Locus 2282

Sequence ID 2R_DroMel_CAF1
Location 8,407,433 – 8,407,567
Length 134
Max. P 0.999875
window3746 window3747 window3748 window3749

overview

Window 6

Location 8,407,433 – 8,407,547
Length 114
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 80.12
Mean single sequence MFE -54.72
Consensus MFE -42.62
Energy contribution -44.50
Covariance contribution 1.88
Combinations/Pair 1.24
Mean z-score -2.35
Structure conservation index 0.78
SVM decision value 1.90
SVM RNA-class probability 0.981811
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8407433 114 + 20766785
GGCAGCUCCCACUCGCCCUGCAGCCCCAUCCUGCCGCCAUCGGUGAGCGCAAAUGCCGCUG---CGGCAGUGGCAGCGGCGGCCCACAAUAGUGCAGCGGCGGCAGUGGCGGUCGCA
.((.(((.(((((.(((((((.(((.......((((((...)))).))......(((((((---(.......))))))))))).(((....)))..)))).)))))))).))).)). ( -54.60)
>DroVir_CAF1 24133 114 + 1
GGCAGCUCUCAUUCGCCCUGCAGCCCCAUCCUGCCGCCCUCGGUGAGCGCCAAUGCAGCCGCAGCGGCUGUUGCCGCCGCC---CAUAACUCAGCGGCCGCAGCCGUUGCGGCGGUG
(((.((((.(....((...((((.......)))).)).....).)))))))...((.((((((((((((((.(((((....---.........))))).)))))))))))))).)). ( -58.12)
>DroGri_CAF1 26126 117 + 1
GGCAGCUCUCACUCCCCCUGCAGCCCCAUAUUGCCGCCGUCGGUGAGCGCCAAUGCGGCAGCAGCAGCUGUUGCCGCCGCCGCACACAAUUCAGCUGCAGCAGCCGUUGCAGCGGUU
(((.((.((((((..(...((.((........)).)).)..)))))).))....((((((((((...)))))))))).)))............((((((((....)))))))).... ( -50.10)
>DroWil_CAF1 22586 117 + 1
GGUAGCUCUCAUUCACCCUGCAGUCCCAUUCUACCGCCUUCGGUGAGCGCCAAUGCUGCAGCAGCAGCUGUUGCCGCCGCUGCACAUAAUUCGGCGGCGGCAGCUGUUGCUGCUGUG
(((.((((.............((.......))((((....)))))))))))......(((((((((((.(((((((((((((.........))))))))))))).))))))))))). ( -58.30)
>DroMoj_CAF1 27451 114 + 1
GGCAGCUCCCAUUCCCCCUGCAGCCCCAUUUUGCCGCCCUCGGUGAGCGCCAAUGCAGCGGCAGCGGCCGUUGCUGCCGCC---CACAAUUCGGCGGCUGCAGCCGUUGCGGCCGUU
(((.((((.....((....((.((........)).))....)).))))))).....((((((.(((((.(((((.((((((---........)))))).))))).))))).)))))) ( -52.50)
>consensus
GGCAGCUCUCAUUCCCCCUGCAGCCCCAUCCUGCCGCCCUCGGUGAGCGCCAAUGCAGCAGCAGCGGCUGUUGCCGCCGCCGC_CACAAUUCAGCGGCGGCAGCCGUUGCGGCCGUG
(((.((((...........((((.......)))).(((...))))))))))...((.((((((((((((((.(((((((............))))))).)))))))))))))).)). (-42.62 = -44.50 +   1.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,407,433 – 8,407,547
Length 114
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 80.12
Mean single sequence MFE -56.86
Consensus MFE -35.20
Energy contribution -35.52
Covariance contribution 0.32
Combinations/Pair 1.22
Mean z-score -1.69
Structure conservation index 0.62
SVM decision value 0.03
SVM RNA-class probability 0.548203
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8407433 114 - 20766785
UGCGACCGCCACUGCCGCCGCUGCACUAUUGUGGGCCGCCGCUGCCACUGCCG---CAGCGGCAUUUGCGCUCACCGAUGGCGGCAGGAUGGGGCUGCAGGGCGAGUGGGAGCUGCC
((((.((.((((((((((((((.(((....)))))).((((((((.......)---)))))))................))))))))..))))).)))).(((.(((....)))))) ( -55.00)
>DroVir_CAF1 24133 114 - 1
CACCGCCGCAACGGCUGCGGCCGCUGAGUUAUG---GGCGGCGGCAACAGCCGCUGCGGCUGCAUUGGCGCUCACCGAGGGCGGCAGGAUGGGGCUGCAGGGCGAAUGAGAGCUGCC
...((((....((((((..(((((((.......---..)))))))..))))))((((((((.(((((.(((((.....))))).))..))).))))))))))))............. ( -61.40)
>DroGri_CAF1 26126 117 - 1
AACCGCUGCAACGGCUGCUGCAGCUGAAUUGUGUGCGGCGGCGGCAACAGCUGCUGCUGCCGCAUUGGCGCUCACCGACGGCGGCAAUAUGGGGCUGCAGGGGGAGUGAGAGCUGCC
..((((.((....)).))(((((((.....(((.(((((((((((....))))))))))))))((((.((((.......)))).))))....)))))))))((.(((....))).)) ( -58.20)
>DroWil_CAF1 22586 117 - 1
CACAGCAGCAACAGCUGCCGCCGCCGAAUUAUGUGCAGCGGCGGCAACAGCUGCUGCUGCAGCAUUGGCGCUCACCGAAGGCGGUAGAAUGGGACUGCAGGGUGAAUGAGAGCUACC
....((((((.((((((..(((((((............)))))))..)))))).))))))(((.((..((.(((((....(((((........)))))..))))).)).)))))... ( -53.30)
>DroMoj_CAF1 27451 114 - 1
AACGGCCGCAACGGCUGCAGCCGCCGAAUUGUG---GGCGGCAGCAACGGCCGCUGCCGCUGCAUUGGCGCUCACCGAGGGCGGCAAAAUGGGGCUGCAGGGGGAAUGGGAGCUGCC
..(((((.((.(..((((((((.(((...((..---(.(((((((.......))))))))..))(((.(((((.....))))).)))..)))))))))))..)...)).).)))).. ( -56.40)
>consensus
AACCGCCGCAACGGCUGCCGCCGCCGAAUUGUG_GCGGCGGCGGCAACAGCCGCUGCUGCUGCAUUGGCGCUCACCGAGGGCGGCAGAAUGGGGCUGCAGGGCGAAUGAGAGCUGCC
....((.(((.((((((..((.((((............)))).))..)))))).))).)).....((((.((((((....(((((........))))).)).....)))).)))).. (-35.20 = -35.52 +   0.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,407,473 – 8,407,567
Length 94
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 75.17
Mean single sequence MFE -52.47
Consensus MFE -34.82
Energy contribution -36.70
Covariance contribution 1.88
Combinations/Pair 1.23
Mean z-score -3.96
Structure conservation index 0.66
SVM decision value 4.34
SVM RNA-class probability 0.999875
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8407473 94 + 20766785
CGGUGAGCGCAAAUGCCGCUG---CGGCAGUGGCAGCGGCGGCCCACAAUAGUGCAGCGGCGGCAGUGGCGGUCGCAGCGAAUCAGGCCAGCUCCUC----------
.((.((((......(((((((---(.......))))))))((((........(((.(((((.((....)).))))).))).....)))).)))))).---------- ( -46.42)
>DroVir_CAF1 24173 94 + 1
CGGUGAGCGCCAAUGCAGCCGCAGCGGCUGUUGCCGCCGCC---CAUAACUCAGCGGCCGCAGCCGUUGCGGCGGUGGCCAAUCAGGCCUCCUCCUC----------
.(((....)))......((((((((((((((.(((((....---.........))))).))))))))))))))((.((((.....)))).)).....---------- ( -55.42)
>DroGri_CAF1 26166 97 + 1
CGGUGAGCGCCAAUGCGGCAGCAGCAGCUGUUGCCGCCGCCGCACACAAUUCAGCUGCAGCAGCCGUUGCAGCGGUUGCGAAUCAAGCCUCCUCCUC----------
.((.(((.((....(((((.(((((....))))).)))))((((.((......((((((((....)))))))).))))))......)))))..))..---------- ( -43.30)
>DroWil_CAF1 22626 107 + 1
CGGUGAGCGCCAAUGCUGCAGCAGCAGCUGUUGCCGCCGCUGCACAUAAUUCGGCGGCGGCAGCUGUUGCUGCUGUGGCAAAUCAGGCCAGUUCAUCCAGUUUGCAA
.((((((((((..(((..((((((((((.(((((((((((((.........))))))))))))).))))))))))..))).....)))..))))))).......... ( -65.40)
>DroMoj_CAF1 27491 94 + 1
CGGUGAGCGCCAAUGCAGCGGCAGCGGCCGUUGCUGCCGCC---CACAAUUCGGCGGCUGCAGCCGUUGCGGCCGUUGCGAAUCAAGCCUCCUCCUC----------
.((.(((.((...(((((((((.(((((.(((((.((((((---........)))))).))))).))))).)))))))))......)))))..))..---------- ( -51.80)
>consensus
CGGUGAGCGCCAAUGCAGCAGCAGCGGCUGUUGCCGCCGCCGC_CACAAUUCAGCGGCGGCAGCCGUUGCGGCCGUGGCGAAUCAGGCCUCCUCCUC__________
.(((((..((....((.((((((((((((((.(((((((............))))))).)))))))))))))).)).))...))..))).................. (-34.82 = -36.70 +   1.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,407,473 – 8,407,567
Length 94
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 75.17
Mean single sequence MFE -46.50
Consensus MFE -23.98
Energy contribution -24.90
Covariance contribution 0.92
Combinations/Pair 1.32
Mean z-score -1.96
Structure conservation index 0.52
SVM decision value 0.85
SVM RNA-class probability 0.866308
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8407473 94 - 20766785
----------GAGGAGCUGGCCUGAUUCGCUGCGACCGCCACUGCCGCCGCUGCACUAUUGUGGGCCGCCGCUGCCACUGCCG---CAGCGGCAUUUGCGCUCACCG
----------(..((((.(((((.....((.(((.(.((....)).).))).))((....)))))))((((((((.......)---)))))))......))))..). ( -41.90)
>DroVir_CAF1 24173 94 - 1
----------GAGGAGGAGGCCUGAUUGGCCACCGCCGCAACGGCUGCGGCCGCUGAGUUAUG---GGCGGCGGCAACAGCCGCUGCGGCUGCAUUGGCGCUCACCG
----------(((..((.((((.....)))).))((((((.((((((..(((((((.......---..)))))))..)))))).)))))).((....)).))).... ( -54.70)
>DroGri_CAF1 26166 97 - 1
----------GAGGAGGAGGCUUGAUUCGCAACCGCUGCAACGGCUGCUGCAGCUGAAUUGUGUGCGGCGGCGGCAACAGCUGCUGCUGCCGCAUUGGCGCUCACCG
----------..((..((((((.((((((.....((((((........))))))))))))..((((((((((((((.....)))))))))))))).))).))).)). ( -46.40)
>DroWil_CAF1 22626 107 - 1
UUGCAAACUGGAUGAACUGGCCUGAUUUGCCACAGCAGCAACAGCUGCCGCCGCCGAAUUAUGUGCAGCGGCGGCAACAGCUGCUGCUGCAGCAUUGGCGCUCACCG
.........((.(((..((((.......))))..(((((....))))).((.(((((....((((((((((((((....)))))))))))).)))))))))))))). ( -46.60)
>DroMoj_CAF1 27491 94 - 1
----------GAGGAGGAGGCUUGAUUCGCAACGGCCGCAACGGCUGCAGCCGCCGAAUUGUG---GGCGGCAGCAACGGCCGCUGCCGCUGCAUUGGCGCUCACCG
----------..((..(((.........((..((((((...))))))..))((((((..((..---(.(((((((.......))))))))..))))))))))).)). ( -42.90)
>consensus
__________GAGGAGGAGGCCUGAUUCGCAACCGCCGCAACGGCUGCCGCCGCCGAAUUGUG_GCGGCGGCGGCAACAGCCGCUGCUGCUGCAUUGGCGCUCACCG
............((....((((..(((((((......(((.((((((..((.((((............)))).))..)))))).)))))))).))..).)))..)). (-23.98 = -24.90 +   0.92)

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 10:25:37 2006