Locus 4242

Sequence ID 2L_DroMel_CAF1
Location 12,117,853 – 12,118,124
Length 271
Max. P 0.979160
window6698 window6699 window6700

overview

Window 8

Location 12,117,853 – 12,117,973
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.16
Mean single sequence MFE -29.58
Consensus MFE -25.26
Energy contribution -26.54
Covariance contribution 1.28
Combinations/Pair 1.06
Mean z-score -2.14
Structure conservation index 0.85
SVM decision value 1.83
SVM RNA-class probability 0.979160
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12117853 120 + 22407834
CCUCACGGCGACGUGCUGCAAGAACAGAGUCGAAGAUAAAACAUUUUAUGGCUCUCUUAGGUGCUUUCCCCACCUGCAGCACGCCCCAUUCCAACGCCAGUUGAAGUACAAAAUACAAAA
......((.(.((((((((((((...(((((((((((.....))))).))))))))))(((((.......))))))))))))).)))....((((....))))................. ( -35.50)
>DroSec_CAF1 19993 120 + 1
CCUCACGGCGACGUGCUGCAAGAACAGAGCCGAAGAUAAAACAUUUUAUGGCUCACUUAGGUGCUUUCCCCACCUGCAGCACGCCCCAUUCCGUCGCCAGUUGAAGUACAAAAUACAAAA
......(((((((((((((.......(((((((((((.....))))).))))))....(((((.......))))))))))))(........)))))))...................... ( -40.10)
>DroSim_CAF1 19874 120 + 1
CCUCGCGGCGACGUGCUGCAAGAACAGACUCGAAGAUAAAACAUUUUAUGGCUCUCUUAGGUGCUUUCCCCACCUGCAGCACGCCCCAUUCCAUCGCCAGUUGAAGUACAAAAUACAAAA
......(((((((((((((((((..((.((..(((((.....)))))..)))).))))(((((.......)))))))))))))..........)))))...................... ( -30.00)
>DroEre_CAF1 20267 109 + 1
CCUCACGACGACGUGCUGCAAGAAAAAAGUCAAAGAUAAAAAAUUUUAUGGCUCUCUUAGGUGAAUUCCCCACCUGCAACACGCCCCAU-C---CACCAGUCAA-------AAGACAAAA
...........((((.(((((((....((((((((((.....))))).))))).))))(((((.......)))))))).))))......-.---.....(((..-------..))).... ( -22.50)
>DroYak_CAF1 20190 112 + 1
CCUCACGGCGACGUGCUGCAAGAACAGCGUCGAAGAUAAAACAUUUUAUGGCUCUCUUAGGAGAUUUCCCCACCUGCAACACGCCCCAU-CUACCACCAGUUGA-------AAUACGAAA
......((.(.((((.((((.(......(((((((((.....))))).))))((((....))))........).)))).)))).)))..-..............-------......... ( -19.80)
>consensus
CCUCACGGCGACGUGCUGCAAGAACAGAGUCGAAGAUAAAACAUUUUAUGGCUCUCUUAGGUGCUUUCCCCACCUGCAGCACGCCCCAUUCCAUCGCCAGUUGAAGUACAAAAUACAAAA
......((.(.((((((((((((...(((((((((((.....))))).))))))))))(((((.......)))))))))))))).))................................. (-25.26 = -26.54 +   1.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,117,973 – 12,118,084
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.47
Mean single sequence MFE -33.86
Consensus MFE -26.93
Energy contribution -27.33
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.98
Structure conservation index 0.80
SVM decision value 1.14
SVM RNA-class probability 0.921489
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12117973 111 + 22407834
ACCAAACCCUGGGCC---ACUCUAAGCCAAAGU------CGGGCCUUGGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGUU
....(((((.(((((---...((.......)).------..))))).))))).....((...((.....))(((((((((((...(((....)))......)))))))))))...))... ( -35.80)
>DroSec_CAF1 20113 111 + 1
UCCAAACCCUGGGCC---ACUUUAAGCCAAAGU------CGGGCCUGAGGUUAUUUAUCAGAACUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGU
.((.((((..(((((---(((((.....)))))------..)))))..))))...................(((((((((((...(((....)))......))))))))))).....)). ( -33.80)
>DroSim_CAF1 19994 111 + 1
UCCAAACCCUGGGCC---ACUUUAAACCAAAGU------CGGGCCUGAGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGU
.((.((((..(((((---(((((.....)))))------..)))))..)))).....((...((.....))(((((((((((...(((....)))......)))))))))))...)))). ( -35.50)
>DroEre_CAF1 20376 114 + 1
UCCAAACAACAGGCCACUACUCUAAGCCAAAGU------CGGGCCUUGGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGU
.((.(((...(((((.(.(((.........)))------.))))))...))).....((...((.....))(((((((((((...(((....)))......)))))))))))...)))). ( -30.00)
>DroYak_CAF1 20302 118 + 1
UCCAAACAACAGGCCA--ACUGUAAGCCAAAGUGGGGCUCGGGCCUUGGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGU
.((.....((((....--.))))..(((((((((((((((((((.((((........)))).))).....)))))).........(((....)))....)))))).)))).......)). ( -34.20)
>consensus
UCCAAACCCUGGGCC___ACUCUAAGCCAAAGU______CGGGCCUUGGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGU
.((.((((..(((((..........((....))........)))))..)))).....((...((.....))(((((((((((...(((....)))......)))))))))))...)))). (-26.93 = -27.33 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,118,004 – 12,118,124
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.59
Mean single sequence MFE -31.52
Consensus MFE -28.54
Energy contribution -28.94
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.91
SVM decision value 1.60
SVM RNA-class probability 0.966414
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12118004 120 + 22407834
GGGCCUUGGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGUUAACCAAUAAAAAAAAAAAACACAAUUGGCUGGCGCAAUGC
.(((.((((........)))).)))(((((((((((((((((...(((....)))......)))))))))))...........((((................))))))))))....... ( -30.49)
>DroSec_CAF1 20144 118 + 1
GGGCCUGAGGUUAUUUAUCAGAACUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGUAACCAAUAAAAC--AAAAACACAAUUGGCUGGCGCAAUGC
((..((((.........))))..))(((((((((((((((((...(((....)))......))))))))))).....((...))........--.............))))))....... ( -30.70)
>DroSim_CAF1 20025 118 + 1
GGGCCUGAGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGUAACCAAUAAAAA--AAAAACACAAUUGGCUGGCGCAAUGC
.(((((((.........)))).)))(((((((((((((((((...(((....)))......))))))))))).....((...))........--.............))))))....... ( -33.20)
>DroEre_CAF1 20410 114 + 1
GGGCCUUGGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGUAACCAAUAAA------AAGUACAAUUGGCUGGCGCAAUGC
(.(((...((((((((......((.....))(((((((((((...(((....)))......)))))))))))....))))))))......------.(((.......)))))).)..... ( -32.20)
>DroYak_CAF1 20340 114 + 1
GGGCCUUGGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGUAACCAAUAAA------AAAUACAAUUGGCUGGCGCAAUGC
.(((.((((........)))).)))(((((((((((((((((...(((....)))......)))))))))))...........((((...------.......))))))))))....... ( -31.00)
>consensus
GGGCCUUGGGUUAUUUAUCAGAGCUGUCAGCGGGCCAUAAAUUCCGACUUUUGUCACUACCAUUUAUGGCCUAAAGAGGUAACCAAUAAAA___AAAAACACAAUUGGCUGGCGCAAUGC
(.(((...((((((((......((.....))(((((((((((...(((....)))......)))))))))))....)))))))).................(....)...))).)..... (-28.54 = -28.94 +   0.40)

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 11:13:17 2006