Locus 2800

Sequence ID 2L_DroMel_CAF1
Location 7,952,114 – 7,952,229
Length 115
Max. P 0.903077
window4446 window4447 window4448

overview

Window 6

Location 7,952,114 – 7,952,206
Length 92
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 80.75
Mean single sequence MFE -18.33
Consensus MFE -13.72
Energy contribution -12.83
Covariance contribution -0.89
Combinations/Pair 1.21
Mean z-score -1.79
Structure conservation index 0.75
SVM decision value 0.73
SVM RNA-class probability 0.835916
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7952114 92 - 22407834
CAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAUUGCCAACGGCCAUGCAGUUUUCCACUCA-CCCGCCGCCC---------CUUAC
.(((((((((..((((.(((((....))))).))))...))).))))))......((((..((.(((.....)))))-...))))...---------..... ( -18.40)
>DroPse_CAF1 151963 100 - 1
CAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAUUGCCACUGGCCACACCACUGGCCCUUC--CCCUUCACCUAGCUCCCCACCAUC
.(((((((((..((((.(((((....))))).))))...))).)))))).((((.(((.....))).)))).....--........................ ( -20.70)
>DroSec_CAF1 123650 90 - 1
CAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCUGUCUGCAAAUUGCCAACGGCCAUGCAGUUUUCACCGC--CCCUCC-CCG---------CACCC
.((((((((((.((((.(((((....))))).))))..)))).))))))(((....((....((.((....)).))--....))-..)---------))... ( -17.20)
>DroSim_CAF1 123691 91 - 1
CAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAUUGCCAACGGCCAUGCAGUUUUCCCCGC--CCCGCCCCCU---------CCCUC
(((((((.......)))))))...((((((......(((((..((.....))..))))).))))))..........--..........---------..... ( -16.70)
>DroAna_CAF1 122055 91 - 1
CAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAUUGCCACUGGCCACAGAGUUCUCCCUUCAACCUGCCACCU---------CCA--
.(((((((((..((((.(((((....))))).))))...))).))))))......((((...((.(((........)))))))))...---------...-- ( -16.30)
>DroPer_CAF1 151428 100 - 1
CAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAUUGCCACUGGCCACACCACUGGCCCUUC--CCCUUCACCUAGCUCCCCACCAUC
.(((((((((..((((.(((((....))))).))))...))).)))))).((((.(((.....))).)))).....--........................ ( -20.70)
>consensus
CAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAUUGCCAACGGCCACACAGUUUUCCCCUC__CCCGCCACCU_________CCAUC
....((((....((((.(((((....))))).))))((((...((.....))...))))))))....................................... (-13.72 = -12.83 +  -0.89)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,952,138 – 7,952,229
Length 91
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 82.61
Mean single sequence MFE -26.67
Consensus MFE -16.37
Energy contribution -16.53
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.95
Structure conservation index 0.61
SVM decision value 0.67
SVM RNA-class probability 0.818501
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7952138 91 + 22407834
AACUG------CAUGGCCGUUGGCA--AUUUGCAGACGGCAAAUUAAUGCAAGCGCAUUUAUUUUUGUCACAAAUGCAAACAACGGCA---GCAAAAGCAAC--
...((------(...(((((((...--.((((((...((((((..(((((....)))))....)))))).....))))))))))))).---)))........-- ( -29.30)
>DroVir_CAF1 136521 92 + 1
GGUAGGAGGCCGCUGGCCACUGGCAA-AAUUGCAGACGGCAAAUUAAUGCCAGCGCAUUUAUUUUUGUCACAAAUGCAAACAACAGCA---ACAA---C-----
(((.....)))(((((((...)))..-..(((((...((((((..(((((....)))))....)))))).....)))))....)))).---....---.----- ( -25.90)
>DroSec_CAF1 123672 91 + 1
AACUG------CAUGGCCGUUGGCA--AUUUGCAGACAGCAAAUUAAUGCAAGCGCAUUUAUUUUUGUCACAAAUGCAAACAACAGCA---GCUAAAGCAAC--
...((------(.((((.((((...--.(((((((((((.((((.(((((....))))).))))))))).....))))))...)))).---))))..)))..-- ( -25.90)
>DroSim_CAF1 123714 91 + 1
AACUG------CAUGGCCGUUGGCA--AUUUGCAGACGGCAAAUUAAUGCAAGCGCAUUUAUUUUUGUCACAAAUGCAAACAACAGCA---GCUAAAGCAAC--
...((------(.((((.((((...--.((((((...((((((..(((((....)))))....)))))).....))))))...)))).---))))..)))..-- ( -26.50)
>DroMoj_CAF1 150900 96 + 1
GUUUGGUGCCCGCUGGCCACUGGCAAAAAUUGCAGACGGCAAAUUAAUGCCAGCGCAUUUAUUUUUGUCACAAAUGCAAACAACAGCA---ACAAGAGC-----
((((((((((....)).)))(((((((((((((.(..((((......))))..))))...))))))))))......))))).......---........----- ( -24.40)
>DroAna_CAF1 122078 96 + 1
AACUC------UGUGGCCAGUGGCA--AUUUGCAGACGGCAAAUUAAUGCAAGCGCAUUUAUUUUUGUCACAAAUGCAAACAACAGCAACGGCAACAGCAACGG
....(------(((.(((.((((((--((((((.....)))))))(((((....))))).......)))))...(((........)))..))).))))...... ( -28.00)
>consensus
AACUG______CAUGGCCAUUGGCA__AUUUGCAGACGGCAAAUUAAUGCAAGCGCAUUUAUUUUUGUCACAAAUGCAAACAACAGCA___GCAAAAGCAAC__
...............(((...))).....(((((...((((((..(((((....)))))....)))))).....)))))......................... (-16.37 = -16.53 +   0.17)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,952,138 – 7,952,229
Length 91
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 82.61
Mean single sequence MFE -29.78
Consensus MFE -22.00
Energy contribution -21.95
Covariance contribution -0.05
Combinations/Pair 1.12
Mean z-score -2.93
Structure conservation index 0.74
SVM decision value 1.03
SVM RNA-class probability 0.903077
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7952138 91 - 22407834
--GUUGCUUUUGC---UGCCGUUGUUUGCAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAU--UGCCAACGGCCAUG------CAGUU
--.......((((---.(((((((...(((((((((((..((((.(((((....))))).))))...))).))))).--))))))))))...)------))).. ( -29.20)
>DroVir_CAF1 136521 92 - 1
-----G---UUGU---UGCUGUUGUUUGCAUUUGUGACAAAAAUAAAUGCGCUGGCAUUAAUUUGCCGUCUGCAAUU-UUGCCAGUGGCCAGCGGCCUCCUACC
-----.---....---.(((((((...((((((((.......))))))))(((((((.....((((.....))))..-.)))))))...)))))))........ ( -31.50)
>DroSec_CAF1 123672 91 - 1
--GUUGCUUUAGC---UGCUGUUGUUUGCAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCUGUCUGCAAAU--UGCCAACGGCCAUG------CAGUU
--........(((---(((.((((((.((((((((((((.((((.(((((....))))).))))..)))).))))).--))).))))))...)------))))) ( -30.40)
>DroSim_CAF1 123714 91 - 1
--GUUGCUUUAGC---UGCUGUUGUUUGCAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAU--UGCCAACGGCCAUG------CAGUU
--........(((---(((.((((((.(((((((((((..((((.(((((....))))).))))...))).))))).--))).))))))...)------))))) ( -28.50)
>DroMoj_CAF1 150900 96 - 1
-----GCUCUUGU---UGCUGUUGUUUGCAUUUGUGACAAAAAUAAAUGCGCUGGCAUUAAUUUGCCGUCUGCAAUUUUUGCCAGUGGCCAGCGGGCACCAAAC
-----....(((.---((((((((...((((((((.......))))))))(((((((..((((.((.....))))))..)))))))...)))).)))).))).. ( -32.00)
>DroAna_CAF1 122078 96 - 1
CCGUUGCUGUUGCCGUUGCUGUUGUUUGCAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAU--UGCCACUGGCCACA------GAGUU
......((((.(((((.((...(((.(((((((((.......)))))))))...)))..(((((((.....))))))--))).)).))).)))------).... ( -27.10)
>consensus
__GUUGCUUUUGC___UGCUGUUGUUUGCAUUUGUGACAAAAAUAAAUGCGCUUGCAUUAAUUUGCCGUCUGCAAAU__UGCCAACGGCCAUG______CAGUU
.................(((((((...((((((((.......))))))))....(((...((((((.....))))))..))))))))))............... (-22.00 = -21.95 +  -0.05)

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 10:36:30 2006