Locus 10085

Sequence ID 3R_DroMel_CAF1
Location 27,014,271 – 27,014,365
Length 94
Max. P 0.993218
window16058 window16059

overview

Window 8

Location 27,014,271 – 27,014,365
Length 94
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 87.09
Mean single sequence MFE -25.38
Consensus MFE -20.78
Energy contribution -20.54
Covariance contribution -0.24
Combinations/Pair 1.06
Mean z-score -2.62
Structure conservation index 0.82
SVM decision value 2.38
SVM RNA-class probability 0.993218
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27014271 94 + 27905053
AAGAAAAACUGUGGCCAAAAACACUUUCA--AGGAACUGA----CUGGCAAGACCAAGAGUGCUAUGUCUGCACUCUAUAAAUUUAAUGAAAGUGACUUU----------
.....................((((((((--..(((....----.(((.....)))(((((((.......))))))).....)))..)))))))).....---------- ( -22.70)
>DroSec_CAF1 61765 96 + 1
AAGAAAAACUUUGGCCAAAAACACUUUUACAGGGAACUGG----CUGGCAAGACCAAGAGUGCUAAGUCUGCACUCUAUAAAUUUAACGAAAGUGACUUU----------
.....................(((((((.(((....))).----.(((.....)))(((((((.......)))))))...........))))))).....---------- ( -23.10)
>DroSim_CAF1 62275 103 + 1
AAGAAAAACUUUGGCCAA-AACACUUUUAC-GGGAACUGG----CUGGCAAGACCAAGAGUGCUAUGUCUGCACUCUAUAAAUUU-ACGAAAGUGACUUUGGCAGUACUC
.............(((((-(.(((((((..-......(((----((....)).)))(((((((.......)))))))........-..)))))))..))))))....... ( -28.90)
>DroEre_CAF1 67309 94 + 1
AAGAAAAACUUUGGCCAAAAACACUUUCG--CGGAACUGG----UUGGCAAGACCAAGAGUGCUAUGUCUGCACUCUAUAAAUUUAAUGAAAGUGACUUU----------
.....................((((((((--..(((.(((----((.....)))))(((((((.......))))))).....)))..)))))))).....---------- ( -25.40)
>DroYak_CAF1 64267 98 + 1
AAGAACAACUUUUGCCAAAAGCACUUUCA--AGCAACUGGCUGGCUGGCAAGACCAAGAGUGCUAUGUCUGCACUCUAUAAAUUUAAUGAAAGUGACUUU----------
.................((((((((((((--(((.....)))((((....)).)).(((((((.......)))))))..........)))))))).))))---------- ( -26.80)
>consensus
AAGAAAAACUUUGGCCAAAAACACUUUCA__AGGAACUGG____CUGGCAAGACCAAGAGUGCUAUGUCUGCACUCUAUAAAUUUAAUGAAAGUGACUUU__________
.....................(((((((.................(((.....)))(((((((.......)))))))...........)))))))............... (-20.78 = -20.54 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 27,014,271 – 27,014,365
Length 94
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 87.09
Mean single sequence MFE -23.76
Consensus MFE -18.78
Energy contribution -19.38
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.79
SVM decision value 0.55
SVM RNA-class probability 0.778822
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27014271 94 - 27905053
----------AAAGUCACUUUCAUUAAAUUUAUAGAGUGCAGACAUAGCACUCUUGGUCUUGCCAG----UCAGUUCCU--UGAAAGUGUUUUUGGCCACAGUUUUUCUU
----------((((.((((((((...((((.(((((((((.......)))))))(((.....))))----).))))...--)))))))).))))................ ( -22.20)
>DroSec_CAF1 61765 96 - 1
----------AAAGUCACUUUCGUUAAAUUUAUAGAGUGCAGACUUAGCACUCUUGGUCUUGCCAG----CCAGUUCCCUGUAAAAGUGUUUUUGGCCAAAGUUUUUCUU
----------......(((((.((((((..((((((((((.......)))))))((((.......)----))).............)))..)))))).)))))....... ( -20.80)
>DroSim_CAF1 62275 103 - 1
GAGUACUGCCAAAGUCACUUUCGU-AAAUUUAUAGAGUGCAGACAUAGCACUCUUGGUCUUGCCAG----CCAGUUCCC-GUAAAAGUGUU-UUGGCCAAAGUUUUUCUU
(((.((((((((((.((((((((.-.((((...(((((((.......)))))))(((.....))).----..))))..)-)..))))))))-)))))...)))..))).. ( -29.30)
>DroEre_CAF1 67309 94 - 1
----------AAAGUCACUUUCAUUAAAUUUAUAGAGUGCAGACAUAGCACUCUUGGUCUUGCCAA----CCAGUUCCG--CGAAAGUGUUUUUGGCCAAAGUUUUUCUU
----------((((.(((((((............((((((.......))))))((((.....))))----.........--.))))))).))))................ ( -21.70)
>DroYak_CAF1 64267 98 - 1
----------AAAGUCACUUUCAUUAAAUUUAUAGAGUGCAGACAUAGCACUCUUGGUCUUGCCAGCCAGCCAGUUGCU--UGAAAGUGCUUUUGGCAAAAGUUGUUCUU
----------((((.((((((((...((((...(((((((.......)))))))((((.......))))...))))...--))))))))))))................. ( -24.80)
>consensus
__________AAAGUCACUUUCAUUAAAUUUAUAGAGUGCAGACAUAGCACUCUUGGUCUUGCCAG____CCAGUUCCC__UGAAAGUGUUUUUGGCCAAAGUUUUUCUU
..........((((.(((((((...........(((((((.......)))))))(((.....))).................))))))).))))................ (-18.78 = -19.38 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:48:33 2006