Locus 7550

Sequence ID X_DroMel_CAF1
Location 18,821,733 – 18,821,829
Length 96
Max. P 0.994890
window12384 window12385

overview

Window 4

Location 18,821,733 – 18,821,829
Length 96
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 77.56
Mean single sequence MFE -29.38
Consensus MFE -16.48
Energy contribution -17.72
Covariance contribution 1.25
Combinations/Pair 1.18
Mean z-score -2.68
Structure conservation index 0.56
SVM decision value 2.00
SVM RNA-class probability 0.985189
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18821733 96 + 22224390
-----AAACAUAUA----UAGAUACAUGCAGGCAAUACGCUCGUACGCAUAUCUA-UCUUG------UGUGUUUGUGCCGAGACAAUUGCCAAAUUAAGUGCAUGCCUCUGU
-----........(----((((..((((((((((((...(((((((((((((...-....)------)))))..))).))))...))))))........))))))..))))) ( -27.80)
>DroSec_CAF1 58754 101 + 1
CACCCAAACGCAUA----UAGAUACAUGCAGGCAAUAUGCUCGUACGCAUAUCUA-UCUUG------UGUGUUUGUGCAGAGACAAUUGCCAAAUUAAGUGCAUGCCUCUGU
....((((((((((----.(((((..((....))((((((......)))))).))-)))))------)))))))).((((((.((..((((.......).))))).)))))) ( -28.70)
>DroEre_CAF1 56755 107 + 1
----UAUGUAUACAUGUAUAAACAUAAGCAUGCAAUACGCA-AUACACGUACACACGCUUGUGCGUUUGUGUUUGUGCAGAGACAAUUGCCAAAUUAAGUGCAUGCCUCUGU
----...........((((((((((((((.(((.....)))-......(((((......)))))))))))))))))))((((.((..((((.......).))))).)))).. ( -29.70)
>DroYak_CAF1 57720 111 + 1
CACAGAAACAUACAUAAAUACAUGCAGGCAGGCAAUACGCUCGUACGCAAACAUA-UCUUGUGCGUUUGUGUUUGUGCAGAGACAAUUGCCAAAUUAAGUGCAUGCCUCUGU
.(((((..(((.(((.......((....))((((((...(((...((((((((((-...........))))))))))..)))...)))))).......))).)))..))))) ( -31.30)
>consensus
_____AAACAUACA____UAGAUACAUGCAGGCAAUACGCUCGUACGCAUACAUA_UCUUG______UGUGUUUGUGCAGAGACAAUUGCCAAAUUAAGUGCAUGCCUCUGU
..................((((..((((((((((((...(((...((((.(((((............))))).))))..)))...))))))........))))))..)))). (-16.48 = -17.72 +   1.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,821,733 – 18,821,829
Length 96
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 77.56
Mean single sequence MFE -31.65
Consensus MFE -17.40
Energy contribution -17.15
Covariance contribution -0.25
Combinations/Pair 1.38
Mean z-score -2.99
Structure conservation index 0.55
SVM decision value 2.52
SVM RNA-class probability 0.994890
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18821733 96 - 22224390
ACAGAGGCAUGCACUUAAUUUGGCAAUUGUCUCGGCACAAACACA------CAAGA-UAGAUAUGCGUACGAGCGUAUUGCCUGCAUGUAUCUA----UAUAUGUUU-----
..(((.(((((((........(((...(((((.(...........------).)))-))(((((((......))))))))))))))))).))).----.........----- ( -24.50)
>DroSec_CAF1 58754 101 - 1
ACAGAGGCAUGCACUUAAUUUGGCAAUUGUCUCUGCACAAACACA------CAAGA-UAGAUAUGCGUACGAGCAUAUUGCCUGCAUGUAUCUA----UAUGCGUUUGGGUG
.(((((((((((.(.......))))..))))))))..(((((...------..((.-..(((((((......)))))))..))((((((....)----)))))))))).... ( -31.70)
>DroEre_CAF1 56755 107 - 1
ACAGAGGCAUGCACUUAAUUUGGCAAUUGUCUCUGCACAAACACAAACGCACAAGCGUGUGUACGUGUAU-UGCGUAUUGCAUGCUUAUGUUUAUACAUGUAUACAUA----
.(((((((((((.(.......))))..))))))))...........((((....))))((((((((((((-.(((((..(....).)))))..))))))))))))...---- ( -35.40)
>DroYak_CAF1 57720 111 - 1
ACAGAGGCAUGCACUUAAUUUGGCAAUUGUCUCUGCACAAACACAAACGCACAAGA-UAUGUUUGCGUACGAGCGUAUUGCCUGCCUGCAUGUAUUUAUGUAUGUUUCUGUG
(((((((((((((........((((((((.((((((.((((((....(......).-..)))))).))).))))).))))))((....))........))))))))))))). ( -35.00)
>consensus
ACAGAGGCAUGCACUUAAUUUGGCAAUUGUCUCUGCACAAACACA______CAAGA_UAGAUAUGCGUACGAGCGUAUUGCCUGCAUGUAUCUA____UAUAUGUUU_____
.(((((((((((.(.......))))..))))))))........................(((((((......)))))))....((.(((((......))))).))....... (-17.40 = -17.15 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:42 2006