGGAUGGUGCAUGGGUAUUUACGGAUUUGUUUCGAGGGGCAGGCAAA
((((((((((.....((.(((((((..((.(....-.).))..)))))))))..........((((.(((((((((....))))).....)))).)))))))))))))).... ( -36.70)
>consensus
U_UGCCAUUCUGACCGCCGGACAAAGUCCGGCCAA_AAGGGGUUCCGUCCGAAAAAA____________________UGGGUAUUUACGGAUUUAUUACGAGGGGUAGGCAAA
..((((..((.....(((((((...)))))))......(..((...(((((....................................)))))..))..)))..))))...... (-19.59 = -19.82 +   0.23)

alignment

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secondary structure

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Window 4

Location 1,676,668 – 1,676,758
Length 90
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 70.00
Mean single sequence MFE -24.83
Consensus MFE -14.79
Energy contribution -15.23
Covariance contribution 0.45
Combinations/Pair 1.06
Mean z-score -1.36
Structure conservation index 0.60
SVM decision value 0.11
SVM RNA-class probability 0.589681
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1676668 90 - 22407834
UUUGCCUACCCCUCGCAAUAAAUCCGUAAAUACCCAA----------------------AUUCGGACGGAACCCCUUUUUGGCCGGACUUUGUCCGGCGGUCAGAAUGGCA-A
.(((((.....((.((......(((((......((..----------------------....)))))))...........(((((((...))))))).)).))...))))-) ( -25.20)
>DroSec_CAF1 3123 85 - 1
UUUGGCUACCCCUCGUAAUAAAUCCCUU--------------------------CAUUUUUUCGGACGGAACCCCUU-UUGGCCGGACUUUGUCCGGCGGUCAGAAUGGCA-A
(((((((...............(((.((--------------------------(........))).))).......-...(((((((...))))))))))))))......-. ( -23.20)
>DroYak_CAF1 4152 112 - 1
UUUGCCUGCCCCUCGAAACAAAUCCGUAAAUACCCAUGCACCAUCCCCCUCGUAAUUUUUUGCGGACAAAACCCCUU-UUAGACGGACUUUGUCCGGCGGUCAGAAAGGCAGA
.....(((((..((...........(((........)))......((((..((((....))))(((((((..((...-......))..))))))))).))...))..))))). ( -26.10)
>consensus
UUUGCCUACCCCUCGAAAUAAAUCCGUAAAUACCCA____________________UUUUUUCGGACGGAACCCCUU_UUGGCCGGACUUUGUCCGGCGGUCAGAAUGGCA_A
..((((.(((.....................................................((........))......(((((((...))))))))))......)))).. (-14.79 = -15.23 +   0.45)

alignment

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secondary structure

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Window 5

Location 1,676,721 – 1,676,838
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.82
Mean single sequence MFE -15.61
Consensus MFE -11.95
Energy contribution -12.20
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.77
SVM decision value 0.67
SVM RNA-class probability 0.818873
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1676721 117 - 22407834
AGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACCGUCCAAAUGGCGAACAACAAAAAUAACAAUUUGCCUACCCCUCGCAAUAAAUCCGUAAAUACCCAA---
.(((((((.......(((.(((((......))))))))............((((.....))))...............)))))))................................--- ( -14.50)
>DroSec_CAF1 3180 108 - 1
AGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACCGGCCAAAUGGCGAACAACAAAAAUAACAAUUUGGCUACCCCUCGUAAUAAAUCCCUU------------
.((............(((.(((((......)))))))).............((((((((....................)))))))).......))............------------ ( -14.15)
>DroSim_CAF1 4088 120 - 1
AGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACCGGCCAAAUGGCGAACAACAAAAAUAACAAUUUGGCUACCCCUCGCAAUAAAUCCGUAAAUACCCACGAA
.((............(((.(((((......)))))))).............((((((((....................)))))))).......))........(((........))).. ( -17.15)
>DroYak_CAF1 4224 120 - 1
AGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACUGGCCAAAUGGCAAACAACAAAAAUAACAAUUUGCCUGCCCCUCGAAACAAAUCCGUAAAUACCCAUGCA
.(((...........(((.(((((......)))))))).............(((.....((((((...............)))))).)))..........................))). ( -16.66)
>consensus
AGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACCGGCCAAAUGGCGAACAACAAAAAUAACAAUUUGCCUACCCCUCGCAAUAAAUCCGUAAAUACCCA____
((((((((.......(((.(((((......))))))))..............(((....)))................)))))).))................................. (-11.95 = -12.20 +   0.25)

alignment

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secondary structure

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Window 6

Location 1,676,758 – 1,676,872
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.51
Mean single sequence MFE -33.17
Consensus MFE -30.46
Energy contribution -29.90
Covariance contribution -0.56
Combinations/Pair 1.06
Mean z-score -3.02
Structure conservation index 0.92
SVM decision value 2.56
SVM RNA-class probability 0.995306
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1676758 114 + 22407834
UUGUUAUUUUUGUUGUUCGCCAUUUGGACGGUUGAUCUUUUGGCUAAUGAAGUUUGUCAUUGAGCUUUAUUUAAUUUGCUGAUGAUGCGAAUGGAAAGAACAACAGAAGGAA------CG
..(((.((((((((((((.(((((((...(((..(....)..)))((((((((((......))))))))))................)))))))...)))))))))))).))------). ( -36.10)
>DroSec_CAF1 3208 116 + 1
UUGUUAUUUUUGUUGUUCGCCAUUUGGCCGGUUGAUCUUUUGGCUAAUGAAGUUUGUCAUUGAGCUUUAUUUAAUUUGCUGAUGAUGCGAAU----AGAACAACAGAAGGAAAGGGAUCG
......(((((((((((((((....))).(((..(....)..)))((((((((((......))))))))))..((((((.......))))))----.))))))))))))........... ( -32.30)
>DroSim_CAF1 4128 116 + 1
UUGUUAUUUUUGUUGUUCGCCAUUUGGCCGGUUGAUCUUUUGGCUAAUGAAGUUUGUCAUUGAGCUUUAUUUAAUUUGCUGAUGAUGCAAAU----AGAACAACAGAAGGAAAGGGAACG
......(((((((((((((((....))).(((..(....)..)))((((((((((......))))))))))..((((((.......))))))----.))))))))))))....(....). ( -32.80)
>DroYak_CAF1 4264 116 + 1
UUGUUAUUUUUGUUGUUUGCCAUUUGGCCAGUUGAUCUUUUGGCUAAUGAAGUUUGUCAUUGAGCUUUAUUUAAUUUGCUGAUGAUGCGAAU----AAAACAACAGAAGGCAAGGGAAUG
((((..((((((((((((.....((((((((........))))))))((((((((......))))))))....((((((.......))))))----.))))))))))))))))....... ( -31.50)
>consensus
UUGUUAUUUUUGUUGUUCGCCAUUUGGCCGGUUGAUCUUUUGGCUAAUGAAGUUUGUCAUUGAGCUUUAUUUAAUUUGCUGAUGAUGCGAAU____AGAACAACAGAAGGAAAGGGAACG
......((((((((((((((((...(..(....)..)...)))).((((((((((......))))))))))..((((((.......)))))).....))))))))))))........... (-30.46 = -29.90 +  -0.56)

alignment

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secondary structure

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Window 7

Location 1,676,758 – 1,676,872
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.51
Mean single sequence MFE -20.85
Consensus MFE -18.48
Energy contribution -18.35
Covariance contribution -0.13
Combinations/Pair 1.05
Mean z-score -3.07
Structure conservation index 0.89
SVM decision value 2.27
SVM RNA-class probability 0.991396
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1676758 114 - 22407834
CG------UUCCUUCUGUUGUUCUUUCCAUUCGCAUCAUCAGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACCGUCCAAAUGGCGAACAACAAAAAUAACAA
.(------((..((.((((((((...(((((.((.......))............(((.(((((......))))))))..................))))).)))))))).))..))).. ( -21.10)
>DroSec_CAF1 3208 116 - 1
CGAUCCCUUUCCUUCUGUUGUUCU----AUUCGCAUCAUCAGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACCGGCCAAAUGGCGAACAACAAAAAUAACAA
...............((((((((.----..((((.......))............(((.(((((......)))))))).....)).......(((....))))))))))).......... ( -21.00)
>DroSim_CAF1 4128 116 - 1
CGUUCCCUUUCCUUCUGUUGUUCU----AUUUGCAUCAUCAGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACCGGCCAAAUGGCGAACAACAAAAAUAACAA
...............((((((((.----((((((.......))))))........(((.(((((......))))))))..............(((....))))))))))).......... ( -23.40)
>DroYak_CAF1 4264 116 - 1
CAUUCCCUUGCCUUCUGUUGUUUU----AUUCGCAUCAUCAGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACUGGCCAAAUGGCAAACAACAAAAAUAACAA
...............((((((((.----..((((.......))............(((.(((((......)))))))).....)).......(((....))))))))))).......... ( -17.90)
>consensus
CGUUCCCUUUCCUUCUGUUGUUCU____AUUCGCAUCAUCAGCAAAUUAAAUAAAGCUCAAUGACAAACUUCAUUAGCCAAAAGAUCAACCGGCCAAAUGGCGAACAACAAAAAUAACAA
...............((((((((.........((.......))............(((.(((((......))))))))..............(((....))))))))))).......... (-18.48 = -18.35 +  -0.13)

alignment

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secondary structure

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Window 8

Location 1,676,872 – 1,676,992
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.68
Mean single sequence MFE -17.61
Consensus MFE -13.83
Energy contribution -13.61
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -1.69
Structure conservation index 0.79
SVM decision value 0.29
SVM RNA-class probability 0.668267
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1676872 120 - 22407834
UUUACAGAUUUUACUUUCAAAUUUCAAAAUCGCUGAUACUCUUCUGUAUCAAUAAUUCCUUUUUAAAAUCAUUAACCCAUCUGGAAUCGAACCUUUUUAGGCCUUUGUUUGAUUGCCACC
......(((((((.(((........))).....((((((......))))))............)))))))...........(((((((((((..............)))))))).))).. ( -16.04)
>DroSec_CAF1 3324 104 - 1
--------------UUUAAAAUUUG--AAUCGCUGAUACACUUCUGUAUCAUAUAUUCCCUUUUAAAAUCAUUAACCCAUCUGGAAUCGAACCUUUUUAAGCCUUUGUUUGAUUGCCGCC
--------------(((((((...(--(((...(((((((....)))))))...))))..)))))))...............((((((((((..............)))))))).))... ( -17.64)
>DroSim_CAF1 4244 118 - 1
CUUACAGAUUUUACUUUCAAAUUUG--AAUCGCUGAUACACGUCUGUAUCAUAUGAUCCCUUUUAAAAUCAUUAACCUAUCUGGAAUCGAACCUUUUUAUGGCUUUGUUUGAUUGCCGCC
......(((((((..((((....))--))....(((((((....)))))))............)))))))............((((((((((..............)))))))).))... ( -19.14)
>consensus
_UUACAGAUUUUACUUUCAAAUUUG__AAUCGCUGAUACACUUCUGUAUCAUAUAUUCCCUUUUAAAAUCAUUAACCCAUCUGGAAUCGAACCUUUUUAAGCCUUUGUUUGAUUGCCGCC
.................................((((((......))))))..............................(((((((((((..............)))))))).))).. (-13.83 = -13.61 +  -0.22)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:46 2006