Locus 215

Sequence ID 2L_DroMel_CAF1
Location 621,395 – 621,767
Length 372
Max. P 0.999928
window331 window332 window333 window334 window335 window336 window337

overview

Window 1

Location 621,395 – 621,513
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.57
Mean single sequence MFE -29.42
Consensus MFE -17.73
Energy contribution -18.40
Covariance contribution 0.67
Combinations/Pair 1.14
Mean z-score -1.75
Structure conservation index 0.60
SVM decision value 0.04
SVM RNA-class probability 0.552369
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 621395 118 + 22407834
--UCUAAUAAAUACAUAACUGGCGAAAAAGAAUGCAGGUAGGAGCACUGCAGAGUUGCUUCUGACCAAUUCACCUACAAUCGAUCAAACGAUAGUCGGGAAAGCGGCGGAUAAACCGCUC
--...................((......((((...((((((((((((....)).))))))).))).)))).(((((.((((......)))).)).)))...))(((((.....))))). ( -31.00)
>DroSec_CAF1 10619 118 + 1
--UGUAAUAAAUACAUCGCUGGCGAAAAAGAAUGCAGGCAAGAGCGAUGCAGAGUUGCUUCUGACCAAUUCACCUACAAUCGAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUC
--((((.....)))).((((.........((((...((((..((((((.....))))))..)).)).)))).(((.....(((((....)))))..)))..))))((((.....)))).. ( -32.90)
>DroSim_CAF1 9832 118 + 1
--UGUAAUAAAUACAUCAGUAGCGAAAAAGAAUGCAGGCAAGAGCGAUGCAGAGUUGCUUCUGACCAAUUCACCUACAAUCGAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUC
--((((.....))))......((......((((...((((..((((((.....))))))..)).)).)))).(((.....(((((....)))))..)))...))(((((.....))))). ( -31.10)
>DroEre_CAF1 14189 92 + 1
GACGUACUUAAAACUUUACUGGCGAAAAGGAAUGUA----------------------------CGAAUUCACCUACAAUCGAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUC
.............((((.(((((......((.((((----------------------------.(......).)))).))((((....))))))))).)))).(((((.....))))). ( -21.60)
>DroYak_CAF1 13176 120 + 1
GACGUAAUAAACACUUUACUGGCGAAAAAGAAUGUAGGCAGAAAAGAUGCAGUGACGCUUCUGACCAAUUCACCUACAAUCAAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUC
...........(.((((.(((((((....((.((((((..(((.(((.((......)).)))......))).)))))).))..((....))))))))).)))).)((((.....)))).. ( -30.50)
>consensus
__UGUAAUAAAUACAUCACUGGCGAAAAAGAAUGCAGGCAAGAGCGAUGCAGAGUUGCUUCUGACCAAUUCACCUACAAUCGAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUC
.....................((......((((...((((.(((((.........))))).)).)).)))).(((((.(((........))).)).)))...))(((((.....))))). (-17.73 = -18.40 +   0.67) 

alignment

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secondary structure

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dotplot

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Window 2

Location 621,395 – 621,513
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.57
Mean single sequence MFE -30.88
Consensus MFE -21.83
Energy contribution -22.68
Covariance contribution 0.85
Combinations/Pair 1.23
Mean z-score -1.58
Structure conservation index 0.71
SVM decision value 0.15
SVM RNA-class probability 0.609760
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 621395 118 - 22407834
GAGCGGUUUAUCCGCCGCUUUCCCGACUAUCGUUUGAUCGAUUGUAGGUGAAUUGGUCAGAAGCAACUCUGCAGUGCUCCUACCUGCAUUCUUUUUCGCCAGUUAUGUAUUUAUUAGA--
(((((((......)))))))..((.((.((((......)))).)).))..(((((((.(((((((....)))(((((........)))))..)))).)))))))..............-- ( -30.00)
>DroSec_CAF1 10619 118 - 1
GAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUCGAUUGUAGGUGAAUUGGUCAGAAGCAACUCUGCAUCGCUCUUGCCUGCAUUCUUUUUCGCCAGCGAUGUAUUUAUUACA--
..((((.....))))((((....(((.((((....))))((.((((((..(..((((((((......)))).))))...)..)))))).))....)))..)))).((((.....))))-- ( -35.70)
>DroSim_CAF1 9832 118 - 1
GAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUCGAUUGUAGGUGAAUUGGUCAGAAGCAACUCUGCAUCGCUCUUGCCUGCAUUCUUUUUCGCUACUGAUGUAUUUAUUACA--
(((((((......)))))))...(((.((((....))))((.((((((..(..((((((((......)))).))))...)..)))))).))....))).......((((.....))))-- ( -34.10)
>DroEre_CAF1 14189 92 - 1
GAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUCGAUUGUAGGUGAAUUCG----------------------------UACAUUCCUUUUCGCCAGUAAAGUUUUAAGUACGUC
(((((((......)))))))((((.((((((........)))))).)).))...((----------------------------(((....((((.(....).))))......))))).. ( -22.80)
>DroYak_CAF1 13176 120 - 1
GAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUUGAUUGUAGGUGAAUUGGUCAGAAGCGUCACUGCAUCUUUUCUGCCUACAUUCUUUUUCGCCAGUAAAGUGUUUAUUACGUC
(((((((......)))))))....(((((((....))))((.((((((((((..((((((........))).)))..))).))))))).))..........((((........))))))) ( -31.80)
>consensus
GAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUCGAUUGUAGGUGAAUUGGUCAGAAGCAACUCUGCAUCGCUCCUGCCUGCAUUCUUUUUCGCCAGUAAUGUAUUUAUUACA__
(((((((......)))))))...(((.((((....))))((.((((((((....((...((.(((....))).))...)))))))))).))....)))...................... (-21.83 = -22.68 +   0.85) 

alignment

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secondary structure

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dotplot

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Window 3

Location 621,473 – 621,581
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.42
Mean single sequence MFE -34.80
Consensus MFE -28.60
Energy contribution -29.16
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.33
Structure conservation index 0.82
SVM decision value 0.05
SVM RNA-class probability 0.560582
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 621473 108 + 22407834
CGAUCAAACGAUAGUCGGGAAAGCGGCGGAUAAACCGCUCAUCGUACGGUAUUG----GAGCAUGUGGCAUCGUUCUGAGAACCGACUGCCAUUCCGCUCCCUCAUCUUUUU--------
.............(((((...(((((........)))))..))).))(((...(----((((..((((((((((((...))).))).))))))...)))))...))).....-------- ( -31.70)
>DroSec_CAF1 10697 112 + 1
CGAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUCAUCUUACGGUAUUGGAUGGAGCAUGUGGCAUCGUUCUGAGAACCGACUGCCAUUCCGCUCUCUCAUCUUUUU--------
(((((....)))))..((((.(((((.((.....))((((((((.........)))).))))..((((((((((((...))).))).)))))).))))).))))........-------- ( -37.00)
>DroSim_CAF1 9910 116 + 1
CGAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUCAUCGUACGGUAUUG----GAGCAUGUGGCAUCGUUCUGAGAACCGACUGCCAUUCCGCUCCCUCAUCUUUUUUUUCCUAG
(((((....)))))..(((((((.(((((.....)))))........(((...(----((((..((((((((((((...))).))).))))))...)))))...)))....))))))).. ( -38.70)
>DroEre_CAF1 14241 107 + 1
CGAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUCAUCGUACGGUAUUG----GAGCAUGUGGUAUCGUUCUGAGAACCGACUGCCUUUCCGCUCCCUCAUCUUUU---------
(((((....))))).((((((.(((((((.....)))))....((.((((.(..----((((..........))))..)..)))))).)).))))))..............--------- ( -32.40)
>DroYak_CAF1 13256 110 + 1
CAAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUCAUCGUACGGUAUUG----GAGCAUGUGGUAUCGUUCUGAGAACCGACUGCCAUUCCGCUCCCUCAUCUUUUUUU------
.....(((((((((((((...(((((........)))))..))).))).....(----((((..((((((((((((...))).))).))))))...)))))...)))))))...------ ( -34.20)
>consensus
CGAUCAAAAGAUCGUCGGGAAAGCGGCGGAUAAACCGCUCAUCGUACGGUAUUG____GAGCAUGUGGCAUCGUUCUGAGAACCGACUGCCAUUCCGCUCCCUCAUCUUUUU________
.....(((((((((((((...(((((........)))))..))).)))..........((((..((((((((((((...))).))).))))))...))))....)))))))......... (-28.60 = -29.16 +   0.56) 

alignment

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secondary structure

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Window 4

Location 621,473 – 621,581
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.42
Mean single sequence MFE -36.64
Consensus MFE -29.08
Energy contribution -30.08
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.79
SVM decision value 0.71
SVM RNA-class probability 0.828512
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 621473 108 - 22407834
--------AAAAAGAUGAGGGAGCGGAAUGGCAGUCGGUUCUCAGAACGAUGCCACAUGCUC----CAAUACCGUACGAUGAGCGGUUUAUCCGCCGCUUUCCCGACUAUCGUUUGAUCG
--------....((((((.((((((...(((((.(((.(((...)))))))))))..)))))----)......((.((..(((((((......)))))))...))))..))))))..... ( -36.40)
>DroSec_CAF1 10697 112 - 1
--------AAAAAGAUGAGAGAGCGGAAUGGCAGUCGGUUCUCAGAACGAUGCCACAUGCUCCAUCCAAUACCGUAAGAUGAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUCG
--------.(((((((((..(((((...(((((.(((.(((...)))))))))))..)))))..))......(((..(..(((((((......)))))))..)..))))))))))..... ( -36.80)
>DroSim_CAF1 9910 116 - 1
CUAGGAAAAAAAAGAUGAGGGAGCGGAAUGGCAGUCGGUUCUCAGAACGAUGCCACAUGCUC----CAAUACCGUACGAUGAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUCG
....((...(((((((...((((((...(((((.(((.(((...)))))))))))..)))))----).....(((.((..(((((((......)))))))...))))))))))))..)). ( -40.90)
>DroEre_CAF1 14241 107 - 1
---------AAAAGAUGAGGGAGCGGAAAGGCAGUCGGUUCUCAGAACGAUACCACAUGCUC----CAAUACCGUACGAUGAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUCG
---------(((((((...((((((....((..((((.(((...))))))).))...)))))----).....(((.((..(((((((......)))))))...))))))))))))..... ( -33.50)
>DroYak_CAF1 13256 110 - 1
------AAAAAAAGAUGAGGGAGCGGAAUGGCAGUCGGUUCUCAGAACGAUACCACAUGCUC----CAAUACCGUACGAUGAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUUG
------...(((((((...((((((...(((..((((.(((...))))))).)))..)))))----).....(((.((..(((((((......)))))))...))))))))))))..... ( -35.60)
>consensus
________AAAAAGAUGAGGGAGCGGAAUGGCAGUCGGUUCUCAGAACGAUGCCACAUGCUC____CAAUACCGUACGAUGAGCGGUUUAUCCGCCGCUUUCCCGACGAUCUUUUGAUCG
.........(((((((....(((((...(((((.(((.(((...)))))))))))..)))))..........(((.....(((((((......))))))).....))))))))))..... (-29.08 = -30.08 +   1.00) 

alignment

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secondary structure

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dotplot

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Window 5

Location 621,581 – 621,687
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.68
Mean single sequence MFE -21.20
Consensus MFE -19.88
Energy contribution -20.08
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.94
SVM decision value 1.53
SVM RNA-class probability 0.961526
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 621581 106 + 22407834
--------------UUUCUUAGCUCCGCUGAGCAGCUGCAGAAGCAACAAAAACAUUAGAAUUGCUAAAAGAUACUCAAAAUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCAC
--------------....(((((((((((((((((((.....)))........(....)...))))....(((.......)))..)))))))......)))))................. ( -20.60)
>DroSec_CAF1 10809 108 + 1
------------UCUUUCUUAGCUCCGCUGAGCAGCUGCAGAAGCAACAAAAACAUUAGAAUUGCUAAAAGAUACUCAAAAUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCAC
------------......(((((((((((((((((((.....)))........(....)...))))....(((.......)))..)))))))......)))))................. ( -20.60)
>DroSim_CAF1 10373 120 + 1
UCCCUCAUCUUUUUUUUCCUAGCUCCGCUGAGCAGCUGCAGAAGCAACAAAAACAUUAGAAUUGCUAAAAGAUACUCAAAAUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCAC
......(((((((.((((..(((((((((((((((((.....)))........(....)...))))....(((.......)))..)))))))......)))))))....)))).)))... ( -19.90)
>DroEre_CAF1 14348 108 + 1
------------UUUUGCUUAGCUCCGCUGAGCAGCUGCAGCAGCAACAAAAACAUUAGAAUUGCUAAAAGAUACUCAAAAUCACCAGCGGACAACGAGCUGAAAUGUUAAAACGAUCAC
------------...((((((((...))))))))((((...))))......((((((.............(((.......)))..((((.........)))).))))))........... ( -22.40)
>DroYak_CAF1 13366 110 + 1
----------UUUUUUGCUUAGCUCCGCUGAGCAGCUGCAGCAGCAACAAAAACAUUAGAAUUGCUAAAAGAUACUCAAAAUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCAC
----------.((((.((((...(((((((((((((((...))))........(....)...))))....(((.......)))..)))))))....)))).))))............... ( -22.50)
>consensus
____________UUUUUCUUAGCUCCGCUGAGCAGCUGCAGAAGCAACAAAAACAUUAGAAUUGCUAAAAGAUACUCAAAAUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCAC
..................(((((((((((((((((((.....)))........(....)...))))....(((.......)))..)))))))......)))))................. (-19.88 = -20.08 +   0.20) 

alignment

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secondary structure

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dotplot

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Window 6

Location 621,647 – 621,767
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.67
Mean single sequence MFE -39.10
Consensus MFE -39.26
Energy contribution -39.30
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -3.46
Structure conservation index 1.00
SVM decision value 4.61
SVM RNA-class probability 0.999928
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 621647 120 + 22407834
AUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCACGUUUUCCUGCAGCAGCAACAACAUUAGUGUGGAAAUCCUUGCGCUGGAGAAAAGCUAGGAAAAAUCUCAGCUGCCGUUGA
.....((((((.(.....((((...(((.((((((....))))))...))).)))).......(((((((((....))..))))))).....((((..((....))..))))))))))). ( -33.90)
>DroSec_CAF1 10877 120 + 1
AUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCACGUUUUCCUGCAGCAGCAAGAACUUCAGUGUGGAAAUCCUUGCGCUGGAGAAAAGCUAGGAAAAAUCUCAGCUGCCGUUGA
.....((((((.(.....((((...(((.((((((....))))))...))).)))).....(((((((((((....))..)))))))))...((((..((....))..))))))))))). ( -40.40)
>DroSim_CAF1 10453 120 + 1
AUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCACGUUUUCCUGCAGCAGCAACAACUUCAGUGUGGAAAUCCUUGCGCUGGAGAAAAGCUAGGAAAAAUCUCAGCUGCCGUUGA
.....((((((.(.....((((...(((.((((((....))))))...))).)))).....(((((((((((....))..)))))))))...((((..((....))..))))))))))). ( -40.40)
>DroEre_CAF1 14416 120 + 1
AUCACCAGCGGACAACGAGCUGAAAUGUUAAAACGAUCACGUUUUCCUGCAGCAGCAACAACUUCAGUGUGGAAAUCCUUGCGCUGGAGAAAAGCUAGGAAAAAUCUCAGCUGCCGUUGA
.....((((((.(.....((((...(((.((((((....))))))...))).)))).....(((((((((((....))..)))))))))...((((..((....))..))))))))))). ( -40.40)
>DroYak_CAF1 13436 120 + 1
AUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCACGUUUUCCUGCAGCAGCAACAACUUCAGUGUGGAAAUCCUUGCGCUGGAGAAAAGCUAGGAAAAAUCUCAGCUGCCGUUGA
.....((((((.(.....((((...(((.((((((....))))))...))).)))).....(((((((((((....))..)))))))))...((((..((....))..))))))))))). ( -40.40)
>consensus
AUCACCAGCGGACAACAAGCUGAAAUGUUAAAACGAUCACGUUUUCCUGCAGCAGCAACAACUUCAGUGUGGAAAUCCUUGCGCUGGAGAAAAGCUAGGAAAAAUCUCAGCUGCCGUUGA
.....((((((.(.....((((...(((.((((((....))))))...))).)))).....(((((((((((....))..)))))))))...((((..((....))..))))))))))). (-39.26 = -39.30 +   0.04) 

alignment

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secondary structure

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dotplot

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Window 7

Location 621,647 – 621,767
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.67
Mean single sequence MFE -37.00
Consensus MFE -35.64
Energy contribution -36.04
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.96
SVM decision value 2.76
SVM RNA-class probability 0.996843
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 621647 120 - 22407834
UCAACGGCAGCUGAGAUUUUUCCUAGCUUUUCUCCAGCGCAAGGAUUUCCACACUAAUGUUGUUGCUGCUGCAGGAAAACGUGAUCGUUUUAACAUUUCAGCUUGUUGUCCGCUGGUGAU
(((.(((((((((((((.............(((.((((((((.(((............))).)))).)))).)))((((((....))))))...)))))))))........)))).))). ( -32.20)
>DroSec_CAF1 10877 120 - 1
UCAACGGCAGCUGAGAUUUUUCCUAGCUUUUCUCCAGCGCAAGGAUUUCCACACUGAAGUUCUUGCUGCUGCAGGAAAACGUGAUCGUUUUAACAUUUCAGCUUGUUGUCCGCUGGUGAU
(((.(((((((((((((.............(((.(((((((((((((((......))))))))))).)))).)))((((((....))))))...)))))))))........)))).))). ( -40.60)
>DroSim_CAF1 10453 120 - 1
UCAACGGCAGCUGAGAUUUUUCCUAGCUUUUCUCCAGCGCAAGGAUUUCCACACUGAAGUUGUUGCUGCUGCAGGAAAACGUGAUCGUUUUAACAUUUCAGCUUGUUGUCCGCUGGUGAU
(((.(((((((((((((.............(((.((((((((.((((((......)))))).)))).)))).)))((((((....))))))...)))))))))........)))).))). ( -37.40)
>DroEre_CAF1 14416 120 - 1
UCAACGGCAGCUGAGAUUUUUCCUAGCUUUUCUCCAGCGCAAGGAUUUCCACACUGAAGUUGUUGCUGCUGCAGGAAAACGUGAUCGUUUUAACAUUUCAGCUCGUUGUCCGCUGGUGAU
(((.(((((((((((((.............(((.((((((((.((((((......)))))).)))).)))).)))((((((....))))))...)))))))))........)))).))). ( -37.40)
>DroYak_CAF1 13436 120 - 1
UCAACGGCAGCUGAGAUUUUUCCUAGCUUUUCUCCAGCGCAAGGAUUUCCACACUGAAGUUGUUGCUGCUGCAGGAAAACGUGAUCGUUUUAACAUUUCAGCUUGUUGUCCGCUGGUGAU
(((.(((((((((((((.............(((.((((((((.((((((......)))))).)))).)))).)))((((((....))))))...)))))))))........)))).))). ( -37.40)
>consensus
UCAACGGCAGCUGAGAUUUUUCCUAGCUUUUCUCCAGCGCAAGGAUUUCCACACUGAAGUUGUUGCUGCUGCAGGAAAACGUGAUCGUUUUAACAUUUCAGCUUGUUGUCCGCUGGUGAU
(((.(((((((((((((.............(((.((((((((.((((((......)))))).)))).)))).)))((((((....))))))...)))))))))........)))).))). (-35.64 = -36.04 +   0.40) 

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 09:30:09 2006