Locus 4439

Sequence ID 2R_DroMel_CAF1
Location 14,597,478 – 14,597,588
Length 110
Max. P 0.779842
window7093 window7094 window7095

overview

Window 3

Location 14,597,478 – 14,597,569
Length 91
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 92.62
Mean single sequence MFE -18.60
Consensus MFE -15.80
Energy contribution -16.20
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.85
SVM decision value 0.55
SVM RNA-class probability 0.779842
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14597478 91 + 20766785
UAUGAGGGCGGUGAAAAGGGAACGAUGCCUCGGGGGUUAUGCCAAUGAAGCACUCUGUCGAUGAGAUAGAGAAAAAAAAAAAAAAACUGAA
........((((.............(((.(((..((.....))..))).)))(((((((.....)))))))..............)))).. ( -21.10)
>DroSec_CAF1 229625 83 + 1
UAUGAGGGCGGUGAAAAGGGAACGAUGCCUCGG-GGUUAUGCCAAUGAAGCACUCCGUCGAUGGGAUAGAGAAAA-------AAAACUGAA
......(((((.(....(....)..(((.(((.-((.....))..))).)))).)))))................-------......... ( -14.80)
>DroSim_CAF1 232908 84 + 1
UAUGAGGGCGGUGAAAAGGGAACGAUGCCUCGGGGGUUAUGCCAAUGAAGCACUCUGUCGAUGGGAUAGAGAAAA-------AAAACUGAA
........((((.............(((.(((..((.....))..))).)))(((((((.....)))))))....-------...)))).. ( -20.50)
>DroEre_CAF1 236985 83 + 1
UAUGAGGGCGGUGAAAAGGGAACGAGGCCUCGGGGGUUAUGCCAAUGAAGCUCUCCGUCGAUGGGAUAGAGAAAA-------AGAA-UGAA
......(((((.((...(....)...((.(((..((.....))..))).)))).)))))................-------....-.... ( -17.50)
>DroYak_CAF1 245098 83 + 1
UAUGAGGGCGGUGAAAAGGGAACGAUGCCUCGGGGGUUAUGCCAAUGAAGCUCUCUGUCGAUGGGAUAGAGAAAA-------AGAA-UGAA
.......((((((....(....)..))))(((..((.....))..))).))((((((((.....))))))))...-------....-.... ( -19.10)
>consensus
UAUGAGGGCGGUGAAAAGGGAACGAUGCCUCGGGGGUUAUGCCAAUGAAGCACUCUGUCGAUGGGAUAGAGAAAA_______AAAACUGAA
.......(((((.....(....)...)))(((..((.....))..))).)).(((((((.....))))))).................... (-15.80 = -16.20 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,597,478 – 14,597,569
Length 91
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 92.62
Mean single sequence MFE -11.76
Consensus MFE -10.74
Energy contribution -10.50
Covariance contribution -0.24
Combinations/Pair 1.08
Mean z-score -1.14
Structure conservation index 0.91
SVM decision value 0.10
SVM RNA-class probability 0.584023
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14597478 91 - 20766785
UUCAGUUUUUUUUUUUUUUUCUCUAUCUCAUCGACAGAGUGCUUCAUUGGCAUAACCCCCGAGGCAUCGUUCCCUUUUCACCGCCCUCAUA
....................((((.((.....)).))))((((((...((.....))...))))))......................... ( -11.50)
>DroSec_CAF1 229625 83 - 1
UUCAGUUUU-------UUUUCUCUAUCCCAUCGACGGAGUGCUUCAUUGGCAUAACC-CCGAGGCAUCGUUCCCUUUUCACCGCCCUCAUA
.........-------....(((..((.....))..)))((((((...((.....))-..))))))......................... ( -11.20)
>DroSim_CAF1 232908 84 - 1
UUCAGUUUU-------UUUUCUCUAUCCCAUCGACAGAGUGCUUCAUUGGCAUAACCCCCGAGGCAUCGUUCCCUUUUCACCGCCCUCAUA
.........-------....((((.((.....)).))))((((((...((.....))...))))))......................... ( -11.00)
>DroEre_CAF1 236985 83 - 1
UUCA-UUCU-------UUUUCUCUAUCCCAUCGACGGAGAGCUUCAUUGGCAUAACCCCCGAGGCCUCGUUCCCUUUUCACCGCCCUCAUA
....-....-------...((((..((.....))..))))(((.....))).........((((...((............)).))))... ( -12.40)
>DroYak_CAF1 245098 83 - 1
UUCA-UUCU-------UUUUCUCUAUCCCAUCGACAGAGAGCUUCAUUGGCAUAACCCCCGAGGCAUCGUUCCCUUUUCACCGCCCUCAUA
....-....-------...(((((.((.....)).)))))(((((...((.....))...))))).......................... ( -12.70)
>consensus
UUCAGUUUU_______UUUUCUCUAUCCCAUCGACAGAGUGCUUCAUUGGCAUAACCCCCGAGGCAUCGUUCCCUUUUCACCGCCCUCAUA
....................((((.((.....)).)))).(((((...((.....))...))))).......................... (-10.74 = -10.50 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,597,498 – 14,597,588
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 84.36
Mean single sequence MFE -19.56
Consensus MFE -15.46
Energy contribution -15.82
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -1.70
Structure conservation index 0.79
SVM decision value 0.37
SVM RNA-class probability 0.710537
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14597498 90 + 20766785
AACGAUGCCUCGGGGGUUAUGCCAAUGAAGCACUCUGUCGAUGAGAUAGAGAAAAAAAAAAAAAAACUGAAAACGAGCAAAGAACUUUGC
..((.(((.(((..((.....))..))).)))(((((((.....)))))))......................)).(((((....))))) ( -22.30)
>DroSec_CAF1 229645 69 + 1
AACGAUGCCUCGG-GGUUAUGCCAAUGAAGCACUCCGUCGAUGGGAUAGAGAAAA-------AAAACUGAAAGCGAG-------------
.....(((.((((-..((.(((.......)))(((..((.....))..)))....-------))..))))..)))..------------- ( -12.00)
>DroSim_CAF1 232928 83 + 1
AACGAUGCCUCGGGGGUUAUGCCAAUGAAGCACUCUGUCGAUGGGAUAGAGAAAA-------AAAACUGAAAGCGAGCAGAGAACUUUGC
..((.(((.(((..((.....))..))).)))(((((((.....)))))))....-------...........)).(((((....))))) ( -21.50)
>DroEre_CAF1 237005 82 + 1
AACGAGGCCUCGGGGGUUAUGCCAAUGAAGCUCUCCGUCGAUGGGAUAGAGAAAA-------AGAA-UGAAAACGAGGCAAGAAUUUUGC
......((((((..((.....))........((((..((.....))..))))...-------....-......))))))........... ( -20.30)
>DroYak_CAF1 245118 82 + 1
AACGAUGCCUCGGGGGUUAUGCCAAUGAAGCUCUCUGUCGAUGGGAUAGAGAAAA-------AGAA-UGAAAACGAGCAAAGAACUUUGC
..((..((.(((..((.....))..))).))((((((((.....))))))))...-------....-......)).(((((....))))) ( -21.70)
>consensus
AACGAUGCCUCGGGGGUUAUGCCAAUGAAGCACUCUGUCGAUGGGAUAGAGAAAA_______AAAACUGAAAACGAGCAAAGAACUUUGC
..((.(((.(((..((.....))..))).)))(((((((.....)))))))......................))............... (-15.46 = -15.82 +   0.36)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:39 2006