Locus 7360

Sequence ID 2L_DroMel_CAF1
Location 20,506,532 – 20,506,661
Length 129
Max. P 0.798024
window11816 window11817 window11818

overview

Window 6

Location 20,506,532 – 20,506,625
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 80.55
Mean single sequence MFE -21.55
Consensus MFE -14.19
Energy contribution -16.07
Covariance contribution 1.88
Combinations/Pair 1.19
Mean z-score -1.91
Structure conservation index 0.66
SVM decision value 0.61
SVM RNA-class probability 0.798024
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20506532 93 + 22407834
GAGCAGAAGGGGCCGCAGGAGCCGGAGGAUAACACGUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCCGGCAAA
..((.(......).))....(((((...........(((((.(((..((((((((...))))))))..))).)))))........)))))... ( -26.51)
>DroSec_CAF1 23571 84 + 1
GAGCAGA---------AGGAGUCGGAGGAUAACACGUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCCGGAAAA
.......---------.....((((...........(((((.(((..((((((((...))))))))..))).)))))........)))).... ( -19.11)
>DroSim_CAF1 28670 84 + 1
GAGCAGA---------AGGAGCCGGAGGAUAACACGUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCCGGCAAA
.......---------....(((((...........(((((.(((..((((((((...))))))))..))).)))))........)))))... ( -25.71)
>DroYak_CAF1 22426 77 + 1
----------------UGGAUCCGGAGGAUAACACAUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCUGCAAAA
----------------........(((.((.((((......)))).)).)))..(((((((..((((.....)))).......)))))))... ( -18.60)
>DroAna_CAF1 14694 71 + 1
----------------AGGCUGCAAGGACUAACACGUGUAGGUGUGAUGUUUAAUGCAGUUAAGCAGUG------CAACAAAAAGCCAGCAAA
----------------.(((((((.((((..((((......))))...))))..)))))))..((.(.(------(........))).))... ( -17.80)
>consensus
GAGCAGA_________AGGAGCCGGAGGAUAACACGUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCCGGCAAA
....................(((((...........(((((.(((..((((((((...))))))))..))).)))))........)))))... (-14.19 = -16.07 +   1.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,506,532 – 20,506,625
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 80.55
Mean single sequence MFE -17.64
Consensus MFE -9.92
Energy contribution -10.72
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.56
SVM decision value 0.08
SVM RNA-class probability 0.571605
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20506532 93 - 22407834
UUUGCCGGCUUUUUGUUGCAGUCGCACUGCUUAACUGCAUUAAGCAUCACACCUACACGUGUUAUCCUCCGGCUCCUGCGGCCCCUUCUGCUC
...((((((((..(((.((((.....))))......)))..))))...((((......)))).......))))....((((......)))).. ( -24.20)
>DroSec_CAF1 23571 84 - 1
UUUUCCGGCUUUUUGUUGCAGUCGCACUGCUUAACUGCAUUAAGCAUCACACCUACACGUGUUAUCCUCCGACUCCU---------UCUGCUC
.....((((((..(((.((((.....))))......)))..))))...((((......)))).......))......---------....... ( -14.50)
>DroSim_CAF1 28670 84 - 1
UUUGCCGGCUUUUUGUUGCAGUCGCACUGCUUAACUGCAUUAAGCAUCACACCUACACGUGUUAUCCUCCGGCUCCU---------UCUGCUC
...((((((((..(((.((((.....))))......)))..))))...((((......)))).......))))....---------....... ( -21.00)
>DroYak_CAF1 22426 77 - 1
UUUUGCAGCUUUUUGUUGCAGUCGCACUGCUUAACUGCAUUAAGCAUCACACCUACAUGUGUUAUCCUCCGGAUCCA----------------
..(((((((.....)))))))......(((((((.....))))))).((((......))))..((((...))))...---------------- ( -16.10)
>DroAna_CAF1 14694 71 - 1
UUUGCUGGCUUUUUGUUG------CACUGCUUAACUGCAUUAAACAUCACACCUACACGUGUUAGUCCUUGCAGCCU----------------
...((..((........)------)...))....(((((........(((........)))........)))))...---------------- ( -12.39)
>consensus
UUUGCCGGCUUUUUGUUGCAGUCGCACUGCUUAACUGCAUUAAGCAUCACACCUACACGUGUUAUCCUCCGGCUCCU_________UCUGCUC
.......((((..(((.((((.....))))......)))..))))...((((......))))............................... ( -9.92 = -10.72 +   0.80)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,506,548 – 20,506,661
Length 113
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 81.71
Mean single sequence MFE -30.85
Consensus MFE -20.34
Energy contribution -21.33
Covariance contribution 0.99
Combinations/Pair 1.14
Mean z-score -1.51
Structure conservation index 0.66
SVM decision value 0.02
SVM RNA-class probability 0.542900
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20506548 113 + 22407834
--AGGAGCCGGAGGAUAACACGUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCCGGCAAAUCCGAGAGAGGAUGCCAACCAUGUGGGGCGGUGGGU
--....(((.............(((((.(((..((((((((...))))))))..))).))))).......(((((((..(((......)))))))..((....)))))))).... ( -35.30)
>DroSec_CAF1 23578 113 + 1
--AGGAGUCGGAGGAUAACACGUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCCGGAAAAUCCGAGUGAGGAUGCCAACCAUGUGGGACGGUGGUA
--.(.(((((.(.....((((......))))..((((((((...)))))))).).))))).)........(((((...((((......)))).))..((....))...))).... ( -31.30)
>DroSim_CAF1 28677 113 + 1
--AGGAGCCGGAGGAUAACACGUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCCGGCAAAUCCGAGUGAGGAUGCCAACCAUGUGGGACGGUGGUA
--.((.(((((...........(((((.(((..((((((((...))))))))..))).)))))........)))))..((((......)))).)).(((((........))))). ( -35.91)
>DroEre_CAF1 22407 104 + 1
UGAGGAUCCGGAGGAUAACACGUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGAAUGCAACAAAAAGCCGGCAAAUCC-A--GAGGAUGCCACCCAUGUGGGG--------
...((((((...((((......(((.(((.((.((((((((...)))))))).(((....))).))....))).))).))))-.--..)))).)).(((....))).-------- ( -30.00)
>DroYak_CAF1 22426 103 + 1
--UGGAUCCGGAGGAUAACACAUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCUGCAAAAUCCGA--GAGGAUGCCAACCAUGUGGGG--------
--(((((((...((((..(((((....)))))........(((((((..((((.....)))).......)))))))..))))..--..)))).))).((....))..-------- ( -30.40)
>DroAna_CAF1 14694 103 + 1
--AGGCUGCAAGGACUAACACGUGUAGGUGUGAUGUUUAAUGCAGUUAAGCAGUG------CAACAAAAAGCCAGCAAAUCCAAAGGAUUCUGCCACACACAUAUA----UAAAU
--.(((((((.((((..((((......))))...))))..)))))))..((((((------(............)))(((((...)))))))))............----..... ( -22.20)
>consensus
__AGGAGCCGGAGGAUAACACGUGUAGGUGUGAUGCUUAAUGCAGUUAAGCAGUGCGACUGCAACAAAAAGCCGGCAAAUCCGAG_GAGGAUGCCAACCAUGUGGGG___UGG__
..................((((((..(((.((.((((((((...)))))))).(((....))).))....)))((((..(((......)))))))...))))))........... (-20.34 = -21.33 +   0.99)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:45 2006