Locus 1118

Sequence ID 3L_DroMel_CAF1
Location 3,276,999 – 3,277,130
Length 131
Max. P 0.891377
window1735 window1736

overview

Window 5

Location 3,276,999 – 3,277,090
Length 91
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 84.23
Mean single sequence MFE -23.32
Consensus MFE -14.98
Energy contribution -14.86
Covariance contribution -0.12
Combinations/Pair 1.20
Mean z-score -2.17
Structure conservation index 0.64
SVM decision value 0.48
SVM RNA-class probability 0.752273
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3276999 91 - 23771897
-AAAGCGAAAGCUGCAGAGGGCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCUAAUA-------------------------UUUAUGACAUUUCUUAUUAAUUAUUUAUCGACGCU
-..(((....)))((.....))...(((.((((...(((((((....)))))))...-------------------------.....((....))..............)))).))) ( -19.40)
>DroSec_CAF1 7155 89 - 1
-AAAGCGAAAGCUGCAGAAGUCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCUAAUA-------------------------UUUAUGGCACUUCUUAUUAAUUAUUUAUCGA--CU
-..(((....)))..((((((....(.(((..(.(.(((((((....))))))).).-------------------------)..))).))))))).................--.. ( -20.00)
>DroSim_CAF1 7788 114 - 1
-AAAGCGAAAGCUGCAGAAGUCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCUAAUAUUUAUGGCCAUUUAAAUGGCUAAUAUUUAUGGCACUUCUUAUUAAUUAUUUAUCGA--CU
-..(((....)))..((((((....(.(((..(.(.((((((((((((((((((.......)))))))))))))))))).).)..))).))))))).................--.. ( -37.60)
>DroEre_CAF1 7129 88 - 1
-AAAGCGAAAGCUGCAGAGGCCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCU-AUA-------------------------UUUAUGGCACUUCUUUUUAAUUAUUUAUCGA--CU
-..(((....)))..(((((....((.(((.(((.((((((((....))))))-)).-------------------------)))))).))))))).................--.. ( -22.10)
>DroYak_CAF1 7472 90 - 1
AAAAGCGAAAGCUACAGAGGCCAAUGGCAUCGGAAAUGGCUAUUUAAACGGCCAAUA-------------------------UUUAUGGCACUUCUUAUUAAUUAUUUAUCGA--CU
...(((....)))..(((((....((.(((..(.(.(((((........))))).).-------------------------)..))).))))))).................--.. ( -17.50)
>consensus
_AAAGCGAAAGCUGCAGAGGCCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCUAAUA_________________________UUUAUGGCACUUCUUAUUAAUUAUUUAUCGA__CU
...(((....)))..((((((((.((....))....(((((((....)))))))................................))))..))))..................... (-14.98 = -14.86 +  -0.12) 

alignment

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secondary structure

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dotplot

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Window 6

Location 3,277,034 – 3,277,130
Length 96
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 86.29
Mean single sequence MFE -26.34
Consensus MFE -18.38
Energy contribution -18.58
Covariance contribution 0.20
Combinations/Pair 1.17
Mean z-score -2.47
Structure conservation index 0.70
SVM decision value 0.97
SVM RNA-class probability 0.891377
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3277034 96 - 23771897
CCCGGAGUUCUAUCUAAAUCACGUACACCCACAGCUGAAA-AAAGCGAAAGCUGCAGAGGGCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCUAAUA--------------------
.((((((......))......(((...(((....(((...-..(((....))).))).)))..)))...))))...(((((((....)))))))...-------------------- ( -24.50)
>DroSec_CAF1 7188 96 - 1
CCCCGAGUUCUAUCAAAAUCACGUACACCCACAGCUGAAA-AAAGCGAAAGCUGCAGAAGUCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCUAAUA--------------------
..((((...((((.........((......))..(((...-..(((....))).)))......))))..))))...(((((((....)))))))...-------------------- ( -22.60)
>DroSim_CAF1 7826 115 - 1
-CCCGAGUUCUAUCAAAAUCACGUACACCCACAGCUGAAA-AAAGCGAAAGCUGCAGAAGUCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCUAAUAUUUAUGGCCAUUUAAAUGGC
-.((((...((((.........((......))..(((...-..(((....))).)))......))))..)))).....((((((((((((((((.......)))))))))))))))) ( -36.50)
>DroEre_CAF1 7162 94 - 1
-CCCGAGUUCUAUCAAAAUCACGUACACCCGCAGCUGAAA-AAAGCGAAAGCUGCAGAGGCCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCU-AUA--------------------
-.((((........................((((((....-........))))))....(((...))).))))..((((((((....))))))-)).-------------------- ( -27.30)
>DroYak_CAF1 7505 97 - 1
CCCUGUGUUCUAUCAAAAUCACGUACACCCACAGCUGAAAAAAAGCGAAAGCUACAGAGGCCAAUGGCAUCGGAAAUGGCUAUUUAAACGGCCAAUA--------------------
..(((((......(........)......)))))((((.....(((....)))......(((...))).))))...(((((........)))))...-------------------- ( -20.80)
>consensus
CCCCGAGUUCUAUCAAAAUCACGUACACCCACAGCUGAAA_AAAGCGAAAGCUGCAGAGGCCAAUGGCAUCGGAAAUGGCCAUUUAAAUGGCUAAUA____________________
..((((...((((.........((......))..(((......(((....))).)))......))))..))))...(((((((....)))))))....................... (-18.38 = -18.58 +   0.20) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:32 2006