Locus 5409

Sequence ID 3L_DroMel_CAF1
Location 14,822,742 – 14,822,886
Length 144
Max. P 0.998085
window8561 window8562 window8563

overview

Window 1

Location 14,822,742 – 14,822,846
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.44
Mean single sequence MFE -33.82
Consensus MFE -22.04
Energy contribution -25.44
Covariance contribution 3.40
Combinations/Pair 1.18
Mean z-score -2.97
Structure conservation index 0.65
SVM decision value 3.00
SVM RNA-class probability 0.998085
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14822742 104 + 23771897
AAAGGCAAAAGGCAAGUGCAACUGCGUUUGCCACUGCAG--------------GUUGCAUAUUGCUCUGCUAUGCUCUUUACAACUUGUAUCAAGUUGU--UUUGGUGCUUUCUAGUUCU
...((((...((((((((((((((((........)))).--------------))))))).))))).))))..((.((..((((((((...))))))))--...)).))........... ( -32.80)
>DroSec_CAF1 57533 104 + 1
AAAAGCAAAAGGCAAGUGCAACUGCGUUUGCCACUGCAG--------------GUUGCAGAUUGCUCUGCUAUGCUCUUUACAACUUGCAUCAAGUUGU--UUUGGUGCUUUCUAGCUCU
...(((((..(((((((((....))))))))).((((..--------------...)))).)))))..((((.((.((..((((((((...))))))))--...)).))....))))... ( -36.70)
>DroSim_CAF1 50733 104 + 1
AAAGGCAAAAGGCAAGUGCAACUGCGUUUGCCACUGCAG--------------GUUGCAGAUUGCUCUGCUAUGCUCUUUACAACUUGCAUCAAGUUGU--UUUGGUGCUUUCUAGCUCU
..((((((..(((((((((....))))))))).((((..--------------...)))).)))).))((((.((.((..((((((((...))))))))--...)).))....))))... ( -36.80)
>DroYak_CAF1 60844 118 + 1
AAAGGCAAAAGGCAAGUGCAACUGCGUUUGCCACUGCAGGUUGCUGGUUGCAGGUUGCAGAUUGCUCUGCAAUGCUCUUUACAACUUCCAUCAAGUUGU--UUUGGUGUUUUUUAGCUCU
..((((((..(((((((((....))))))))).((((((.((((.....)))).)))))).)))).))((((.((.((..(((((((.....)))))))--...)).))...)).))... ( -39.80)
>DroAna_CAF1 54928 102 + 1
AAAGCCAAAAGGCAAAGGCAAACGUAAACGCAAUUCAAA--------------A--CCAGGUUGCUAUGCCAUGCUCUUUAGAACUUGUUUCGAGUUUUGAGUCUCUGCUUUUCAAA--U
.......(((((((.((((....(((...((((((....--------------.--...))))))..)))........((((((((((...)))))))))))))).)))))))....--. ( -23.00)
>consensus
AAAGGCAAAAGGCAAGUGCAACUGCGUUUGCCACUGCAG______________GUUGCAGAUUGCUCUGCUAUGCUCUUUACAACUUGCAUCAAGUUGU__UUUGGUGCUUUCUAGCUCU
...(((((..(((((((((....))))))))).((((((.((((.....)))).)))))).)))))..((((.((.((..((((((((...)))))))).....)).))....))))... (-22.04 = -25.44 +   3.40)

alignment

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secondary structure

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Window 2

Location 14,822,742 – 14,822,846
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.44
Mean single sequence MFE -29.98
Consensus MFE -17.38
Energy contribution -19.38
Covariance contribution 2.00
Combinations/Pair 1.06
Mean z-score -2.51
Structure conservation index 0.58
SVM decision value 1.95
SVM RNA-class probability 0.983720
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14822742 104 - 23771897
AGAACUAGAAAGCACCAAA--ACAACUUGAUACAAGUUGUAAAGAGCAUAGCAGAGCAAUAUGCAAC--------------CUGCAGUGGCAAACGCAGUUGCACUUGCCUUUUGCCUUU
...................--((((((((...))))))))((((.(((....((.((((..((((((--------------.(((.((.....))))))))))).))))))..))))))) ( -27.30)
>DroSec_CAF1 57533 104 - 1
AGAGCUAGAAAGCACCAAA--ACAACUUGAUGCAAGUUGUAAAGAGCAUAGCAGAGCAAUCUGCAAC--------------CUGCAGUGGCAAACGCAGUUGCACUUGCCUUUUGCUUUU
.......(((((((.....--((((((((...))))))))((((.(((..(((((....)))))...--------------.(((((..((....))..)))))..)))))))))))))) ( -33.90)
>DroSim_CAF1 50733 104 - 1
AGAGCUAGAAAGCACCAAA--ACAACUUGAUGCAAGUUGUAAAGAGCAUAGCAGAGCAAUCUGCAAC--------------CUGCAGUGGCAAACGCAGUUGCACUUGCCUUUUGCCUUU
((((.(((((.((......--((((((((...)))))))).(((.(((..(((((....)))))...--------------((((.((.....)))))).))).))))).))))).)))) ( -31.20)
>DroYak_CAF1 60844 118 - 1
AGAGCUAAAAAACACCAAA--ACAACUUGAUGGAAGUUGUAAAGAGCAUUGCAGAGCAAUCUGCAACCUGCAACCAGCAACCUGCAGUGGCAAACGCAGUUGCACUUGCCUUUUGCCUUU
...(((.............--(((((((.....))))))).....((((((((((....)))))))..)))....))).....((((.(((((..((....))..)))))..)))).... ( -34.90)
>DroAna_CAF1 54928 102 - 1
A--UUUGAAAAGCAGAGACUCAAAACUCGAAACAAGUUCUAAAGAGCAUGGCAUAGCAACCUGG--U--------------UUUGAAUUGCGUUUACGUUUGCCUUUGCCUUUUGGCUUU
.--.(..(((.((((((..((((((((.(...((.((((....)))).))((...))...).))--)--------------)))))...(((........))))))))).)))..).... ( -22.60)
>consensus
AGAGCUAGAAAGCACCAAA__ACAACUUGAUGCAAGUUGUAAAGAGCAUAGCAGAGCAAUCUGCAAC______________CUGCAGUGGCAAACGCAGUUGCACUUGCCUUUUGCCUUU
.......(((.(((.......(((((((.....)))))))((((.(((..(((((....)))))..................(((((..((....))..)))))..)))))))))).))) (-17.38 = -19.38 +   2.00)

alignment

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secondary structure

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Window 3

Location 14,822,781 – 14,822,886
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.52
Mean single sequence MFE -27.31
Consensus MFE -19.85
Energy contribution -20.93
Covariance contribution 1.08
Combinations/Pair 1.10
Mean z-score -2.17
Structure conservation index 0.73
SVM decision value 1.11
SVM RNA-class probability 0.916772
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14822781 105 - 23771897
AAGAUGUGGCCACUUCAGACUUUCAACAUGUGGCUGCCACAGAACUAGAAAGCACCAAA--ACAACUUGAUACAAGUUGUAAAGAGCAUAGCAGAGCAAUAUGCAAC-------------
.....(..(((((................)))))..)......................--((((((((...)))))))).....(((((.........)))))...------------- ( -22.99)
>DroSec_CAF1 57572 105 - 1
AAGAUGUGGCCACUUCAGACUUUCAACAUGUGGCUGCCACAGAGCUAGAAAGCACCAAA--ACAACUUGAUGCAAGUUGUAAAGAGCAUAGCAGAGCAAUCUGCAAC-------------
.....(..(((((................)))))..)......(((....)))......--((((((((...))))))))..........(((((....)))))...------------- ( -29.69)
>DroSim_CAF1 50772 105 - 1
AAGAUGUGGCCACUUCAGACUUUCAACAUGUGGCUGCCACAGAGCUAGAAAGCACCAAA--ACAACUUGAUGCAAGUUGUAAAGAGCAUAGCAGAGCAAUCUGCAAC-------------
.....(..(((((................)))))..)......(((....)))......--((((((((...))))))))..........(((((....)))))...------------- ( -29.69)
>DroYak_CAF1 60884 118 - 1
AAGAUGUGGCCACUUCAGACUUUCAGCAUGUGGCUGCCACAGAGCUAAAAAACACCAAA--ACAACUUGAUGGAAGUUGUAAAGAGCAUUGCAGAGCAAUCUGCAACCUGCAACCAGCAA
.....(..(((((................)))))..)......(((.............--(((((((.....))))))).....((((((((((....)))))))..)))....))).. ( -34.09)
>DroAna_CAF1 54967 103 - 1
UAGAUGCAGCCACUUCAGACUUCCAACAUGUUGCUGCCACA--UUUGAAAAGCAGAGACUCAAAACUCGAAACAAGUUCUAAAGAGCAUGGCAUAGCAACCUGG--U-------------
..........................((.((((((((((..--...........(((........))).......((((....)))).))))..)))))).)).--.------------- ( -20.10)
>consensus
AAGAUGUGGCCACUUCAGACUUUCAACAUGUGGCUGCCACAGAGCUAGAAAGCACCAAA__ACAACUUGAUGCAAGUUGUAAAGAGCAUAGCAGAGCAAUCUGCAAC_____________
.....((((((((................))))))))........................(((((((.....)))))))..........(((((....)))))................ (-19.85 = -20.93 +   1.08)

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 11:49:41 2006