Locus 3382

Sequence ID 2R_DroMel_CAF1
Location 11,443,521 – 11,443,637
Length 116
Max. P 0.773251
window5523 window5524 window5525

overview

Window 3

Location 11,443,521 – 11,443,612
Length 91
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 80.17
Mean single sequence MFE -25.37
Consensus MFE -16.83
Energy contribution -16.99
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.66
SVM decision value 0.44
SVM RNA-class probability 0.735999
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11443521 91 + 20766785
AUCACUUUUCAUUCUACGUUAAAAUGCAAUCAAAUGCAAACAAGCGCGUGCUCUGG--CGUUUUUACGAU-UGUUUGCACGUGAGUGAAUC----GCG
.......(((((((.((((......((((((((((((.....(((....)))...)--)))))....)))-)))....)))))))))))..----... ( -22.00)
>DroVir_CAF1 80221 92 + 1
UUUUCUUCGCAUGAU--AGCCAAGUGCAAUCAAAUGCAAACAAGCGCGUGCUUACAGC----UUUAUGAUAUGUUUGCACGUGAGUGGACCCUAGGCG
...............--.(((.((((((......))))..((..(((((((..(((.(----.....)...)))..)))))))..))....)).))). ( -26.50)
>DroPse_CAF1 59824 90 + 1
AUCAGCUGGCGUUAUAUGCAAAAAUGCAAUCAAAUGCAAACAAGCGCGUGCUCUCA---GCUUUUACGAU-UGUUUGCACGUGAGUGAAUC----GCG
.(((.((.((((....((((....)))).......((((((((...(((((.....---))....))).)-))))))))))).)))))...----... ( -24.30)
>DroEre_CAF1 59351 91 + 1
AUCACUUUGCAUUAAAUGGAAAAAUGCAAUCAAAUGCAAACAAGCGCGUGCUCUGG--CGUUUUUACGAU-UGUUUGCACGUGAGUGAAUC----GCG
.((((.(((((((.........)))))))(((..(((((((((((((........)--)))........)-))))))))..)))))))...----... ( -26.00)
>DroAna_CAF1 42528 89 + 1
AUCAGCUCGCAUUAAGUGCAAAAAUGCAAUCAAAUGCAAACAAGCGCGUGCUCUGG--CGUU--UAUGGA-UGUUUGCACGUGAGUGCGCC----GCU
...(((.((((((..(((((((..((((......))))...((((((........)--))))--).....-..)))))))...))))))..----))) ( -29.10)
>DroPer_CAF1 62617 90 + 1
AUCAGCUGGCGUUAUAUGCAAAAAUGCAAUCAAAUGCAAACAAGCGCGUGCUCUCA---GCUUUUACGAU-UGUUUGCACGUGAGUGAAUC----GCG
.(((.((.((((....((((....)))).......((((((((...(((((.....---))....))).)-))))))))))).)))))...----... ( -24.30)
>consensus
AUCACCUCGCAUUAUAUGCAAAAAUGCAAUCAAAUGCAAACAAGCGCGUGCUCUCA___GUUUUUACGAU_UGUUUGCACGUGAGUGAAUC____GCG
........((..............((((......))))..((..(((((((.........................)))))))..))........)). (-16.83 = -16.99 +   0.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,443,521 – 11,443,612
Length 91
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 80.17
Mean single sequence MFE -25.32
Consensus MFE -14.36
Energy contribution -14.37
Covariance contribution 0.00
Combinations/Pair 1.18
Mean z-score -2.14
Structure conservation index 0.57
SVM decision value 0.51
SVM RNA-class probability 0.763690
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11443521 91 - 20766785
CGC----GAUUCACUCACGUGCAAACA-AUCGUAAAAACG--CCAGAGCACGCGCUUGUUUGCAUUUGAUUGCAUUUUAACGUAGAAUGAAAAGUGAU
...----...(((((((.(((((((((-(.(((......(--(....))..))).)))))))))).)))...(((((((...)))))))....)))). ( -22.80)
>DroVir_CAF1 80221 92 - 1
CGCCUAGGGUCCACUCACGUGCAAACAUAUCAUAAA----GCUGUAAGCACGCGCUUGUUUGCAUUUGAUUGCACUUGGCU--AUCAUGCGAAGAAAA
.(((...(((.((.(((.(((((((((........(----(((((....))).)))))))))))).))).)).))).))).--............... ( -23.40)
>DroPse_CAF1 59824 90 - 1
CGC----GAUUCACUCACGUGCAAACA-AUCGUAAAAGC---UGAGAGCACGCGCUUGUUUGCAUUUGAUUGCAUUUUUGCAUAUAACGCCAGCUGAU
.((----(......(((.(((((((((-(.(((....((---.....))..))).)))))))))).))).((((....)))).....)))........ ( -25.90)
>DroEre_CAF1 59351 91 - 1
CGC----GAUUCACUCACGUGCAAACA-AUCGUAAAAACG--CCAGAGCACGCGCUUGUUUGCAUUUGAUUGCAUUUUUCCAUUUAAUGCAAAGUGAU
...----...(((((((.(((((((((-(.(((......(--(....))..))).)))))))))).)))(((((((.........))))))).)))). ( -25.90)
>DroAna_CAF1 42528 89 - 1
AGC----GGCGCACUCACGUGCAAACA-UCCAUA--AACG--CCAGAGCACGCGCUUGUUUGCAUUUGAUUGCAUUUUUGCACUUAAUGCGAGCUGAU
..(----((((((.(((.(((((((((-......--..((--(........)))..))))))))).))).)))....(((((.....))))))))).. ( -28.00)
>DroPer_CAF1 62617 90 - 1
CGC----GAUUCACUCACGUGCAAACA-AUCGUAAAAGC---UGAGAGCACGCGCUUGUUUGCAUUUGAUUGCAUUUUUGCAUAUAACGCCAGCUGAU
.((----(......(((.(((((((((-(.(((....((---.....))..))).)))))))))).))).((((....)))).....)))........ ( -25.90)
>consensus
CGC____GAUUCACUCACGUGCAAACA_AUCGUAAAAAC___CCAGAGCACGCGCUUGUUUGCAUUUGAUUGCAUUUUUGCAUAUAAUGCAAACUGAU
.......(((.((.(((.((((((((.....((....))......((((....)))))))))))).))).)).)))...................... (-14.36 = -14.37 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,443,546 – 11,443,637
Length 91
Sequences 6
Columns 91
Reading direction forward
Mean pairwise identity 81.32
Mean single sequence MFE -21.40
Consensus MFE -16.66
Energy contribution -16.85
Covariance contribution 0.19
Combinations/Pair 1.06
Mean z-score -1.64
Structure conservation index 0.78
SVM decision value 0.54
SVM RNA-class probability 0.773251
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11443546 91 + 20766785
GCAAUCAAAUGCAAACAAGCGCGUGCUCUGGCGUUUUUACGAUUGUUUGCACGUGAGUGAAUCGCGUCUAUAAAAAAUGAAAAAAAAAAAA
....(((...((((((((((((........))))........))))))))((((((.....))))))..........)))........... ( -20.20)
>DroSec_CAF1 62475 91 + 1
GCAAUCAAAUGCAAACAAGCGCGUGCUCUGGCGUUUUUACGAUUGUUUGCACGUGAGUGAAUCGCGUCUAUAAAAAAUGAAAAAAAAAAAA
....(((...((((((((((((........))))........))))))))((((((.....))))))..........)))........... ( -20.20)
>DroEre_CAF1 59376 87 + 1
GCAAUCAAAUGCAAACAAGCGCGUGCUCUGGCGUUUUUACGAUUGUUUGCACGUGAGUGAAUCGCGACAAUAAAAAAUAUGAAAAAA----
....(((..(((((((((((((........))))........)))))))))(((((.....))))).............))).....---- ( -20.40)
>DroYak_CAF1 58088 86 + 1
GCAAUCAAAUGCAAACAAGCGCGUGCUCUGGCGUUUUUACGAUUGUUUGCACGUGAGUGAAUCGCGUCAAGAAAAAAUAUGAAAAA-----
....(((...((((((((((((........))))........))))))))((((((.....))))))............)))....----- ( -20.20)
>DroAna_CAF1 42553 88 + 1
GCAAUCAAAUGCAAACAAGCGCGUGCUCUGGCGUU--UAUGGAUGUUUGCACGUGAGUGCGCCGCUCCGCAAACAAGUGCCAGCAAAAAC-
(((.(((..(((((((((((((........)))))--......))))))))..))).)))...(((..(((......))).)))......- ( -26.50)
>DroPer_CAF1 62642 75 + 1
GCAAUCAAAUGCAAACAAGCGCGUGCUCUCA-GCUUUUACGAUUGUUUGCACGUGAGUGAAUCGCGUCCGCCAACA---------------
((........((((((((...(((((.....-))....))).))))))))((((((.....))))))..)).....--------------- ( -20.90)
>consensus
GCAAUCAAAUGCAAACAAGCGCGUGCUCUGGCGUUUUUACGAUUGUUUGCACGUGAGUGAAUCGCGUCAAUAAAAAAUGAAAAAAAA____
.((.(((..(((((((((((((........)))))........))))))))..))).))................................ (-16.66 = -16.85 +   0.19)

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 10:54:09 2006