Locus 1393

Sequence ID X_DroMel_CAF1
Location 4,187,913 – 4,188,091
Length 178
Max. P 0.924069
window2221 window2222 window2223

overview

Window 1

Location 4,187,913 – 4,188,029
Length 116
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 89.43
Mean single sequence MFE -39.47
Consensus MFE -31.42
Energy contribution -32.05
Covariance contribution 0.63
Combinations/Pair 1.12
Mean z-score -2.27
Structure conservation index 0.80
SVM decision value 1.16
SVM RNA-class probability 0.924069
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4187913 116 - 22224390
CGU--GAGAGUAUGAAAAUAUGCAAAGGGCAGAACACAAUUUGCGUGUUGUGAUUCGACAAAGGUUUUGUGAAAAACCUUUGGCCUCACCGUGGUUUUCCGGCAUGGGAAAGCGGCCC
.((--(((.((((....)))).)....(((.(((((((((......)))))).)))..((((((((((....))))))))))))))))).((.(((((((......))))))).)).. ( -41.40)
>DroSec_CAF1 19564 116 - 1
CGU--GAGGGUAUGAAAAUAUGCAAAGGGCAGAACACAAUUUGCGUGUUGUGAUUCGACAAAGGUUUUGCGAAAAACCUUUGGCCUCACAGUGCUUUUCCGGCAUGGGAAAGCGGCCC
.((--(((.((((....)))).)....(((.(((((((((......)))))).)))..((((((((((....)))))))))))))))))..(((((((((.....))))))))).... ( -43.80)
>DroEre_CAF1 21067 114 - 1
CGU--GAGGGUAUGAAAAUAUGCAAAGGGGAAAACACAAUUUGCGUGUUGUGAUUCGACAAAGGUU-UGCGAG-AACCUUUGGCCUCGUGGUGGUUUCUCGGCAUGGAAAAGCGGCCC
...--((((...((((((((((((((..(.......)..))))))))))....)))).((((((((-(....)-)))))))).))))..(((.((((.((......)).)))).))). ( -36.40)
>DroYak_CAF1 24145 116 - 1
CGUAUGAGGGCAUGAAAAUAUGCAAAGGGCAGCACACAAUUUGCGUGUUGUGAUUCGACGAAGGUU-UGCGAG-AACCUUUGGCCUCGUGGUGGUUUCUCGACAUGGUAAAGUGGCCC
.......((((.........(((.....)))...(((..(((((((((((.((..(..((((((((-(....)-))))))))(((....))).)..)).)))))).)))))))))))) ( -36.30)
>consensus
CGU__GAGGGUAUGAAAAUAUGCAAAGGGCAGAACACAAUUUGCGUGUUGUGAUUCGACAAAGGUU_UGCGAA_AACCUUUGGCCUCACGGUGGUUUCCCGGCAUGGGAAAGCGGCCC
.....(((.((.((((((((((((((..(.......)..))))))))))....)))).((((((((((....)))))))))))))))..(((.(((((((......))))))).))). (-31.42 = -32.05 +   0.63)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,187,953 – 4,188,065
Length 112
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 92.90
Mean single sequence MFE -28.60
Consensus MFE -20.83
Energy contribution -22.45
Covariance contribution 1.62
Combinations/Pair 1.11
Mean z-score -2.22
Structure conservation index 0.73
SVM decision value 0.01
SVM RNA-class probability 0.539193
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4187953 112 + 22224390
GGUUUUUCACAAAACCUUUGUCGAAUCACAACACGCAAAUUGUGUUCUGCCCUUUGCAUAUUUUCAUACUCUC--ACGGAGCGUGGAAACCACUGAAAAGUGGAUGUACUAAUU
((((((....))))))...((.(((.(((((........)))))))).))....(((((.((((((..(((..--...)))..))))))(((((....))))))))))...... ( -29.30)
>DroSec_CAF1 19604 112 + 1
GGUUUUUCGCAAAACCUUUGUCGAAUCACAACACGCAAAUUGUGUUCUGCCCUUUGCAUAUUUUCAUACCCUC--ACGGAGCGUGAAAACCACUGAAAAGUGGAUGUACUAAUU
((((((....))))))...((.(((.(((((........)))))))).))....(((((.((((((..(((..--..)).)..))))))(((((....))))))))))...... ( -27.70)
>DroEre_CAF1 21107 110 + 1
GGUU-CUCGCA-AACCUUUGUCGAAUCACAACACGCAAAUUGUGUUUUCCCCUUUGCAUAUUUUCAUACCCUC--ACGGAGCGUGAAAACCACUGAAAAGUGGAUGUACUAAUU
((((-(..(((-(....)))).)))))..((((((.....))))))........(((((.((((((..(((..--..)).)..))))))(((((....))))))))))...... ( -26.80)
>DroYak_CAF1 24185 112 + 1
GGUU-CUCGCA-AACCUUCGUCGAAUCACAACACGCAAAUUGUGUGCUGCCCUUUGCAUAUUUUCAUGCCCUCAUACGGAGCGUGAAAGCCACUGAAAAGUGUAUGUACUAAUU
((((-(..((.-.......)).))))).((.(((((.....))))).)).....(((((((((((((((((......)).))))))))).((((....))))))))))...... ( -30.60)
>consensus
GGUU_CUCGCA_AACCUUUGUCGAAUCACAACACGCAAAUUGUGUUCUGCCCUUUGCAUAUUUUCAUACCCUC__ACGGAGCGUGAAAACCACUGAAAAGUGGAUGUACUAAUU
(((((......)))))...((.(((.(((((........)))))))).))....(((((.(((((((.(((......)).).)))))))(((((....))))))))))...... (-20.83 = -22.45 +   1.62)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,187,993 – 4,188,091
Length 98
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 85.69
Mean single sequence MFE -26.32
Consensus MFE -18.34
Energy contribution -19.52
Covariance contribution 1.19
Combinations/Pair 1.10
Mean z-score -1.88
Structure conservation index 0.70
SVM decision value 0.48
SVM RNA-class probability 0.751472
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4187993 98 - 22224390
-----AUCGCU---------CACGAUGACACCGAUAAUUGAAUUAGUACAUCCACUUUUCAGUGGUUUCCACGCUCCGU--GAGAGUAUGAAAAUAUGCAAAGGGCAGAACACA
-----...(((---------(..((((..((..((......))..)).))))...((((((((((...))))(((.(..--..)))).))))))........))))........ ( -19.80)
>DroSec_CAF1 19644 103 - 1
UUUAAAUCGCU---------CACGAUGACACUGAUAAUUGAAUUAGUACAUCCACUUUUCAGUGGUUUUCACGCUCCGU--GAGGGUAUGAAAAUAUGCAAAGGGCAGAACACA
........(((---------(..((((..((((((......)))))).))))((((....))))(((((((..(.((..--..)))..))))))).......))))........ ( -27.80)
>DroEre_CAF1 21145 98 - 1
-----GUCGCC---------CAUGAUGAUACUGAUAAUUGAAUUAGUACAUCCACUUUUCAGUGGUUUUCACGCUCCGU--GAGGGUAUGAAAAUAUGCAAAGGGGAAAACACA
-----((..((---------(..((((.(((((((......)))))))))))..((((.((...(((((((..(.((..--..)))..))))))).)).)))))))...))... ( -31.70)
>DroYak_CAF1 24223 109 - 1
-----AUCGCUGAUACAGAUCACGAUGAUACUGAUAAUUCAAUUAGUACAUACACUUUUCAGUGGCUUUCACGCUCCGUAUGAGGGCAUGAAAAUAUGCAAAGGGCAGCACACA
-----...((((...(........(((.(((((((......))))))))))....((((((...(((((((..(...)..))))))).))))))........)..))))..... ( -26.00)
>consensus
_____AUCGCU_________CACGAUGACACUGAUAAUUGAAUUAGUACAUCCACUUUUCAGUGGUUUUCACGCUCCGU__GAGGGUAUGAAAAUAUGCAAAGGGCAGAACACA
........(((............((((.(((((((......)))))))))))..((((.((...(((((((.((((.......)))).))))))).)).)))))))........ (-18.34 = -19.52 +   1.19)

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 10:08:17 2006