Locus 3731

Sequence ID 2R_DroMel_CAF1
Location 12,341,257 – 12,341,408
Length 151
Max. P 0.948702
window6059 window6060 window6061

overview

Window 9

Location 12,341,257 – 12,341,377
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.06
Mean single sequence MFE -49.03
Consensus MFE -24.42
Energy contribution -25.03
Covariance contribution 0.62
Combinations/Pair 1.58
Mean z-score -1.85
Structure conservation index 0.50
SVM decision value 0.43
SVM RNA-class probability 0.734829
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12341257 120 - 20766785
CAGGCAGCCUUGUAGGCGGCCUGCUUGGUCUUCUCAUAGUCGUCGUGGGCACUCACCAGUUGCUUUUGGAGCAUGGCCAUCCGGUUGCGAGCCGCUUCCAGGAGCUGUGUCUUGGCGGCC
(((((.(((.....))).)))))...............(((((((.((((((.........(((((((((((..((....))(((.....))))).))))))))).))))))))))))). ( -47.00)
>DroPse_CAF1 25691 120 - 1
CAGGCAGCCUUAUAAGCUGCCUGUUUGGUCUUCUCGUAGUCCUCUUUGGAGAUCUGGAGUUGCUGCCGGAGCAUUGCAAUCCGGCUUUGAGCGGCCUCGACCAGCUGCGUCUUGGAGGCC
((((((((.......))))))))...(((((((.((((((((.....)))...((((.(..(((((((((((...........)))))).)))))..)..)))))))))....))))))) ( -51.20)
>DroEre_CAF1 1757 120 - 1
CAGGCUGCCUUGUAGGCGGCCUGCUUGGUCUUCUCAUAGUCGUCGUGGGCACUCACCAAAUGCUUUUGGAGCACGGCCAACCGGUUGCGAGCGGCUUCCAGGAGCUGCGACUUGGUGGCC
(((((((((.....)))))))))...((((...(((.((((.(((..(.(.....(((((....))))).....((....))).)..)))(((((((....)))))))))))))).)))) ( -51.40)
>DroWil_CAF1 44951 120 - 1
CAAGCUGCUUUGUAGGCGGCUUGUUUCGUCUUCUCAAAGUCUUCGCGAGCACUUUGCAAUUGCUUUUGGAGCAAACCUACACGGUUUUUGGCUGCCUCGAGUAAUUGAGUUUUCGAAGCC
.((((((((.....))))))))((((((....(((((((((((...))).))))))(((((((((..((((((((((.....)))))...))).))..)))))))))))....)))))). ( -40.40)
>DroMoj_CAF1 753 120 - 1
CAGGCCGCCCGAUAGGCCGCCUGCUUGGUCUUCUCAUAGUCAUCGCGUGCGUUGUCCAGCUGCUUUUGGAGCGUGGCCAGGCGGUUUUUGGCCGCCUCGAGCAGCUGCACCUUGGUGGUC
..(((((((.((((((((((.(((((((.....))).)).))..))).)).)))))(((((((((...(((.(((((((((.....)))))))))))))))))))))......))))))) ( -52.20)
>DroPer_CAF1 25709 120 - 1
CAGGCAGCCUUAUAAGCUGCCUGUUUGGUCUUCUCGUAGUCCUCUUUGGAGAUCUGGAGUUGCUGCCGGAGCAUUGCAAUCCGGCUUUGAGCGGCCUCGAGCAGCUGCGUCUUGGAGGCC
((((((((.......))))))))...(((((((.((((((.(((....)))..((.((((((((((((((.........))))))....))))).))).))..))))))....))))))) ( -52.00)
>consensus
CAGGCAGCCUUAUAGGCGGCCUGCUUGGUCUUCUCAUAGUCCUCGUGGGCACUCUCCAGUUGCUUUUGGAGCAUGGCCAUCCGGUUUUGAGCGGCCUCGAGCAGCUGCGUCUUGGAGGCC
(((((((((.....)))))))))...............((((((((....))....((((((((...((.((..((((....))))....))..))...))))))))......)))))). (-24.42 = -25.03 +   0.62)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,341,297 – 12,341,408
Length 111
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 75.58
Mean single sequence MFE -40.20
Consensus MFE -22.92
Energy contribution -23.03
Covariance contribution 0.12
Combinations/Pair 1.38
Mean z-score -1.89
Structure conservation index 0.57
SVM decision value 1.01
SVM RNA-class probability 0.899284
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12341297 111 + 20766785
AUGGCCAUGCUCCAAAAGCAACUGGUGAGUGCCCACGACGACUAUGAGAAGACCAAGCAGGCCGCCUACAAGGCUGCCUGUGCCGCCGUGGAAGCCAAACAGAGGGCUGGA------
..((((.((((.....)))).(((.((.((..(((((.((.((......)).....((((((.(((.....))).))))))..)).)))))..))))..)))..))))...------ ( -39.60)
>DroPse_CAF1 25731 111 + 1
AUUGCAAUGCUCCGGCAGCAACUCCAGAUCUCCAAAGAGGACUACGAGAAGACCAAACAGGCAGCUUAUAAGGCUGCCUGUGCCGCCAUCGAGGCCAAGCAGAAGGCCGCC------
...((........(((.((..(((.((.((((....)))).))..)))........((((((((((.....)))))))))))).))).....((((........)))))).------ ( -42.00)
>DroWil_CAF1 44991 111 + 1
GUAGGUUUGCUCCAAAAGCAAUUGCAAAGUGCUCGCGAAGACUUUGAGAAGACGAAACAAGCCGCCUACAAAGCAGCUUGUGCUGCGGUUGAGGCCAAACAGAAGGCAUCA------
(((((((((((.....)))))...((((((.((.....)))))))).................))))))...(((((....)))))...(((.(((........))).)))------ ( -31.60)
>DroYak_CAF1 661 111 + 1
UUGGCCUUGCUCCAAAAGCAACUGGUGAGUGCCCACGACGACUAUGAGAAGACCAAGCAGGCCGCCUACAAGGCAGCCUGUGCCGCCGUGGAGGCCAAACAGAGGGCUGGA------
(..((((((((.....)))..(((.((.((..(((((.((.((......)).....((((((.(((.....))).))))))..)).)))))..))))..))))))))..).------ ( -41.10)
>DroMoj_CAF1 793 117 + 1
CUGGCCACGCUCCAAAAGCAGCUGGACAACGCACGCGAUGACUAUGAGAAGACCAAGCAGGCGGCCUAUCGGGCGGCCUGCGCUGCCGUCGAGGCCAAGCAGAAGGCGGCCAACAGC
.(((((...(((.....((((((((.((.((....)).)).((......)).))).((((((.(((.....))).)))))))))))....)))(((........))))))))..... ( -49.10)
>DroPer_CAF1 25749 111 + 1
AUUGCAAUGCUCCGGCAGCAACUCCAGAUCUCCAAAGAGGACUACGAGAAGACCAAACAGGCAGCUUAUAAGGCUGCCUGUGCCGCCAUCGAGGCCAAGCAGAAAGCCGCC------
...((..((((..(((.....(((.((.((((....)))).))..)))........((((((((((.....)))))))))))))(((.....)))..))))....))....------ ( -37.80)
>consensus
AUGGCCAUGCUCCAAAAGCAACUGCAGAGCGCCCACGACGACUAUGAGAAGACCAAACAGGCCGCCUACAAGGCUGCCUGUGCCGCCGUCGAGGCCAAACAGAAGGCCGCA______
.((((..((((.....))))....................................((((((.(((.....))).)))))))))).......((((........))))......... (-22.92 = -23.03 +   0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,341,297 – 12,341,408
Length 111
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 75.58
Mean single sequence MFE -44.02
Consensus MFE -27.72
Energy contribution -28.42
Covariance contribution 0.70
Combinations/Pair 1.35
Mean z-score -1.90
Structure conservation index 0.63
SVM decision value 1.38
SVM RNA-class probability 0.948702
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12341297 111 - 20766785
------UCCAGCCCUCUGUUUGGCUUCCACGGCGGCACAGGCAGCCUUGUAGGCGGCCUGCUUGGUCUUCUCAUAGUCGUCGUGGGCACUCACCAGUUGCUUUUGGAGCAUGGCCAU
------..............((((((((((((((((.(((((.(((.....))).)))))..(((.....)))..)))))))))))......((((......)))).....))))). ( -41.90)
>DroPse_CAF1 25731 111 - 1
------GGCGGCCUUCUGCUUGGCCUCGAUGGCGGCACAGGCAGCCUUAUAAGCUGCCUGUUUGGUCUUCUCGUAGUCCUCUUUGGAGAUCUGGAGUUGCUGCCGGAGCAUUGCAAU
------.((((((........))))....((((((((((((((((.......)))))))))..(((((((....((....))..))))))).......)))))))..))........ ( -45.80)
>DroWil_CAF1 44991 111 - 1
------UGAUGCCUUCUGUUUGGCCUCAACCGCAGCACAAGCUGCUUUGUAGGCGGCUUGUUUCGUCUUCUCAAAGUCUUCGCGAGCACUUUGCAAUUGCUUUUGGAGCAAACCUAC
------(((.(((........))).)))...(((((....)))))...(((((..((((((...(.(((....))).)...)))))).........((((((...)))))).))))) ( -32.60)
>DroYak_CAF1 661 111 - 1
------UCCAGCCCUCUGUUUGGCCUCCACGGCGGCACAGGCUGCCUUGUAGGCGGCCUGCUUGGUCUUCUCAUAGUCGUCGUGGGCACUCACCAGUUGCUUUUGGAGCAAGGCCAA
------.............(((((((((((((((((.(((((((((.....)))))))))..(((.....)))..)))))))))))..........((((((...)))))))))))) ( -49.60)
>DroMoj_CAF1 793 117 - 1
GCUGUUGGCCGCCUUCUGCUUGGCCUCGACGGCAGCGCAGGCCGCCCGAUAGGCCGCCUGCUUGGUCUUCUCAUAGUCAUCGCGUGCGUUGUCCAGCUGCUUUUGGAGCGUGGCCAG
.....((((((((........)((..(((.((((((((((((.(((.....))).)))))).(((.(..(.(((.((....))))).)..).))))))))).)))..))))))))). ( -50.60)
>DroPer_CAF1 25749 111 - 1
------GGCGGCUUUCUGCUUGGCCUCGAUGGCGGCACAGGCAGCCUUAUAAGCUGCCUGUUUGGUCUUCUCGUAGUCCUCUUUGGAGAUCUGGAGUUGCUGCCGGAGCAUUGCAAU
------((((((.(((((((..(((.....))))))(((((((((.......)))))))))..(((((((....((....))..))))))).))))..))))))............. ( -43.60)
>consensus
______GGCAGCCUUCUGCUUGGCCUCGACGGCGGCACAGGCAGCCUUAUAGGCGGCCUGCUUGGUCUUCUCAUAGUCCUCGUGGGCACUCUCCAGUUGCUUUUGGAGCAUGGCCAU
.................((...((..(((.((((((((((((((((.....))))))))))...(.((......)).).................)))))).)))..))...))... (-27.72 = -28.42 +   0.70)

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 11:02:58 2006