Locus 8305

Sequence ID 3R_DroMel_CAF1
Location 22,179,855 – 22,179,988
Length 133
Max. P 0.985251
window13391 window13392 window13393

overview

Window 1

Location 22,179,855 – 22,179,948
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.14
Mean single sequence MFE -25.32
Consensus MFE -15.31
Energy contribution -15.57
Covariance contribution 0.25
Combinations/Pair 1.13
Mean z-score -2.36
Structure conservation index 0.60
SVM decision value 0.06
SVM RNA-class probability 0.563415
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22179855 93 - 27905053
ACCGUUCUUGC-------------------------AGCUUAAUGUUUAAUGGCACGCUACGUGCAACGUAGCAUUAAAGUGGCAAUCAAAGCGGUUG--AAACACAUCAACACUUCAUC
..((((.((((-------------------------.((((((((((.....(((((...))))).....)))))).)))).))))....))))((((--(......)))))........ ( -25.10)
>DroSec_CAF1 24369 93 - 1
ACAGUUCUUGC-------------------------AGCUUAAUGCUUAAUGGCACGCCACGUGCAACGUAGCAUUAAAGUGGCAAUCAAAGCGGUUG--AAACACAUCAACACUUCAUC
...(((.((((-------------------------.((((((((((.....(((((...))))).....)))))).)))).))))....))).((((--(......)))))........ ( -25.40)
>DroSim_CAF1 23216 93 - 1
ACAGUUCUUGC-------------------------AGCUUAAUGCUUAAUGGCACGCCACGUGCAACGUAGCAUUAAAGUGGCAAUCAAAGCGGUUG--AAACACAUCAACACUUCAUC
...(((.((((-------------------------.((((((((((.....(((((...))))).....)))))).)))).))))....))).((((--(......)))))........ ( -25.40)
>DroEre_CAF1 38592 92 - 1
AC-GUUCUUGC-------------------------AGCUUAAUGCUUAAUAGCACGCUACGUGCAACGUUGCAUUAAAGUGGCAAUCAAAGUGGUUG--AAUCACAUCAACACUUCAUC
..-....((((-------------------------.(((((((((......(((((...)))))......))))).)))).))))...(((((.(((--(......))))))))).... ( -24.30)
>DroYak_CAF1 30700 93 - 1
ACAGUUCUUGC-------------------------AGCUUAAUGCUUAAUAGCACGCUACGUGCAACGUAGCAUUAAAGUGGCAAUCAAAGUGGUUG--AAUCACAUCAACACUUCAUC
.......((((-------------------------.((((((((((.....(((((...))))).....)))))).)))).))))...(((((.(((--(......))))))))).... ( -25.90)
>DroPer_CAF1 43760 120 - 1
CCAAUUUUUGCGGAGCAGCAUCAGCAGCAGCAAAGGAGCUUAAUGCAUAAUAACAUGCCACGUGCAACAUCGCAUUAAAAUGCCAAUCAAAGUGGUUGUGGAAACCAUCAGCACUUCAUC
....(((((((...((.((....)).)).)))))))........((((......))))...((((......((((....))))........((((((.....))))))..))))...... ( -25.80)
>consensus
ACAGUUCUUGC_________________________AGCUUAAUGCUUAAUAGCACGCCACGUGCAACGUAGCAUUAAAGUGGCAAUCAAAGCGGUUG__AAACACAUCAACACUUCAUC
...(((..((.............................((((((((.....(((((...))))).....)))))))).....(((((.....))))).......))..)))........ (-15.31 = -15.57 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,179,893 – 22,179,988
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 89.86
Mean single sequence MFE -26.40
Consensus MFE -21.46
Energy contribution -21.90
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.33
Structure conservation index 0.81
SVM decision value 2.00
SVM RNA-class probability 0.985251
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22179893 95 + 27905053
CUUUAAUGCUACGUUGCACGUAGCGUGCCAUUAAACAUUAAGCUGCAAGAACGGUAGCACAAAAAACUAUAGGCUUACGGAUUUUAUCGAGAGUU
.(((((((.(((((((....))))))).)))))))......(((((.......))))).............(((((.(((......))).))))) ( -21.60)
>DroSec_CAF1 24407 95 + 1
CUUUAAUGCUACGUUGCACGUGGCGUGCCAUUAAGCAUUAAGCUGCAAGAACUGUAGCAUAAAAAACUGUAGGCUUACGGAUUUUAUCGUGAGUA
..((((((((..((.(((((...))))).))..))))))))((((((.....))))))..............((((((((......)))))))). ( -29.50)
>DroSim_CAF1 23254 95 + 1
CUUUAAUGCUACGUUGCACGUGGCGUGCCAUUAAGCAUUAAGCUGCAAGAACUGUAGCAUAAAAAACUGUAGGCUUACGGCUUGUAUCGUGAGUU
..((((((((..((.(((((...))))).))..))))))))((((((.....)))))).............(((((((((......))))))))) ( -29.50)
>DroEre_CAF1 38630 89 + 1
CUUUAAUGCAACGUUGCACGUAGCGUGCUAUUAAGCAUUAAGCUGCAAGAAC-GUAGCACAAAAAA-----GGCUCACGGUUUUUAUCGAGAGUU
..(((((((......(((((...)))))......)))))))(((((......-)))))........-----(((((.((((....)))).))))) ( -27.00)
>DroYak_CAF1 30738 92 + 1
CUUUAAUGCUACGUUGCACGUAGCGUGCUAUUAAGCAUUAAGCUGCAAGAACUGUAGCACAAAAAAAC---GGCUUACGGAUUUUAUCAAGAGUU
..((((((((.....(((((...))))).....))))))))((((((.....))))))...((((..(---(.....))..)))).......... ( -24.40)
>consensus
CUUUAAUGCUACGUUGCACGUAGCGUGCCAUUAAGCAUUAAGCUGCAAGAACUGUAGCACAAAAAACU_UAGGCUUACGGAUUUUAUCGAGAGUU
..((((((((.....(((((...))))).....))))))))(((((.......)))))..............((((.(((......))).)))). (-21.46 = -21.90 +   0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,179,893 – 22,179,988
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 89.86
Mean single sequence MFE -21.06
Consensus MFE -17.58
Energy contribution -17.38
Covariance contribution -0.20
Combinations/Pair 1.10
Mean z-score -1.30
Structure conservation index 0.83
SVM decision value -0.02
SVM RNA-class probability 0.521393
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22179893 95 - 27905053
AACUCUCGAUAAAAUCCGUAAGCCUAUAGUUUUUUGUGCUACCGUUCUUGCAGCUUAAUGUUUAAUGGCACGCUACGUGCAACGUAGCAUUAAAG
..((..((........))..)).........(((.(((((((((((...(((......)))..))))(((((...)))))...))))))).))). ( -18.90)
>DroSec_CAF1 24407 95 - 1
UACUCACGAUAAAAUCCGUAAGCCUACAGUUUUUUAUGCUACAGUUCUUGCAGCUUAAUGCUUAAUGGCACGCCACGUGCAACGUAGCAUUAAAG
..((.(((........))).)).........(((.(((((((.......(((......)))......(((((...)))))...))))))).))). ( -20.40)
>DroSim_CAF1 23254 95 - 1
AACUCACGAUACAAGCCGUAAGCCUACAGUUUUUUAUGCUACAGUUCUUGCAGCUUAAUGCUUAAUGGCACGCCACGUGCAACGUAGCAUUAAAG
..............((.(((((.((..(((.......)))..))..))))).))((((((((.....(((((...))))).....)))))))).. ( -22.70)
>DroEre_CAF1 38630 89 - 1
AACUCUCGAUAAAAACCGUGAGCC-----UUUUUUGUGCUAC-GUUCUUGCAGCUUAAUGCUUAAUAGCACGCUACGUGCAACGUUGCAUUAAAG
..(((.((........)).))).(-----(((...((((.((-(((...(((......)))......(((((...)))))))))).)))).)))) ( -23.00)
>DroYak_CAF1 30738 92 - 1
AACUCUUGAUAAAAUCCGUAAGCC---GUUUUUUUGUGCUACAGUUCUUGCAGCUUAAUGCUUAAUAGCACGCUACGUGCAACGUAGCAUUAAAG
.....(((((((((..((.....)---)..)))).((((((..((....))(((.....)))...))))))((((((.....))))))))))).. ( -20.30)
>consensus
AACUCUCGAUAAAAUCCGUAAGCCUA_AGUUUUUUGUGCUACAGUUCUUGCAGCUUAAUGCUUAAUGGCACGCUACGUGCAACGUAGCAUUAAAG
...............................(((.(((((((.(((...(((......)))......(((((...))))))))))))))).))). (-17.58 = -17.38 +  -0.20)

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 13:08:25 2006