Locus 8009

Sequence ID 3L_DroMel_CAF1
Location 21,123,591 – 21,124,029
Length 438
Max. P 0.998324
window13082 window13083 window13084 window13085 window13086

overview

Window 2

Location 21,123,591 – 21,123,711
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.33
Mean single sequence MFE -38.30
Consensus MFE -35.10
Energy contribution -35.70
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.92
SVM decision value 2.01
SVM RNA-class probability 0.985436
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21123591 120 - 23771897
AAGGAUUUGUUAUUGGCCGAAAAGGCAAAAAUCAAUAAAAACGCCACAUGUAAGAGGACACCGGACACAAGCGACAUGGUGUCCAAUCGGCAGGGCAUGGGGCUCACGACACCUAGACUC
.(((..((((.....(((((...(((................)))..........((((((((..(......)...))))))))..))))).((((.....))))))))..)))...... ( -33.69)
>DroSec_CAF1 174298 120 - 1
AAGGAUUUGUGAUUGGCCGAAAAGGCAAAAAUCAAUAAAAGCGCCACAUGUAAGAGGACACCGGGCACAAGCGACAUGGUGGCCAAUCGGCAGGGCAUGGGGCUCACGACUCCUAGCCUC
.((((.((((((...(((.....)))................(((.(((((.......(((((.((....))....)))))(((....)))...))))).))))))))).))))...... ( -39.70)
>DroSim_CAF1 85996 120 - 1
AAGGAUUUGUGAUUGGCCGAAAAGGCAAAAAUCAAUAAAAGCGCCACAUGUAAGAGGACACCGGGCACAAGCGACAUGGUGGCCAAUCGGCAGGGCAUGGGGCUCACGACUCCUAGCCUC
.((((.((((((...(((.....)))................(((.(((((.......(((((.((....))....)))))(((....)))...))))).))))))))).))))...... ( -39.70)
>DroEre_CAF1 96719 120 - 1
AAGGAUUUGUGAUUGGCCGAAACGGCAAAAAUCAAUAAAAGCGCCACAUGUAAGAGGACACCGGGCACAAGCGACAUGGUGGCCAAUCGGCAGGGCAUGGGGCUCACGACUCCUAGCCUC
.((((.((((((...((((...))))................(((.(((((.......(((((.((....))....)))))(((....)))...))))).))))))))).))))...... ( -39.80)
>DroYak_CAF1 67686 120 - 1
AAGGAUUUGUGAUUGGCCGAAAAGGCAAAAAUCAAUAAAAGCGCCACAUGUAAGAGGACACCGGGCACAACCGACAUGGUGGCCAAUCGGCAGGGCAUGGGGCUCACGACUCCUAGCCUC
.((((.((((((...(((.....)))................(((.(((((.......(((((..(......)...)))))(((....)))...))))).))))))))).))))...... ( -38.60)
>consensus
AAGGAUUUGUGAUUGGCCGAAAAGGCAAAAAUCAAUAAAAGCGCCACAUGUAAGAGGACACCGGGCACAAGCGACAUGGUGGCCAAUCGGCAGGGCAUGGGGCUCACGACUCCUAGCCUC
.((((.((((((...(((.....)))................(((.(((((.......(((((..(......)...)))))(((....)))...))))).))))))))).))))...... (-35.10 = -35.70 +   0.60)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,123,671 – 21,123,791
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -27.50
Consensus MFE -24.92
Energy contribution -25.52
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.91
SVM decision value 3.07
SVM RNA-class probability 0.998324
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21123671 120 - 23771897
GUGUUGCGAAAAUUGAUUCGAACAUAAAUAAAGGGCAGCCAAGCGUGGCCAGACAAGGACAACAAAGGCAAGGGAAGCCGAAGGAUUUGUUAUUGGCCGAAAAGGCAAAAAUCAAUAAAA
(((((.((((......)))))))))............(((.....((((((((((((..(......(((.......)))...)..))))))..))))))....))).............. ( -29.50)
>DroSec_CAF1 174378 120 - 1
GUGUGGCGAAAAUUGAUUCGAACAUAAAUAAAGGGCAGCCAAGCGUGGCCAGACAAGGACAACAAAAGCAAGGGAAGCCGAAGGAUUUGUGAUUGGCCGAAAAGGCAAAAAUCAAUAAAA
...........((((((((((.(((((((....(((..((..((.((.((......))....))...))...))..))).....))))))).)))(((.....)))...))))))).... ( -28.20)
>DroSim_CAF1 86076 120 - 1
GUGUGGCGAAAAUUGAUUCGAACAUAAAUAAAGGGCAGCCAAGCGUGGCCAGACAAGGACAACAAAAGCAAGGGAAGCCGAAGGAUUUGUGAUUGGCCGAAAAGGCAAAAAUCAAUAAAA
...........((((((((((.(((((((....(((..((..((.((.((......))....))...))...))..))).....))))))).)))(((.....)))...))))))).... ( -28.20)
>DroEre_CAF1 96799 120 - 1
GUGUGGCGAAAAUUGAUUCGAACAUAAAUAAAGGGCAGCCAAGCGUGGCCAGACAAGGACAACAGAAGCAAGGGAAGCCGAAGGAUUUGUGAUUGGCCGAAACGGCAAAAAUCAAUAAAA
...........((((((((((.(((((((....(((..((..((.((.((......))....))...))...))..))).....))))))).)))((((...))))...))))))).... ( -27.20)
>DroYak_CAF1 67766 115 - 1
GUGUGGCGAAAAUUGAUUCGAACAUAAAUAAAGGGCAGCCAAGCGUGGCCAGACAAGGACAACAAAAGCA-----AGCCGAAGGAUUUGUGAUUGGCCGAAAAGGCAAAAAUCAAUAAAA
...........((((((((((.(((((((....(((.((((....)))).......(.....).......-----.))).....))))))).)))(((.....)))...))))))).... ( -24.40)
>consensus
GUGUGGCGAAAAUUGAUUCGAACAUAAAUAAAGGGCAGCCAAGCGUGGCCAGACAAGGACAACAAAAGCAAGGGAAGCCGAAGGAUUUGUGAUUGGCCGAAAAGGCAAAAAUCAAUAAAA
...........((((((((((.(((((((....(((..((..((.((.((......))....))...))...))..))).....))))))).)))(((.....)))...))))))).... (-24.92 = -25.52 +   0.60)

alignment

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secondary structure

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Window 4

Location 21,123,791 – 21,123,911
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.49
Mean single sequence MFE -22.16
Consensus MFE -20.12
Energy contribution -20.36
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.36
Structure conservation index 0.91
SVM decision value 0.89
SVM RNA-class probability 0.875355
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21123791 120 - 23771897
UGUCGUGGCAUUAACACUCACACGGGACAUACUAUUUCCAACUGAUAAUAAAGCCACCUCCCUUGCUCACUUCUUCUUUUCAUUCGCUCCAUUCACAGGAGGACAAUAAGAAAACUGCAA
....(((((.(((....(((...((((........))))...)))...))).)))))......(((.......(((((.....((.((((.......))))))....)))))....))). ( -21.50)
>DroSec_CAF1 174498 120 - 1
CGUCGUGGCAUUAACACUCACACGGGACAUACUAUUUCCAACUGAUAAUAAAGCCACCUCCCUUGCUCACUUCUUCUUUUCUUUCGCUCCAUUCACAGGAGGACAAUAAGAAAACUGCAA
.(..(((((.(((....(((...((((........))))...)))...))).)))))..)...(((....(((((.((.((((((............)))))).)).)))))....))). ( -22.60)
>DroSim_CAF1 86196 120 - 1
UGUCGUGGCAUUAACACUCGCACGGGACAUACUAUUUCCAACUGAUAAUAAAGCCACCUCCCUUGCUCACUUCUUCUUUUCUUUCGCUCCAUUCACAGGAGGACAAUAAGAAAACUGCAA
....(((((.(((....(((...((((........))))...)))...))).)))))......(((....(((((.((.((((((............)))))).)).)))))....))). ( -21.80)
>DroEre_CAF1 96919 116 - 1
UGUCGUGGCAUUAACACUCACACGGGACACACUAUUUCCAACUGAUAAUAAAGCCACCUC-CUUGCUCUC---UUCCUUUCUUUCGCUCCAUUCACAGGACGACAAUAAGAAAACUGCAA
....(((((.(((....(((...((((........))))...)))...))).)))))...-..(((....---....(((((((((.(((.......))))))....))))))...))). ( -19.60)
>DroYak_CAF1 67881 117 - 1
UGUCGUGGCAUUAGCACUCACACGGGACAUAGUAUUUCCAUCUGAUAAUAAAGCCACAUCCCUUGCUCAC---UUCUUUUCUUUCGCUCCAUUCACAGGAGGACAAUAAGAAAACUGCAA
....(((((.(((....(((...((((........))))...)))...))).)))))......(((....---(((((.....((.((((.......))))))....)))))....))). ( -25.30)
>consensus
UGUCGUGGCAUUAACACUCACACGGGACAUACUAUUUCCAACUGAUAAUAAAGCCACCUCCCUUGCUCACUUCUUCUUUUCUUUCGCUCCAUUCACAGGAGGACAAUAAGAAAACUGCAA
....(((((.(((....(((...((((........))))...)))...))).)))))......(((.......(((((.....((.((((.......))))))....)))))....))). (-20.12 = -20.36 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,123,871 – 21,123,991
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -30.36
Consensus MFE -27.74
Energy contribution -28.18
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.19
Structure conservation index 0.91
SVM decision value 0.12
SVM RNA-class probability 0.591808
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21123871 120 - 23771897
AAUUGUCUCGUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUUGGGCCGUCAAAUGUCGUGGCAUUAACACUCACACGGGACAUACUAUUUCCA
...((((((((((..(.(((((...)))))..)..))))......(((((.((((((.(((.......))).......)))))))))))..............))))))........... ( -31.00)
>DroSec_CAF1 174578 120 - 1
AAUUGUCUCAUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUUGGGCCGUCAAACGUCGUGGCAUUAACACUCACACGGGACAUACUAUUUCCA
...((((((.......(((....)))((..((((((.(((.....(((...)))....(((.......)))..))).)))))..)..))..............))))))........... ( -27.20)
>DroSim_CAF1 86276 120 - 1
AAUUGUCUCGUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUUGGGCCGUCAAAUGUCGUGGCAUUAACACUCGCACGGGACAUACUAUUUCCA
...((((((((((..(.(((((...)))))..)..))))......(((((.((((((.(((.......))).......)))))))))))..............))))))........... ( -31.00)
>DroEre_CAF1 96995 120 - 1
AAUUGUCUCGUUAUUCCUUGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUGGGGCCGUCAAAUGUCGUGGCAUUAACACUCACACGGGACACACUAUUUCCA
...((((((((.......((((((((((.................)))...(((....(((......))).))).........)))))))...........))))))))........... ( -30.90)
>DroYak_CAF1 67958 120 - 1
AAUUGUCUCGUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCGUUGGGCCGUCAAAUGUCGUGGCAUUAGCACUCACACGGGACAUAGUAUUUCCA
...((((((((....((((....)))).(((((......(....)(((((.((((((.(((.......))).......)))))))))))..))))).....))))))))........... ( -31.70)
>consensus
AAUUGUCUCGUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUUGGGCCGUCAAAUGUCGUGGCAUUAACACUCACACGGGACAUACUAUUUCCA
...((((((((((..(.(((((...)))))..)..))))......(((((.((((((.......((....))......)))))))))))..............))))))........... (-27.74 = -28.18 +   0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,123,911 – 21,124,029
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.90
Mean single sequence MFE -37.70
Consensus MFE -29.94
Energy contribution -30.62
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.67
Structure conservation index 0.79
SVM decision value 0.06
SVM RNA-class probability 0.562182
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21123911 118 - 23771897
GGCCCGAUGUUAAUUGAAUUGUCUGCGGCCC--CGAGCGCAAUUGUCUCGUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUUGGGCCGUCAAA
(((((((.(..(((.(...((((...(((..--.(((.((....)))))((((..(.(((((...)))))..)..))))......)))...))))...).)))..).)))))))...... ( -35.80)
>DroSec_CAF1 174618 118 - 1
GGCCCGAUGUUAAUUGAAUUGUCUGCGGCCC--CGAGCGCAAUUGUCUCAUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUUGGGCCGUCAAA
(((((((.(..(((.(((((((..(((((..--.(((.((....)))))......((((....))))..)))))...))))).))(((...)))......)))..).)))))))...... ( -34.30)
>DroSim_CAF1 86316 118 - 1
GGCCCGAUGUUAAUUGAAUUGUCUGCGGCCC--CGAGCGCAAUUGUCUCGUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUUGGGCCGUCAAA
(((((((.(..(((.(...((((...(((..--.(((.((....)))))((((..(.(((((...)))))..)..))))......)))...))))...).)))..).)))))))...... ( -35.80)
>DroEre_CAF1 97035 119 - 1
GGC-CGAUGUUAAUUGAAUUGUCUGCGGCCCUUUGAGCGCAAUUGUCUCGUUAUUCCUUGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUGGGGCCGUCAAA
(((-((((((((((((((((((..(((((((...(((.((....)))))((........))...)))))))......))))).)))..))))))))).(((......)))))))...... ( -36.40)
>DroYak_CAF1 67998 120 - 1
GGCCCGAUGUUAAUUGAAUUGUCUGCGGUCCUCCGCGCGCAAUUGUCUCGUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCGUUGGGCCGUCAAA
(((((((((..(((.(((((((.(((((....))))).))))))...((((((..(.(((((...)))))..)..))))))....(((...)))....).)))..)))))))))...... ( -46.20)
>consensus
GGCCCGAUGUUAAUUGAAUUGUCUGCGGCCC__CGAGCGCAAUUGUCUCGUUAUUCCCAGCCAUGGGCUGCUGUUUAACGAUCUCGCCAUUGGCAUUACCAUUUCCUUUGGGCCGUCAAA
(((((((.(..(((.(...((((...(((.....(((.((....)))))((((..(.(((((...)))))..)..))))......)))...))))...).)))..).)))))))...... (-29.94 = -30.62 +   0.68)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:48 2006