Locus 80

Sequence ID X_DroMel_CAF1
Location 330,384 – 330,538
Length 154
Max. P 0.911853
window102 window103 window104 window105

overview

Window 2

Location 330,384 – 330,504
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.28
Mean single sequence MFE -45.02
Consensus MFE -25.53
Energy contribution -25.92
Covariance contribution 0.39
Combinations/Pair 1.33
Mean z-score -2.00
Structure conservation index 0.57
SVM decision value 0.51
SVM RNA-class probability 0.764197
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 330384 120 + 22224390
CAAUGGGGGAGGCAGCCGUUAAGGAUCCAUUGCAUGCGAAAAUGCUGCCCAGGAUAGCAAACAGGCGGUGCAGCAGUUCCUCGCCGCUCAUGGCUUUCGUUAGCGGAAAGAUGCUCCUCA
.....((((((.((.(((((((.((.((((.((..((((...((((((((......((......)))).)))))).....)))).))..))))...)).))))))).....)))))))). ( -44.70)
>DroPse_CAF1 1637 120 + 1
CAAUGGGCGAGGCGGCCGACAGCGAGUUAUUGAAGGCAAAGAUGCUGCCCAAUAUGGCGAAGAGGCGAUGCAGCAGCUCCUCGCUGCUCAUCGCCUUCGACAGCGGGAAGAUGCUGCGUA
...(((((..(((((((..(((.......)))..))).....))))))))).....(((..(((((((((.((((((.....)))))))))))))))...(((((......)))))))). ( -48.70)
>DroGri_CAF1 39492 120 + 1
CAAUCGGCGAUGCAGCCGAUGGUGAAUUGUUGCCAGCAAAUAUGCUGCCCAAUAUGGCAAAUAAACGAUGCAGCAGCUGUUCGCUGUUCAGCGAUUUUGACAGCGGGAAUAUGCUGCGUA
..((((((......))))))((..(....)..))((((....))))(((......))).........((((((((....((((((((.(((.....)))))))))))....)))))))). ( -45.20)
>DroWil_CAF1 1611 120 + 1
CAAUCGGCGAGGCGGCUGAUAAUGAAUUGUUGCAGGCAAAGAUGCUGCCCAAUAUGACAAAAAGGCGAUGCAAUAACUCCUCACUGCCCAUGGCCUUGGACAGUGGGAAUAUGCUGCGUA
...........(((((.......((.((((((((((((....))))(((..............)))..)))))))).))(((((((.(((......))).))))))).....)))))... ( -37.44)
>DroMoj_CAF1 107262 120 + 1
CUAUGGGCGAGGCAGCCGACGGCGAGGCAUUGCCCGCAAAUAUGCUGCCCAAUAUGGCAAACAAGCGAUGCAGCAGCUGCUCGCUGUUCAGGGACUUGGACAUCGGAAAGAUGCUGCGUA
....((((((.((.(((...)))...)).))))))(((....)))((((......))))........((((((((.((..(((.(((((((....))))))).)))..)).)))))))). ( -47.50)
>DroPer_CAF1 1621 120 + 1
CAAUGGGCGAGGCGGCCGACAGCGAGUUAUUGAAGGCAAAGAUGCUACCCAAUAUGGCGAAGAGGCGAUGCAGCAGCUCCUCGCUGCUCAUCGCCUUCGACAGCGGGAAGAUGCUGCGUA
.....(((......)))(.(((((..........((((....)))).(((....((.(((..((((((((.((((((.....))))))))))))))))).))..)))....))))))... ( -46.60)
>consensus
CAAUGGGCGAGGCAGCCGACAGCGAGUUAUUGCAGGCAAAGAUGCUGCCCAAUAUGGCAAACAGGCGAUGCAGCAGCUCCUCGCUGCUCAUCGCCUUCGACAGCGGGAAGAUGCUGCGUA
........(.((((((.(((.....))).(((....)))....))))))).................((((((((.((.(((((((..............))))))).)).)))))))). (-25.53 = -25.92 +   0.39)

alignment

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secondary structure

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dotplot

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Window 3

Location 330,384 – 330,504
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.28
Mean single sequence MFE -41.06
Consensus MFE -24.06
Energy contribution -24.07
Covariance contribution 0.01
Combinations/Pair 1.44
Mean z-score -1.70
Structure conservation index 0.59
SVM decision value 0.19
SVM RNA-class probability 0.627255
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 330384 120 - 22224390
UGAGGAGCAUCUUUCCGCUAACGAAAGCCAUGAGCGGCGAGGAACUGCUGCACCGCCUGUUUGCUAUCCUGGGCAGCAUUUUCGCAUGCAAUGGAUCCUUAACGGCUGCCUCCCCCAUUG
.(((((((..(((((.......)))))((((..((((((((((..((((((.(((..............)))))))))))))))).))).))))..........))).))))........ ( -38.14)
>DroPse_CAF1 1637 120 - 1
UACGCAGCAUCUUCCCGCUGUCGAAGGCGAUGAGCAGCGAGGAGCUGCUGCAUCGCCUCUUCGCCAUAUUGGGCAGCAUCUUUGCCUUCAAUAACUCGCUGUCGGCCGCCUCGCCCAUUG
...(((((..........((.(((((((((((((((((.....)))))).))))))))..))).))((((((((((.....)))))..)))))....))))).(((......)))..... ( -45.90)
>DroGri_CAF1 39492 120 - 1
UACGCAGCAUAUUCCCGCUGUCAAAAUCGCUGAACAGCGAACAGCUGCUGCAUCGUUUAUUUGCCAUAUUGGGCAGCAUAUUUGCUGGCAACAAUUCACCAUCGGCUGCAUCGCCGAUUG
...((((((.......(((((.....(((((....))))))))))))))))..........((((......))))(((....)))((....)).......((((((......)))))).. ( -38.71)
>DroWil_CAF1 1611 120 - 1
UACGCAGCAUAUUCCCACUGUCCAAGGCCAUGGGCAGUGAGGAGUUAUUGCAUCGCCUUUUUGUCAUAUUGGGCAGCAUCUUUGCCUGCAACAAUUCAUUAUCAGCCGCCUCGCCGAUUG
...((((((.((((((((((((((......))))))))).)))))...)))...((((..(......)..)))).(((....))).)))...........(((.((......)).))).. ( -36.80)
>DroMoj_CAF1 107262 120 - 1
UACGCAGCAUCUUUCCGAUGUCCAAGUCCCUGAACAGCGAGCAGCUGCUGCAUCGCUUGUUUGCCAUAUUGGGCAGCAUAUUUGCGGGCAAUGCCUCGCCGUCGGCUGCCUCGCCCAUAG
...((.(((((.....)))))..........(((((((((((((...)))).)))).))))))).....(((((.(((....)))(((((..(((........)))))))).)))))... ( -41.70)
>DroPer_CAF1 1621 120 - 1
UACGCAGCAUCUUCCCGCUGUCGAAGGCGAUGAGCAGCGAGGAGCUGCUGCAUCGCCUCUUCGCCAUAUUGGGUAGCAUCUUUGCCUUCAAUAACUCGCUGUCGGCCGCCUCGCCCAUUG
...(((((.....((((.((.(((((((((((((((((.....)))))).))))))))..))).))...))))..(((....)))............))))).(((......)))..... ( -45.10)
>consensus
UACGCAGCAUCUUCCCGCUGUCGAAGGCCAUGAGCAGCGAGGAGCUGCUGCAUCGCCUCUUUGCCAUAUUGGGCAGCAUCUUUGCCUGCAAUAACUCGCUAUCGGCCGCCUCGCCCAUUG
...((((((..((((((((((............)))))).)))).))))))...(((.....(((......))).(((....)))..................))).............. (-24.06 = -24.07 +   0.01)

alignment

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secondary structure

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dotplot

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Window 4

Location 330,424 – 330,538
Length 114
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 78.62
Mean single sequence MFE -38.70
Consensus MFE -26.35
Energy contribution -27.02
Covariance contribution 0.67
Combinations/Pair 1.30
Mean z-score -1.75
Structure conservation index 0.68
SVM decision value 0.91
SVM RNA-class probability 0.880538
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 330424 114 + 22224390
AAUGCUGCCCAGGAUAGCAAACAGGCGGUGCAGCAGUUCCUCGCCGCUCAUGGCUUUCGUUAGCGGAAAGAUGCUCCUCAUGGCCAGUAGAACUUGAGCGUAUCUGAAG---GAUCA-
..((((((((......((......)))).))))))(.(((((.(((((.(((.....))).)))))..((((((..((((.(..(....)..).)))).))))))).))---)).).- ( -35.00)
>DroPse_CAF1 1677 114 + 1
GAUGCUGCCCAAUAUGGCGAAGAGGCGAUGCAGCAGCUCCUCGCUGCUCAUCGCCUUCGACAGCGGGAAGAUGCUGCGUAUGGCCAGCAGAACUUGAGCGUAGCUAGAA---GAUUA-
..(((((.(((.((((.(((..((((((((.((((((.....))))))))))))))))).(((((......)))))))))))).)))))...(((.(((...)))..))---)....- ( -47.70)
>DroGri_CAF1 39532 113 + 1
UAUGCUGCCCAAUAUGGCAAAUAAACGAUGCAGCAGCUGUUCGCUGUUCAGCGAUUUUGACAGCGGGAAUAUGCUGCGUAUGGCUAGCAAAACUUGAGCGUAACUG----CAAAUAU-
(((((((((......)))...((..((((((((((....((((((((.(((.....)))))))))))....)))))))).))..))..........))))))....----.......- ( -35.00)
>DroWil_CAF1 1651 116 + 1
GAUGCUGCCCAAUAUGACAAAAAGGCGAUGCAAUAACUCCUCACUGCCCAUGGCCUUGGACAGUGGGAAUAUGCUGCGUAUGGCCAGCAGAACUUGAGCGUAGCUAAAAAG-AAAAU-
...(((((...............(((.(((((.((..(((.(((((.(((......))).))))))))...)).)))))...))).((.........))))))).......-.....- ( -31.70)
>DroMoj_CAF1 107302 118 + 1
UAUGCUGCCCAAUAUGGCAAACAAGCGAUGCAGCAGCUGCUCGCUGUUCAGGGACUUGGACAUCGGAAAGAUGCUGCGUAUGGCCAGUAGAACUUGUGCAUAGCUAUCGGGAUAUCAA
..(((((.(((.....((......)).((((((((.((..(((.(((((((....))))))).)))..)).)))))))).))).)))))...((((.((...))...))))....... ( -36.50)
>DroPer_CAF1 1661 114 + 1
GAUGCUACCCAAUAUGGCGAAGAGGCGAUGCAGCAGCUCCUCGCUGCUCAUCGCCUUCGACAGCGGGAAGAUGCUGCGUAUGGCCAGCAGAACUUGAGCGUAGCUAGAA---GAUUA-
...(((((......((((...(((((((((.((((((.....)))))))))))))))((.(((((......)))))))....))))((.........))))))).....---.....- ( -46.30)
>consensus
GAUGCUGCCCAAUAUGGCAAACAGGCGAUGCAGCAGCUCCUCGCUGCUCAUCGCCUUCGACAGCGGGAAGAUGCUGCGUAUGGCCAGCAGAACUUGAGCGUAGCUAAAA___GAUAA_
..(((((.(((.....((......)).((((((((.((.(((((((..............))))))).)).)))))))).))).)))))............................. (-26.35 = -27.02 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 330,424 – 330,538
Length 114
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 78.62
Mean single sequence MFE -37.32
Consensus MFE -25.46
Energy contribution -25.97
Covariance contribution 0.51
Combinations/Pair 1.35
Mean z-score -1.88
Structure conservation index 0.68
SVM decision value 1.08
SVM RNA-class probability 0.911853
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 330424 114 - 22224390
-UGAUC---CUUCAGAUACGCUCAAGUUCUACUGGCCAUGAGGAGCAUCUUUCCGCUAACGAAAGCCAUGAGCGGCGAGGAACUGCUGCACCGCCUGUUUGCUAUCCUGGGCAGCAUU
-...((---(((..(...((((((.(((((.(.......).)))))..(((((.......)))))...)))))).))))))..((((((.(((..............))))))))).. ( -31.44)
>DroPse_CAF1 1677 114 - 1
-UAAUC---UUCUAGCUACGCUCAAGUUCUGCUGGCCAUACGCAGCAUCUUCCCGCUGUCGAAGGCGAUGAGCAGCGAGGAGCUGCUGCAUCGCCUCUUCGCCAUAUUGGGCAGCAUC
-.....---.....(((..((((((.......((((....((((((........)))).)).((((((((((((((.....)))))).))))))))....))))..)))))))))... ( -46.30)
>DroGri_CAF1 39532 113 - 1
-AUAUUUG----CAGUUACGCUCAAGUUUUGCUAGCCAUACGCAGCAUAUUCCCGCUGUCAAAAUCGCUGAACAGCGAACAGCUGCUGCAUCGUUUAUUUGCCAUAUUGGGCAGCAUA
-..(((((----.((.....)))))))..((((.(((....((((((.......(((((.....(((((....))))))))))))))))...((......)).......))))))).. ( -31.81)
>DroWil_CAF1 1651 116 - 1
-AUUUU-CUUUUUAGCUACGCUCAAGUUCUGCUGGCCAUACGCAGCAUAUUCCCACUGUCCAAGGCCAUGGGCAGUGAGGAGUUAUUGCAUCGCCUUUUUGUCAUAUUGGGCAGCAUC
-.....-.......((((.((.........)))))).....((.(((.((((((((((((((......))))))))).)))))...)))...((((..(......)..)))).))... ( -37.60)
>DroMoj_CAF1 107302 118 - 1
UUGAUAUCCCGAUAGCUAUGCACAAGUUCUACUGGCCAUACGCAGCAUCUUUCCGAUGUCCAAGUCCCUGAACAGCGAGCAGCUGCUGCAUCGCUUGUUUGCCAUAUUGGGCAGCAUA
.((....(((((((((...))...........((((........(((((.....)))))..........(((((((((((((...)))).)))).))))))))))))))))...)).. ( -30.70)
>DroPer_CAF1 1661 114 - 1
-UAAUC---UUCUAGCUACGCUCAAGUUCUGCUGGCCAUACGCAGCAUCUUCCCGCUGUCGAAGGCGAUGAGCAGCGAGGAGCUGCUGCAUCGCCUCUUCGCCAUAUUGGGUAGCAUC
-.....---.....(((((((.........))((((....((((((........)))).)).((((((((((((((.....)))))).))))))))....))))......)))))... ( -46.10)
>consensus
_UAAUC___UUCUAGCUACGCUCAAGUUCUGCUGGCCAUACGCAGCAUCUUCCCGCUGUCGAAGGCCAUGAGCAGCGAGGAGCUGCUGCAUCGCCUCUUUGCCAUAUUGGGCAGCAUC
.............................(((((.(((...((((((..((((((((((............)))))).)))).))))))...((......)).....))).))))).. (-25.46 = -25.97 +   0.51)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:29 2006