Locus 3289

Sequence ID 2L_DroMel_CAF1
Location 9,528,884 – 9,529,109
Length 225
Max. P 0.999931
window5217 window5218 window5219 window5220 window5221 window5222 window5223 window5224

overview

Window 7

Location 9,528,884 – 9,528,989
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.79
Mean single sequence MFE -34.46
Consensus MFE -12.18
Energy contribution -14.46
Covariance contribution 2.28
Combinations/Pair 1.19
Mean z-score -2.71
Structure conservation index 0.35
SVM decision value 3.15
SVM RNA-class probability 0.998593
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9528884 105 + 22407834
GGUGGAAGUCCUAAGGAUAAGCCUGUAGAAAGUUCU------------GGAGCAAGUCCUGGAGAAAAACCA---GCAGGUAGUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCU
..((((...(((.(((((..((.(.((((....)))------------).)))..)))))((.......)).---..)))...))))...(((..(((((((.....)))))))...))) ( -29.30)
>DroSec_CAF1 36491 108 + 1
GGUGGAAGUCCUAAGGAUAAGCCUGUAGAAAGUUCU------------GGAGGAAAUCCUGGAGCAAAACCAGGAGCAGGUAUUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCU
..(((((..(((.........(((.((((....)))------------).)))...((((((.......))))))..)))..)))))...(((..(((((((.....)))))))...))) ( -35.50)
>DroSim_CAF1 39604 105 + 1
GGUGGAAGUCCUAAGGAUAAGCCUGUAGAAAGUUCU------------GGAGGAAAUCCUGCAGCAAAACCU---GCAGGUAUUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCU
..(((((((((...))))..((((((((......((------------(.(((....))).)))......))---)))))).)))))...(((..(((((((.....)))))))...))) ( -38.00)
>DroEre_CAF1 40389 117 + 1
GCAGGAAGUCCUGAGAGCAAGCCAGCAGAUAGUUCUGGCGGAGCAGCUGGAGGAAGUCCUGCAGGGAAACCU---GUAGUAGGUCCAGAAGGAAAACCAGGAGAUAAUUCUGGCAAAGGC
.((((....)))).......(((..........((..((......))..))(((..(.(((((((....)))---)))).)..)))..........((((((.....))))))....))) ( -41.70)
>DroYak_CAF1 44576 87 + 1
GGGGGAAGUCCUCAGGUUAAGCCUGUAGAAGGUUCU------------GAAAGAAAUCCUGGGGCCAAACCA---GCAGGACGUCCUGAGAGCAAACCAGGA------------------
..((...(..((((((.....(((((.(..((((((------------(..(....)..)))))))....).---)))))....))))))..)...))....------------------ ( -27.80)
>consensus
GGUGGAAGUCCUAAGGAUAAGCCUGUAGAAAGUUCU____________GGAGGAAAUCCUGGAGCAAAACCA___GCAGGUAGUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCU
...(((.((((...))))..(((((((((....)))............(((.....)))................))))))..))).........(((((((.....)))))))...... (-12.18 = -14.46 +   2.28)

alignment

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secondary structure

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Window 8

Location 9,528,884 – 9,528,989
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.79
Mean single sequence MFE -29.50
Consensus MFE -9.75
Energy contribution -11.87
Covariance contribution 2.12
Combinations/Pair 1.15
Mean z-score -3.14
Structure conservation index 0.33
SVM decision value 3.97
SVM RNA-class probability 0.999736
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9528884 105 - 22407834
AGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGACUACCUGC---UGGUUUUUCUCCAGGACUUGCUCC------------AGAACUUUCUACAGGCUUAUCCUUAGGACUUCCACC
(((...(((((((.....)))))))..))).((((((..(((...---.))).....)))((((...(((..------------(((....)))...)))...))))..)))........ ( -25.40)
>DroSec_CAF1 36491 108 - 1
AGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGAAUACCUGCUCCUGGUUUUGCUCCAGGAUUUCCUCC------------AGAACUUUCUACAGGCUUAUCCUUAGGACUUCCACC
(((...(((((((.....)))))))..)))....((((..((((.((((((.......))))))...(((..------------(((....)))..)))........))))..))))... ( -29.90)
>DroSim_CAF1 39604 105 - 1
AGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGAAUACCUGC---AGGUUUUGCUGCAGGAUUUCCUCC------------AGAACUUUCUACAGGCUUAUCCUUAGGACUUCCACC
(((...(((((((.....)))))))..)))....((((..(((((---((......)))))))..))))...------------.(((..(((((.(((.....)))))))).))).... ( -31.80)
>DroEre_CAF1 40389 117 - 1
GCCUUUGCCAGAAUUAUCUCCUGGUUUUCCUUCUGGACCUACUAC---AGGUUUCCCUGCAGGACUUCCUCCAGCUGCUCCGCCAGAACUAUCUGCUGGCUUGCUCUCAGGACUUCCUGC
((((..(((((.........)))))..(((....)))........---))))......((((((..((((..(((....(((.((((....)))).)))...)))...))))..)))))) ( -33.60)
>DroYak_CAF1 44576 87 - 1
------------------UCCUGGUUUGCUCUCAGGACGUCCUGC---UGGUUUGGCCCCAGGAUUUCUUUC------------AGAACCUUCUACAGGCUUAACCUGAGGACUUCCCCC
------------------((((((.......)))))).(((((.(---.((((.((((...(((.(((....------------.)))...)))...)))).)))).))))))....... ( -26.80)
>consensus
AGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGACUACCUGC___UGGUUUUGCUCCAGGAUUUCCUCC____________AGAACUUUCUACAGGCUUAUCCUUAGGACUUCCACC
......(((((((.....))))))).........(((...((((.....((((((......(((.....)))............)))))).....))))((((....))))...)))... ( -9.75 = -11.87 +   2.12)

alignment

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secondary structure

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Window 9

Location 9,528,920 – 9,529,029
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.38
Mean single sequence MFE -38.77
Consensus MFE -16.59
Energy contribution -19.40
Covariance contribution 2.81
Combinations/Pair 1.15
Mean z-score -3.42
Structure conservation index 0.43
SVM decision value 2.24
SVM RNA-class probability 0.990943
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9528920 109 + 22407834
--------GGAGCAAGUCCUGGAGAAAAACCA---GCAGGUAGUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCUGCUGAAGUUGGAGCUGCUGGAGAAAAGCCUGUUGAUAUUC
--------(((.....)))...........((---((((((..(((((..(((...((((..((((((((.....))))))))....)))).))).))))).....))))))))...... ( -36.60)
>DroSec_CAF1 36527 112 + 1
--------GGAGGAAAUCCUGGAGCAAAACCAGGAGCAGGUAUUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCUGCUAAAGGUGGAGCUACUGGACAAAAUCCUAUUGAAAUUC
--------..((((..((((((.......))))))........(((((..(((..(((....((((((((.....))))))))...)))...))).))))).....)))).......... ( -35.50)
>DroSim_CAF1 39640 109 + 1
--------GGAGGAAAUCCUGCAGCAAAACCU---GCAGGUAUUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCUGCUGAAGGUGGAGCUACUGGAGAAAAUCCUGUUGAAAUUC
--------..((((...(((((((......))---)))))..((((((..(((..(((....((((((((.....))))))))...)))...))).))))))....)))).......... ( -39.70)
>DroEre_CAF1 40429 114 + 1
GAGCAGCUGGAGGAAGUCCUGCAGGGAAACCU---GUAGUAGGUCCAGAAGGAAAACCAGGAGAUAAUUCUGGCAAAGGCACUGG---GGGAAGUCCCCAGGAUAAGCCUGUAGAAAGUC
..((.((..(((((..(.(((((((....)))---)))).)..)))....((....))..........))..))..((((.((((---((.....)))))).....))))))........ ( -43.30)
>consensus
________GGAGGAAAUCCUGCAGCAAAACCA___GCAGGUAGUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCUGCUGAAGGUGGAGCUACUGGAGAAAAGCCUGUUGAAAUUC
........(((.....(((.(.(((...(((....((((.(...((((((.....(((....)))..))))))...).))))....)))...))).).))).....)))........... (-16.59 = -19.40 +   2.81)

alignment

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secondary structure

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Window 0

Location 9,528,920 – 9,529,029
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 74.38
Mean single sequence MFE -30.39
Consensus MFE -15.35
Energy contribution -15.97
Covariance contribution 0.62
Combinations/Pair 1.27
Mean z-score -2.96
Structure conservation index 0.51
SVM decision value 2.68
SVM RNA-class probability 0.996338
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9528920 109 - 22407834
GAAUAUCAACAGGCUUUUCUCCAGCAGCUCCAACUUCAGCAGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGACUACCUGC---UGGUUUUUCUCCAGGACUUGCUCC--------
...........((.......(((((((.(((......(((((....(((((((.....))))))))))))....)))....))))---))).......)).(((.....)))-------- ( -27.34)
>DroSec_CAF1 36527 112 - 1
GAAUUUCAAUAGGAUUUUGUCCAGUAGCUCCACCUUUAGCAGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGAAUACCUGCUCCUGGUUUUGCUCCAGGAUUUCCUCC--------
..........((((....((((.(.(((...(((...((((((...(((((((.....)))))))..)).....((....))))))...)))...))).).)))).))))..-------- ( -30.00)
>DroSim_CAF1 39640 109 - 1
GAAUUUCAACAGGAUUUUCUCCAGUAGCUCCACCUUCAGCAGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGAAUACCUGC---AGGUUUUGCUGCAGGAUUUCCUCC--------
...........(((............(((........)))(((...(((((((.....)))))))..))).)))((((..(((((---((......)))))))..))))...-------- ( -33.00)
>DroEre_CAF1 40429 114 - 1
GACUUUCUACAGGCUUAUCCUGGGGACUUCCC---CCAGUGCCUUUGCCAGAAUUAUCUCCUGGUUUUCCUUCUGGACCUACUAC---AGGUUUCCCUGCAGGACUUCCUCCAGCUGCUC
..........((((.....((((((.....))---)))).))))..(((((.........))))).......(((((.......(---(((....))))..((....)))))))...... ( -31.20)
>consensus
GAAUUUCAACAGGAUUUUCUCCAGUAGCUCCACCUUCAGCAGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGAAUACCUGC___AGGUUUUGCUCCAGGACUUCCUCC________
......................(((((.(((.....((((((..(((((((((.....)))))))........(((.....))).....))..))))))..))).))))).......... (-15.35 = -15.97 +   0.62)

alignment

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secondary structure

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Window 1

Location 9,528,949 – 9,529,069
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.50
Mean single sequence MFE -41.12
Consensus MFE -27.55
Energy contribution -27.80
Covariance contribution 0.25
Combinations/Pair 1.31
Mean z-score -2.86
Structure conservation index 0.67
SVM decision value 3.33
SVM RNA-class probability 0.999014
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9528949 120 + 22407834
UAGUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCUGCUGAAGUUGGAGCUGCUGGAGAAAAGCCUGUUGAUAUUCCACAACAAAAACCAGAAGAUAGUUCUGGCGGAGGCUCUGG
...(((((..(((...((((..((((((((.....))))))))....)))).))).)))))....(((((((((........)))).....((((((.....))))))...))))).... ( -39.60)
>DroSec_CAF1 36559 120 + 1
UAUUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCUGCUAAAGGUGGAGCUACUGGACAAAAUCCUAUUGAAAUUCCACCAGGAAAACCAGAAGAUAGUUCUGGCGGAGGCUCGGG
....((.(((..(...(((((((((..(((((((((((((.(.......).)))....(((.....))).........))))))))))..))).........))))))..)...))).)) ( -39.10)
>DroSim_CAF1 39669 120 + 1
UAUUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCUGCUGAAGGUGGAGCUACUGGAGAAAAUCCUGUUGAAAUUCCACCAGGAAAACCAGAAGAUAGUUCUGGCGGAGGCUCUGG
....((((((..(...(((((((((..(((((((((((((.(.......).))).((.(((.....))).))......))))))))))..))).........))))))..)...)))))) ( -42.60)
>DroEre_CAF1 40466 117 + 1
AGGUCCAGAAGGAAAACCAGGAGAUAAUUCUGGCAAAGGCACUGG---GGGAAGUCCCCAGGAUAAGCCUGUAGAAAGUCCUGAGAGCAAGCCAGGAGGUAGUUCUGGCGGAGCAGUUGG
.(.(((...((((...((((((.....))))))...((((.((((---((.....)))))).....))))........))))........(((((((.....)))))))))).)...... ( -43.20)
>consensus
UAGUCCGGAGAGCAAACCAGAAGGUAGUUCUGGUGGAGCUGCUGAAGGUGGAGCUACUGGAGAAAAGCCUGUUGAAAUUCCACAAGGAAAACCAGAAGAUAGUUCUGGCGGAGGCUCUGG
....((((((......((((((.((..(((((((..((((.(.......).))))...........((((..((......))..))))..))))))).))..))))))......)))))) (-27.55 = -27.80 +   0.25)

alignment

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secondary structure

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Window 2

Location 9,528,949 – 9,529,069
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.50
Mean single sequence MFE -35.88
Consensus MFE -26.95
Energy contribution -26.70
Covariance contribution -0.25
Combinations/Pair 1.34
Mean z-score -3.56
Structure conservation index 0.75
SVM decision value 4.63
SVM RNA-class probability 0.999931
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9528949 120 - 22407834
CCAGAGCCUCCGCCAGAACUAUCUUCUGGUUUUUGUUGUGGAAUAUCAACAGGCUUUUCUCCAGCAGCUCCAACUUCAGCAGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGACUA
..((((((...(((((((.....)))))))...(((((........)))))))))))..(((....(((........)))(((...(((((((.....)))))))..)))....)))... ( -34.70)
>DroSec_CAF1 36559 120 - 1
CCCGAGCCUCCGCCAGAACUAUCUUCUGGUUUUCCUGGUGGAAUUUCAAUAGGAUUUUGUCCAGUAGCUCCACCUUUAGCAGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGAAUA
((.((((..(((((((((.....)))))))....((((((((.........((((...)))).((.(((........))).))))))))))...........))...))))...)).... ( -36.40)
>DroSim_CAF1 39669 120 - 1
CCAGAGCCUCCGCCAGAACUAUCUUCUGGUUUUCCUGGUGGAAUUUCAACAGGAUUUUCUCCAGUAGCUCCACCUUCAGCAGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGAAUA
(((((((..(((((((((.....)))))))....((((((((.........(((.....))).((.(((........))).))))))))))...........))...)))))..)).... ( -37.50)
>DroEre_CAF1 40466 117 - 1
CCAACUGCUCCGCCAGAACUACCUCCUGGCUUGCUCUCAGGACUUUCUACAGGCUUAUCCUGGGGACUUCCC---CCAGUGCCUUUGCCAGAAUUAUCUCCUGGUUUUCCUUCUGGACCU
(((...((...(((((.........)))))..))....((((........((((.....((((((.....))---)))).))))..(((((.........)))))..))))..))).... ( -34.90)
>consensus
CCAGAGCCUCCGCCAGAACUAUCUUCUGGUUUUCCUGGUGGAAUUUCAACAGGAUUUUCUCCAGUAGCUCCACCUUCAGCAGCUCCACCAGAACUACCUUCUGGUUUGCUCUCCGGAAUA
(((((((....(((((((.....(((((((..(((((.(((....))).)))))........(((.(((........))).)))..))))))).....)))))))..)))))..)).... (-26.95 = -26.70 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,528,989 – 9,529,109
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 75.87
Mean single sequence MFE -38.67
Consensus MFE -20.71
Energy contribution -22.15
Covariance contribution 1.44
Combinations/Pair 1.31
Mean z-score -2.80
Structure conservation index 0.54
SVM decision value 2.39
SVM RNA-class probability 0.993348
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9528989 120 + 22407834
GCUGAAGUUGGAGCUGCUGGAGAAAAGCCUGUUGAUAUUCCACAACAAAAACCAGAAGAUAGUUCUGGCGGAGGCUCUGGGGGAAGUCCUCAGAAUAAGCCUGUAGAAAGUUCUAAAGGA
(((...((..((((((((((((......))((((........)))).....))))....))))))..))...)))(((((((.....))))))).....(((.((((....)))).))). ( -37.40)
>DroSec_CAF1 36599 119 + 1
GCUAAAGGUGGAGCUACUGGACAAAAUCCUAUUGAAAUUCCACCAGGAAAACCAGAAGAUAGUUCUGGCGGAGGCUCGGGGGGAAGUCCCAAGGAUAAGCCUGUAGAAAGUCCUAAAGG-
.((..(((.....((((.((.....(((((.((((..((((.((((((....(....)....)))))).))))..)))).(((....))).)))))...)).)))).....)))..)).- ( -35.20)
>DroSim_CAF1 39709 119 + 1
GCUGAAGGUGGAGCUACUGGAGAAAAUCCUGUUGAAAUUCCACCAGGAAAACCAGAAGAUAGUUCUGGCGGAGGCUCUGGGGGAAGUCCUCAGAAUAAGCCUGUAGAAAGUCCUAAAGG-
......(((((((..((.(((.....))).)).....)))))))((((...((((((.....)))))).(.(((((((((((.....)))))))....)))).)......)))).....- ( -39.60)
>DroEre_CAF1 40506 115 + 1
ACUGG---GGGAAGUCCCCAGGAUAAGCCUGUAGAAAGUCCUGAGAGCAAGCCAGGAGGUAGUUCUGGCGGAGCAGUUGGAGGAAGUCCUGGAGGGAGACCUGUAGUAAAACCAGAAG--
((((.---(((...((((((((((...(((.(((....(((((....)).(((((((.....))))))))))....))).)))..))))))).)))...))).))))...........-- ( -42.50)
>consensus
GCUGAAGGUGGAGCUACUGGAGAAAAGCCUGUUGAAAUUCCACAAGGAAAACCAGAAGAUAGUUCUGGCGGAGGCUCUGGGGGAAGUCCUCAGAAUAAGCCUGUAGAAAGUCCUAAAGG_
.(((.((((((((((.(((.......((((..((......))..))))...((((((.....))))))))).)))))).((((....)))).......)))).))).............. (-20.71 = -22.15 +   1.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,528,989 – 9,529,109
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 75.87
Mean single sequence MFE -32.48
Consensus MFE -17.01
Energy contribution -17.20
Covariance contribution 0.19
Combinations/Pair 1.46
Mean z-score -2.85
Structure conservation index 0.52
SVM decision value 2.34
SVM RNA-class probability 0.992644
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9528989 120 - 22407834
UCCUUUAGAACUUUCUACAGGCUUAUUCUGAGGACUUCCCCCAGAGCCUCCGCCAGAACUAUCUUCUGGUUUUUGUUGUGGAAUAUCAACAGGCUUUUCUCCAGCAGCUCCAACUUCAGC
.(((.((((....)))).)))......((((((....))....((((....(((((((.....)))))))...(((((..(((..((....))...)))..))))))))).....)))). ( -28.70)
>DroSec_CAF1 36599 119 - 1
-CCUUUAGGACUUUCUACAGGCUUAUCCUUGGGACUUCCCCCCGAGCCUCCGCCAGAACUAUCUUCUGGUUUUCCUGGUGGAAUUUCAAUAGGAUUUUGUCCAGUAGCUCCACCUUUAGC
-.((..(((.....((((.(((..(((((.(((....)))...(((..(((((((((((((.....)))))...))))))))..)))...)))))...)))..)))).....)))..)). ( -35.50)
>DroSim_CAF1 39709 119 - 1
-CCUUUAGGACUUUCUACAGGCUUAUUCUGAGGACUUCCCCCAGAGCCUCCGCCAGAACUAUCUUCUGGUUUUCCUGGUGGAAUUUCAACAGGAUUUUCUCCAGUAGCUCCACCUUCAGC
-.((..(((.....((((.(((....((((.((......)))))))))(((((((((((((.....)))))...)))))))).........(((.....))).)))).....)))..)). ( -32.80)
>DroEre_CAF1 40506 115 - 1
--CUUCUGGUUUUACUACAGGUCUCCCUCCAGGACUUCCUCCAACUGCUCCGCCAGAACUACCUCCUGGCUUGCUCUCAGGACUUUCUACAGGCUUAUCCUGGGGACUUCCC---CCAGU
--...((((........((((....(((..((((..((((......((...(((((.........)))))..))....))))..))))..))).....))))(((....)))---)))). ( -32.90)
>consensus
_CCUUUAGGACUUUCUACAGGCUUAUCCUGAGGACUUCCCCCAGAGCCUCCGCCAGAACUAUCUUCUGGUUUUCCUGGUGGAAUUUCAACAGGAUUUUCUCCAGUAGCUCCACCUUCAGC
...................((......(((((((.................(((((((.....)))))))..(((((.(((....))).)))))...))))))).....))......... (-17.01 = -17.20 +   0.19)

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 10:48:58 2006