Locus 5413

Sequence ID 2R_DroMel_CAF1
Location 17,464,432 – 17,464,606
Length 174
Max. P 0.908698
window8633 window8634 window8635

overview

Window 3

Location 17,464,432 – 17,464,532
Length 100
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.53
Mean single sequence MFE -30.13
Consensus MFE -26.13
Energy contribution -26.47
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.18
Structure conservation index 0.87
SVM decision value 0.00
SVM RNA-class probability 0.533793
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17464432 100 + 20766785
CGCACAUAUGAGUCGGUGG---------AUGAGGCGGCCGAAUUUGCCGGCCCCAUUUUCAUGCAAUUUUUAUGACUUGGCUCUGUGCGCUGUUCUUUAUUUUUUUUU------U-----
((((((..(((((((.((.---------((((((.(((((.......)))))))....)))).)).......)))))))....))))))...................------.----- ( -29.30)
>DroSim_CAF1 438 98 + 1
CGCACAUAUGAGUCGGUGG---------AAGAGGCGGCCGAAUUUGCCGGCCCCAUUUUCAUGCAAUUUUUAUGACUUGGCUCUGUGCGCUGUUCUUUAUUCUUUUU-------------
((((((...((((((((((---------(((.((.(((((.......))))))).))))))).((.......))...))))))))))))..................------------- ( -30.60)
>DroYak_CAF1 456 119 + 1
C-CACAUAUGAGUCGCGGGAUGAGGCGAAUGAGGCGGCCGAAUUUGCCGGCCCCAUUUUCAUGCAAUUUUUAUGACUUGGCUCUGUGCGCUGUUCUUUAUUCUUUGUUGGGUUGUUGGCU
(-((((...((((...((((...((((...(((..(((((.......)))))(((...(((((.......)))))..))))))....))))..)))).))))..)).))).......... ( -30.50)
>consensus
CGCACAUAUGAGUCGGUGG_________AUGAGGCGGCCGAAUUUGCCGGCCCCAUUUUCAUGCAAUUUUUAUGACUUGGCUCUGUGCGCUGUUCUUUAUUCUUUUUU______U_____
((((((...((((((.................((.(((((.......)))))))....(((((.......)))))..))))))))))))............................... (-26.13 = -26.47 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,464,432 – 17,464,532
Length 100
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.53
Mean single sequence MFE -24.63
Consensus MFE -22.63
Energy contribution -22.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.92
SVM decision value 1.06
SVM RNA-class probability 0.908698
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17464432 100 - 20766785
-----A------AAAAAAAAAUAAAGAACAGCGCACAGAGCCAAGUCAUAAAAAUUGCAUGAAAAUGGGGCCGGCAAAUUCGGCCGCCUCAU---------CCACCGACUCAUAUGUGCG
-----.------...................((((((......((((..........(((....))).((((((.....)))))).......---------.....))))....)))))) ( -24.90)
>DroSim_CAF1 438 98 - 1
-------------AAAAAGAAUAAAGAACAGCGCACAGAGCCAAGUCAUAAAAAUUGCAUGAAAAUGGGGCCGGCAAAUUCGGCCGCCUCUU---------CCACCGACUCAUAUGUGCG
-------------..................((((((......((((..........(((....))).((((((.....)))))).......---------.....))))....)))))) ( -24.90)
>DroYak_CAF1 456 119 - 1
AGCCAACAACCCAACAAAGAAUAAAGAACAGCGCACAGAGCCAAGUCAUAAAAAUUGCAUGAAAAUGGGGCCGGCAAAUUCGGCCGCCUCAUUCGCCUCAUCCCGCGACUCAUAUGUG-G
.................................((((((((((..((((.........))))...)))((((((.....))))))..)))..((((........))))......))))-. ( -24.10)
>consensus
_____A______AAAAAAGAAUAAAGAACAGCGCACAGAGCCAAGUCAUAAAAAUUGCAUGAAAAUGGGGCCGGCAAAUUCGGCCGCCUCAU_________CCACCGACUCAUAUGUGCG
...............................((((((......((((..........(((....))).((((((.....)))))).....................))))....)))))) (-22.63 = -22.97 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,464,503 – 17,464,606
Length 103
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.05
Mean single sequence MFE -30.31
Consensus MFE -24.37
Energy contribution -25.03
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.80
SVM decision value 0.27
SVM RNA-class probability 0.661627
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17464503 103 - 20766785
UUUGCAGACCUGCAGAGAAAGGUCCAUUGGGGCGGAUUAUGAGUAAGAUGCUCUCGAUUCGCCCCCCCCCCCCA-----------A------AAAAAAAAAUAAAGAACAGCGCACAGAG
..(((.(((((........)))))....((((((((((..((((.....))))..)))))))))).........-----------.------....................)))..... ( -32.30)
>DroSim_CAF1 509 97 - 1
UUUGCAGACCUGCAGAGAAAGGUCCAUUGGGGCGGAUUAUGAGUAAGAUGCUCUCGAUUCGCCGCCCCCC-----------------------AAAAAGAAUAAAGAACAGCGCACAGAG
..(((.(((((........)))))....(((((((.....((((.....))))........)))))))..-----------------------...................)))..... ( -29.12)
>DroYak_CAF1 535 120 - 1
UUUGCAGACCUGCUGGGAAAGGUCCAUUGGGGCGGAUUAUGAGUAAGAUGGUCCCGAUUCACCGCCGCCCCCCUUGAACAAGCCAACAACCCAACAAAGAAUAAAGAACAGCGCACAGAG
..(((.(((((........)))))((..(((((((....(((((..(......)..)))))...)))))))...))....................................)))..... ( -29.50)
>consensus
UUUGCAGACCUGCAGAGAAAGGUCCAUUGGGGCGGAUUAUGAGUAAGAUGCUCUCGAUUCGCCGCCCCCCCCC____________A______AAAAAAGAAUAAAGAACAGCGCACAGAG
..(((.(((((........)))))....((((((((((..((((.....))))..)))))))).))..............................................)))..... (-24.37 = -25.03 +   0.67)

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 11:44:10 2006