Locus 3533

Sequence ID 2R_DroMel_CAF1
Location 11,818,888 – 11,819,007
Length 119
Max. P 0.893593
window5751 window5752 window5753

overview

Window 1

Location 11,818,888 – 11,818,990
Length 102
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 82.34
Mean single sequence MFE -36.15
Consensus MFE -25.08
Energy contribution -26.44
Covariance contribution 1.36
Combinations/Pair 1.14
Mean z-score -2.01
Structure conservation index 0.69
SVM decision value 0.42
SVM RNA-class probability 0.729627
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11818888 102 - 20766785
ACAGGCGAACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGCCAUAAAGCUCCACGAUCCCACAGAUCGACGGUGGCGA------------UGUCAGCUACUGGCGAUCAGUCAC
...(((.......(((.(..((..(((....)))(((((((......)))))))))..)))).(((((.(((((((..------------.....))))))).))))).))).. ( -38.90)
>DroPse_CAF1 8421 106 - 1
ACAGCUGAACAAAGUGUGUGUCAGUAGCAGUCAAGUGGAGCCAUAAAGCUCCA-------AGAGAUCGACGGUGGCGAUGGCGAUGCCUGUGUCAGCUACU-GCGAUCAGUCAC
...((((((((.....))).))))).....((...((((((......))))))-------.))(((((.(((((((((((((...)))...))).))))))-))))))...... ( -36.90)
>DroEre_CAF1 9224 102 - 1
ACAGGCGAACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGCCACAAAGCUCCCCGAUCCCACAGAUCGACGGUGGCGA------------UGUCAGCUACUGGCGAUCAGUCAC
...(((.......(((.(..((..(((....)))(.(((((......))))).)))..)))).(((((.(((((((..------------.....))))))).))))).))).. ( -34.10)
>DroWil_CAF1 14584 94 - 1
ACAGUUGAACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGUCAUAAAGCUCAACA-----AGAUCUCGACGGUUG--G------------UGGCAACAACU-GCGAUCAGUCAA
(((.((.....)).)))......((((..(((..((.((((......)))).)).-----.)))..))))(..((--(------------(.(((.....)-)).))))..).. ( -22.80)
>DroAna_CAF1 8787 112 - 1
ACAGCUGAACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGCCAUAAAGCUCCACGAUCCCACAGAUCGACGGUGGCGAUUCCGAUGCC-GUGUCAGCUACC-GCGAUCAGUCAC
.((((((((((.....))).))))))).......(((((((......))))))).........(((((.((((((((((..((....)-).))).))))))-))))))...... ( -44.20)
>DroPer_CAF1 9206 106 - 1
ACAGCUGAACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGCCAUAAAGCUCCA-------AGAGAUCGACGGUGGCGAUGGCGAUGCCUGUGUCAGCUACU-GCGAUCAGUCAC
.((((((((((.....))).)))))))...((...((((((......))))))-------.))(((((.(((((((((((((...)))...))).))))))-))))))...... ( -40.00)
>consensus
ACAGCUGAACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGCCAUAAAGCUCCACG_____ACAGAUCGACGGUGGCGA____________UGUCAGCUACU_GCGAUCAGUCAC
.((((((((((.....))).))))))).......(((((((......))))))).........(((((.(((((((...................)))))).))))))...... (-25.08 = -26.44 +   1.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,818,912 – 11,819,007
Length 95
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 80.04
Mean single sequence MFE -29.15
Consensus MFE -18.10
Energy contribution -19.63
Covariance contribution 1.53
Combinations/Pair 1.05
Mean z-score -1.61
Structure conservation index 0.62
SVM decision value 0.19
SVM RNA-class probability 0.625274
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11818912 95 + 20766785
-UCGCCACCGUCGAUCUGUGGGAUCGUGGAGCUUUAUGGCUCCACUUGACUGCAACUGACACACACUUUGU-UCGCCUGUCGACCGGGCGGUCUUGG
-(((((.(.(((((((.....))))((((((((....))))))))..(((.(((((.............))-).))..)))))).))))))...... ( -34.82)
>DroPse_CAF1 8455 89 + 1
AUCGCCACCGUCGAUCUCU-------UGGAGCUUUAUGGCUCCACUUGACUGCUACUGACACACACUUUGU-UCAGCUGUCGCCCAGGCGGUCUCGA
.(((..((((((.......-------(((((((....)))))))...(((.(((...((((.......)))-).))).))).....))))))..))) ( -29.90)
>DroGri_CAF1 24490 86 + 1
A--GCCACC---GAUCA---UGGUCCCGAAGCUUUAUGACUGCACCUGACUCCAACUGACACACACUUUGUUUCAGCUGUCGUCUGGGCGGUCC---
(--((....---(((..---..))).....)))....((((((.((.(((..((.((((.(((.....))).)))).))..))).)))))))).--- ( -26.00)
>DroWil_CAF1 14607 88 + 1
-C--CAACCGUCGAGAUCU-----UGUUGAGCUUUAUGACUCCACUUGACUGCAACUGACACACACUUUGU-UCAACUGUCGUCCGGGCGGGUCCGG
-.--...(((..(((.((.-----....)).)))...(((((..((.(((.(((..(((.(((.....)))-)))..))).))).))..)))))))) ( -18.90)
>DroAna_CAF1 8820 96 + 1
AUCGCCACCGUCGAUCUGUGGGAUCGUGGAGCUUUAUGGCUCCACUUGACUGCAACUGACACACACUUUGU-UCAGCUGUCGCCCGGGCGGUCUCCA
((((((...(((((((.....))))((((((((....))))))))..))).(((.((((.(((.....)))-)))).)))......))))))..... ( -36.20)
>DroPer_CAF1 9240 89 + 1
AUCGCCACCGUCGAUCUCU-------UGGAGCUUUAUGGCUCCACUUGACUGCAACUGACACACACUUUGU-UCAGCUGUCGCCCAGGCGGUCUCGA
.(((..((((((..((...-------(((((((....)))))))...))..(((.((((.(((.....)))-)))).)))......))))))..))) ( -29.10)
>consensus
AUCGCCACCGUCGAUCUCU_____CGUGGAGCUUUAUGGCUCCACUUGACUGCAACUGACACACACUUUGU_UCAGCUGUCGCCCGGGCGGUCUCGA
......((((((...............((((((....))))))....(((.....((((.(((.....))).))))..))).....))))))..... (-18.10 = -19.63 +   1.53)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,818,912 – 11,819,007
Length 95
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 80.04
Mean single sequence MFE -32.18
Consensus MFE -25.55
Energy contribution -26.08
Covariance contribution 0.53
Combinations/Pair 1.17
Mean z-score -1.83
Structure conservation index 0.79
SVM decision value 0.98
SVM RNA-class probability 0.893593
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11818912 95 - 20766785
CCAAGACCGCCCGGUCGACAGGCGA-ACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGCCAUAAAGCUCCACGAUCCCACAGAUCGACGGUGGCGA-
....((((....))))((((.(((.-......))).)))).((..(.(((..(((((((......)))))))((((.....))))))).)..))..- ( -39.80)
>DroPse_CAF1 8455 89 - 1
UCGAGACCGCCUGGGCGACAGCUGA-ACAAAGUGUGUGUCAGUAGCAGUCAAGUGGAGCCAUAAAGCUCCA-------AGAGAUCGACGGUGGCGAU
(((..((((.(..(((..(.(((((-(((.....))).))))).)..)))...((((((......))))))-------.......).))))..))). ( -28.80)
>DroGri_CAF1 24490 86 - 1
---GGACCGCCCAGACGACAGCUGAAACAAAGUGUGUGUCAGUUGGAGUCAGGUGCAGUCAUAAAGCUUCGGGACCA---UGAUC---GGUGGC--U
---.(((.((((.(((..(((((((.(((.....))).)))))))..))).)).)).)))....((((((((.....---...))---)).)))--) ( -31.20)
>DroWil_CAF1 14607 88 - 1
CCGGACCCGCCCGGACGACAGUUGA-ACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGUCAUAAAGCUCAACA-----AGAUCUCGACGGUUG--G-
((((((((((...(((..((..(((-(((.....))).)))..))..)))..)))).)))....((.((....-----.)).))...)))...--.- ( -22.30)
>DroAna_CAF1 8820 96 - 1
UGGAGACCGCCCGGGCGACAGCUGA-ACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGCCAUAAAGCUCCACGAUCCCACAGAUCGACGGUGGCGAU
....(.(((((..(((..(((((((-(((.....))).)))))))..)))..(((((((......)))))))((((.....))))...))))))... ( -38.40)
>DroPer_CAF1 9240 89 - 1
UCGAGACCGCCUGGGCGACAGCUGA-ACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGCCAUAAAGCUCCA-------AGAGAUCGACGGUGGCGAU
(((..((((.(..(((..(((((((-(((.....))).)))))))..)))...((((((......))))))-------.......).))))..))). ( -32.60)
>consensus
UCGAGACCGCCCGGGCGACAGCUGA_ACAAAGUGUGUGUCAGUUGCAGUCAAGUGGAGCCAUAAAGCUCCACG_____AGAGAUCGACGGUGGCGAU
......(((((..(((..(((((((.(((.....))).)))))))..)))...((((((......)))))).................))))).... (-25.55 = -26.08 +   0.53)

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 10:57:50 2006