Locus 3431

Sequence ID X_DroMel_CAF1
Location 9,167,307 – 9,167,519
Length 212
Max. P 0.800808
window5618 window5619 window5620

overview

Window 8

Location 9,167,307 – 9,167,405
Length 98
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 68.41
Mean single sequence MFE -30.42
Consensus MFE -15.99
Energy contribution -16.93
Covariance contribution 0.94
Combinations/Pair 1.11
Mean z-score -1.67
Structure conservation index 0.53
SVM decision value 0.55
SVM RNA-class probability 0.779515
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9167307 98 + 22224390
UUUAUGCCGGCCCUGUCGAGGGGUGCCUUGGAACAGGCCAUCCAACAGGUGGGCAUAAAGCCGCGAGAGAUUAAG--------------CUGAAAAGCAAAAAAAAUCAAAU
((((((((.(((.(((....((((((((......))).))))).)))))).))))))))..(....).......(--------------((....))).............. ( -33.00)
>DroVir_CAF1 86487 107 + 1
UUUAUGCCUUCACUUACGCGUACGGCCUUAGAGCAGGCUAUAAAGCAAGCAGGAAUUGAUUUUAGUUGUAAUAUGGGUCAAACCUGCGACUGGAA-----CCAAAAACAAAU
......(((...(((.(...((..((((......))))..))..).))).)))..(((.(((((((((((....((......)))))))))))))-----.)))........ ( -23.00)
>DroSim_CAF1 1994 98 + 1
UUUAUGCCGGCCCUGUCGAGGGGUGCCUUGGAACAGGCCAUCCAACAGGUGGGCAUCAGGCCGCGAGAGAUUAGG--------------CUGAAAAGCAAAAAAAAUCAAAU
....((((.(((.(((....((((((((......))).))))).)))))).))))((((.((.(....)....))--------------))))................... ( -31.30)
>DroYak_CAF1 1987 98 + 1
UUUAUGCCGGCCCUGUCGCGGGGUGCCUUGGAACAGGCCAUCCAACAGGUGGGCAUCAAGCCGCGUGGGCGUAAG--------------GCGACAAACAAAGCAAAUCAAAU
....((((.((((...((((((((((((((((........))))......)))))))...))))).))))....)--------------))).................... ( -34.40)
>consensus
UUUAUGCCGGCCCUGUCGAGGGGUGCCUUGGAACAGGCCAUCCAACAGGUGGGCAUCAAGCCGCGAGAGAUUAAG______________CUGAAAAGCAAAAAAAAUCAAAU
...(((((.(((.(((...(((..((((......))))..))).)))))).)))))........................................................ (-15.99 = -16.93 +   0.94)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,167,307 – 9,167,405
Length 98
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 68.41
Mean single sequence MFE -28.04
Consensus MFE -18.62
Energy contribution -17.25
Covariance contribution -1.38
Combinations/Pair 1.38
Mean z-score -1.22
Structure conservation index 0.66
SVM decision value 0.41
SVM RNA-class probability 0.726108
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9167307 98 - 22224390
AUUUGAUUUUUUUUGCUUUUCAG--------------CUUAAUCUCUCGCGGCUUUAUGCCCACCUGUUGGAUGGCCUGUUCCAAGGCACCCCUCGACAGGGCCGGCAUAAA
....((((......(((....))--------------)..))))..........(((((((..((((((((...((((......)))).....))))))))...))))))). ( -29.20)
>DroVir_CAF1 86487 107 - 1
AUUUGUUUUUGG-----UUCCAGUCGCAGGUUUGACCCAUAUUACAACUAAAAUCAAUUCCUGCUUGCUUUAUAGCCUGCUCUAAGGCCGUACGCGUAAGUGAAGGCAUAAA
........(((.-----...)))..(((((.((((..................))))..))))).((((((...((((......))))....(((....))))))))).... ( -24.37)
>DroSim_CAF1 1994 98 - 1
AUUUGAUUUUUUUUGCUUUUCAG--------------CCUAAUCUCUCGCGGCCUGAUGCCCACCUGUUGGAUGGCCUGUUCCAAGGCACCCCUCGACAGGGCCGGCAUAAA
...................((((--------------((...........)).))))((((..((((((((...((((......)))).....))))))))...)))).... ( -28.40)
>DroYak_CAF1 1987 98 - 1
AUUUGAUUUGCUUUGUUUGUCGC--------------CUUACGCCCACGCGGCUUGAUGCCCACCUGUUGGAUGGCCUGUUCCAAGGCACCCCGCGACAGGGCCGGCAUAAA
....(((..((...))..)))((--------------(....((((.((((((.....)))........((...((((......))))...)))))...)))).)))..... ( -30.20)
>consensus
AUUUGAUUUUUUUUGCUUUUCAG______________CUUAAUCCCACGCGGCUUGAUGCCCACCUGUUGGAUGGCCUGUUCCAAGGCACCCCGCGACAGGGCCGGCAUAAA
..................................................(((.....)))....((((((...((((......))))..(((......))))))))).... (-18.62 = -17.25 +  -1.38)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,167,405 – 9,167,519
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.66
Mean single sequence MFE -38.60
Consensus MFE -16.40
Energy contribution -19.40
Covariance contribution 3.00
Combinations/Pair 1.23
Mean z-score -1.85
Structure conservation index 0.42
SVM decision value 0.62
SVM RNA-class probability 0.800808
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9167405 114 + 22224390
UGCUGUGGAGGAUAACUCGCUGCGGAUCGGCUCCACCC----G--UUGGCCACUGGGCAAUCCGACUCAGGCGCAGCUAUCCAAGGUGCCGCACACCUUGUUCUACGAGAUGCCGCAGCA
.(((((((.(((((....((((((....((((......----.--..)))).(((((........))))).)))))))))))((((((.....)))))).............))))))). ( -45.50)
>DroVir_CAF1 86594 114 + 1
CAGCGUAGUGCACAACAAACUACUCAUUGGCAAAACUCUGAUGCAGUUGCCA--GAGAAAUC----ACUGGAGCAGCAAUCGAAGGUGCCUAGCACCCUGUUCUACGAAAUGCCACAACA
..(.(((((.........))))).)..(((((...(((((..((....))))--))).....----..((((((((........(((((...))))))))))))).....)))))..... ( -32.40)
>DroSim_CAF1 2092 114 + 1
UGCUGUGGAGGAUAACUCGCUGCGGAUCGGCUCCACCC----G--CUGGCCACUGGGCAAUCCUACUCAGGCGCAGCUAUCCAAGGUGCCGCACACCUUGUUCUACGAGAUGCCGCAGCA
.(((((((.(((((....(((((((.(((((.......----)--)))))).(((((........)))))..))))))))))((((((.....)))))).............))))))). ( -47.10)
>DroYak_CAF1 2085 114 + 1
AGCUGUGGAGGAUAACUCGCUGCGCAUCGGCUCCACAC----G--CUGGCCACUGGGCAAUCCCACGCAGGCGCAGCUAUCCAAAGUGCCACACACCUUGUUCUACGAGAUGCCGCAGCA
.(((((((.(((((....(((((((..((((.......----)--)))((...((((....)))).))..))))))))))))...........((.((((.....)))).))))))))). ( -45.30)
>DroMoj_CAF1 413358 114 + 1
UAGUGUAGUGAACAAUAAACUACGAAUUGGAGAAACAGAAAUGGAGCUGUCA--GAGAUAUC----ACGGGAUCAGCAAUCAAAAGUGCCCAGCACACUAUUCUAUGAUAUGCCACAGCA
...((((((.........))))))...........((....))..(((((..--(..(((((----(..((((.....)))....((((...))))......)..))))))..)))))). ( -22.70)
>consensus
UGCUGUGGAGGAUAACUCGCUGCGCAUCGGCUCCACAC____G__CUGGCCACUGGGCAAUCC_ACACAGGCGCAGCUAUCCAAGGUGCCGCACACCUUGUUCUACGAGAUGCCGCAGCA
.(((((((..........((((((....((((...............))))...((....)).........))))))....(((((((.....)))))))............))))))). (-16.40 = -19.40 +   3.00)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:18 2006