Locus 6118

Sequence ID 2L_DroMel_CAF1
Location 17,118,208 – 17,118,436
Length 228
Max. P 0.997650
window9750 window9751 window9752 window9753 window9754

overview

Window 0

Location 17,118,208 – 17,118,328
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.83
Mean single sequence MFE -34.30
Consensus MFE -27.70
Energy contribution -28.06
Covariance contribution 0.36
Combinations/Pair 1.14
Mean z-score -1.52
Structure conservation index 0.81
SVM decision value 0.38
SVM RNA-class probability 0.711963
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17118208 120 - 22407834
ACCAAAACCAACCGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGCUGCUCCAGCUGAAUUUGCAGCACCCUUUGACCCCGAACUAAGCAGCUCUGGCCCAUGGCUCCCCAUCUCCCACC
.............((((((((((...(((((((((((((...(.((((...)))).)......))))).)))))).))...))))...))))))(((...((((....))))...))).. ( -35.60)
>DroSec_CAF1 82053 120 - 1
ACCAAAACCAACCGAGUCGGGUUAAUGGCAAAGGUGCUGAUGCUGCUGCUCCAGCUGAAUUUGCAGCACCCUUUGACCCCGAACUAAGCAGCCCUGGCCCAUGGCUCCCCAUCUCCCACC
.............(((((((((((..(((...(((((((...(.((((...)))).)......))))))).((((....)))).......))).))))))..)))))............. ( -34.00)
>DroSim_CAF1 98118 118 - 1
ACCAAAACCAACUGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGCUGCUCCAGCUGA-UUUGCAGCACCCUUUGACCCCGAAAAAAACAAACCUGGCCCAUGGUUC-CCAUCUCCCAAC
...............((((((...(((((((((((((((...(.((((...)))).).-....))))).))))))...............((((........)))).-))))..)))))) ( -34.10)
>DroEre_CAF1 84098 119 - 1
ACCAAAACCAACCGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGGUGCUCCAGCUGAAUUUGCAGCACCCUUUGACCCCGAACUAAGCAGCCCUUGCCCAUGGCUCC-CAUCUUCCACC
.............(((((((((....(((...(((((((..(((((....)))))........))))))).((((....)))).......)))...)))))..)))).-........... ( -35.70)
>DroYak_CAF1 83971 119 - 1
ACCAGAACCAACCGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGGUGCUCCACCUGAAUUUGCAGCACCCUUUGACCCCGAACUAAGCAGCCCUUGCCCAUGACUCC-CCAUCCCCACC
.............(((((((((....(((...(((((((...(.((((...)))).)......))))))).((((....)))).......)))...)))))..)))).-........... ( -32.10)
>consensus
ACCAAAACCAACCGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGCUGCUCCAGCUGAAUUUGCAGCACCCUUUGACCCCGAACUAAGCAGCCCUGGCCCAUGGCUCCCCAUCUCCCACC
.............(((((((((((..(((...(((((((..((((......))))........))))))).((((....)))).......))).))))))..)))))............. (-27.70 = -28.06 +   0.36)

alignment

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secondary structure

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Window 1

Location 17,118,248 – 17,118,356
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.05
Mean single sequence MFE -47.84
Consensus MFE -38.70
Energy contribution -39.62
Covariance contribution 0.92
Combinations/Pair 1.08
Mean z-score -3.09
Structure conservation index 0.81
SVM decision value 2.90
SVM RNA-class probability 0.997650
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17118248 108 + 22407834
GGGGUCAAAGGGUGCUGCAAAUUCAGCUGGAGCAGCAGCAUCAGCACCUUUGCCAUUAACCCAACUCGGUUGGUUUUGGUUCGGUUUUUGCUGGGUGCUG------------GUGCUUCC
((((........((((((...(((....)))))))))((((((((((((..((.(..((((.(((.(((......)))))).))))..))).))))))))------------)))))))) ( -41.30)
>DroSec_CAF1 82093 117 + 1
GGGGUCAAAGGGUGCUGCAAAUUCAGCUGGAGCAGCAGCAUCAGCACCUUUGCCAUUAACCCGACUCGGUUGGUUUUGGUUCGGUUUUUGCUGGGUGCUGAUGCUAC---UGGUGCUUCC
((((.((..((..(((((...(((....))))))))(((((((((((((..((.(..((((.(((.(((......)))))).))))..))).))))))))))))).)---)..)))))). ( -47.10)
>DroSim_CAF1 98157 116 + 1
GGGGUCAAAGGGUGCUGCAAA-UCAGCUGGAGCAGCAGCAUCAGCACCUUUGCCAUUAACCCAACUCAGUUGGUUUUGGUUUGGUUUUUGCUGGGUGCUGCUGCUUC---GAGUGCUUCC
(((((........((((....-.))))(((((((((((((((((((((...((((.....(((((...)))))...))))..)))....))).))))))))))))))---)...))))). ( -47.60)
>DroEre_CAF1 84137 117 + 1
GGGGUCAAAGGGUGCUGCAAAUUCAGCUGGAGCACCAGCAUCAGCACCUUUGCCAUUAACCCAACUCGGUUGGUUUUGGUUCGCUUUUUGCUGGGUGCUGAUGCUAC---UGGUGCUUCC
(((((...((((((((.((........)).))))))(((((((((((((..((((.....(((((...)))))...))))..((.....)).))))))))))))).)---)...))))). ( -49.80)
>DroYak_CAF1 84010 120 + 1
GGGGUCAAAGGGUGCUGCAAAUUCAGGUGGAGCACCAGCAUCAGCACCUUUGCCAUUAACCCAACUCGGUUGGUUCUGGUUCGGUUUUUGCUGGGUGCUGAUGCUACCUCUGGUGCUUCC
(((((.....((((((.((........)).))))))(((((((((((((..((.(..((((.(((.(((......)))))).))))..))).)))))))))))))))))).......... ( -53.40)
>consensus
GGGGUCAAAGGGUGCUGCAAAUUCAGCUGGAGCAGCAGCAUCAGCACCUUUGCCAUUAACCCAACUCGGUUGGUUUUGGUUCGGUUUUUGCUGGGUGCUGAUGCUAC___UGGUGCUUCC
(((((.....(.((((.((........)).)))).)(((((((((((((..((.(..((((.(((.(((......)))))).))))..))).))))))))))))).........))))). (-38.70 = -39.62 +   0.92)

alignment

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secondary structure

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Window 2

Location 17,118,248 – 17,118,356
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.05
Mean single sequence MFE -42.76
Consensus MFE -32.24
Energy contribution -34.12
Covariance contribution 1.88
Combinations/Pair 1.03
Mean z-score -3.66
Structure conservation index 0.75
SVM decision value 2.10
SVM RNA-class probability 0.987933
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17118248 108 - 22407834
GGAAGCAC------------CAGCACCCAGCAAAAACCGAACCAAAACCAACCGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGCUGCUCCAGCUGAAUUUGCAGCACCCUUUGACCCC
(((.(((.------------(((((..((((....(((...(((...(((((...))))).....)))....))))))).))))).)))))).((((......))))............. ( -35.40)
>DroSec_CAF1 82093 117 - 1
GGAAGCACCA---GUAGCAUCAGCACCCAGCAAAAACCGAACCAAAACCAACCGAGUCGGGUUAAUGGCAAAGGUGCUGAUGCUGCUGCUCCAGCUGAAUUUGCAGCACCCUUUGACCCC
(((.(((...---((((((((((((((..((.....((((..(..........)..)))).......))...)))))))))))))))))))).((((......))))............. ( -44.80)
>DroSim_CAF1 98157 116 - 1
GGAAGCACUC---GAAGCAGCAGCACCCAGCAAAAACCAAACCAAAACCAACUGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGCUGCUCCAGCUGA-UUUGCAGCACCCUUUGACCCC
((........---(.((((((((((..((((....(((...(((...(((((...))))).....)))....))))))).)))))))))).).((((.-....))))..))......... ( -39.30)
>DroEre_CAF1 84137 117 - 1
GGAAGCACCA---GUAGCAUCAGCACCCAGCAAAAAGCGAACCAAAACCAACCGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGGUGCUCCAGCUGAAUUUGCAGCACCCUUUGACCCC
(((.((((((---...(((((((((((..((.....))...(((...(((((...))))).....)))....)))))))))))))))))))).((((......))))............. ( -48.50)
>DroYak_CAF1 84010 120 - 1
GGAAGCACCAGAGGUAGCAUCAGCACCCAGCAAAAACCGAACCAGAACCAACCGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGGUGCUCCACCUGAAUUUGCAGCACCCUUUGACCCC
........(((((((((((((((((((..((...((((.(((..(.......)..))).))))....))...)))))))))))))(((((.((........)).)))))))))))..... ( -45.80)
>consensus
GGAAGCACCA___GUAGCAUCAGCACCCAGCAAAAACCGAACCAAAACCAACCGAGUUGGGUUAAUGGCAAAGGUGCUGAUGCUGCUGCUCCAGCUGAAUUUGCAGCACCCUUUGACCCC
(((.(((.(......((((((((((((..((...((((.((((..........).))).))))....))...))))))))))))).)))))).((((......))))............. (-32.24 = -34.12 +   1.88)

alignment

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secondary structure

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Window 3

Location 17,118,328 – 17,118,436
Length 108
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 88.18
Mean single sequence MFE -32.67
Consensus MFE -22.60
Energy contribution -24.85
Covariance contribution 2.25
Combinations/Pair 1.15
Mean z-score -1.83
Structure conservation index 0.69
SVM decision value 0.23
SVM RNA-class probability 0.642605
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17118328 108 + 22407834
UCGGUUUUUGCUGGGUGCUG---------GUGCUUCCUCUUUUUUGCUAUUAGUUUUCGCCACAUGUUUGUGUGCGCCUGCAGCACCACCCCACCGAAAGACCCCCACUCGACAACC
..((((((((.((((.(.((---------(((((....(......)......((...(((((((....)))).)))...)))))))))))))).).))))))).............. ( -31.30)
>DroSec_CAF1 82173 117 + 1
UCGGUUUUUGCUGGGUGCUGAUGCUACUGGUGCUUCCUCUUUUUUGCUAUUAGUUUUCGCCACAUGUUUGUGUGUGCCAGCAUCACCACCCCACCGAAAGACCCCCACUCGACAACC
..((((((((..(((((.(((((((((((((((............)).))))))....(((((((....))))).)).))))))).)))))...).))))))).............. ( -36.10)
>DroSim_CAF1 98236 117 + 1
UUGGUUUUUGCUGGGUGCUGCUGCUUCGAGUGCUUCCUCUUUUUUGUUAUUAGUUUUCGCGACAUGUUUGUGUGUGCCAGCAGCACCACCCCACCGAAAGACCCCCACUCGACAACC
..((((((((..(((((.(((((((..(((.(((....(......).....))).)))(((((((....)))).))).))))))).)))))...).))))))).............. ( -32.80)
>DroEre_CAF1 84217 115 + 1
UCGCUUUUUGCUGGGUGCUGAUGCUACUGGUGCUUCCUCUUUUUUGCUAUUAGUUUUCGCCGCUUGUUUGUGUGUGCCAGCAGCAACACCCCACCGAAAGCCCCAC--UCUACAAGC
..((((((.(.((((.(.((.((((.((((..(............((...........))(((......))).)..)))).)))).)))))))).)))))).....--......... ( -30.50)
>consensus
UCGGUUUUUGCUGGGUGCUGAUGCUACUGGUGCUUCCUCUUUUUUGCUAUUAGUUUUCGCCACAUGUUUGUGUGUGCCAGCAGCACCACCCCACCGAAAGACCCCCACUCGACAACC
..((((.(((..(((((.(((((((.(((((((............)).))))).....(((((((....))))).)).))))))).)))))...(....).........))).)))) (-22.60 = -24.85 +   2.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,118,328 – 17,118,436
Length 108
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 88.18
Mean single sequence MFE -34.48
Consensus MFE -24.33
Energy contribution -25.95
Covariance contribution 1.62
Combinations/Pair 1.10
Mean z-score -1.60
Structure conservation index 0.71
SVM decision value 0.08
SVM RNA-class probability 0.575522
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17118328 108 - 22407834
GGUUGUCGAGUGGGGGUCUUUCGGUGGGGUGGUGCUGCAGGCGCACACAAACAUGUGGCGAAAACUAAUAGCAAAAAAGAGGAAGCAC---------CAGCACCCAGCAAAAACCGA
((((...(((.........)))(.((((((((((((.(...(((.((((....)))))))....((.............))).)))))---------)).).)))).)...)))).. ( -29.92)
>DroSec_CAF1 82173 117 - 1
GGUUGUCGAGUGGGGGUCUUUCGGUGGGGUGGUGAUGCUGGCACACACAAACAUGUGGCGAAAACUAAUAGCAAAAAAGAGGAAGCACCAGUAGCAUCAGCACCCAGCAAAAACCGA
((((..((((.........))))((.(((((.((((((((((.((((......)))))).....................((.....))..)))))))).))))).))...)))).. ( -37.00)
>DroSim_CAF1 98236 117 - 1
GGUUGUCGAGUGGGGGUCUUUCGGUGGGGUGGUGCUGCUGGCACACACAAACAUGUCGCGAAAACUAAUAACAAAAAAGAGGAAGCACUCGAAGCAGCAGCACCCAGCAAAAACCAA
((((..((((.........))))((.(((((.(((((((.(((((........))).))...................(((......)))..))))))).))))).))...)))).. ( -37.20)
>DroEre_CAF1 84217 115 - 1
GCUUGUAGA--GUGGGGCUUUCGGUGGGGUGUUGCUGCUGGCACACACAAACAAGCGGCGAAAACUAAUAGCAAAAAAGAGGAAGCACCAGUAGCAUCAGCACCCAGCAAAAAGCGA
.........--.....(((((..((.(((((((((((((((................((...........))........(....).)))))))))...)))))).))..))))).. ( -33.80)
>consensus
GGUUGUCGAGUGGGGGUCUUUCGGUGGGGUGGUGCUGCUGGCACACACAAACAUGUGGCGAAAACUAAUAGCAAAAAAGAGGAAGCACCAGUAGCAUCAGCACCCAGCAAAAACCGA
((((..((((.((...)).))))((.(((((.(((((((.((.(((........))))).....................(....)......))))))).))))).))...)))).. (-24.33 = -25.95 +   1.62)

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 12:02:29 2006