Locus 3179

Sequence ID X_DroMel_CAF1
Location 8,440,956 – 8,441,103
Length 147
Max. P 0.776953
window5215 window5216 window5217 window5218

overview

Window 5

Location 8,440,956 – 8,441,075
Length 119
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.96
Mean single sequence MFE -41.60
Consensus MFE -26.55
Energy contribution -26.72
Covariance contribution 0.17
Combinations/Pair 1.24
Mean z-score -2.06
Structure conservation index 0.64
SVM decision value 0.34
SVM RNA-class probability 0.697716
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8440956 119 + 22224390
GCCUUUCUGCUCUUCAUGGCCAGCAUUCUGCGCGGCUACAGAGACUUUCUGGUGCCCAUAUCCAAGGCACCAUCGGUGGGAGCCACCGAUCCAAGUGCCCUCUUCCAGCUGAAGGCUUU
((((((..(((.....(((((.((.....))..))))).((((((((...((((((.........))))))((((((((...))))))))..))))...))))...))).))))))... ( -44.90)
>DroGri_CAF1 59418 119 + 1
GCAUUUCUGCUCUUUAUGGCGUCCAUAUUGCGUGGCUAUCGUGACUACUUGGUGCCCAUAUCAAGGGCGCCCUCCGUUGGCGCCACGGAUCCAAGUGCCUUAUUUCAGCUAAAGGCUUU
(((....)))..((..(((((.(((......(((((......).))))..(((((((.......)))))))......))))))))..)).......(((((..........)))))... ( -36.60)
>DroEre_CAF1 3860 119 + 1
GCCUUUCUGCUUUUUAUGGCCAGCAUUCUGCGCGGUUACAGAGAUUUUCUGGUGCCCAUUUCCAAGGCACCCUCGGUGGGAGCCACUGAUCCGAGUGCCCUCUUUCAGCUGAAGGCCUU
((((((..(((.....(((((.((.....))..))))).((((...(((.((((((.........)))))).(((((((...)))))))...)))....))))...))).))))))... ( -38.50)
>DroWil_CAF1 2098 119 + 1
GCAUUUCUACUCUUCAUGGCAUCGAUAUUGCGUGGAUAUCGCGACUAUUUGGUACCCAUAUCGAAGGCACCUUCAGUGGGUGCCACAGAUCCGAAUGCCUUAUUCCAGCACAAGGCUUU
((...............(((((((...(((((.......))))).....((((((((((...((((....)))).))))))))))......)).)))))...............))... ( -35.51)
>DroMoj_CAF1 91797 119 + 1
GCAUUUCUGCUCUUCAUGGCGUGCAUAUUGCGCGGCUAUCGUGACUAUCUGGUGCCAAUUUCAAAGGCACCCUCUGUGGGCGCCACGGAUCCGAGUGCCUUAUUUCAGCUGAAAGCUUU
((.((((.(((.........((((.....))))(((..(((.((......((((((.........)))))).(((((((...))))))))))))..))).......))).))))))... ( -40.00)
>DroAna_CAF1 2264 119 + 1
GCCUUUCUGCUCUUCAUGGCGAGCAUAUUGCGCGGCUACCGGGACUUCCUGGUGCCCAUUUCCAAGGCGCCCUCAGUGGGCGCCACUGAUCCAAGCGCCCUGUUCCAGCUGAAGGCCUU
((((((..(((...((.(((..((.....))(((((.((((((....))))))))).........(((((((.....)))))))..........))))).))....))).))))))... ( -54.10)
>consensus
GCAUUUCUGCUCUUCAUGGCGAGCAUAUUGCGCGGCUACCGAGACUAUCUGGUGCCCAUAUCCAAGGCACCCUCAGUGGGCGCCACGGAUCCAAGUGCCCUAUUCCAGCUGAAGGCUUU
((.((((.(((......(((..............................((((((.........)))))).(((((((...))))))).......))).......))).))))))... (-26.55 = -26.72 +   0.17)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,440,956 – 8,441,075
Length 119
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 81.96
Mean single sequence MFE -41.38
Consensus MFE -25.59
Energy contribution -26.65
Covariance contribution 1.06
Combinations/Pair 1.29
Mean z-score -1.75
Structure conservation index 0.62
SVM decision value -0.01
SVM RNA-class probability 0.526338
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8440956 119 - 22224390
AAAGCCUUCAGCUGGAAGAGGGCACUUGGAUCGGUGGCUCCCACCGAUGGUGCCUUGGAUAUGGGCACCAGAAAGUCUCUGUAGCCGCGCAGAAUGCUGGCCAUGAAGAGCAGAAAGGC
...((((((.(((.....((((((((...((((((((...))))))))))))))))...(((((((..((((.....))))..)))((.(((....)))))))))...))).).))))) ( -47.10)
>DroGri_CAF1 59418 119 - 1
AAAGCCUUUAGCUGAAAUAAGGCACUUGGAUCCGUGGCGCCAACGGAGGGCGCCCUUGAUAUGGGCACCAAGUAGUCACGAUAGCCACGCAAUAUGGACGCCAUAAAGAGCAGAAAUGC
..(((.....))).......(((((((((.((((((....).)))))....((((.......)))).)))))).(((...((.((...)).))...)))))).......(((....))) ( -37.00)
>DroEre_CAF1 3860 119 - 1
AAGGCCUUCAGCUGAAAGAGGGCACUCGGAUCAGUGGCUCCCACCGAGGGUGCCUUGGAAAUGGGCACCAGAAAAUCUCUGUAACCGCGCAGAAUGCUGGCCAUAAAAAGCAGAAAGGC
...((((((.(((.....(((((((((...((.((((...)))).)))))))))))....((((...((((...((.(((((......))))))).))))))))....))).).))))) ( -39.00)
>DroWil_CAF1 2098 119 - 1
AAAGCCUUGUGCUGGAAUAAGGCAUUCGGAUCUGUGGCACCCACUGAAGGUGCCUUCGAUAUGGGUACCAAAUAGUCGCGAUAUCCACGCAAUAUCGAUGCCAUGAAGAGUAGAAAUGC
...(((((((......))))))).(((...(((((((((...((((..(((((((.......)))))))...))))..((((((.......)))))).))))))..)))...))).... ( -37.50)
>DroMoj_CAF1 91797 119 - 1
AAAGCUUUCAGCUGAAAUAAGGCACUCGGAUCCGUGGCGCCCACAGAGGGUGCCUUUGAAAUUGGCACCAGAUAGUCACGAUAGCCGCGCAAUAUGCACGCCAUGAAGAGCAGAAAUGC
..(((.....))).......(((...(((...((((((((((.....))))(((.........)))........))))))....))).((.....))..))).......(((....))) ( -35.00)
>DroAna_CAF1 2264 119 - 1
AAGGCCUUCAGCUGGAACAGGGCGCUUGGAUCAGUGGCGCCCACUGAGGGCGCCUUGGAAAUGGGCACCAGGAAGUCCCGGUAGCCGCGCAAUAUGCUCGCCAUGAAGAGCAGAAAGGC
...((((((.((.....(((((((((....(((((((...))))))).)))))))))......((((((.((....)).))).)))))......(((((........)))))).))))) ( -52.70)
>consensus
AAAGCCUUCAGCUGAAAUAAGGCACUCGGAUCAGUGGCGCCCACCGAGGGUGCCUUGGAAAUGGGCACCAGAAAGUCACGAUAGCCGCGCAAUAUGCACGCCAUGAAGAGCAGAAAGGC
......(((.(((.......(((...(((.(((((((...))))))).(((((((.......)))))))...............))).((.....))..)))......))).))).... (-25.59 = -26.65 +   1.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,440,995 – 8,441,103
Length 108
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 79.50
Mean single sequence MFE -38.18
Consensus MFE -28.01
Energy contribution -27.98
Covariance contribution -0.02
Combinations/Pair 1.26
Mean z-score -1.43
Structure conservation index 0.73
SVM decision value 0.55
SVM RNA-class probability 0.776953
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8440995 108 + 22224390
AGAGACUUUCUGGUGCCCAUAUCCAAGGCACCAUCGGUGGGAGCCACCGAUCCAAGUGCCCUCUUCCAGCUGAAGGCUUUUUUGCGAUCGCGUGAUAAGGUAAGAA--AA
......(((((((((((.........))))))((((((((...)))))((((((((.(((.((........)).)))...)))).))))....)))......))))--). ( -34.90)
>DroVir_CAF1 2104 110 + 1
CGUGACUACUUGGUGCCUAUUUCAAAGGCGCCUUCCGUGGGCGCCACGGAUCCAAGUGCCUUAUUUCAGCUGAAAGCUUUUCUGCGCUCGCGCGAUAAGGUAAGUGCAAA
.((.((((((((((((((.......))))))).(((((((...)))))))...))))((((((((...((.((..((......))..))))..)))))))).)))))... ( -40.00)
>DroPse_CAF1 4021 108 + 1
CGCGACUAUUUGGUGCCCAUAUCGAAGGCACCAUCGGUGGGGGCCACCGAUCCGAGUGCCUUAUUCCAGCUGAAGGCCUUUCUGCGUUCGCGCGAUAAGGUAACGA--GU
((.((.....(((((((.........)))))))(((((((...)))))))))))..(((((((((...((.(((.((......)).)))))..)))))))))....--.. ( -40.00)
>DroGri_CAF1 59457 110 + 1
CGUGACUACUUGGUGCCCAUAUCAAGGGCGCCCUCCGUUGGCGCCACGGAUCCAAGUGCCUUAUUUCAGCUAAAGGCUUUUCUGCGCUCGCGCGACAAGGUAAGAGUGAA
......((((((((((((.......))))))).(((((.(....))))))......((((((.....(((.....)))....((((....))))..)))))).))))).. ( -34.40)
>DroWil_CAF1 2137 110 + 1
CGCGACUAUUUGGUACCCAUAUCGAAGGCACCUUCAGUGGGUGCCACAGAUCCGAAUGCCUUAUUCCAGCACAAGGCUUUUCUGAGAUCACGUGAUAAGGUGAGAGUUGA
..(((((...((((((((((...((((....)))).))))))))))((((...(((.(((((..........))))))))))))...((((.(....).)))).))))). ( -36.70)
>DroAna_CAF1 2303 104 + 1
CGGGACUUCCUGGUGCCCAUUUCCAAGGCGCCCUCAGUGGGCGCCACUGAUCCAAGCGCCCUGUUCCAGCUGAAGGCCUUUUUGCGUUCCCGCGAUAAGGUGAG------
.(((((.....(((((.....((...(((((((.....)))))))...)).....)))))..)))))........(((((.(((((....))))).)))))...------ ( -43.10)
>consensus
CGCGACUACUUGGUGCCCAUAUCAAAGGCACCAUCAGUGGGCGCCACCGAUCCAAGUGCCUUAUUCCAGCUGAAGGCUUUUCUGCGAUCGCGCGAUAAGGUAAGAG__AA
...........((((((.........)))))).(((((((...)))))))......(((((((((...((.....))......(((....))))))))))))........ (-28.01 = -27.98 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,440,995 – 8,441,103
Length 108
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 79.50
Mean single sequence MFE -37.18
Consensus MFE -25.99
Energy contribution -25.60
Covariance contribution -0.39
Combinations/Pair 1.30
Mean z-score -1.34
Structure conservation index 0.70
SVM decision value 0.31
SVM RNA-class probability 0.682342
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8440995 108 - 22224390
UU--UUCUUACCUUAUCACGCGAUCGCAAAAAAGCCUUCAGCUGGAAGAGGGCACUUGGAUCGGUGGCUCCCACCGAUGGUGCCUUGGAUAUGGGCACCAGAAAGUCUCU
((--((((..((.......((....))......((((((........))))))....))((((((((...))))))))(((((((.......)))))))))))))..... ( -39.50)
>DroVir_CAF1 2104 110 - 1
UUUGCACUUACCUUAUCGCGCGAGCGCAGAAAAGCUUUCAGCUGAAAUAAGGCACUUGGAUCCGUGGCGCCCACGGAAGGCGCCUUUGAAAUAGGCACCAAGUAGUCACG
..((.(((..(((((((((....)))......(((.....)))...)))))).((((((.(((((((...)))))))....((((.......)))).))))))))))).. ( -37.20)
>DroPse_CAF1 4021 108 - 1
AC--UCGUUACCUUAUCGCGCGAACGCAGAAAGGCCUUCAGCUGGAAUAAGGCACUCGGAUCGGUGGCCCCCACCGAUGGUGCCUUCGAUAUGGGCACCAAAUAGUCGCG
..--..............(((((.((.((....(((((..........))))).)))).((((((((...))))))))(((((((.......)))))))......))))) ( -36.90)
>DroGri_CAF1 59457 110 - 1
UUCACUCUUACCUUGUCGCGCGAGCGCAGAAAAGCCUUUAGCUGAAAUAAGGCACUUGGAUCCGUGGCGCCAACGGAGGGCGCCCUUGAUAUGGGCACCAAGUAGUCACG
............(((.(((....))))))....(((((..........)))))((((((.((((((....).)))))....((((.......)))).))))))....... ( -36.20)
>DroWil_CAF1 2137 110 - 1
UCAACUCUCACCUUAUCACGUGAUCUCAGAAAAGCCUUGUGCUGGAAUAAGGCAUUCGGAUCUGUGGCACCCACUGAAGGUGCCUUCGAUAUGGGUACCAAAUAGUCGCG
.........(((((((((((.(((((..(((..(((((((......))))))).)))))))))))((((((.......))))))...)))).)))).............. ( -33.00)
>DroAna_CAF1 2303 104 - 1
------CUCACCUUAUCGCGGGAACGCAAAAAGGCCUUCAGCUGGAACAGGGCGCUUGGAUCAGUGGCGCCCACUGAGGGCGCCUUGGAAAUGGGCACCAGGAAGUCCCG
------...........(((....))).....((.((((..((((..(((((((((....(((((((...))))))).)))))))))(.......).)))))))).)).. ( -40.30)
>consensus
UU__CUCUUACCUUAUCGCGCGAACGCAGAAAAGCCUUCAGCUGGAAUAAGGCACUUGGAUCCGUGGCGCCCACCGAAGGCGCCUUCGAUAUGGGCACCAAAUAGUCACG
..........((.....(((....)))......(((((..........)))))....)).(((((((...))))))).((.((((.......)))).))........... (-25.99 = -25.60 +  -0.39)

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 10:53:09 2006