Locus 1005

Sequence ID 3R_DroMel_CAF1
Location 3,197,602 – 3,197,743
Length 141
Max. P 0.994217
window1626 window1627 window1628 window1629

overview

Window 6

Location 3,197,602 – 3,197,703
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.07
Mean single sequence MFE -30.83
Consensus MFE -16.68
Energy contribution -18.06
Covariance contribution 1.38
Combinations/Pair 1.11
Mean z-score -2.24
Structure conservation index 0.54
SVM decision value 0.64
SVM RNA-class probability 0.807854
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3197602 101 + 27905053
GGUG-------UAGAUACAAUAUGGGCCUUCUUCUC-----G-------GUUGCGUAUACGCAACAUAUGCGAGAAUGAAAAAUGAAAAUAAUUGUUGAAAAACUGAUAGCUAUUCGGCU
....-------.............((((((((((((-----(-------((((((....)))))).....)))))).)))..............(((....)))............)))) ( -22.70)
>DroSec_CAF1 17172 108 + 1
GGUG-------UAGAUACAAUAUUUGCCUUCUUCUC-----GGGCACGCGUUGCGUAUACGCAACGUAUGCGAGAAUGAAAAAUGAAAAUAAUUGUUGAAAACCUGCUAGCCAUUCGGCU
(((.-------.....(((((((((...((((((((-----..(((..(((((((....)))))))..)))))))).)))......)))).))))).....)))....((((....)))) ( -34.00)
>DroSim_CAF1 23984 108 + 1
GGUG-------UAGAUACAAUAUGUGCCUUCUUCUC-----GGGCACGCGUUGCGUAUACGCAACGUAUGCGAGAAUGAAAAAUGAAAAUAAUUGUUGAAAACCUGCUAGCCAUUCGGCU
(((.-------.....(((((.......((((((((-----..(((..(((((((....)))))))..)))))))).)))..((....)).))))).....)))....((((....)))) ( -33.00)
>DroEre_CAF1 16777 109 + 1
UGUGCCUACAAUAUAUACCAUAUGUGCCUCCAACUCUGUUGGGCCACACGUUGCGUAUACGCAACGUAUGCGGGAAUGAAAA-----------UUUUUAAAAACUGCCCGCUAUGCGGCU
...(((................((((.(.(((((...)))))).)))).((((((....))))))(((((((((........-----------.............))))).))))))). ( -33.60)
>consensus
GGUG_______UAGAUACAAUAUGUGCCUUCUUCUC_____GGGCACGCGUUGCGUAUACGCAACGUAUGCGAGAAUGAAAAAUGAAAAUAAUUGUUGAAAAACUGCUAGCCAUUCGGCU
.........................(((...............(((.((((((((....)))))))).)))..(((((.................................)))))))). (-16.68 = -18.06 +   1.38)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,197,602 – 3,197,703
Length 101
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.07
Mean single sequence MFE -31.09
Consensus MFE -17.52
Energy contribution -20.34
Covariance contribution 2.81
Combinations/Pair 1.07
Mean z-score -2.95
Structure conservation index 0.56
SVM decision value 2.46
SVM RNA-class probability 0.994217
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3197602 101 - 27905053
AGCCGAAUAGCUAUCAGUUUUUCAACAAUUAUUUUCAUUUUUCAUUCUCGCAUAUGUUGCGUAUACGCAAC-------C-----GAGAAGAAGGCCCAUAUUGUAUCUA-------CACC
.((((((.(((.....))).))).................(((.((((((.....((((((....))))))-------)-----)))))))))))..............-------.... ( -23.60)
>DroSec_CAF1 17172 108 - 1
AGCCGAAUGGCUAGCAGGUUUUCAACAAUUAUUUUCAUUUUUCAUUCUCGCAUACGUUGCGUAUACGCAACGCGUGCCC-----GAGAAGAAGGCAAAUAUUGUAUCUA-------CACC
((((....))))....(((.....(((((.((((....(((((.((((((((..(((((((....)))))))..)))..-----)))))))))).))))))))).....-------.))) ( -31.10)
>DroSim_CAF1 23984 108 - 1
AGCCGAAUGGCUAGCAGGUUUUCAACAAUUAUUUUCAUUUUUCAUUCUCGCAUACGUUGCGUAUACGCAACGCGUGCCC-----GAGAAGAAGGCACAUAUUGUAUCUA-------CACC
.((((((.((((....))))))).................(((.((((((((..(((((((....)))))))..)))..-----)))))))))))..............-------.... ( -30.80)
>DroEre_CAF1 16777 109 - 1
AGCCGCAUAGCGGGCAGUUUUUAAAAA-----------UUUUCAUUCCCGCAUACGUUGCGUAUACGCAACGUGUGGCCCAACAGAGUUGGAGGCACAUAUGGUAUAUAUUGUAGGCACA
.((((((..(((((.(((.........-----------.....))))))))((((((((((....))))))(((((.((((((...))))).).)))))...))))....))).)))... ( -38.84)
>consensus
AGCCGAAUAGCUAGCAGGUUUUCAACAAUUAUUUUCAUUUUUCAUUCUCGCAUACGUUGCGUAUACGCAACGCGUGCCC_____GAGAAGAAGGCACAUAUUGUAUCUA_______CACC
.((((((.(((.....))).))).................(((.(((((((((.(((((((....))))))).)))).......)))))))))))......................... (-17.52 = -20.34 +   2.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,197,631 – 3,197,743
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.38
Mean single sequence MFE -33.21
Consensus MFE -22.84
Energy contribution -23.52
Covariance contribution 0.69
Combinations/Pair 1.11
Mean z-score -1.82
Structure conservation index 0.69
SVM decision value 0.41
SVM RNA-class probability 0.725124
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3197631 112 + 27905053
-G-------GUUGCGUAUACGCAACAUAUGCGAGAAUGAAAAAUGAAAAUAAUUGUUGAAAAACUGAUAGCUAUUCGGCUCACUCCUCUCAGCAGUGUUCGUCCCAUCCUAGCUCCCAUG
-.-------((((((....)))))).((((.(((...((...(((((....((((((((.........((((....))))........)))))))).)))))....))....))).)))) ( -26.33)
>DroSec_CAF1 17201 119 + 1
-GGGCACGCGUUGCGUAUACGCAACGUAUGCGAGAAUGAAAAAUGAAAAUAAUUGUUGAAAACCUGCUAGCCAUUCGGCUCACUCCUCUCAGGAGUGUUCGUCCUAUCCUAGCUCCCAUG
-(((((..(((((((....)))))))..)))(((...((...(((((.....................((((....))))((((((.....)))))))))))....))....)))))... ( -37.90)
>DroSim_CAF1 24013 119 + 1
-GGGCACGCGUUGCGUAUACGCAACGUAUGCGAGAAUGAAAAAUGAAAAUAAUUGUUGAAAACCUGCUAGCCAUUCGGCUCACUCCUCUCAGGAGUGUUCGUCCUAUCCUAGCUCCCAUG
-(((((..(((((((....)))))))..)))(((...((...(((((.....................((((....))))((((((.....)))))))))))....))....)))))... ( -37.90)
>DroEre_CAF1 16817 109 + 1
GGGCCACACGUUGCGUAUACGCAACGUAUGCGGGAAUGAAAA-----------UUUUUAAAAACUGCCCGCUAUGCGGCUCACUCCUCUCAGCAGUAUUCGUGUUAUCCUAGCUCCCAUC
(((((....((((((....))))))(((((((((........-----------.............))))).))))))))).........(((((.((.......)).)).)))...... ( -30.70)
>consensus
_GGGCACGCGUUGCGUAUACGCAACGUAUGCGAGAAUGAAAAAUGAAAAUAAUUGUUGAAAAACUGCUAGCCAUUCGGCUCACUCCUCUCAGCAGUGUUCGUCCUAUCCUAGCUCCCAUG
.......((((((((....))))))))(((.(((.(((((.............................(((....))).((((((.....)))))))))))..........))).))). (-22.84 = -23.52 +   0.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,197,631 – 3,197,743
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.38
Mean single sequence MFE -35.70
Consensus MFE -23.77
Energy contribution -25.65
Covariance contribution 1.88
Combinations/Pair 1.07
Mean z-score -1.62
Structure conservation index 0.67
SVM decision value 0.07
SVM RNA-class probability 0.570312
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3197631 112 - 27905053
CAUGGGAGCUAGGAUGGGACGAACACUGCUGAGAGGAGUGAGCCGAAUAGCUAUCAGUUUUUCAACAAUUAUUUUCAUUUUUCAUUCUCGCAUAUGUUGCGUAUACGCAAC-------C-
.......((.((((((..(....((((.((....))))))....(((.(((.....))).)))................)..)))))).))....((((((....))))))-------.- ( -28.90)
>DroSec_CAF1 17201 119 - 1
CAUGGGAGCUAGGAUAGGACGAACACUCCUGAGAGGAGUGAGCCGAAUGGCUAGCAGGUUUUCAACAAUUAUUUUCAUUUUUCAUUCUCGCAUACGUUGCGUAUACGCAACGCGUGCCC-
..((..((((.............((((((.....))))))((((....))))....))))..)).........................(((..(((((((....)))))))..)))..- ( -38.80)
>DroSim_CAF1 24013 119 - 1
CAUGGGAGCUAGGAUAGGACGAACACUCCUGAGAGGAGUGAGCCGAAUGGCUAGCAGGUUUUCAACAAUUAUUUUCAUUUUUCAUUCUCGCAUACGUUGCGUAUACGCAACGCGUGCCC-
..((..((((.............((((((.....))))))((((....))))....))))..)).........................(((..(((((((....)))))))..)))..- ( -38.80)
>DroEre_CAF1 16817 109 - 1
GAUGGGAGCUAGGAUAACACGAAUACUGCUGAGAGGAGUGAGCCGCAUAGCGGGCAGUUUUUAAAAA-----------UUUUCAUUCCCGCAUACGUUGCGUAUACGCAACGUGUGGCCC
...(((((..(((((.....(((.((((((....).......((((...))))))))).)))....)-----------))))..))))).(((((((((((....))))))))))).... ( -36.30)
>consensus
CAUGGGAGCUAGGAUAGGACGAACACUCCUGAGAGGAGUGAGCCGAAUAGCUAGCAGGUUUUCAACAAUUAUUUUCAUUUUUCAUUCUCGCAUACGUUGCGUAUACGCAACGCGUGCCC_
...(((((..((((.........((((((.....))))))(((......)))..........................))))..)))))((((.(((((((....))))))).))))... (-23.77 = -25.65 +   1.88)

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 09:58:10 2006